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Conserved domains on  [gi|568933163|ref|XP_006535763|]
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histone-lysine N-methyltransferase 2C isoform X22 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4693-4845 7.28e-118

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


:

Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 369.84  E-value: 7.28e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4693 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDA 4772
Cdd:cd19171     1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4773 TLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4845
Cdd:cd19171    81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4341-4445 2.03e-73

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


:

Pssm-ID: 277167  Cd Length: 105  Bit Score: 240.72  E-value: 2.03e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4420
Cdd:cd15697     1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                          90       100
                  ....*....|....*....|....*
gi 568933163 4421 IYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:cd15697    81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1640-1720 1.79e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


:

Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 1.79e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1640 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 1719
Cdd:cd22026     1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                  .
gi 568933163 1720 N 1720
Cdd:cd22026    81 N 81
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 247-330 1.16e-53

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


:

Pssm-ID: 277166  Cd Length: 90  Bit Score: 183.61  E-value: 1.16e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15696     7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                  ....
gi 568933163  327 CPEH 330
Cdd:cd15696    87 CPTH 90
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 947-1003 3.79e-36

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


:

Pssm-ID: 277071  Cd Length: 57  Bit Score: 132.45  E-value: 3.79e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163  947 KFTLQQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 1003
Cdd:cd15596     1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1081-1131 4.21e-32

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


:

Pssm-ID: 277073  Cd Length: 51  Bit Score: 120.42  E-value: 4.21e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163 1081 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1131
Cdd:cd15600     1 TCPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1004-1050 6.25e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


:

Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.11  E-value: 6.25e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1050
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 390-435 1.13e-28

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


:

Pssm-ID: 277069  Cd Length: 46  Bit Score: 110.80  E-value: 1.13e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 466-517 2.57e-27

PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the third PHD finger.


:

Pssm-ID: 276986  Cd Length: 52  Bit Score: 106.80  E-value: 2.57e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  466 LCPFCGKCYHPELQKDMLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYC 517
Cdd:cd15511     1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4549-4636 8.48e-25

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


:

Pssm-ID: 197781  Cd Length: 86  Bit Score: 100.83  E-value: 8.48e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163   4549 VFVIRIVEQGheDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYTF 4628
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 568933163   4629 RYGRNPLM 4636
Cdd:smart00542   79 RYHRSPLL 86
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 343-388 2.24e-23

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


:

Pssm-ID: 276984  Cd Length: 48  Bit Score: 95.45  E-value: 2.24e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163  343 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV--TPLKRAGWQCPEC 388
Cdd:cd15509     1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 1880-2370 2.90e-21

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 103.86  E-value: 2.90e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1880 ESLSQSQNSQPP---SPQMFSPGSSHSRPPSPvdpYAkmvgtPRPP-PGGHSFPRRNSVTPvencvplssvprpihmnet 1955
Cdd:PHA03247 2541 EELASDDAGDPPpplPPAAPPAAPDRSVPPPR---PA-----PRPSePAVTSRARRPDAPP------------------- 2593

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1956 SATRPSPARDLCASSMTNSDPYAKPPDTPRPmmtdqfsKPFSLPRSPVISEQSTKGPLTTGTSDHFTKPS--PRTDAFQR 2033
Cdd:PHA03247 2594 QSARPRAPVDDRGDPRGPAPPSPLPPDTHAP-------DPPPPSPSPAANEPDPHPPPTVPPPERPRDDPapGRVSRPRR 2666

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2034 QRLPDPYAGPSLTPaplgNGPfktplHPPPSQDPYGSVSQTSRRLSVDPYERPA------LTPRPVDNFSHSQSNDPYSH 2107
Cdd:PHA03247 2667 ARRLGRAAQASSPP----QRP-----RRRAARPTVGSLTSLADPPPPPPTPEPAphalvsATPLPPGPAAARQASPALPA 2737

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2108 PPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTP-----RPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTI 2182
Cdd:PHA03247 2738 APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPprrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAA 2817

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2183 DPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYT------------HHLGPPRPGISVPYSQP---------PAVPRPRTS 2241
Cdd:PHA03247 2818 LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLplggsvapggdvRRRPPSRSPAAKPAAPArppvrrlarPAVSRSTES 2897

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2242 EGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPdtcsqtPRPPGPGRIDTFTHAS---SSAVRDPYDQPPVTPR 2318
Cdd:PHA03247 2898 FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP------PRPQPPLAPTTDPAGAgepSGAVPQPWLGALVPGR 2971

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568933163 2319 PHSESFGTSQvvhDLVDRPVPGSEGNFSTSSNLP-VSSQGQQFS-SVSQLPGPV 2370
Cdd:PHA03247 2972 VAVPRFRVPQ---PAPSREAPASSTPPLTGHSLSrVSSWASSLAlHEETDPPPV 3022
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4490-4541 4.60e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


:

Pssm-ID: 461787  Cd Length: 51  Bit Score: 80.63  E-value: 4.60e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  4490 GSLIFHTIGQLLPQQMqAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSI 4541
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 2146-2753 8.65e-13

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 75.75  E-value: 8.65e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2146 PGTP---RPLIDSYSQTSGTArsnPDPYSQPPgtPRPNTIDPYSQQPPTPRPSPQTDMFV-----------SSVANQRHT 2211
Cdd:PHA03247 2475 PGAPvyrRPAEARFPFAAGAA---PDPGGGGP--PDPDAPPAPSRLAPAILPDEPVGEPVhprmltwirglEELASDDAG 2549

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2212 DPythhlGPPRPGISVP----YSQPPAVPRPRTSEGFTRPSSARPALMPnqdpflQAAQNRVPGlpGPLIRPPDTCSQTP 2287
Cdd:PHA03247 2550 DP-----PPPLPPAAPPaapdRSVPPPRPAPRPSEPAVTSRARRPDAPP------QSARPRAPV--DDRGDPRGPAPPSP 2616

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2288 RPPGPgridtfthasssavrDPYDQPPVTPRPH-SESFGTSQVVHDLVDRPVPGSEGNfSTSSNLPVSSQGQQFSSVSQL 2366
Cdd:PHA03247 2617 LPPDT---------------HAPDPPPPSPSPAaNEPDPHPPPTVPPPERPRDDPAPG-RVSRPRRARRLGRAAQASSPP 2680

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2367 PGPVPTSGGTDTQNTVNMSQA-DTEKLRQRQKLREIILQQQQQKKIASRQEKGPQDTAVVPHPVPLPHWQPESINQAFTR 2445
Cdd:PHA03247 2681 QRPRRRAARPTVGSLTSLADPpPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2446 PPPPYPGSTRSPVIPPLGPRyavfpkdQRGPYPPEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPhir 2525
Cdd:PHA03247 2761 PTTAGPPAPAPPAAPAAGPP-------RRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--- 2830

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2526 rPMSMemprpsnnpplnnpvgLPQHFPPQGLPVQQHNILGQAFielrhrAPDGR-SRLPFAASPSSVIESPSHPRHGNF- 2603
Cdd:PHA03247 2831 -PTSA----------------QPTAPPPPPGPPPPSLPLGGSV------APGGDvRRRPPSRSPAAKPAAPARPPVRRLa 2887

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2604 ---LPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP------------------LNHP 2662
Cdd:PHA03247 2888 rpaVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPttdpagagepsgavpqpwLGAL 2967

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2663 LSGEFS-------------EAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKE-LDVKDlegvevkDLDDEDLE 2728
Cdd:PHA03247 2968 VPGRVAvprfrvpqpapsrEAPASSTPPLTGHSLSRVSSWASSLALHEETDPPPVSLKQtLWPPD-------DTEDSDAD 3040

                         650       660
                  ....*....|....*....|....*.
gi 568933163 2729 NLNL-DTEDGKGDDLDTLDNlETNDP 2753
Cdd:PHA03247 3041 SLFDsDSERSDLEALDPLPP-EPHDP 3065
Myosin_tail_1 super family cl37647
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 3192-3274 9.81e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


The actual alignment was detected with superfamily member pfam01576:

Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 45.55  E-value: 9.81e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3192 EEWLQETQQLLQmqqkylEEQigahrKSKKALSAKQRT--AKKAG-REFPEEDAEQLKHVTEQQSMVQKQLEQIRKQQKE 3268
Cdd:pfam01576  467 ESQLQDTQELLQ------EET-----RQKLNLSTRLRQleDERNSlQEQLEEEEEAKRNVERQLSTLQAQLSDMKKKLEE 535


                   ....*.
gi 568933163  3269 HAELIE 3274
Cdd:pfam01576  536 DAGTLE 541
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3289-3601 3.65e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.60  E-value: 3.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3289 LAPPILM----PGVQPQPPLV-------PGATSLTMSQPNFPMVPQQLQHQQHTAVISGHTSPARMPSLPgwQSNSASAH 3357
Cdd:pfam03154  169 TQPPVLQaqsgAASPPSPPPPgttqaatAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLH--PQRLPSPH 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3358 LPLNPPRIQPPIAQLSLKTcTPAPGTVSSANP-----QNGPPPRVEFDDNNPFSESFQERERKERLREQQE--RQRVQLM 3430
Cdd:pfam03154  247 PPLQPMTQPPPPSQVSPQP-LPQPSLHGQMPPmphslQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAapGQSQQRI 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3431 QEVDRQRALQQRMEMEQHCLMGAELA-------NRTPVSQMPFYGSDRPCDFLQPPRP--LQQSPQHQQQIGPVLQQQNV 3501
Cdd:pfam03154  326 HTPPSQSQLQSQQPPREQPLPPAPLSmphikppPTTPIPQLPNPQSHKHPPHLSGPSPfqMNSNLPPPPALKPLSSLSTH 405

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3502 QQGSVNSPPNQTFMQTneqRQVGPPsfvPDSPSASGGSPNFHSvkPGHGNLPGSSFQQSPLRPPFT--PILPGTSP--VA 3577
Cdd:pfam03154  406 HPPSAHPPPLQLMPQS---QQLPPP---PAQPPVLTQSQSLPP--PAASHPPTSGLHQVPSQSPFPqhPFVPGGPPpiTP 477

                          330       340
                   ....*....|....*....|....
gi 568933163  3578 NSNVPCGQDPAVTQGQNYSGSSQS 3601
Cdd:pfam03154  478 PSGPPTSTSSAMPGIQPPSSASVS 501
 
Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4693-4845 7.28e-118

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 369.84  E-value: 7.28e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4693 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDA 4772
Cdd:cd19171     1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4773 TLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4845
Cdd:cd19171    81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4341-4445 2.03e-73

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 240.72  E-value: 2.03e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4420
Cdd:cd15697     1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                          90       100
                  ....*....|....*....|....*
gi 568933163 4421 IYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:cd15697    81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1640-1720 1.79e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 1.79e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1640 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 1719
Cdd:cd22026     1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                  .
gi 568933163 1720 N 1720
Cdd:cd22026    81 N 81
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 247-330 1.16e-53

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 183.61  E-value: 1.16e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15696     7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                  ....
gi 568933163  327 CPEH 330
Cdd:cd15696    87 CPTH 90
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
4705-4844 4.89e-38

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 140.48  E-value: 4.89e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4705 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgvYMFRMDNDHVIDATLTGGPARYINH 4784
Cdd:COG2940     5 HPRIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINH 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4785 SCAPNCVAEvvtfERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHkiPCHCGavNCRKW 4844
Cdd:COG2940    83 SCDPNCEAD----EEDGRIFIVALRDIAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 947-1003 3.79e-36

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 132.45  E-value: 3.79e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163  947 KFTLQQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 1003
Cdd:cd15596     1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 4707-4828 1.16e-35

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 133.61  E-value: 1.16e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163   4707 NVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNR-GVYMFRMDNDHVIDATLTGGPARYINHS 4785
Cdd:smart00317    2 KLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAkAFYLFDIDSDLCIDARRKGNLARFINHS 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|...
gi 568933163   4786 CAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDD 4828
Cdd:smart00317   82 CEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1081-1131 4.21e-32

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


Pssm-ID: 277073  Cd Length: 51  Bit Score: 120.42  E-value: 4.21e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163 1081 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1131
Cdd:cd15600     1 TCPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1004-1050 6.25e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.11  E-value: 6.25e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1050
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 4717-4822 3.83e-29

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 114.54  E-value: 3.83e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  4717 GLGLYAARDIEKHTMVIEYIGT-IIRNEVANRKEKLYESQNR----GVYMFRMDND--HVIDATLT--GGPARYINHSCA 4787
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDEDseYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 568933163  4788 PNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYK 4822
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDYG 115
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 390-435 1.13e-28

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 110.80  E-value: 1.13e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 466-517 2.57e-27

PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the third PHD finger.


Pssm-ID: 276986  Cd Length: 52  Bit Score: 106.80  E-value: 2.57e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  466 LCPFCGKCYHPELQKDMLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYC 517
Cdd:cd15511     1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4549-4636 8.48e-25

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 100.83  E-value: 8.48e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163   4549 VFVIRIVEQGheDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYTF 4628
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 568933163   4629 RYGRNPLM 4636
Cdd:smart00542   79 RYHRSPLL 86
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4547-4631 8.99e-25

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 100.76  E-value: 8.99e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  4547 RPVFVIRIVEqgHEDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENY 4626
Cdd:pfam05965    1 GPLFRVTVEE--DPDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 568933163  4627 TFRYG 4631
Cdd:pfam05965   79 KFRYG 83
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 343-388 2.24e-23

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 95.45  E-value: 2.24e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163  343 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV--TPLKRAGWQCPEC 388
Cdd:cd15509     1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1880-2370 2.90e-21

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 103.86  E-value: 2.90e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1880 ESLSQSQNSQPP---SPQMFSPGSSHSRPPSPvdpYAkmvgtPRPP-PGGHSFPRRNSVTPvencvplssvprpihmnet 1955
Cdd:PHA03247 2541 EELASDDAGDPPpplPPAAPPAAPDRSVPPPR---PA-----PRPSePAVTSRARRPDAPP------------------- 2593

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1956 SATRPSPARDLCASSMTNSDPYAKPPDTPRPmmtdqfsKPFSLPRSPVISEQSTKGPLTTGTSDHFTKPS--PRTDAFQR 2033
Cdd:PHA03247 2594 QSARPRAPVDDRGDPRGPAPPSPLPPDTHAP-------DPPPPSPSPAANEPDPHPPPTVPPPERPRDDPapGRVSRPRR 2666

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2034 QRLPDPYAGPSLTPaplgNGPfktplHPPPSQDPYGSVSQTSRRLSVDPYERPA------LTPRPVDNFSHSQSNDPYSH 2107
Cdd:PHA03247 2667 ARRLGRAAQASSPP----QRP-----RRRAARPTVGSLTSLADPPPPPPTPEPAphalvsATPLPPGPAAARQASPALPA 2737

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2108 PPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTP-----RPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTI 2182
Cdd:PHA03247 2738 APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPprrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAA 2817

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2183 DPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYT------------HHLGPPRPGISVPYSQP---------PAVPRPRTS 2241
Cdd:PHA03247 2818 LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLplggsvapggdvRRRPPSRSPAAKPAAPArppvrrlarPAVSRSTES 2897

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2242 EGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPdtcsqtPRPPGPGRIDTFTHAS---SSAVRDPYDQPPVTPR 2318
Cdd:PHA03247 2898 FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP------PRPQPPLAPTTDPAGAgepSGAVPQPWLGALVPGR 2971

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568933163 2319 PHSESFGTSQvvhDLVDRPVPGSEGNFSTSSNLP-VSSQGQQFS-SVSQLPGPV 2370
Cdd:PHA03247 2972 VAVPRFRVPQ---PAPSREAPASSTPPLTGHSLSrVSSWASSLAlHEETDPPPV 3022
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4490-4541 4.60e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 80.63  E-value: 4.60e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  4490 GSLIFHTIGQLLPQQMqAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSI 4541
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 4500-4543 1.50e-16

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 76.17  E-value: 1.50e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 568933163   4500 LLPQQMQAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEE 4543
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 4368-4445 2.42e-14

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 71.21  E-value: 2.42e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  4368 HLNCALWSTEVYetQAGA------LINVELALRRGLQMKCVFCH-KTGATSGCHRFRCTNIYHFTCATKAQCMF-FKDKT 4439
Cdd:pfam13771    1 HVVCALWSPELV--QRGNdsmgfpIEDIEKIPKRRWKLKCYLCKkKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDN 78

                           90
                   ....*....|
gi 568933163  4440 ----MLCPMH 4445
Cdd:pfam13771   79 gtfkSYCKKH 88
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1884-2305 3.50e-14

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 79.81  E-value: 3.50e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1884 QSQNSQPPSPQMFSPGSShsrPPSPVDPYAKMVGTPRPPPGGHSFPrrnsvtpvencvplssvprpihmnetsatrpspa 1963
Cdd:pfam03154  165 QILQTQPPVLQAQSGAAS---PPSPPPPGTTQAATAGPTPSAPSVP---------------------------------- 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1964 rdlcassmtnsdPYAKPPDTPRPMMTDQFSKPFSLPRSpviseqstkgplttgtsdhftkpsprTDAFQRQRLPDPYagP 2043
Cdd:pfam03154  208 ------------PQGSPATSQPPNQTQSTAAPHTLIQQ--------------------------TPTLHPQRLPSPH--P 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2044 SLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSVDPYERP-ALTPRPVDNFSH-SQSNDPYSHPPLTPHPAMTESFT 2121
Cdd:pfam03154  248 PLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQhPVPPQPFPLTPQsSQSQVPPGPSPAAPGQSQQRIHT 327

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2122 HASRAFPQPGTISRSASQDP-------YSQPPGTPRP-LIDSYSQTSGTARSNPDPYSQPPGTPRPNTIDPYS----QQP 2189
Cdd:pfam03154  328 PPSQSQLQSQQPPREQPLPPaplsmphIKPPPTTPIPqLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSslstHHP 407

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2190 PTPRPSPQTDMFVSS----------VANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTR--PSSARPALMPN 2257
Cdd:pfam03154  408 PSAHPPPLQLMPQSQqlppppaqppVLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPitPPSGPPTSTSS 487

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2258 QDPFLQAAQNRVPGLPGPLI--------------RPPDTCSQTPRPPGPGR--------IDTFTHASSSA 2305
Cdd:pfam03154  488 AMPGIQPPSSASVSSSGPVPaavscplppvqikeEALDEAEEPESPPPPPRspspeptvVNTPSHASQSA 557
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2146-2753 8.65e-13

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 75.75  E-value: 8.65e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2146 PGTP---RPLIDSYSQTSGTArsnPDPYSQPPgtPRPNTIDPYSQQPPTPRPSPQTDMFV-----------SSVANQRHT 2211
Cdd:PHA03247 2475 PGAPvyrRPAEARFPFAAGAA---PDPGGGGP--PDPDAPPAPSRLAPAILPDEPVGEPVhprmltwirglEELASDDAG 2549

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2212 DPythhlGPPRPGISVP----YSQPPAVPRPRTSEGFTRPSSARPALMPnqdpflQAAQNRVPGlpGPLIRPPDTCSQTP 2287
Cdd:PHA03247 2550 DP-----PPPLPPAAPPaapdRSVPPPRPAPRPSEPAVTSRARRPDAPP------QSARPRAPV--DDRGDPRGPAPPSP 2616

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2288 RPPGPgridtfthasssavrDPYDQPPVTPRPH-SESFGTSQVVHDLVDRPVPGSEGNfSTSSNLPVSSQGQQFSSVSQL 2366
Cdd:PHA03247 2617 LPPDT---------------HAPDPPPPSPSPAaNEPDPHPPPTVPPPERPRDDPAPG-RVSRPRRARRLGRAAQASSPP 2680

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2367 PGPVPTSGGTDTQNTVNMSQA-DTEKLRQRQKLREIILQQQQQKKIASRQEKGPQDTAVVPHPVPLPHWQPESINQAFTR 2445
Cdd:PHA03247 2681 QRPRRRAARPTVGSLTSLADPpPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2446 PPPPYPGSTRSPVIPPLGPRyavfpkdQRGPYPPEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPhir 2525
Cdd:PHA03247 2761 PTTAGPPAPAPPAAPAAGPP-------RRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--- 2830

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2526 rPMSMemprpsnnpplnnpvgLPQHFPPQGLPVQQHNILGQAFielrhrAPDGR-SRLPFAASPSSVIESPSHPRHGNF- 2603
Cdd:PHA03247 2831 -PTSA----------------QPTAPPPPPGPPPPSLPLGGSV------APGGDvRRRPPSRSPAAKPAAPARPPVRRLa 2887

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2604 ---LPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP------------------LNHP 2662
Cdd:PHA03247 2888 rpaVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPttdpagagepsgavpqpwLGAL 2967

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2663 LSGEFS-------------EAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKE-LDVKDlegvevkDLDDEDLE 2728
Cdd:PHA03247 2968 VPGRVAvprfrvpqpapsrEAPASSTPPLTGHSLSRVSSWASSLALHEETDPPPVSLKQtLWPPD-------DTEDSDAD 3040

                         650       660
                  ....*....|....*....|....*.
gi 568933163 2729 NLNL-DTEDGKGDDLDTLDNlETNDP 2753
Cdd:PHA03247 3041 SLFDsDSERSDLEALDPLPP-EPHDP 3065
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 252-330 1.60e-12

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 66.20  E-value: 1.60e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163   252 HHRCVEWSLGICQ-----MEEPLLvNVDKAVVSGSTERCAFCKH-LGATIKCCEEKCTQMYHYPCAAGAGTFQDFSH--- 322
Cdd:pfam13771    1 HVVCALWSPELVQrgndsMGFPIE-DIEKIPKRRWKLKCYLCKKkGGACIQCSKKNCRRAFHVTCALEAGLLMQFDEdng 79


                   ....*....
gi 568933163   323 -FFLLCPEH 330
Cdd:pfam13771   80 tFKSYCKKH 88
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1004-1050 2.40e-12

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 64.44  E-value: 2.40e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 568933163  1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQT--VPKGGWKCKWCV 1050
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECK 49
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1004-1049 2.85e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 61.07  E-value: 2.85e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 568933163   1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1049
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 390-438 7.27e-11

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 60.20  E-value: 7.27e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 568933163   390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPV--MKSVPTNGWKCKNCRIC 438
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPldPAEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 390-435 5.68e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 57.61  E-value: 5.68e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 568933163    390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKS-VPTNGWKCKNC 435
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 955-1005 8.97e-10

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.12  E-value: 8.97e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163   955 CVVCGsfGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKG-WRCLECTVC 1005
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 954-1002 1.08e-09

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.84  E-value: 1.08e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 568933163    954 MCVVCGSFGqgAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 1002
Cdd:smart00249    1 YCSVCGKPD--DGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 344-391 1.45e-08

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 53.65  E-value: 1.45e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 568933163   344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVT--PLKRAGWQCPECKVC 391
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 344-388 9.99e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.36  E-value: 9.99e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 568933163    344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTP-LKRAGWQCPEC 388
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 467-517 1.10e-06

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.36  E-value: 1.10e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 568933163    467 CPFCGKCYHPElqkDMLHCNMCKRWVHLECDKPTdqELDSQLKEDYICMYC 517
Cdd:smart00249    2 CSVCGKPDDGG---ELLQCDGCDRWYHQTCLGPP--LLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 467-518 2.55e-06

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 47.10  E-value: 2.55e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163   467 CPFCGKcyhPELQKDMLHCNMCKRWVHLECDKPTDQELDsQLKEDYICMYCK 518
Cdd:pfam00628    2 CAVCGK---SDDGGELVQCDGCDDWFHLACLGPPLDPAE-IPSGEWLCPECK 49
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2175-2597 3.57e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 53.62  E-value: 3.57e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2175 GTPRPNTIDPYSQQPPTPRPSPQ---TDMFVSSVANQRHTDP-----YTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTR 2246
Cdd:pfam03154  130 GSSDPKDIDQDNRSTSPSIPSPQdneSDSDSSAQQQILQTQPpvlqaQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQ 209

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2247 PSSarPALMPNQDPFLQAA-----QNRVPGLPGPLIRPPDTCSQTPRPPGPGRIdtfthaSSSAVRDPYDQPPVTPRPHS 2321
Cdd:pfam03154  210 GSP--ATSQPPNQTQSTAAphtliQQTPTLHPQRLPSPHPPLQPMTQPPPPSQV------SPQPLPQPSLHGQMPPMPHS 281

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2322 ESFGTSQVVHDLVDRPVPGSegnfstssnlPVSSQGQQfssvsqLPGPVPTSGGTDTQNTvnMSQADTEKLRQRQKLREI 2401
Cdd:pfam03154  282 LQTGPSHMQHPVPPQPFPLT----------PQSSQSQV------PPGPSPAAPGQSQQRI--HTPPSQSQLQSQQPPREQ 343

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2402 ILQQQQqkkIASRQEKGPQDTAVVPHPVPLPHWQPESINQAF------TRPPPPY--PGSTRSPVIPPLG--PRYAVFPK 2471
Cdd:pfam03154  344 PLPPAP---LSMPHIKPPPTTPIPQLPNPQSHKHPPHLSGPSpfqmnsNLPPPPAlkPLSSLSTHHPPSAhpPPLQLMPQ 420

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2472 DQRGPYPPE-----VAGMGMRPHGFRFGFPGAGHgPMPSQDRFhvPQQIQGSGIPPHIRRPMSmemprpsnnPPLNNPVG 2546
Cdd:pfam03154  421 SQQLPPPPAqppvlTQSQSLPPPAASHPPTSGLH-QVPSQSPF--PQHPFVPGGPPPITPPSG---------PPTSTSSA 488

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568933163  2547 LPQHFPPQGLPVQQHNILGQAF------IELRHRAPDG----RSRLPFAASPS---SVIESPSH 2597
Cdd:pfam03154  489 MPGIQPPSSASVSSSGPVPAAVscplppVQIKEEALDEaeepESPPPPPRSPSpepTVVNTPSH 552
HMG_box pfam00505
HMG (high mobility group) box;
1661-1712 1.22e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 45.68  E-value: 1.22e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 568933163  1661 VLYTNINFPNLKEEFPDWTTR--VKQIAKLWRKASSQERAPYVQKARDNRAALR 1712
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
HMG smart00398
high mobility group;
1659-1712 1.34e-05

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 45.77  E-value: 1.34e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 568933163   1659 APVLYTNINFPNLKEEFPDWTT--RVKQIAKLWRKASSQERAPYVQKARDNRAALR 1712
Cdd:smart00398    8 AFMLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1082-1133 8.93e-05

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 42.86  E-value: 8.93e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  1082 CPVCcRNYREEDLILQCRQCDRWMHAVCqnLNTEEEVENVADIGFDCSMCRP 1133
Cdd:pfam00628    2 CAVC-GKSDDGGELVQCDGCDDWFHLAC--LGPPLDPAEIPSGEWLCPECKP 50
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 2024-2341 3.77e-04

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 46.60  E-value: 3.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2024 PSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQ--DPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQS 2101
Cdd:COG5180   138 TREATSASAGVALAAALLQRSDPILAKDPDGDSASTLPPPAEklDKVLTEPRDALKDSPEKLDRPKVEVKDEAQEEPPDL 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2102 NDPYSHPPLtphPAMTESFthasraFPQPGTiSRSASQDPYSQPPGTPRPLIDSysqtsgtARSNPDPYSQPPGTPRPNt 2181
Cdd:COG5180   218 TGGADHPRP---EAASSPK------VDPPST-SEARSRPATVDAQPEMRPPADA-------KERRRAAIGDTPAAEPPG- 279

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2182 idpysQQPPTPRPSPQTDMfvSSVANQRHTDPYTHHLGPP--RPGISVPYSQPPAVPRPRTSEGftRPSSA-RPALMPNQ 2258
Cdd:COG5180   280 -----LPVLEAGSEPQSDA--PEAETARPIDVKGVASAPPatRPVRPPGGARDPGTPRPGQPTE--RPAGVpEAASDAGQ 350

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2259 DP-FLQAAQNRVPGLPGPLIRPPDTCSQTPRPPGpgridtfthasssavrDPYDQPPVTPRPHSESFGTSQVVHDLVDRP 2337
Cdd:COG5180   351 PPsAYPPAEEAVPGKPLEQGAPRPGSSGGDGAPF----------------QPPNGAPQPGLGRRGAPGPPMGAGDLVQAA 414


                  ....
gi 568933163 2338 VPGS 2341
Cdd:COG5180   415 LDGG 418
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 3192-3274 9.81e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 45.55  E-value: 9.81e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3192 EEWLQETQQLLQmqqkylEEQigahrKSKKALSAKQRT--AKKAG-REFPEEDAEQLKHVTEQQSMVQKQLEQIRKQQKE 3268
Cdd:pfam01576  467 ESQLQDTQELLQ------EET-----RQKLNLSTRLRQleDERNSlQEQLEEEEEAKRNVERQLSTLQAQLSDMKKKLEE 535


                   ....*.
gi 568933163  3269 HAELIE 3274
Cdd:pfam01576  536 DAGTLE 541
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
4366-4449 1.32e-03

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.97  E-value: 1.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4366 WVHLNCALWSTEVY--ETQAGALINVELALRRGL-QMKCVFCHKTGATS-GCHRFRCTNIYHFTCATKAqCMFFK----- 4436
Cdd:COG5141   268 WGHVICAMFNPELSfgHLLSKDPIDNIASVSSSRwKLGCLICKEFGGTCiQCSYFNCTRAYHVTCARRA-GYFDLniysh 346

                          90       100
                  ....*....|....*....|
gi 568933163 4437 -------DKTMLCPMHKPKG 4449
Cdd:COG5141   347 ngisyciDHEPLCRKHYPLG 366
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 4401-4445 2.17e-03

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 38.73  E-value: 2.17e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 568933163   4401 CVFCHKTGATS---GCHRfrCTNIYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1082-1131 2.32e-03

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 38.73  E-value: 2.32e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 568933163   1082 CPVCcRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVadiGFDCSMC 1131
Cdd:smart00249    2 CSVC-GKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDG---KWYCPKC 47
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3289-3601 3.65e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.60  E-value: 3.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3289 LAPPILM----PGVQPQPPLV-------PGATSLTMSQPNFPMVPQQLQHQQHTAVISGHTSPARMPSLPgwQSNSASAH 3357
Cdd:pfam03154  169 TQPPVLQaqsgAASPPSPPPPgttqaatAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLH--PQRLPSPH 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3358 LPLNPPRIQPPIAQLSLKTcTPAPGTVSSANP-----QNGPPPRVEFDDNNPFSESFQERERKERLREQQE--RQRVQLM 3430
Cdd:pfam03154  247 PPLQPMTQPPPPSQVSPQP-LPQPSLHGQMPPmphslQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAapGQSQQRI 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3431 QEVDRQRALQQRMEMEQHCLMGAELA-------NRTPVSQMPFYGSDRPCDFLQPPRP--LQQSPQHQQQIGPVLQQQNV 3501
Cdd:pfam03154  326 HTPPSQSQLQSQQPPREQPLPPAPLSmphikppPTTPIPQLPNPQSHKHPPHLSGPSPfqMNSNLPPPPALKPLSSLSTH 405

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3502 QQGSVNSPPNQTFMQTneqRQVGPPsfvPDSPSASGGSPNFHSvkPGHGNLPGSSFQQSPLRPPFT--PILPGTSP--VA 3577
Cdd:pfam03154  406 HPPSAHPPPLQLMPQS---QQLPPP---PAQPPVLTQSQSLPP--PAASHPPTSGLHQVPSQSPFPqhPFVPGGPPpiTP 477

                          330       340
                   ....*....|....*....|....
gi 568933163  3578 NSNVPCGQDPAVTQGQNYSGSSQS 3601
Cdd:pfam03154  478 PSGPPTSTSSAMPGIQPPSSASVS 501
mukB PRK04863
chromosome partition protein MukB;
3189-3279 5.41e-03

chromosome partition protein MukB;


Pssm-ID: 235316 [Multi-domain]  Cd Length: 1486  Bit Score: 43.41  E-value: 5.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 3189 KQYEEWLQETQQLLQMQQKY--LEEQIGAHRKSKKALsakQRTAKKAGREFPEEDA---------EQLKHVTEQQSMVQK 3257
Cdd:PRK04863  503 RRLREQRHLAEQLQQLRMRLseLEQRLRQQQRAERLL---AEFCKRLGKNLDDEDEleqlqeeleARLESLSESVSEARE 579

                          90       100
                  ....*....|....*....|..
gi 568933163 3258 QLEQIRKQQKEHAELIEDYRIK 3279
Cdd:PRK04863  580 RRMALRQQLEQLQARIQRLAAR 601
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 3183-3274 5.71e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 42.44  E-value: 5.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 3183 VNDSQRKQYEEwLQETQQLLQMQQKYLEEQigahRKSKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQLEQI 3262
Cdd:COG4942   144 LAPARREQAEE-LRADLAELAALRAELEAE----RAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAEL 218

                          90
                  ....*....|..
gi 568933163 3263 RKQQKEHAELIE 3274
Cdd:COG4942   219 QQEAEELEALIA 230
 
Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4693-4845 7.28e-118

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 369.84  E-value: 7.28e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4693 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDA 4772
Cdd:cd19171     1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4773 TLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4845
Cdd:cd19171    81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
SET_KMT2C cd19208
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) ...
 4692-4845 9.22e-108

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C (EC2.1.1.43; also termed lysine N-methyltransferase 2C, homologous to ALR protein (HALR) myeloid/lymphoid, or mixed-lineage leukemia protein 3 (MLL3)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me) and may be involved in leukemogenesis and developmental disorder. KMT2C is a catalytic subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Overexpression of KMT2C is associated with estrogen receptor-positive breast cancer; KMT2C mediates the estrogen dependence of breast cancer through regulation of estrogen receptor alpha (ERalpha) enhancer function. KMT2C is frequently mutated in certain populations with diffuse-type gastric adenocarcinomas (DGA); its loss promotes epithelial-to-mesenchymal transition (EMT) and is associated with worse overall survival.


Pssm-ID: 380985 [Multi-domain]  Cd Length: 154  Bit Score: 340.84  E-value: 9.22e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4692 SKSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVID 4771
Cdd:cd19208     1 SKSSQYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRIDNDHVID 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568933163 4772 ATLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4845
Cdd:cd19208    81 ATLTGGPARYINHSCAPNCVAEVVTFEKGHKIIISSSRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 154
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 4691-4845 1.37e-94

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380986 [Multi-domain]  Cd Length: 155  Bit Score: 303.54  E-value: 1.37e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4691 HSKSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVI 4770
Cdd:cd19209     1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568933163 4771 DATLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4845
Cdd:cd19209    81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4341-4445 2.03e-73

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 240.72  E-value: 2.03e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4420
Cdd:cd15697     1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                          90       100
                  ....*....|....*....|....*
gi 568933163 4421 IYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:cd15697    81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
SET_SETD1-like cd10518
SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), ...
 4694-4842 1.38e-72

SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), histone-lysine N-methyltransferases (KMT2A/KMT2B/KMT2C/KMT2D) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A), 1B (SETD1B), as well as histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B), 2C (KMT2C), 2D (KMT2D). These proteins are histone-lysine N-methyltransferases (EC 2.1.1.43) that specifically methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380916  Cd Length: 150  Bit Score: 240.19  E-value: 1.38e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4694 SSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQN-RGVYMFRMDNDHVIDA 4772
Cdd:cd10518     2 SKRFRQLRSRLKERLRVGKSGIHGWGLFAKRPIAAGEMVIEYVGEVIRPIVADKREKRYDEEGgGGTYMFRIDEDLVIDA 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4773 TLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQhKIPCHCGAVNCR 4842
Cdd:cd10518    82 TKKGNIARFINHSCDPNCYAKIITVDGEKHIVIFAKRDIAPGEELTYDYKFPIEDEE-KIPCLCGAPNCR 150
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 4341-4445 7.55e-70

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 230.27  E-value: 7.55e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4420
Cdd:cd15666     1 CVLCGGEGDGDTDGPGRLLNLDVDKWVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCAN 80

                          90       100
                  ....*....|....*....|....*
gi 568933163 4421 IYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:cd15666    81 VYHLPCAIKDGCMFFKDKTMLCPSH 105
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4341-4446 1.43e-64

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 215.30  E-value: 1.43e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4420
Cdd:cd15698     1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                          90       100
                  ....*....|....*....|....*.
gi 568933163 4421 IYHFTCATKAQCMFFKDKTMLCPMHK 4446
Cdd:cd15698    81 VYHFACAIRAKCMFFKDKTMLCPMHK 106
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 4694-4846 3.75e-59

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins; This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380947 [Multi-domain]  Cd Length: 152  Bit Score: 201.85  E-value: 3.75e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4694 SSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDAT 4773
Cdd:cd19170     2 AMRFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDAT 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4774 LTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCRKWMN 4846
Cdd:cd19170    82 MHGNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIEDV--KIPCTCGSKKCRKYLN 152
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1640-1720 1.79e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 1.79e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1640 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 1719
Cdd:cd22026     1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                  .
gi 568933163 1720 N 1720
Cdd:cd22026    81 N 81
SET_SETD1 cd19169
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ...
 4705-4842 2.82e-54

SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated.


Pssm-ID: 380946  Cd Length: 148  Bit Score: 187.54  E-value: 2.82e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4705 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRG-VYMFRMDNDHVIDATLTGGPARYIN 4783
Cdd:cd19169    12 KKQLKFAKSRIHDWGLFALEPIAADEMVIEYVGQVIRQSVADEREKRYEAIGIGsSYLFRVDDDTIIDATKCGNLARFIN 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 4784 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCR 4842
Cdd:cd19169    92 HSCNPNCYAKIITVESQKKIVIYSKRPIAVNEEITYDYKFPIEDE--KIPCLCGAPQCR 148
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 247-330 1.16e-53

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 183.61  E-value: 1.16e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15696     7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                  ....
gi 568933163  327 CPEH 330
Cdd:cd15696    87 CPTH 90
SET_SET1 cd20072
SET domain (including post-SET domain) found in catalytic component of the Saccharomyces ...
 4705-4842 6.83e-49

SET domain (including post-SET domain) found in catalytic component of the Saccharomyces cerevisiae COMPASS complex and similar proteins; The family contains mostly fungal SET domains, including SET1 found in the catalytic component of the Saccharomyces cerevisiae COMPASS (complex of proteins associated with Set1). SET1 is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex. The activity of this catalytic domain is established through forming a complex with a set of core proteins; it is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3).


Pssm-ID: 380998  Cd Length: 148  Bit Score: 172.22  E-value: 6.83e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4705 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRG-VYMFRMDNDHVIDATLTGGPARYIN 4783
Cdd:cd20072    12 KKQLKFARSAIHNWGLYAMENISAKDMVIEYVGEVIRQQVADEREKRYLRQGIGsSYLFRIDDDTVVDATKKGNIARFIN 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 4784 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCR 4842
Cdd:cd20072    92 HCCDPNCTAKIIKVEGEKRIVIYAKRDIAAGEELTYDYKFPREED--KIPCLCGAPNCR 148
SET_KMT2A cd19206
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) ...
 4696-4846 6.58e-47

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) and similar proteins; KMT2A (EC2.1.1.43; also termed lysine N-methyltransferase 2A, ALL-1, CXXC-type zinc finger protein 7 (CXXC7), myeloid/lymphoid or mixed-lineage leukemia (MLL), myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (TRX1), or zinc finger protein HRX) acts as a histone methyltransferase that plays an essential role in early development and hematopoiesis. It is a catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac).


Pssm-ID: 380983 [Multi-domain]  Cd Length: 154  Bit Score: 166.74  E-value: 6.58e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4696 QYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLT 4775
Cdd:cd19206     4 RFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYSGNVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMH 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568933163 4776 GGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN 4846
Cdd:cd19206    84 GNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 154
SET_KMT2B cd19207
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) ...
 4696-4846 4.62e-44

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) and similar proteins; KMT2B (EC2.1.1.43; also termed lysine N-methyltransferase 2B, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL2/MLL4), trithorax homolog 2 (TRX2), or WW domain-binding protein 7 (WBP-7)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is required during the transcriptionally active period of oocyte growth for the establishment and/or maintenance of bulk H3K4 trimethylation (H3K4me3), global transcriptional silencing that precedes resumption of meiosis, oocyte survival and normal zygotic genome activation.


Pssm-ID: 380984 [Multi-domain]  Cd Length: 154  Bit Score: 158.65  E-value: 4.62e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4696 QYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLT 4775
Cdd:cd19207     4 RFRHLKKTSKEAVGVYRSAIHGRGLFCKRNIDAGEMVIEYSGIVIRSVLTDKREKFYDSKGIGCYMFRIDDFDVVDATMH 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568933163 4776 GGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN 4846
Cdd:cd19207    84 GNAARFINHSCEPNCYSRVIHVEGQKHIVIFALRKIYRGEELTYDYKFPIEDASNKLPCNCGAKRCRRFLN 154
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 247-330 2.74e-42

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 150.93  E-value: 2.74e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15665     7 GEVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSKSFHFPCAAAAGCFQDIKTLTLF 86


                  ....
gi 568933163  327 CPEH 330
Cdd:cd15665    87 CPEH 90
HMG_KMT2C-like cd21997
high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and ...
 1645-1711 1.01e-41

high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and similar proteins; This subfamily includes KMT2C and KMT2D. KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, and farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. All subfamily members contain one HMG-box domain.


Pssm-ID: 438813  Cd Length: 67  Bit Score: 148.66  E-value: 1.01e-41
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163 1645 KWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAAL 1711
Cdd:cd21997     1 KWEKDEPLGDMATISPVLYANINHPNLKQEYPDWTDRAKQIAKLWRKLSAEERAPYLQKARENRAAL 67
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1636-1717 2.43e-40

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438836  Cd Length: 84  Bit Score: 145.23  E-value: 2.43e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1636 LSNAQRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINK 1715
Cdd:cd22027     2 LSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRINK 81


                  ..
gi 568933163 1716 VQ 1717
Cdd:cd22027    82 VQ 83
SET_SETD1A cd19204
SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and ...
 4705-4846 1.18e-39

SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and similar proteins; SETD1A (EC2.1.1.43), also termed lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit SET1, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Human SET domain containing protein 1A (hSETD1A) expression occurs at a high rate in hepatocellular carcinoma patients and controls tumor metastasis in breast cancer by activating MMP expression.


Pssm-ID: 380981 [Multi-domain]  Cd Length: 153  Bit Score: 145.94  E-value: 1.18e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4705 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGV-YMFRMDNDHVIDATLTGGPARYIN 4783
Cdd:cd19204    13 KKKLRFGRSRIHEWGLFAMEPIAADEMVIEYVGQNIRQVVADMREKRYVQEGIGSsYLFRVDHDTIIDATKCGNLARFIN 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4784 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCRKWMN 4846
Cdd:cd19204    93 HCCTPNCYAKVITIESQKKIVIYSKQPIGVNEEITYDYKFPIEDN--KIPCLCGTENCRGTLN 153
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
4705-4844 4.89e-38

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 140.48  E-value: 4.89e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4705 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgvYMFRMDNDHVIDATLTGGPARYINH 4784
Cdd:COG2940     5 HPRIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINH 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4785 SCAPNCVAEvvtfERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHkiPCHCGavNCRKW 4844
Cdd:COG2940    83 SCDPNCEAD----EEDGRIFIVALRDIAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
SET_SETD1B cd19205
SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and ...
 4705-4846 1.05e-37

SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and similar proteins; SETD1B (EC2.1.1.43), also termed lysine N-methyltransferase 2G, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Loss of SETD1B occurs in up to half the gastric and colorectal cancers, most commonly via SETD1B mutations, while de novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.


Pssm-ID: 380982 [Multi-domain]  Cd Length: 153  Bit Score: 140.58  E-value: 1.05e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4705 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGV-YMFRMDNDHVIDATLTGGPARYIN 4783
Cdd:cd19205    13 KKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSsYMFRVDHDTIIDATKCGNFARFIN 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4784 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCRKWMN 4846
Cdd:cd19205    93 HSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDV--KIPCLCGSENCRGTLN 153
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 4341-4445 1.45e-37

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 138.31  E-value: 1.45e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4420
Cdd:cd15664     1 CALCGVYGDDEPNDAGRLLYCGQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPA 80

                          90       100
                  ....*....|....*....|....*
gi 568933163 4421 IYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:cd15664    81 NYHFMCARKAECVFQDDKKVFCPAH 105
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 947-1003 3.79e-36

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 132.45  E-value: 3.79e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163  947 KFTLQQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 1003
Cdd:cd15596     1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 4707-4828 1.16e-35

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 133.61  E-value: 1.16e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163   4707 NVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNR-GVYMFRMDNDHVIDATLTGGPARYINHS 4785
Cdd:smart00317    2 KLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAkAFYLFDIDSDLCIDARRKGNLARFINHS 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|...
gi 568933163   4786 CAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDD 4828
Cdd:smart00317   82 CEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 4339-4446 3.93e-34

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 128.58  E-value: 3.93e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4339 RKCCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRC 4418
Cdd:cd15693     1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                          90       100
                  ....*....|....*....|....*...
gi 568933163 4419 TNIYHFTCATKAQCMFFKDKTMLCPMHK 4446
Cdd:cd15693    81 TSNYHFMCSRAKNCVFLEDKKVYCQRHK 108
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1081-1131 4.21e-32

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


Pssm-ID: 277073  Cd Length: 51  Bit Score: 120.42  E-value: 4.21e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163 1081 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1131
Cdd:cd15600     1 TCPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
SET_SETD2-like cd10531
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), ...
 4707-4842 6.32e-32

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2), ASH1-like protein (ASH1L) and similar proteins; This family includes SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2) and ASH1-like protein (ASH1L), which function as histone-lysine N-methyltransferases. SETD2 specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. NSD2 shows histone H3 'Lys-27' (H3K27me) methyltransferase activity. ASH1L specifically methylates 'Lys-36' of histone H3 (H3K36me). The family also includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins.


Pssm-ID: 380929  Cd Length: 136  Bit Score: 123.13  E-value: 6.32e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4707 NVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQN-RGVYMFRMDNDHVIDATLTGGPARYINHS 4785
Cdd:cd10531     1 KLELFRTEKKGWGVKAKEDIQKGEFIIEYVGEVIDKKEFKERLDEYEELGkSNFYILSLSDDVVIDATRKGNLSRFINHS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568933163 4786 CAPNCVAEvVTFERGHKII-ISSNRRIQKGEELCYDYKFDFEDDQhKIPCHCGAVNCR 4842
Cdd:cd10531    81 CEPNCETQ-KWIVNGEYRIgIFALRDIPAGEELTFDYNFVNYNEA-KQVCLCGAQNCR 136
SET_SETD2 cd19172
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and ...
 4706-4845 6.66e-32

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins; SETD2 (also termed HIF-1, huntingtin yeast partner B, huntingtin-interacting protein 1 (HIP-1), huntingtin-interacting protein B, lysine N-methyltransferase 3A or protein-lysine N-methyltransferase SETD2) acts as histone-lysine N-methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. It has been shown that methylation is a posttranslational modification of dynamic microtubules and that SETD2 methylates alpha-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy.


Pssm-ID: 380949 [Multi-domain]  Cd Length: 142  Bit Score: 123.46  E-value: 6.66e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4706 SNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRM-DNDHVIDATLTGGPARYINH 4784
Cdd:cd19172     2 AKVEVFRTEKKGWGLRAAEDLPKGTFVIEYVGEVLDEKEFKRRMKEYAREGNRHYYFMAlKSDEIIDATKKGNLSRFINH 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4785 SCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFD--FEDDQhkiPCHCGAVNCRKWM 4845
Cdd:cd19172    82 SCEPNCETQKWTVNGELRVGFFAKRDIPAGEELTFDYQFEryGKEAQ---KCYCGSPNCRGYI 141
SET_ASHR3-like cd19175
SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 ...
 4717-4845 2.70e-31

SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins; This family includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3, also termed protein SET DOMAIN GROUP 4 or protein stamen loss), ASH1 homolog 3 (ASHH3, also termed protein SET DOMAIN GROUP 7) and homolog 4 (ASHH4, also termed protein SET DOMAIN GROUP 24). They all function as histone-lysine N-methyltransferases (EC 2.1.1.43).


Pssm-ID: 380952 [Multi-domain]  Cd Length: 139  Bit Score: 121.37  E-value: 2.70e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKHTMVIEYIGTIIRNEVAnrKEKLYESQNRG---VYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAE 4793
Cdd:cd19175    11 GWGLVADEDINAGEFIIEYVGEVIDDKTC--EERLWDMKHKGeknFYMCEIDKDMVIDATFKGNLSRFINHSCDPNCELQ 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4794 VVTFERGHKIIISSNRRIQKGEELCYDYKF-DFEDDQHkipCHCGAVNCRKWM 4845
Cdd:cd19175    89 KWQVDGETRIGVFAIRDIKKGEELTYDYQFvQFGADQD---CHCGSKNCRGKL 138
SET_EZH cd10519
SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar ...
 4708-4821 3.54e-31

SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both, EZH1 and EZH2, can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380917  Cd Length: 117  Bit Score: 120.43  E-value: 3.54e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4708 VYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGvYMFRMDNDHVIDATLTGGPARYINHSCA 4787
Cdd:cd10519     3 LLLGKSDVAGWGLFLKEPIKKDEFIGEYTGELISQDEADRRGKIYDKYNSS-YLFNLNDQFVVDATRKGNKIRFANHSSN 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 568933163 4788 PNCVAEVVTFERGHKIIISSNRRIQKGEELCYDY 4821
Cdd:cd10519    82 PNCYAKVMMVNGDHRIGIFAKRDIEAGEELFFDY 115
SET_NSD cd19173
SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, ...
 4717-4841 4.69e-31

SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, NSD2, NSD3 and similar proteins; The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2, and NSD3, which are primarily known to be involved in chromatin integrity and gene expression through mono-, di-, or tri-methylating lysine 36 of histone H3 (H3K36), respectively. NSD1 (EC 2.1.1.43; also termed histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B) or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3.


Pssm-ID: 380950 [Multi-domain]  Cd Length: 142  Bit Score: 120.88  E-value: 4.69e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVV 4795
Cdd:cd19173    13 GWGLRTKRDIKKGDFVIEYVGELIdEEECRRRLKKAHENNITNFYMLTLDKDRIIDAGPKGNLSRFMNHSCQPNCETQKW 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 4796 TFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQhKIPCHCGAVNC 4841
Cdd:cd19173    93 TVNGDTRVGLFAVRDIPAGEELTFNYNLDCLGNE-KKVCRCGAPNC 137
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1004-1050 6.25e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.11  E-value: 6.25e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1050
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 954-1002 3.08e-29

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 112.17  E-value: 3.08e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  954 MCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 1002
Cdd:cd15512     1 MCVSCGSFGRGAEGRLIACSQCGQCYHPYCVNVKVTKVILSKGWRCLDC 49
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 4717-4822 3.83e-29

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 114.54  E-value: 3.83e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  4717 GLGLYAARDIEKHTMVIEYIGT-IIRNEVANRKEKLYESQNR----GVYMFRMDND--HVIDATLT--GGPARYINHSCA 4787
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDEDseYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 568933163  4788 PNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYK 4822
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDYG 115
SET_SUV39H cd10542
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4717-4845 6.91e-29

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homologs, SUV39H1, SUV39H2 and similar proteins; This family includes SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. Also included are Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (SUV39H homolog) and Neurospora crassa DIM-5, both of which also methylate 'Lys-9' of histone H3.


Pssm-ID: 380940 [Multi-domain]  Cd Length: 245  Bit Score: 118.55  E-value: 6.91e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgVYMFRMD-----NDHVIDATLTGGPARYINHSCAPN-- 4789
Cdd:cd10542    99 GWGVKTLEDIKKGTFVMEYVGEIITSEEAERRGKIYDANGR-TYLFDLDyndddCEYTVDAAYYGNISHFINHSCDPNla 177

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 4790 ---CVAEVVtFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQH----------KIPCHCGAVNCRKWM 4845
Cdd:cd10542   178 vyaVWINHL-DPRLPRIAFFAKRDIKAGEELTFDYLMTGTGGSSestipkpkdvRVPCLCGSKNCRKYL 245
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 390-435 1.13e-28

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 110.80  E-value: 1.13e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 247-330 1.87e-28

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 111.55  E-value: 1.87e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15695     7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                  ....
gi 568933163  327 CPEH 330
Cdd:cd15695    87 CPEH 90
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 4341-4445 6.85e-28

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 110.75  E-value: 6.85e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPArLLNLDLDLWVHLNCALWSTEVYETQAGAL--INVELALRRGLQMKCVFCHKT-GATSGCHRFR 4417
Cdd:cd15571     1 CALCPRSGGALKGGGA-LKTTSDGLWVHVVCALWSPEVYFDDGTLLevEGVSKIPKRRKKLKCSICGKRgGACIQCSYPG 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 568933163 4418 CTNIYHFTCATKAQCMF-----FKDKTMLCPMH 4445
Cdd:cd15571    80 CPRSFHVSCAIRAGCLFefedgPGNFVVYCPKH 112
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 466-517 2.57e-27

PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the third PHD finger.


Pssm-ID: 276986  Cd Length: 52  Bit Score: 106.80  E-value: 2.57e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  466 LCPFCGKCYHPELQKDMLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYC 517
Cdd:cd15511     1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 4341-4445 2.89e-27

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277164  Cd Length: 105  Bit Score: 108.59  E-value: 2.89e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4420
Cdd:cd15694     1 CALCLKYGDADSKDAGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLS 80

                          90       100
                  ....*....|....*....|....*
gi 568933163 4421 IYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:cd15694    81 NFHFMCARASRCCFQDDKKVFCQKH 105
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 953-1002 7.36e-27

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 105.50  E-value: 7.36e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163  953 DMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 1002
Cdd:cd15597     1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 50
SET_ASH1L cd19174
SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ...
 4717-4846 6.80e-26

SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ASH1L (EC 2.1.1.43; also termed absent small and homeotic disks protein 1 homolog, KMT2H, or lysine N-methyltransferase 2H) acts as histone-lysine N-methyltransferase that specifically methylates 'Lys-36' of histone H3 (H3K36me). It plays important roles in development; heterozygous mutation of ASH1L is associated with severe intellectual disability (ID) and multiple congenital anomaly (MCA).


Pssm-ID: 380951 [Multi-domain]  Cd Length: 141  Bit Score: 106.22  E-value: 6.80e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYeSQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCvaEVV 4795
Cdd:cd19174    11 GWGVRTKEPIKAGQFIIEYVGEVVsEQEFRRRMIEQY-HNHSHHYCLNLDSGMVIDGYRMGNEARFVNHSCDPNC--EMQ 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4796 TFE-RG-HKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN 4846
Cdd:cd19174    88 KWSvNGvYRIGLFALKDIPAGEELTYDYNFHSFNVEKQQPCKCGSPNCRGVIG 140
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 390-435 4.10e-25

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 100.59  E-value: 4.10e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15510     1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4549-4636 8.48e-25

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 100.83  E-value: 8.48e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163   4549 VFVIRIVEQGheDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYTF 4628
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 568933163   4629 RYGRNPLM 4636
Cdd:smart00542   79 RYHRSPLL 86
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4547-4631 8.99e-25

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 100.76  E-value: 8.99e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  4547 RPVFVIRIVEqgHEDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENY 4626
Cdd:pfam05965    1 GPLFRVTVEE--DPDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 568933163  4627 TFRYG 4631
Cdd:pfam05965   79 KFRYG 83
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 1081-1131 1.80e-24

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D.


Pssm-ID: 276989  Cd Length: 51  Bit Score: 98.90  E-value: 1.80e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163 1081 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1131
Cdd:cd15514     1 KCPVCSRSYNEGELIIQCSQCERWLHGACDSLRTEEEAERAADNGYRCLLC 51
SET_EZH2 cd19218
SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43) ...
 4704-4823 1.52e-23

SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43), also termed lysine N-methyltransferase 6, or ENX-1, or histone-lysine N-methyltransferase EZH2, is a catalytic subunit of the polycomb repressive complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380995  Cd Length: 120  Bit Score: 98.83  E-value: 1.52e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4704 WKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYEsQNRGVYMFRMDNDHVIDATLTGGPARYIN 4783
Cdd:cd19218     2 SKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYD-KYMCSFLFNLNNDFVVDATRKGNKIRFAN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 568933163 4784 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKF 4823
Cdd:cd19218    81 HSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRY 120
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 343-388 2.24e-23

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 95.45  E-value: 2.24e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163  343 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV--TPLKRAGWQCPEC 388
Cdd:cd15509     1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 390-435 9.92e-23

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 93.91  E-value: 9.92e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
SET_EZH1 cd19217
SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43) ...
 4705-4827 4.93e-22

SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43), also termed ENX-2, or histone-lysine N-methyltransferase EZH1, is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380994  Cd Length: 136  Bit Score: 95.13  E-value: 4.93e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4705 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYEsQNRGVYMFRMDNDHVIDATLTGGPARYINH 4784
Cdd:cd19217     5 KKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYD-KYMSSFLFNLNNDFVVDATRKGNKIRFANH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 568933163 4785 SCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFED 4827
Cdd:cd19217    84 SVNPNCYAKVVMVNGDHRIGIFAKRAIQQGEELFFDYRYSQAD 126
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1081-1131 5.14e-22

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 91.89  E-value: 5.14e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163 1081 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1131
Cdd:cd15601     1 TCPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1880-2370 2.90e-21

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 103.86  E-value: 2.90e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1880 ESLSQSQNSQPP---SPQMFSPGSSHSRPPSPvdpYAkmvgtPRPP-PGGHSFPRRNSVTPvencvplssvprpihmnet 1955
Cdd:PHA03247 2541 EELASDDAGDPPpplPPAAPPAAPDRSVPPPR---PA-----PRPSePAVTSRARRPDAPP------------------- 2593

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1956 SATRPSPARDLCASSMTNSDPYAKPPDTPRPmmtdqfsKPFSLPRSPVISEQSTKGPLTTGTSDHFTKPS--PRTDAFQR 2033
Cdd:PHA03247 2594 QSARPRAPVDDRGDPRGPAPPSPLPPDTHAP-------DPPPPSPSPAANEPDPHPPPTVPPPERPRDDPapGRVSRPRR 2666

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2034 QRLPDPYAGPSLTPaplgNGPfktplHPPPSQDPYGSVSQTSRRLSVDPYERPA------LTPRPVDNFSHSQSNDPYSH 2107
Cdd:PHA03247 2667 ARRLGRAAQASSPP----QRP-----RRRAARPTVGSLTSLADPPPPPPTPEPAphalvsATPLPPGPAAARQASPALPA 2737

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2108 PPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTP-----RPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTI 2182
Cdd:PHA03247 2738 APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPprrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAA 2817

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2183 DPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYT------------HHLGPPRPGISVPYSQP---------PAVPRPRTS 2241
Cdd:PHA03247 2818 LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLplggsvapggdvRRRPPSRSPAAKPAAPArppvrrlarPAVSRSTES 2897

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2242 EGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPdtcsqtPRPPGPGRIDTFTHAS---SSAVRDPYDQPPVTPR 2318
Cdd:PHA03247 2898 FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP------PRPQPPLAPTTDPAGAgepSGAVPQPWLGALVPGR 2971

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568933163 2319 PHSESFGTSQvvhDLVDRPVPGSEGNFSTSSNLP-VSSQGQQFS-SVSQLPGPV 2370
Cdd:PHA03247 2972 VAVPRFRVPQ---PAPSREAPASSTPPLTGHSLSrVSSWASSLAlHEETDPPPV 3022
SET_SETDB-like cd10538
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 4712-4821 2.20e-20

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins; The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380936 [Multi-domain]  Cd Length: 217  Bit Score: 92.82  E-value: 2.20e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4712 RSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYeSQNRGVYMFRMDND---------HVIDATLTGGPARYI 4782
Cdd:cd10538    95 RTSKKGWGVRSLEFIPKGSFVCEYVGEVITTSEADRRGKIY-DKSGGSYLFDLDEFsdsdgdgeeLCVDATFCGNVSRFI 173

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 568933163 4783 NHSCAPN----CVAEVVTFERGHKIIISSNRRIQKGEELCYDY 4821
Cdd:cd10538   174 NHSCDPNlfpfNVVIDHDDLRYPRIALFATRDILPGEELTFDY 216
SET_NSD2 cd19211
SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) ...
 4710-4841 6.16e-20

SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems, and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness. WHSC1 is frequently deleted in Wolf-Hirschhorn syndrome (WHS).


Pssm-ID: 380988 [Multi-domain]  Cd Length: 142  Bit Score: 89.28  E-value: 6.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4710 LARSRIQGLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAP 4788
Cdd:cd19211     6 IIKTEGKGWGLIAKRDIKKGEFVNEYVGELIdEEECMARIKHAHENDITHFYMLTIDKDRIIDAGPKGNYSRFMNHSCQP 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4789 NCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIpCHCGAVNC 4841
Cdd:cd19211    86 NCETQKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCLGNEKTV-CRCGAPNC 137
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 4341-4445 2.19e-19

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 86.21  E-value: 2.19e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFC--HEEGDGLTD--GPArllnldLDLWVHLNCALWSTEVYETqAGALINVELALRRGLQMKCVFCHKTGATSGCHRF 4416
Cdd:cd15668     1 CVFCkrGPHYKGLGDlfGPY------YEVWVHEDCAVWAPGVYLV-GGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHK 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 568933163 4417 RCTNIYHFTCATKAQCMFFKDK-TMLCPMH 4445
Cdd:cd15668    74 GCKAKYHYPCAVESGCQLDEENfSLLCPKH 103
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 241-330 9.18e-19

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 84.56  E-value: 9.18e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  241 ALFDSTGTCWAHHRCVEWS--LGICQMEEPLLVNVDKAVVSGSTERCAFCKH-LGATIKCCEEKCTQMYHYPCAAGAGTF 317
Cdd:cd15571    16 ALKTTSDGLWVHVVCALWSpeVYFDDGTLLEVEGVSKIPKRRKKLKCSICGKrGGACIQCSYPGCPRSFHVSCAIRAGCL 95

                          90
                  ....*....|....*..
gi 568933163  318 QDFS----HFFLLCPEH 330
Cdd:cd15571    96 FEFEdgpgNFVVYCPKH 112
SET_SETD8 cd10528
SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2. ...
 4714-4821 1.07e-18

SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2.1.1.43; also termed N-lysine methyltransferase KMT5A, H4-K20-HMTase KMT5A, lysine N-methyltransferase 5A, lysine-specific methylase 5A, PR/SET domain-containing protein 07, PR-Set7 or PR/SET07) is a nucleosomal histone-lysine N-methyltransferase that specifically monomethylates 'Lys-20' of histone H4 (H4K20me1). It plays a central role in the silencing of euchromatic genes.


Pssm-ID: 380926 [Multi-domain]  Cd Length: 141  Bit Score: 85.71  E-value: 1.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4714 RIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYES-QNRGVYM--FRMDN-DHVIDATL-TGGPARYINHSC-A 4787
Cdd:cd10528    25 DGKGRGVIATRPFEKGDFVVEYHGDLITITEAKKREALYAKdPSTGCYMyyFQYKGkTYCVDATKeSGRLGRLINHSKkK 104

                          90       100       110
                  ....*....|....*....|....*....|....
gi 568933163 4788 PNCVAEVVTFERGHKIIISSNRRIQKGEELCYDY 4821
Cdd:cd10528   105 PNLKTKLLVIDGVPHLILVAKRDIKPGEELLYDY 138
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4490-4541 4.60e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 80.63  E-value: 4.60e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  4490 GSLIFHTIGQLLPQQMqAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSI 4541
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
SET_EHMT cd10543
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4705-4842 5.51e-18

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase EHMT1, EHMT2 and similar proteins; This family includes EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380941 [Multi-domain]  Cd Length: 231  Bit Score: 86.24  E-value: 5.51e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4705 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKlyESqnrgvYMFRMDND----HVIDATLTGGPAR 4780
Cdd:cd10543    90 RYRLQLFRTRGMGWGVRALQDIPKGTFVCEYIGELISDSEADSRED--DS-----YLFDLDNKdgetYCIDARRYGNISR 162

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 4781 YINHSCAPNCVAevVTFERGH------KIIISSNRRIQKGEELCYDYKFDFEDDQHK-IPCHCGAVNCR 4842
Cdd:cd10543   163 FINHLCEPNLIP--VRVFVEHqdlrfpRIAFFASRDIKAGEELGFDYGEKFWRIKGKyFTCRCGSPKCK 229
SET_NSD3 cd19212
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 4716-4841 1.43e-17

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 3 (NSD3) and similar proteins; NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. NSD3 is amplified and overexpressed in multiple cancer types, including acute myeloid leukemia (AML), breast, lung, pancreatic and bladder cancers, as well as squamous cell carcinoma of the head and neck (SCCHN). NSD3 contributes to tumorigenesis by interacting with bromodomain-containing protein 4 (BRD4), the bromodomain and extraterminal (BET) protein, which is a potential therapeutic target in acute myeloid leukemia (AML). NSD3 is amplified in primary tumors and cell lines from breast carcinoma, and can promote the cell viability of small-cell lung cancer and pancreatic ductal adenocarcinoma. High NSD3 expression is implicated in poor grade and heavy smoking history in SCCHN. Thus, NSD3 may serve as a potential druggable target for selective cancer therapy.


Pssm-ID: 380989 [Multi-domain]  Cd Length: 142  Bit Score: 82.28  E-value: 1.43e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4716 QGLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEV 4794
Cdd:cd19212    12 RGWGLRTKRSIKKGEFVNEYVGELIdEEECRLRIKRAHENSVTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCETQK 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 4795 VTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIpCHCGAVNC 4841
Cdd:cd19212    92 WTVNGDVRVGLFALCDIPAGMELTFNYNLDCLGNGRTE-CHCGADNC 137
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 4341-4445 1.61e-17

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 80.44  E-value: 1.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCheegdgltdgparllNLDlDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4420
Cdd:cd15665     1 CALC---------------NLG-EVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSK 64

                          90       100
                  ....*....|....*....|....*.
gi 568933163 4421 IYHFTCATKAQCM-FFKDKTMLCPMH 4445
Cdd:cd15665    65 SFHFPCAAAAGCFqDIKTLTLFCPEH 90
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1961-2606 8.46e-17

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 89.23  E-value: 8.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1961 SPARDLCASSMTNSDPYAKPPDTPRPMMTDQFSKPfSLPRSPVISEQS-TKGPLTTGTSdhftkPSPRTDAfqrqrLPDP 2039
Cdd:PHA03247 2438 SPGGDVLAGLAADGDPFFARTILGAPFSLSLLLGE-LFPGAPVYRRPAeARFPFAAGAA-----PDPGGGG-----PPDP 2506

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2040 YAGP---SLTPAPLGNGPFKTPLHPppsqdpygsvsqtsrrlsvdpyeRPALTPRPVDNFSHSQSNDPYSHPPLTPHPAM 2116
Cdd:PHA03247 2507 DAPPapsRLAPAILPDEPVGEPVHP-----------------------RMLTWIRGLEELASDDAGDPPPPLPPAAPPAA 2563

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2117 TESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPlidsysqtsgtaRSNPDPYSQPPGTPRPNTIDPYSQQPPTPRPSP 2196
Cdd:PHA03247 2564 PDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARP------------RAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSP 2631

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2197 qtdmfvSSVANQRhtdPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTRPSSA--------RPALMPNQDPFLQAAQNR 2268
Cdd:PHA03247 2632 ------SPAANEP---DPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQAssppqrprRRAARPTVGSLTSLADPP 2702

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2269 VPGlPGPLIRPPDTCSQTPRPPGPgridtfthassSAVRDPYDQPPVTPRPHSESFGTSqvvhdlvdrpVPGSEGNFSTs 2348
Cdd:PHA03247 2703 PPP-PTPEPAPHALVSATPLPPGP-----------AAARQASPALPAAPAPPAVPAGPA----------TPGGPARPAR- 2759

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2349 snlPVSSQGQQFSSVSQLP--GPVPTSggtdTQNTVNMSQADTEKLrqrqklreiilqqqqqkkiasrqeKGPQDTAVVP 2426
Cdd:PHA03247 2760 ---PPTTAGPPAPAPPAAPaaGPPRRL----TRPAVASLSESRESL------------------------PSPWDPADPP 2808

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2427 HPVPLPH-WQPESINQAFTRPPPPY-----PGSTRSPVIPPLGPRYAVFPK---DQRGP--YPPEVAGMGMRPHGFRFGF 2495
Cdd:PHA03247 2809 AAVLAPAaALPPAASPAGPLPPPTSaqptaPPPPPGPPPPSLPLGGSVAPGgdvRRRPPsrSPAAKPAAPARPPVRRLAR 2888

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2496 PGaghgPMPSQDRFHVPQ-QIQGSGIPPHIRRPMSMEMPRPSNNPPLNNPV-GLPQ-HFPPQGLPVQQHNILGQA-FIEL 2571
Cdd:PHA03247 2889 PA----VSRSTESFALPPdQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPpPRPQpPLAPTTDPAGAGEPSGAVpQPWL 2964

                         650       660       670
                  ....*....|....*....|....*....|....*....
gi 568933163 2572 RHRAPDG----RSRLPFAASPSSVIESPSHPRHGNFLPR 2606
Cdd:PHA03247 2965 GALVPGRvavpRFRVPQPAPSREAPASSTPPLTGHSLSR 3003
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1870-2373 9.13e-17

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 88.84  E-value: 9.13e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1870 PSTPSRIPVQESLS-QSQNSQPPSPQMFSPGSSHSRPPSPVDPYAKmvgTPRPPPGGHSfPRRNSVTPVEncvPLSSVPR 1948
Cdd:PHA03247 2577 PSEPAVTSRARRPDaPPQSARPRAPVDDRGDPRGPAPPSPLPPDTH---APDPPPPSPS-PAANEPDPHP---PPTVPPP 2649

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1949 PIHMNETSATRPSPARDlcASSMTNSDPYAKPPDTPRPMMTDQFSKP---FSLPRSPVISEQSTKGPLTTGTsdhftkPS 2025
Cdd:PHA03247 2650 ERPRDDPAPGRVSRPRR--ARRLGRAAQASSPPQRPRRRAARPTVGSltsLADPPPPPPTPEPAPHALVSAT------PL 2721

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2026 PRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSVDPyERPALTPRPVDNFSHSQSN--- 2102
Cdd:PHA03247 2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAG-PPRRLTRPAVASLSESRESlps 2800

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2103 --DPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNP--DPYSQPPGTPR 2178
Cdd:PHA03247 2801 pwDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPsrSPAAKPAAPAR 2880

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2179 P-----------NTIDPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTRP 2247
Cdd:PHA03247 2881 PpvrrlarpavsRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2248 SSARPALMPNQDPflqAAQNRVPGlPGPLIRPPDTCSQTPRPPGPGRIDTFthASSSAVRDPYDQPPVT-------PRPH 2320
Cdd:PHA03247 2961 QPWLGALVPGRVA---VPRFRVPQ-PAPSREAPASSTPPLTGHSLSRVSSW--ASSLALHEETDPPPVSlkqtlwpPDDT 3034

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 2321 SESFGTSQVVHDLVDR------PVPGSEGNFSTSSNLPVSSQGQQFSSVSQLPGPVPTS 2373
Cdd:PHA03247 3035 EDSDADSLFDSDSERSdlealdPLPPEPHDPFAHEPDPATPEAGARESPSSQFGPPPLS 3093
SET_LegAS4-like cd10522
SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and ...
 4717-4827 9.16e-17

SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and similar proteins; LegAS4 is a type IV secretion system effector of Legionella pneumophila. It contains a SET domain that is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. It also contains an ankyrin repeat domain of unknown function at its C-terminal region.


Pssm-ID: 380920 [Multi-domain]  Cd Length: 122  Bit Score: 79.31  E-value: 9.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNrgvYMFRMDNDH-VIDATLTGGPARYINHSCAPNCVAEVV 4795
Cdd:cd10522    14 GLGLFAAETIAKGEFVGEYTGEVLDRWEEDRDSVYHYDPL---YPFDLNGDIlVIDAGKKGNLTRFINHSDQPNLELIVR 90

                          90       100       110
                  ....*....|....*....|....*....|..
gi 568933163 4796 TFERGHKIIISSNRRIQKGEELCYDYKFDFED 4827
Cdd:cd10522    91 TLKGEQHIGFVAIRDIKPGEELFISYGPKYWK 122
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 4500-4543 1.50e-16

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 76.17  E-value: 1.50e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 568933163   4500 LLPQQMQAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEE 4543
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1894-2470 1.63e-16

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 88.07  E-value: 1.63e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1894 QMFSPGSSHSRPPSPVDPYAkmvGTPRPPPGGhsfprrnSVTPVENCVPLSSVPRPIHMNETSATRPSPARDLC------ 1967
Cdd:PHA03247 2472 ELFPGAPVYRRPAEARFPFA---AGAAPDPGG-------GGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTwirgle 2541

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1968 -ASSMTNSDPYAKPPDTPRPMMTDQfSKPFSLP-------------RSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQR 2033
Cdd:PHA03247 2542 eLASDDAGDPPPPLPPAAPPAAPDR-SVPPPRPaprpsepavtsraRRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPD 2620

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2034 QRLPDPyagPSLTPAPLGN-----GPFKTPLHPPPSQDPYGSVSQTSRRLSvdpyeRPALTPRPvdnfshsqsndpySHP 2108
Cdd:PHA03247 2621 THAPDP---PPPSPSPAANepdphPPPTVPPPERPRDDPAPGRVSRPRRAR-----RLGRAAQA-------------SSP 2679

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2109 PLTPHPamtesfthasRAFPqPGTISRSASQDPYSQPPgTPRPlidsysqtSGTARSNPDPysQPPGTPRPNTIDPYSQQ 2188
Cdd:PHA03247 2680 PQRPRR----------RAAR-PTVGSLTSLADPPPPPP-TPEP--------APHALVSATP--LPPGPAAARQASPALPA 2737

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2189 PPTPRPSPQTDmfVSSVANQRHTDPYTHHlGPPRPgisVPYSQPPAVPRPRTsegfTRPSSARPALMPNQDPFLQAAQNR 2268
Cdd:PHA03247 2738 APAPPAVPAGP--ATPGGPARPARPPTTA-GPPAP---APPAAPAAGPPRRL----TRPAVASLSESRESLPSPWDPADP 2807

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2269 VPGLPGPliRPPDTCSQTPRPPGPgridTFTHASSSAvrdpydqPPVTPRPHSESFGTSQVVH---DLVDRPVPGSEGNF 2345
Cdd:PHA03247 2808 PAAVLAP--AAALPPAASPAGPLP----PPTSAQPTA-------PPPPPGPPPPSLPLGGSVApggDVRRRPPSRSPAAK 2874

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2346 STSSNLPvssqgqqfsSVSQLPGPVPTsggtdtQNTVNMSQADTEKLRQRQklreiilqqqqqkkiasrqekgpqdtavv 2425
Cdd:PHA03247 2875 PAAPARP---------PVRRLARPAVS------RSTESFALPPDQPERPPQ----------------------------- 2910

                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 2426 PHPVPLPHWQPESINQAFTRPPPPYPGSTRSPVIPPLGPRYAVFP 2470
Cdd:PHA03247 2911 PQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEP 2955
SET_SUV39H_Clr4-like cd20073
SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 ...
 4716-4845 2.48e-16

SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 methyltransferase Clr4, and similar proteins; This subfamily contains fission yeast Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (also known as Suv39h), the sole homolog of the mammalian SUV39H1 and SUV39H2 enzymes, that has a critical role in preventing aberrant heterochromatin formation. It is known to di- and tri-methylate Lys-9 of histone H3, a central heterochromatic histone modification, with its specificity profile most similar to that of the human SUV39H2 homolog.


Pssm-ID: 380999 [Multi-domain]  Cd Length: 259  Bit Score: 82.23  E-value: 2.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4716 QGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYEsqNRGV-YMFRMD-------NDHVIDATLTGGPARYINHSCA 4787
Cdd:cd20073   103 KGWGLRCPRFIKAGTFIGVYLGEVITQSEAEIRGKKYD--NVGVtYLFDLDlfedqvdEYYTVDAQYCGDVTRFINHSCD 180

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568933163 4788 PNCVAEVV----TFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQ----------------HKIPCHCGAVNCRKWM 4845
Cdd:cd20073   181 PNLAIYSVlrdkSDSKIYDLAFFAIKDIPALEELTFDYSGRNNFDQlgfignrsnskyinlkNKRPCYCGSANCRGWL 258
SET_SETMAR cd10544
SET domain (including pre-SET and post-SET domains) found in SET domain and mariner ...
 4717-4845 2.48e-16

SET domain (including pre-SET and post-SET domains) found in SET domain and mariner transposase fusion protein (SETMAR) and similar proteins; SETMAR (also termed metnase) is a DNA-binding protein that is indirectly recruited to sites of DNA damage through protein-protein interactions. It has a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity. SETMAR also acts as a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3. It specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining.


Pssm-ID: 380942 [Multi-domain]  Cd Length: 254  Bit Score: 81.96  E-value: 2.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKlyeSQNRG----VYMFR--MDNDHV----IDATLTGGPARYINHSC 4786
Cdd:cd10544   101 GWGLRTLEFIPKGRFVCEYAGEVIGFEEARRRTK---SQTKGdmnyIIVLRehLSSGKVletfVDPTYIGNIGRFLNHSC 177

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568933163 4787 APNCVAEVVtfeRGH----KIIISSNRRIQKGEELCYDY------------KFDFEDDQHKIPCHCGAVNCRKWM 4845
Cdd:cd10544   178 EPNLFMVPV---RVDsmvpKLALFAARDIVAGEELSFDYsgefsnsvesvtLARQDESKSRKPCLCGAENCRGFL 249
SET_NSD1 cd19210
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 4706-4841 7.91e-16

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins; NSD1 (EC 2.1.1.43; also termed Histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD1 is altered in approximately 10% of head and neck cancer patients with 55% decrease in risk of death in NSD1-mutated versus non-mutated patients; its disruption promotes favorable chemotherapeutic responses linked to hypomethylation.


Pssm-ID: 380987 [Multi-domain]  Cd Length: 142  Bit Score: 77.27  E-value: 7.91e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4706 SNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINH 4784
Cdd:cd19210     2 PEVEIFRTLGRGWGLRCKTDIKKGEFVNEYVGELIdEEECRARIRYAQEHDITNFYMLTLDKDRIIDAGPKGNYARFMNH 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163 4785 SCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQhKIPCHCGAVNC 4841
Cdd:cd19210    82 CCQPNCETQKWTVNGDTRVGLFALCDIKAGTELTFNYNLECLGNG-KTVCKCGAPNC 137
SET_EHMT1 cd10535
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4693-4842 8.38e-16

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins; EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, or lysine N-methyltransferase 1D (KMT1D)) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380933 [Multi-domain]  Cd Length: 231  Bit Score: 79.98  E-value: 8.38e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4693 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKlyesqnrGVYMFRMDND----H 4768
Cdd:cd10535    78 RNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREE-------DSYLFDLDNKdgevY 150

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 4769 VIDATLTGGPARYINHSCAPNCVAEVVTFE----RGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKI-PCHCGAVNCR 4842
Cdd:cd10535   151 CIDARFYGNVSRFINHHCEPNLVPVRVFMAhqdlRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLfSCRCGSPKCR 229
SET cd08161
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ...
 4707-4821 1.86e-15

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site.


Pssm-ID: 380914 [Multi-domain]  Cd Length: 72  Bit Score: 73.82  E-value: 1.86e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4707 NVYLARSRIQGLGLYAARDIEKhtmvieyiGTIIrnevanrkeklyesqnrgvymfrmdndhvidatltgGPARYINHSC 4786
Cdd:cd08161     1 EIRPSTIPGAGFGLFATRDIPK--------GEVI------------------------------------GLARFINHSC 36

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 568933163 4787 APNCVAEVVTFERGHKIIISSNRRIQKGEELCYDY 4821
Cdd:cd08161    37 EPNCEFEEVYVGGKPRVFIVALRDIKAGEELTVDY 71
SET_EZH-like cd19168
SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb ...
 4708-4825 2.28e-15

SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb repressive complex 2 (PRC2), and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both EZH1 and EZH2 can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380945  Cd Length: 124  Bit Score: 75.30  E-value: 2.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4708 VYLARSRIQ-GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgVYMFRMDNDHVIDATLTGGPARYINH-- 4784
Cdd:cd19168     3 VVLGKSQLEcGLGLFAAEDIKEGEFVIEYTGELISHDEGVRREHRRGDVSY-LYLFEEQEGIWVDAAIYGNLSRYINHat 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 568933163 4785 --SCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDF 4825
Cdd:cd19168    82 dkVKTGNCMPKIMYVNHEWRIKFTAIKDIKIGEELFFNYGDNF 124
SET_SUV39H_DIM5-like cd19473
SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; ...
 4717-4845 2.62e-15

SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; This subfamily contains Neurospora crassa DIM-5 (also termed H3-K9-HMTase dim-5, or HKMT) which functions as histone-lysine N-methyltransferase that specifically trimethylates histone H3 to form H3K9me3.


Pssm-ID: 380996 [Multi-domain]  Cd Length: 274  Bit Score: 79.67  E-value: 2.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKHTMVIEYIGTIIRNEVAN-RKEKLYESQNRGVYMFRMD---NDHVIDATLTG-----------GPARY 4781
Cdd:cd19473   117 GWGVRSTVDIKRGQFVDCYVGEIITPEEAQrRRDAATIAQRKDVYLFALDkfsDPDSLDPRLRGdpyeidgefmsGPTRF 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4782 INHSCAPNC-VAEVVT------FergHKIIISSNRRIQKGEELCYDY----------KFDFEDDQHKIPCHCGAVNCRKW 4844
Cdd:cd19473   197 INHSCDPNLrIFARVGdhadkhI---HDLAFFAIKDIPRGTELTFDYvdgvtgldddAGDEEKEKEMTKCLCGSPKCRGY 273


                  .
gi 568933163 4845 M 4845
Cdd:cd19473   274 L 274
SET_SETD5-like cd10529
SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine ...
 4719-4825 3.39e-15

SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. KMT2E (also termed inactive lysine N-methyltransferase 2E or myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. The family also includes Saccharomyces cerevisiae SET domain-containing proteins, SET3 and SET4, and Schizosaccharomyces pombe SET3. Most of these family members contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380927  Cd Length: 127  Bit Score: 75.00  E-value: 3.39e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4719 GLYAARDIEKHTMVIEYIGTI-IRNEVANRKEKLYESQNRgVYMF--RMDNDHVIDATLTGGPARYINHSCAPNCVAEVV 4795
Cdd:cd10529    18 GLVATEDISPGEPILEYKGEVsLRSEFKEDNGFFKRPSPF-VFFYdgFEGLPLCVDARKYGNEARFIRRSCRPNAELRHV 96

                          90       100       110
                  ....*....|....*....|....*....|.
gi 568933163 4796 TFERG-HKIIISSNRRIQKGEELCYDYKFDF 4825
Cdd:cd10529    97 VVSNGeLRLFIFALKDIRKGTEITIPFDYDY 127
SET_SUV39H2 cd10532
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4716-4845 3.89e-15

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins; SUV39H2 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B (KMT1B), or Su(var)3-9 homolog 2) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380930 [Multi-domain]  Cd Length: 243  Bit Score: 78.39  E-value: 3.89e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4716 QGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgVYMFRMD---NDHVIDATLTGGPARYINHSCAPNCVA 4792
Cdd:cd10532    95 RGWGVKTLQKIKKNSFVMEYVGEVITSEEAERRGQFYDSKGI-TYLFDLDyesDEFTVDAARYGNVSHFVNHSCDPNLQV 173

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4793 EVVTFE----RGHKIIISSNRRIQKGEELCYDYKFDFEDD-------------QHKIPCHCGAVNCRKWM 4845
Cdd:cd10532   174 FNVFIDnldtRLPRIALFSTRTIKAGEELTFDYQMKGSGDlssdsidnspakkRVRTVCKCGAVTCRGYL 243
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 1004-1049 4.02e-15

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 72.11  E-value: 4.02e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15519     1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
SET_SUV39H1 cd10525
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4716-4845 6.62e-15

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins; SUV39H1 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A (KMT1A), position-effect variegation 3-9 homolog (SUV39H), or Su(var)3-9 homolog 1) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380923 [Multi-domain]  Cd Length: 255  Bit Score: 78.01  E-value: 6.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4716 QGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNrGVYMFRMD---NDHVIDATLTGGPARYINHSCAPNCVA 4792
Cdd:cd10525    97 RGWGVRTLEKIRKNSFVMEYVGEIITSEEAERRGQIYDRQG-ATYLFDLDyveDVYTVDAAYYGNISHFVNHSCDPNLQV 175

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 4793 EVVTF----ERGHKIIISSNRRIQKGEELCYDYKF-----DFEDDQH-----------------KIPCHCGAVNCRKWM 4845
Cdd:cd10525   176 YNVFIdnldERLPRIALFATRTIRAGEELTFDYNMqvdpvDAESTKMdsnfglaglpgspkkrvRIECKCGVRSCRKYL 254
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 1004-1049 1.04e-14

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 70.75  E-value: 1.04e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 391-435 1.06e-14

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 70.88  E-value: 1.06e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 249-330 1.44e-14

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 72.44  E-value: 1.44e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  249 CWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAG-TFQDFSHFFllC 327
Cdd:cd15664    25 EWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPANYHFMCARKAEcVFQDDKKVF--C 102


                  ...
gi 568933163  328 PEH 330
Cdd:cd15664   103 PAH 105
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 1004-1049 1.66e-14

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 70.11  E-value: 1.66e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15515     1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 4368-4445 2.42e-14

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 71.21  E-value: 2.42e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  4368 HLNCALWSTEVYetQAGA------LINVELALRRGLQMKCVFCH-KTGATSGCHRFRCTNIYHFTCATKAQCMF-FKDKT 4439
Cdd:pfam13771    1 HVVCALWSPELV--QRGNdsmgfpIEDIEKIPKRRWKLKCYLCKkKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDN 78

                           90
                   ....*....|
gi 568933163  4440 ----MLCPMH 4445
Cdd:pfam13771   79 gtfkSYCKKH 88
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1884-2305 3.50e-14

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 79.81  E-value: 3.50e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1884 QSQNSQPPSPQMFSPGSShsrPPSPVDPYAKMVGTPRPPPGGHSFPrrnsvtpvencvplssvprpihmnetsatrpspa 1963
Cdd:pfam03154  165 QILQTQPPVLQAQSGAAS---PPSPPPPGTTQAATAGPTPSAPSVP---------------------------------- 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1964 rdlcassmtnsdPYAKPPDTPRPMMTDQFSKPFSLPRSpviseqstkgplttgtsdhftkpsprTDAFQRQRLPDPYagP 2043
Cdd:pfam03154  208 ------------PQGSPATSQPPNQTQSTAAPHTLIQQ--------------------------TPTLHPQRLPSPH--P 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2044 SLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSVDPYERP-ALTPRPVDNFSH-SQSNDPYSHPPLTPHPAMTESFT 2121
Cdd:pfam03154  248 PLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQhPVPPQPFPLTPQsSQSQVPPGPSPAAPGQSQQRIHT 327

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2122 HASRAFPQPGTISRSASQDP-------YSQPPGTPRP-LIDSYSQTSGTARSNPDPYSQPPGTPRPNTIDPYS----QQP 2189
Cdd:pfam03154  328 PPSQSQLQSQQPPREQPLPPaplsmphIKPPPTTPIPqLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSslstHHP 407

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2190 PTPRPSPQTDMFVSS----------VANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTR--PSSARPALMPN 2257
Cdd:pfam03154  408 PSAHPPPLQLMPQSQqlppppaqppVLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPitPPSGPPTSTSS 487

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2258 QDPFLQAAQNRVPGLPGPLI--------------RPPDTCSQTPRPPGPGR--------IDTFTHASSSA 2305
Cdd:pfam03154  488 AMPGIQPPSSASVSSSGPVPaavscplppvqikeEALDEAEEPESPPPPPRspspeptvVNTPSHASQSA 557
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 4341-4445 4.03e-14

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 71.10  E-value: 4.03e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGD----GLTDGPArllnldLDLWVHLNCALWSTEVYETqAGALINVELALRRGLQMKCVFCHKTGATSGCHRF 4416
Cdd:cd15699     1 CCLCGKWANyrnlGDLFGPF------YEFWVHEGCILWANGIYLV-CGRLYGLQEALDIAREMKCSHCQEAGATLGCYNK 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 568933163 4417 RCTNIYHFTCATKAQCMFFKDK-TMLCPMH 4445
Cdd:cd15699    74 GCSFRYHYPCAIDADCLLNEENfSVRCPKH 103
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 250-330 4.09e-14

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 71.18  E-value: 4.09e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGT--FQDFShffLLC 327
Cdd:cd15666    26 WVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCANVYHLPCAIKDGCmfFKDKT---MLC 102


                  ...
gi 568933163  328 PEH 330
Cdd:cd15666   103 PSH 105
SET_EHMT2 cd10533
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4693-4842 6.27e-14

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 2 (EHMT2) and similar proteins; EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C (KMT1C), or protein G9a) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380931 [Multi-domain]  Cd Length: 239  Bit Score: 74.67  E-value: 6.27e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4693 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKlyesqnrGVYMFRMDND----H 4768
Cdd:cd10533    78 RNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVRED-------DSYLFDLDNKdgevY 150

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 4769 VIDATLTGGPARYINHSCAPNCVAEVVTFE----RGHKIIISSNRRIQKGEELCYDYKFDFEDDQHK-IPCHCGAVNCR 4842
Cdd:cd10533   151 CIDARYYGNISRFINHLCDPNIIPVRVFMLhqdlRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKyFTCQCGSEKCK 229
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 1005-1049 1.18e-13

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 67.68  E-value: 1.18e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1004-1049 1.26e-13

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 67.66  E-value: 1.26e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 250-330 1.94e-13

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 69.26  E-value: 1.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  250 WAHHRCVEWSLGICqMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLLCPE 329
Cdd:cd15668    24 WVHEDCAVWAPGVY-LVGGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHKGCKAKYHYPCAVESGCQLDEENFSLLCPK 102


                  .
gi 568933163  330 H 330
Cdd:cd15668   103 H 103
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 1004-1049 2.60e-13

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 67.09  E-value: 2.60e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15605     1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1810-2248 2.94e-13

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 77.29  E-value: 2.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1810 APGSDTPSSGAQSPLTPqagngnvSPAQTfhkdlfskHLPGTPASTPSDGVFVKPQPPPPPSTPSRIPVQE------SLS 1883
Cdd:PHA03247 2600 APVDDRGDPRGPAPPSP-------LPPDT--------HAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDpapgrvSRP 2664

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1884 QSQNSQPPSPQMFSPGSSHSRP--PSPVDPYAKMVGTPRPPPGGHSFPRRNSVTPVENCVPLSSVPRPIHMNETSATRPS 1961
Cdd:PHA03247 2665 RRARRLGRAAQASSPPQRPRRRaaRPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAV 2744

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1962 PARDLCASSMTN--SDPYAKPPDTPRPMMTDQFSKPFSLPRSPV--ISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLP 2037
Cdd:PHA03247 2745 PAGPATPGGPARpaRPPTTAGPPAPAPPAAPAAGPPRRLTRPAVasLSESRESLPSPWDPADPPAAVLAPAAALPPAASP 2824

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2038 DPYAGPSLTPAPLGngPFKTPLHPPPSQDPYGSVS---QTSRR-LSVDPYERPALTPRP----VDNFSHSQSNDPYSHPP 2109
Cdd:PHA03247 2825 AGPLPPPTSAQPTA--PPPPPGPPPPSLPLGGSVApggDVRRRpPSRSPAAKPAAPARPpvrrLARPAVSRSTESFALPP 2902

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2110 LTPHPAMTESFTHASRAFPQPGTISRSASQD---PYSQPPGTPRPLIDSYSQTSGTArSNPDPYSQPPG----------T 2176
Cdd:PHA03247 2903 DQPERPPQPQAPPPPQPQPQPPPPPQPQPPPpppPRPQPPLAPTTDPAGAGEPSGAV-PQPWLGALVPGrvavprfrvpQ 2981

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2177 PRPNTIDPYSQQPP----------------------TPRPS-------PQTDMFVSSVANQRHTDPYTHHLGPPRPGISV 2227
Cdd:PHA03247 2982 PAPSREAPASSTPPltghslsrvsswasslalheetDPPPVslkqtlwPPDDTEDSDADSLFDSDSERSDLEALDPLPPE 3061

                         490       500
                  ....*....|....*....|.
gi 568933163 2228 PYSQPPAVPRPRTSEGFTRPS 2248
Cdd:PHA03247 3062 PHDPFAHEPDPATPEAGARES 3082
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1004-1049 3.10e-13

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 66.69  E-value: 3.10e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15510     1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 1005-1049 3.32e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 66.65  E-value: 3.32e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4364-4445 3.36e-13

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 68.05  E-value: 3.36e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4364 DLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMF-FKDKTMLC 4442
Cdd:cd15696     8 ECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQdFSRRLLLC 87


                  ...
gi 568933163 4443 PMH 4445
Cdd:cd15696    88 PTH 90
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4364-4445 3.67e-13

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 68.02  E-value: 3.67e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4364 DLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATkAQCMFFKDKT--ML 4441
Cdd:cd15695     8 ECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAA-ASGSFQSMKTllLL 86


                  ....
gi 568933163 4442 CPMH 4445
Cdd:cd15695    87 CPEH 90
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 250-330 3.68e-13

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 68.54  E-value: 3.68e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAG-TFqdFSHFFLLCP 328
Cdd:cd15697    26 WVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTNVYHFTCAIKAQcMF--FKDKTMLCP 103


                  ..
gi 568933163  329 EH 330
Cdd:cd15697   104 MH 105
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 1004-1050 4.57e-13

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 66.51  E-value: 4.57e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1050
Cdd:cd15602     1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCV 47
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 391-435 5.45e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 65.80  E-value: 5.45e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15545     2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 4341-4445 5.89e-13

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 67.98  E-value: 5.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEegdgltdgPARLLNL-DL------DLWVHLNCALWSTEVYETqAGALINVELALRRGLQMKCVFCHKTGATSGC 4413
Cdd:cd15700     1 CCLCRN--------PANYKDLgDLcgpyypEHWVHEACAVWTTGVYLV-AGKLFGLQEAVQKAADAKCSSCQGAGATVGC 71

                          90       100       110
                  ....*....|....*....|....*....|...
gi 568933163 4414 HRFRCTNIYHFTCATKAQCMFFKDK-TMLCPMH 4445
Cdd:cd15700    72 CHKGCTQSYHYICAVEAGCLFEEENfSLRCPKH 104
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 1005-1049 7.97e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 65.51  E-value: 7.97e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 4341-4445 8.34e-13

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 67.80  E-value: 8.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGParLLNLDLDLWVHLNCALWSTEVYETQ-------AGALIN-VELALRRGLQMKCVFCHKTGATSG 4412
Cdd:cd15673     1 CGFCKSGEENKETGG--KLASGEKIAAHHNCMLFSSGLVQYVspnendfGGFDIEdVKKEIKRGRKLKCNLCKKTGATIG 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 568933163 4413 CHRFRCTNIYHFTCATKAQCMFFKDK-----TMLCPMH 4445
Cdd:cd15673    79 CDVKQCKKTYHYHCAKKDDAKIIERNsqgiyRVYCKNH 116
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2146-2753 8.65e-13

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 75.75  E-value: 8.65e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2146 PGTP---RPLIDSYSQTSGTArsnPDPYSQPPgtPRPNTIDPYSQQPPTPRPSPQTDMFV-----------SSVANQRHT 2211
Cdd:PHA03247 2475 PGAPvyrRPAEARFPFAAGAA---PDPGGGGP--PDPDAPPAPSRLAPAILPDEPVGEPVhprmltwirglEELASDDAG 2549

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2212 DPythhlGPPRPGISVP----YSQPPAVPRPRTSEGFTRPSSARPALMPnqdpflQAAQNRVPGlpGPLIRPPDTCSQTP 2287
Cdd:PHA03247 2550 DP-----PPPLPPAAPPaapdRSVPPPRPAPRPSEPAVTSRARRPDAPP------QSARPRAPV--DDRGDPRGPAPPSP 2616

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2288 RPPGPgridtfthasssavrDPYDQPPVTPRPH-SESFGTSQVVHDLVDRPVPGSEGNfSTSSNLPVSSQGQQFSSVSQL 2366
Cdd:PHA03247 2617 LPPDT---------------HAPDPPPPSPSPAaNEPDPHPPPTVPPPERPRDDPAPG-RVSRPRRARRLGRAAQASSPP 2680

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2367 PGPVPTSGGTDTQNTVNMSQA-DTEKLRQRQKLREIILQQQQQKKIASRQEKGPQDTAVVPHPVPLPHWQPESINQAFTR 2445
Cdd:PHA03247 2681 QRPRRRAARPTVGSLTSLADPpPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2446 PPPPYPGSTRSPVIPPLGPRyavfpkdQRGPYPPEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPhir 2525
Cdd:PHA03247 2761 PTTAGPPAPAPPAAPAAGPP-------RRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--- 2830

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2526 rPMSMemprpsnnpplnnpvgLPQHFPPQGLPVQQHNILGQAFielrhrAPDGR-SRLPFAASPSSVIESPSHPRHGNF- 2603
Cdd:PHA03247 2831 -PTSA----------------QPTAPPPPPGPPPPSLPLGGSV------APGGDvRRRPPSRSPAAKPAAPARPPVRRLa 2887

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2604 ---LPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP------------------LNHP 2662
Cdd:PHA03247 2888 rpaVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPttdpagagepsgavpqpwLGAL 2967

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2663 LSGEFS-------------EAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKE-LDVKDlegvevkDLDDEDLE 2728
Cdd:PHA03247 2968 VPGRVAvprfrvpqpapsrEAPASSTPPLTGHSLSRVSSWASSLALHEETDPPPVSLKQtLWPPD-------DTEDSDAD 3040

                         650       660
                  ....*....|....*....|....*.
gi 568933163 2729 NLNL-DTEDGKGDDLDTLDNlETNDP 2753
Cdd:PHA03247 3041 SLFDsDSERSDLEALDPLPP-EPHDP 3065
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 390-435 1.39e-12

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 64.80  E-value: 1.39e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 252-330 1.60e-12

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 66.20  E-value: 1.60e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163   252 HHRCVEWSLGICQ-----MEEPLLvNVDKAVVSGSTERCAFCKH-LGATIKCCEEKCTQMYHYPCAAGAGTFQDFSH--- 322
Cdd:pfam13771    1 HVVCALWSPELVQrgndsMGFPIE-DIEKIPKRRWKLKCYLCKKkGGACIQCSKKNCRRAFHVTCALEAGLLMQFDEdng 79


                   ....*....
gi 568933163   323 -FFLLCPEH 330
Cdd:pfam13771   80 tFKSYCKKH 88
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 251-330 1.98e-12

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 66.50  E-value: 1.98e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  251 AHHRCVEWSLGICQMEEP-------LLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGT-FQDFSH 322
Cdd:cd15669    25 AHYFCLLFSSGLPQRGEDnegiygfLPEDIRKEVRRASRLRCFYCKKKGASIGCAVKGCRRSFHFPCGLENGCvTQFFGE 104


                  ....*...
gi 568933163  323 FFLLCPEH 330
Cdd:cd15669   105 YRSFCWEH 112
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1004-1050 2.40e-12

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 64.44  E-value: 2.40e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 568933163  1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQT--VPKGGWKCKWCV 1050
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECK 49
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 4717-4843 2.79e-12

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes.


Pssm-ID: 380915 [Multi-domain]  Cd Length: 288  Bit Score: 70.78  E-value: 2.79e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLY--------------ESQNRGVYMFRMDNDHVIDATLTGGPARYI 4782
Cdd:cd10517   140 GWGIRCLDDIPKGSFVCIYAGQILTEDEANEEGLQYgdeyfaeldyievvEKLKEGYESDVEEHCYIIDAKSEGNLGRYL 219

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163 4783 NHSCAPNCVAEVVtFERGHKIIIS-----SNRRIQKGEELCYDYKFDFEDDQHKI-PCHCGAVNCRK 4843
Cdd:cd10517   220 NHSCSPNLFVQNV-FVDTHDLRFPwvaffASRYIRAGTELTWDYNYEVGSVPGKVlYCYCGSSNCRG 285
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 1004-1049 2.99e-12

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 64.09  E-value: 2.99e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15604     1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 250-330 3.89e-12

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 65.67  E-value: 3.89e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  250 WAHHRCVEWSLGICQMEEPLLvNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLLCPE 329
Cdd:cd15700    25 WVHEACAVWTTGVYLVAGKLF-GLQEAVQKAADAKCSSCQGAGATVGCCHKGCTQSYHYICAVEAGCLFEEENFSLRCPK 103


                  .
gi 568933163  330 H 330
Cdd:cd15700   104 H 104
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 390-435 4.98e-12

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 63.09  E-value: 4.98e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQpvMKSVPTNGWKCKNC 435
Cdd:cd15529     1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 391-435 6.20e-12

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 62.81  E-value: 6.20e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 250-311 1.01e-11

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 64.64  E-value: 1.01e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568933163  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA 311
Cdd:cd15693    28 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCS 89
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 391-435 1.17e-11

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 62.29  E-value: 1.17e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 1005-1049 1.18e-11

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 62.05  E-value: 1.18e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 1005-1049 1.35e-11

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 62.00  E-value: 1.35e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGG-WKCKWC 1049
Cdd:cd15525     2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 1005-1049 1.71e-11

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 61.91  E-value: 1.71e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVP-KGGWKCKWC 1049
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
4339-4434 2.05e-11

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 63.52  E-value: 2.05e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  4339 RKCCFCHEEGDGL---TDGparllnldldLWVHLNCALWSTEVY--ETQAGALINVELALRRGLQMKCVFCHK-TGATSG 4412
Cdd:pfam13832    1 VRCCLCPLRGGALkqtSDG----------RWVHVLCAIFVPEVRfgNVATMEPIDVSRIPPERWKLKCVFCKKrSGACIQ 70

                           90       100
                   ....*....|....*....|..
gi 568933163  4413 CHRFRCTNIYHFTCATKAQCMF 4434
Cdd:pfam13832   71 CSKGRCTTAFHVTCAQAAGVYM 92
SET_SETDB2 cd10523
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) ...
 4716-4845 2.42e-11

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins; SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380921 [Multi-domain]  Cd Length: 266  Bit Score: 67.55  E-value: 2.42e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4716 QGLGLYAARDIEKHTMVIEYIGTI---IRNEVANRKEKLYESQNRGVYMFRM-----------DNDHVIDATLTGGPARY 4781
Cdd:cd10523   118 KGWGVRCLDDIDKGTFVCIYAGRVlsrARSPTEPLPPKLELPSENEVEVVTSwlilskkrklrENVCFLDASKEGNVGRF 197

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163 4782 INHSCAPNCVAEVVTFERGHK----IIISSNRRIQKGEELCYDYKFDFEDDQHK-IPCHCGAVNCRKWM 4845
Cdd:cd10523   198 LNHSCCPNLFVQNVFVDTHDKnfpwVAFFTNRVVKAGTELTWDYSYDAGTSPEQeIPCLCGVNKCQKKI 266
SET_SETDB cd10541
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), ...
 4716-4843 2.46e-11

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), SET domain bifurcated 2 (SETDB2), and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380939 [Multi-domain]  Cd Length: 236  Bit Score: 66.80  E-value: 2.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4716 QGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVV 4795
Cdd:cd10541   102 KGWGIRCLDDIAKGTFVCIYAGKILTDDFADKEGLEMGDEYFANLDHIEESCYIIDAKLEGNLGRYLNHSCSPNLFVQNV 181

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568933163 4796 tFERGHK-----IIISSNRRIQKGEELCYDYKFDFEDDQHK-IPCHCGAVNCRK 4843
Cdd:cd10541   182 -FVDTHDlrfpwVAFFASKRIKAGTELTWDYNYEVGSVEGKeLLCCCGSNECRG 234
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1004-1049 2.69e-11

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 61.16  E-value: 2.69e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1004-1049 2.85e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 61.07  E-value: 2.85e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 568933163   1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1049
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 250-330 3.28e-11

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277164  Cd Length: 105  Bit Score: 63.14  E-value: 3.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA-AGAGTFQDFSHFFllCP 328
Cdd:cd15694    26 WTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLSNFHFMCArASRCCFQDDKKVF--CQ 103


                  ..
gi 568933163  329 EH 330
Cdd:cd15694   104 KH 105
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 4341-4445 5.87e-11

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 62.27  E-value: 5.87e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGlTDGPARLLNLDlDLWVHLNCALWSTEVYETQ------AGALIN-VELALRRGLQMKCVFCHKTGATSGC 4413
Cdd:cd15669     1 CVLCGRSDDD-PDKYGEKLQKD-GICAHYFCLLFSSGLPQRGednegiYGFLPEdIRKEVRRASRLRCFYCKKKGASIGC 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 568933163 4414 HRFRCTNIYHFTCATKAQC--MFFKDKTMLCPMH 4445
Cdd:cd15669    79 AVKGCRRSFHFPCGLENGCvtQFFGEYRSFCWEH 112
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 390-438 7.27e-11

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 60.20  E-value: 7.27e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 568933163   390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPV--MKSVPTNGWKCKNCRIC 438
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPldPAEIPSGEWLCPECKPK 51
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 1002-1049 8.53e-11

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 59.70  E-value: 8.53e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163 1002 CTVCEACGKATDpgrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15527     2 CSVCQDSGNADN---LLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 1005-1049 8.85e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 59.63  E-value: 8.85e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15545     2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 1005-1049 9.37e-11

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 59.70  E-value: 9.37e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15530     2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 390-435 1.22e-10

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 59.33  E-value: 1.22e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15515     1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
SET_SMYD cd20071
SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing ...
 4717-4821 1.57e-10

SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing protein, and similar proteins; The family includes SET and MYND domain-containing proteins, SMYD1-SYMD5. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. SMYD5 (also termed protein NN8-4AG, or retinoic acid-induced protein 15) functions as histone lysine methyltransferase that mediates H4K20me3 at heterochromatin regions.


Pssm-ID: 380997 [Multi-domain]  Cd Length: 122  Bit Score: 61.62  E-value: 1.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4717 GLGLYAARDIEKhtmvieyiGTIIRNE------VANRKEKLYESQNRGVYMFRMdndhvidatltggpARYINHSCAPNC 4790
Cdd:cd20071    10 GRGLVATRDIEP--------GELILVEkplvsvPSNSFSLTDGLNEIGVGLFPL--------------ASLLNHSCDPNA 67

                          90       100       110
                  ....*....|....*....|....*....|.
gi 568933163 4791 VaevVTFERGHKIIISSNRRIQKGEELCYDY 4821
Cdd:cd20071    68 V---VVFDGNGTLRVRALRDIKAGEELTISY 95
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 390-435 2.20e-10

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 58.70  E-value: 2.20e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15604     1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
GGN pfam15685
Gametogenetin; GGN is a family of proteins largely found in mammals. It reacts with POG in the ...
 1890-2377 2.91e-10

Gametogenetin; GGN is a family of proteins largely found in mammals. It reacts with POG in the maturation of sperm and is expressed virtually only in the testis. It is found to be associated with the intracellular membrane, binds with GGNBP1 and may be involved in vesicular trafficking.


Pssm-ID: 434857 [Multi-domain]  Cd Length: 668  Bit Score: 66.71  E-value: 2.91e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1890 PPSPQMF-SPGSSHSRPPSPVDP-----YAKMVGTPRPPPGGhsfprrnsvtpvencvplSSVPRPIHMNETSATRPSPA 1963
Cdd:pfam15685   64 PPEPQASpSPLPLTLELPLPVTPppeeaAAAAVSTAPPPAVG------------------SLLPAPSKWRKPTGTAVARI 125

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1964 RDLC-ASSMTNSDPYAKPPDTprPMMTDQFSKPFSLPRSPViseqstkGPLTTGTSDHFTKPSPRTDAFQRQRLPDPYAG 2042
Cdd:pfam15685  126 RGLLeASHRGQGDPLSLRPLL--PLLPRQLIEKDPAPGAPA-------PPPPTPLEPRKPPPLPPSDRQPPNRGITPALA 196

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2043 PSLTPaplgngpfktplhPPPSQDPYGSVSQTSRrlSVDPYERPALTPRPVDNFSHSQSNDPY-------SHPPLTPHPA 2115
Cdd:pfam15685  197 TSATS-------------PTDSQAKHIAEGKTAG--GACGGAPPQAGEGEMARFAASESGLSLlckvtfkSAAPLCPAAA 261

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2116 MTESFTHASRAFPQPGTISRSASQDPYSQ-------PPGTPRPL--IDSYSQTSGTARSNPDPYSQPPGTPRPNTidpYS 2186
Cdd:pfam15685  262 SGPLAAKASLGGGGGGGLFAASGAISCAEvlkqgplAPGAARPLgeVPRAALETEGGEGDGEGCSGGPAAPASHA---RA 338

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2187 QQPPT----PRPSPQTDMFVSSVANQRH--TDPYTHHLGPPR---PGISVPYSQPPavPRPRTSEGFTRPSSARPALMPN 2257
Cdd:pfam15685  339 LPPPAyttfPGSKPKFDWVSPPDGPERHfrFNGAGGGIGAPRrraAALSGPWGSPP--PPPGKAHPIPGPRRPAPALLAP 416

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2258 QDPFLQAAQNRVPGLPGplirPPDTCSQTPRPPGPGRIDTFTHASSSAVRDPYDQPPVTP--RPHSESFGTSQVVHDLVD 2335
Cdd:pfam15685  417 PMFIFPAPTNGEPVRPG----PPAPQALLPRPPPPTPPATPPPVPPPIPQLPALQPMPLAaaRPPTPRPCPGHGESALAP 492

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|..
gi 568933163  2336 RPVPgsegnfSTSSNLPVSSQGQQFSSVSQLPGPVPTSGGTD 2377
Cdd:pfam15685  493 APTA------PLPPALAADQAPAPALAAAPAPSPAPAPATAD 528
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 1005-1049 3.14e-10

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 58.04  E-value: 3.14e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKG-GWKCKWC 1049
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 250-330 3.15e-10

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 60.07  E-value: 3.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGT--FQDFShffLLC 327
Cdd:cd15698    26 WVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPNVYHFACAIRAKCmfFKDKT---MLC 102


                  ...
gi 568933163  328 PEH 330
Cdd:cd15698   103 PMH 105
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 391-435 3.35e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 58.22  E-value: 3.35e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15628     2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 391-435 4.11e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 57.94  E-value: 4.11e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
SET_SpSET3-like cd19183
SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET ...
 4718-4832 4.11e-10

SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET domain-containing protein 3 (SETD3) and similar proteins; Schizosaccharomyces pombe SETD3 functions as a transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. It is required for both, gene activation and repression.


Pssm-ID: 380960  Cd Length: 173  Bit Score: 62.04  E-value: 4.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4718 LGLYAARDIEKHTMVIEYIGtiirnEVANRKEKLYESQNRgvY----------MFRMDNDHVIDATLTGGPARYINHSCA 4787
Cdd:cd19183    14 FGLFADRPIPAGDPIQELLG-----EIGLQSEYIADPENQ--YqilgapkphvFFHPQSPLYIDTRRSGSVARFIRRSCR 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 4788 PNCVAEVVTFERGH--KIIISSNRRIQKGEELCYDYKFDFEDDQHKI 4832
Cdd:cd19183    87 PNAELVTVASDSGSvlKFVLYASRDISPGEEITIGWDWDNPHPFRRF 133
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1810-2197 5.13e-10

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 66.33  E-value: 5.13e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1810 APGSDTPSSGAQ-SPLTPQAGNGNVSPA----------QTFHKDLFSKHLPGTPASTPSdgvfvkpqppPPPSTPSRIPV 1878
Cdd:pfam03154  198 GPTPSAPSVPPQgSPATSQPPNQTQSTAaphtliqqtpTLHPQRLPSPHPPLQPMTQPP----------PPSQVSPQPLP 267

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1879 QESLsqsQNSQPPSPQMFSPGSSHSRPPSPVDPYakmvgtPRPPPGGHSfprrnsvtpveNCVPLSSVPRPIHMNETSAT 1958
Cdd:pfam03154  268 QPSL---HGQMPPMPHSLQTGPSHMQHPVPPQPF------PLTPQSSQS-----------QVPPGPSPAAPGQSQQRIHT 327

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  1959 RPSpardlcASSMTNSDPYAKPPDTPRPMMTDQFSKPFSLPRSPVISEQSTKGPlttgtsDHFTKPSPrtdaFQ-RQRLP 2037
Cdd:pfam03154  328 PPS------QSQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQSHKHP------PHLSGPSP----FQmNSNLP 391

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2038 DPYA-----------GPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTsrrlsvdpyerpaLTPRPVDNFSHSQSNDPYS 2106
Cdd:pfam03154  392 PPPAlkplsslsthhPPSAHPPPLQLMPQSQQLPPPPAQPPVLTQSQS-------------LPPPAASHPPTSGLHQVPS 458

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2107 HPPLTPHPAMTESfthASRAFPQPGTISRSASQDPYSQPPGTPRPlidSYSQTSGTARSNPDPYSQPPGTPRPNTIDPYS 2186
Cdd:pfam03154  459 QSPFPQHPFVPGG---PPPITPPSGPPTSTSSAMPGIQPPSSASV---SSSGPVPAAVSCPLPPVQIKEEALDEAEEPES 532

                          410
                   ....*....|.
gi 568933163  2187 QQPPTPRPSPQ 2197
Cdd:pfam03154  533 PPPPPRSPSPE 543
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 390-435 5.68e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 57.61  E-value: 5.68e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 568933163    390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKS-VPTNGWKCKNC 435
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 390-435 6.01e-10

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 57.29  E-value: 6.01e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15532     1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 390-435 8.74e-10

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 57.07  E-value: 8.74e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15605     1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 955-1005 8.97e-10

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.12  E-value: 8.97e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163   955 CVVCGsfGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKG-WRCLECTVC 1005
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 954-1002 1.08e-09

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.84  E-value: 1.08e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 568933163    954 MCVVCGSFGqgAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 1002
Cdd:smart00249    1 YCSVCGKPD--DGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1804-2283 1.14e-09

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 65.19  E-value: 1.14e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1804 SQHLLVAPGSD---TPSSGAQSPLTPQAGNGNVSPAQTFHKDLFSKHLPGTPASTPSDGVFVKPQPPPPpstpsripvqe 1880
Cdd:PHA03307   46 DSAELAAVTVVagaAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSP----------- 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1881 slsqsqnsqPPSPQMFSPGSSHSRPPSPVDPYAKMVGTPRPPPGG--------HSFPRRNSVTPVENCVPLSSVPrpihm 1952
Cdd:PHA03307  115 ---------DPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAAsppaagasPAAVASDAASSRQAALPLSSPE----- 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1953 nETSATRPSPArdlcASSMTNSDPYAKPPDTPRPMMTDQFSKPFSLPRSPviseQSTKGPLTTGTSDHFTKPSPRTDAFQ 2032
Cdd:PHA03307  181 -ETARAPSSPP----AEPPPSTPPAAASPRPPRRSSPISASASSPAPAPG----RSAADDAGASSSDSSSSESSGCGWGP 251

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2033 RQRLPDPYAGPSLTPAPLGNGpfKTPLHPPPSQDPYGSVSQTSRRlsvdpyerpalTPRPvdnfshsQSNDPYSHPPLTP 2112
Cdd:PHA03307  252 ENECPLPRPAPITLPTRIWEA--SGWNGPSSRPGPASSSSSPRER-----------SPSP-------SPSSPGSGPAPSS 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2113 HPAMtesfthASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPySQPPGTPRPNTIDPYSQQPPTP 2192
Cdd:PHA03307  312 PRAS------SSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADP-SSPRKRPRPSRAPSSPAASAGR 384

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2193 RPSPQTDMFVSSVANQRHTdpythhlGPPRPGisvpySQPPAVPrPRTSEGFTRPSSARPALMPNQDPFlqaaqnrvPGL 2272
Cdd:PHA03307  385 PTRRRARAAVAGRARRRDA-------TGRFPA-----GRPRPSP-LDAGAASGAFYARYPLLTPSGEPW--------PGS 443

                         490
                  ....*....|.
gi 568933163 2273 PGPlirPPDTC 2283
Cdd:PHA03307  444 PPP---PPGRV 451
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 388-435 1.51e-09

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 56.23  E-value: 1.51e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163  388 CKVCQNckqSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15527     2 CSVCQD---SGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 1004-1049 1.51e-09

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 56.16  E-value: 1.51e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1049
Cdd:cd15529     1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 250-330 1.71e-09

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 58.00  E-value: 1.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  250 WAHHRCVEWSLGIcQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLLCPE 329
Cdd:cd15699    24 WVHEGCILWANGI-YLVCGRLYGLQEALDIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAIDADCLLNEENFSVRCPK 102


                  .
gi 568933163  330 H 330
Cdd:cd15699   103 H 103
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1004-1049 1.83e-09

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 55.75  E-value: 1.83e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGkatDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15532     1 FCRVCK---DGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 1005-1049 2.39e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 55.52  E-value: 2.39e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15628     2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 1004-1049 4.24e-09

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 54.71  E-value: 4.24e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1004 VCEACGKAtdpGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15523     1 FCSVCRKS---GELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 1001-1049 4.64e-09

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 54.76  E-value: 4.64e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163 1001 ECTVCeacgkaTDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15539     1 ECAVC------GDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 390-435 4.84e-09

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 54.96  E-value: 4.84e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15602     1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 391-435 5.86e-09

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 54.73  E-value: 5.86e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 4364-4445 6.27e-09

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277182 [Multi-domain]  Cd Length: 115  Bit Score: 56.83  E-value: 6.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4364 DLWVHLNCALWSTEVYETQAGALINVELA---------LRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMF 4434
Cdd:cd15712    20 NIAAHQNCLLYSSGFVESEEYNPLNLDRRfdvesvlneIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCALCDDAAI 99

                          90
                  ....*....|....*.
gi 568933163 4435 FKDKT-----MLCPMH 4445
Cdd:cd15712   100 ETDEVrgiyrVFCQKH 115
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1004-1049 6.84e-09

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 54.33  E-value: 6.84e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKG----GWKCKWC 1049
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKtknsGWQCSEC 50
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1809-2146 6.99e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 63.03  E-value: 6.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1809 VAPGSDTPssgaqsPLTPQAGNGNVSPAQtfhkdlfskhlPGTPASTPsdgvfvkPQPPPPPSTPSRIPVQESLSQSQNS 1888
Cdd:PHA03247 2749 ATPGGPAR------PARPPTTAGPPAPAP-----------PAAPAAGP-------PRRLTRPAVASLSESRESLPSPWDP 2804

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1889 QPPSPQMFSPGSS---HSRPPSPVDPYAKMVGTPRPPPGGhsfPRRNSVTPVENCVPLSSV-----PRPIHMNETSATRP 1960
Cdd:PHA03247 2805 ADPPAAVLAPAAAlppAASPAGPLPPPTSAQPTAPPPPPG---PPPPSLPLGGSVAPGGDVrrrppSRSPAAKPAAPARP 2881

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1961 sPARDLCASSMTNS-DPYAKPPDTPRPMMTDQFSKPFSLPRSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQR--LP 2037
Cdd:PHA03247 2882 -PVRRLARPAVSRStESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSgaVP 2960

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2038 DPYAGP----------SLTPAPLGNGPFKTPLHPPPSQDPYGSVSQ--TSRRLSVDPYERPA---LTPRPVDN------- 2095
Cdd:PHA03247 2961 QPWLGAlvpgrvavprFRVPQPAPSREAPASSTPPLTGHSLSRVSSwaSSLALHEETDPPPVslkQTLWPPDDtedsdad 3040

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568933163 2096 ---FSHSQSNDPYSHPPLTPHPamTESFTHAsrafPQPGTISRSASQDPYSQ--PP 2146
Cdd:PHA03247 3041 slfDSDSERSDLEALDPLPPEP--HDPFAHE----PDPATPEAGARESPSSQfgPP 3090
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 390-435 8.90e-09

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 54.19  E-value: 8.90e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1004-1049 1.33e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 53.47  E-value: 1.33e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163 1004 VCEACGKATD-PGRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1049
Cdd:cd15489     1 SCIVCGKGGDlGGELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 344-391 1.45e-08

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 53.65  E-value: 1.45e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 568933163   344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVT--PLKRAGWQCPECKVC 391
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 390-435 1.48e-08

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 53.62  E-value: 1.48e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15519     1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2118-2461 1.53e-08

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 61.73  E-value: 1.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2118 ESFTHASRAFPQPGTISRSASQDPYSQPPG----TPRPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTIDPYSQQPPTPR 2193
Cdd:PHA03307   12 EAAAEGGEFFPRPPATPGDAADDLLSGSQGqlvsDSAELAAVTVVAGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2194 PSPQTdmfVSSVANQRHTDPYTHHLGPPRPGISVPYSQPP-----AVPRPRTSEGFTRPSSARPALMPNQDPFLQAAQNR 2268
Cdd:PHA03307   92 LSTLA---PASPAREGSPTPPGPSSPDPPPPTPPPASPPPspapdLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAAS 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2269 VPGLPGPLIRPPDT--CSQTPRPPGPGRIDTFTHASSSAVRDPYDQPPV---TPRP----------------HSESFGTS 2327
Cdd:PHA03307  169 SRQAALPLSSPEETarAPSSPPAEPPPSTPPAAASPRPPRRSSPISASAsspAPAPgrsaaddagasssdssSSESSGCG 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2328 QVVHDLVDRPVP-----------GSEGNFSTSSNLPVSSqgqqfSSVSQLPGPVPTSGGTDTQNTVNMSQADTEKLRQRq 2396
Cdd:PHA03307  249 WGPENECPLPRPapitlptriweASGWNGPSSRPGPASS-----SSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSR- 322

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568933163 2397 klreiilqqqqQKKIASRQEKGPQDTAVVPHPVPLPHWQPESinqafTRPPPPYPGSTRSPVIPP 2461
Cdd:PHA03307  323 -----------ESSSSSTSSSSESSRGAAVSPGPSPSRSPSP-----SRPPPPADPSSPRKRPRP 371
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 249-330 1.93e-08

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 55.48  E-value: 1.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  249 CWAHHRCVEWSLGICQMEEPLLVN--------VDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAA--GAGTFQ 318
Cdd:cd15673    23 IAAHHNCMLFSSGLVQYVSPNENDfggfdiedVKKEIKRGRKLKCNLCKKTGATIGCDVKQCKKTYHYHCAKkdDAKIIE 102

                          90
                  ....*....|....
gi 568933163  319 DFSH--FFLLCPEH 330
Cdd:cd15673   103 RNSQgiYRVYCKNH 116
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 391-435 2.78e-08

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 52.77  E-value: 2.78e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15530     2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 1005-1050 3.20e-08

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 52.55  E-value: 3.20e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1050
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNCV 47
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 388-435 4.52e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 52.32  E-value: 4.52e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  388 CKVCQNCKQSGEDskMLVCDTCDKGYHTFCLQPVMKS-VPTNGWKCKNC 435
Cdd:cd15489     2 CIVCGKGGDLGGE--LLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 466-517 6.14e-08

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277067  Cd Length: 57  Bit Score: 51.91  E-value: 6.14e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163  466 LCPFCGKCYHP-ELQKDMLHCNMCKRWVHLECDKPTDQ--ELDSQLKED--YICMYC 517
Cdd:cd15592     1 FCPLCDKCYDDdDYESKMMQCGKCDRWVHSKCENLSDEmyEILSNLPESvaYTCINC 57
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 388-435 7.67e-08

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 51.60  E-value: 7.67e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  388 CKVCQNcKQsgEDSKMLVCDTCDKGYHTFCLQPVMKSVP-TNGWKCKNC 435
Cdd:cd15525     2 CHVCGG-KQ--DPEKQLLCDECDMAYHLYCLDPPLTSLPdDDEWYCPDC 47
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 954-1002 8.05e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 51.55  E-value: 8.05e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  954 MCVVCGSFGQGaEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 1002
Cdd:cd15489     1 SCIVCGKGGDL-GGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 467-517 8.38e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 51.55  E-value: 8.38e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163  467 CPFCGKCYHPElqKDMLHCNMCKRWVHLECDKPTdqELDSQLKEDYICMYC 517
Cdd:cd15489     2 CIVCGKGGDLG--GELLQCDGCGKWFHADCLGPP--LSSFVPNGKWICPVC 48
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 1004-1049 9.14e-08

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 51.20  E-value: 9.14e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163 1004 VCEACGkatDPGRLLLCDDCDISYHTYCLDPPL--QTVPKGGWKCKWC 1049
Cdd:cd15533     1 YCDSCG---EGGDLLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1001-1049 1.59e-07

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 50.47  E-value: 1.59e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568933163 1001 ECTVCEACGKATDpgrLLLCDDCDISYHTYCLDPPLQTVPKG---GWKCKWC 1049
Cdd:cd15563     1 ECCVCKQTGDNSQ---LVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
SET_Suv4-20-like cd10524
SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of ...
 4704-4843 1.71e-07

SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of variegation 4-20 (Suv4-20) and similar proteins; Suv4-20 (also termed Su(var)4-20) is a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-20' of histone H4. It acts as a dominant suppressor of position-effect variegation. The family also includes Suv4-20 homologs, lysine N-methyltransferase 5B (KMT5B) and lysine N-methyltransferase 5C (KMT5C). Both KMT5B (also termed lysine-specific methyltransferase 5B, or suppressor of variegation 4-20 homolog 1, or Su(var)4-20 homolog 1, or Suv4-20h1) and KMT5C (also termed lysine-specific methyltransferase 5C, or suppressor of variegation 4-20 homolog 2, or Su(var)4-20 homolog 2, or Suv4-20h2) are histone methyltransferases that specifically trimethylate 'Lys-20' of histone H4 (H4K20me3). They play central roles in the establishment of constitutive heterochromatin in pericentric heterochromatin regions.


Pssm-ID: 380922 [Multi-domain]  Cd Length: 141  Bit Score: 53.44  E-value: 1.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4704 WKSNVYLARSRiQGLGLYAARDIEKHTMVIEYIGTIIRNEVAnrkEKLYESQNRG----VYMFRMDNDHVIDatltgGPA 4779
Cdd:cd10524     7 CPCNRYSLENH-YGAKIIATKPIKKGEKIHELCGCIAELSEE---EEALLRPGGNdfsvMYSSRKKCSQLWL-----GPA 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568933163 4780 RYINHSCAPNCvaEVVTFERGhKIIISSNRRIQKGEELCYDYKFDFEDDQHkipCHCGAVNCRK 4843
Cdd:cd10524    78 AFINHDCRPNC--KFVPTGKS-TACVKVLRDIEPGEEITVYYGDNYFGENN---EECECETCER 135
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 391-435 2.68e-07

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 49.91  E-value: 2.68e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15531     2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1081-1131 2.96e-07

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 50.01  E-value: 2.96e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163 1081 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVadiGFDCSMC 1131
Cdd:cd15489     1 SCIVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNG---KWICPVC 48
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 466-517 3.04e-07

PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins; This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277087  Cd Length: 57  Bit Score: 50.17  E-value: 3.04e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163  466 LCPFCGKCYHP--ELQKDMLHCNMCKRWVHLECDKPTDQELDSQLKED---YICMYC 517
Cdd:cd15615     1 FCILCGQVYEEneGDEKEWVQCDSCSEWVHFECDGRTGLGAFKYAKSDglqYVCPRC 57
PHA03377 PHA03377
EBNA-3C; Provisional
 1811-2193 3.30e-07

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 56.98  E-value: 3.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1811 PGSDTPSSGAQSPLTPQAGNGNVSPAQTFHKDLfSKHLPGTPASTPSDgvfvKPQPPPPPSTPSRIPVQESLSQSQNSQP 1890
Cdd:PHA03377  568 PVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQ-AKCKDGPPASGPHE----KQPPSSAPRDMAPSVVRMFLRERLLEQS 642

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1891 --PSPQMF------SPGSSHSRPPSPVDPYAKMVGTPRPP--PGGHSFPrrnsVTPVENCVPLSSVprpiHMNETSATRP 1960
Cdd:PHA03377  643 tgPKPKSFwemragRDGSGIQQEPSSRRQPATQSTPPRPSwlPSVFVLP----SVDAGRAQPSEES----HLSSMSPTQP 714

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1961 SPA------RDLCASSMTNSDPYAKPPDTPR--------PMMTDQFSKPFSLPRSPVISEQSTKGPLTTGTSDH----FT 2022
Cdd:PHA03377  715 ISHeeqpryEDPDDPLDLSLHPDQAPPPSHQapysgheePQAQQAPYPGYWEPRPPQAPYLGYQEPQAQGVQVSsypgYA 794

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2023 KPSPRTDAFQRQRLP------DPYAGPSLTP-APlgngpfkTPLHPPPSQDPYGSVSQTSrrlsvdpyerpaltprpVDN 2095
Cdd:PHA03377  795 GPWGLRAQHPRYRHSwaywsqYPGHGHPQGPwAP-------RPPHLPPQWDGSAGHGQDQ-----------------VSQ 850

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2096 FSHSQSNDPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQDPY-SQPPGTPRPLIDSYS---QTSGTARSN---PD 2168
Cdd:PHA03377  851 FPHLQSETGPPRLQLSQVPQLPYSQTLVSSSAPSWSSPQPRAPIRPIpTRFPPPPMPLQDSMAvgcDSSGTACPSmpfAS 930

                         410       420
                  ....*....|....*....|....*
gi 568933163 2169 PYSQPPGTPrpntIDPYSQQPPTPR 2193
Cdd:PHA03377  931 DYSQGAFTP----LDINAQTPKRPR 951
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 390-435 3.58e-07

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 49.32  E-value: 3.58e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15523     1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 1005-1050 3.65e-07

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 49.59  E-value: 3.65e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1050
Cdd:cd15630     3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACI 48
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1005-1049 4.08e-07

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 49.14  E-value: 4.08e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKAtdpGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15531     2 CEVCQQG---GEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2090-2319 4.41e-07

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 56.70  E-value: 4.41e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2090 PRPVDNFSHSQSNDPYS------------HPPLTPHPAMTESFTHASRAFPQPGTISRSASQDP-YSQPPGTPRPLIDSY 2156
Cdd:pfam03154  149 PSPQDNESDSDSSAQQQilqtqppvlqaqSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPaTSQPPNQTQSTAAPH 228

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2157 SQTSGTarsnpdPYSQPPGTPRPNT-------IDPYSQQPPTPRPSPQTDMFVSSVANQRHTDP-YTHHLGPPRPGISVP 2228
Cdd:pfam03154  229 TLIQQT------PTLHPQRLPSPHPplqpmtqPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPsHMQHPVPPQPFPLTP 302

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2229 YSQPPAVPrPRTSEGFTRPSSARPALMPNQDPFLQAAQNRVPGLPG-----PLIRPPDTcsqTPRPPGPGRiDTFTHASS 2303
Cdd:pfam03154  303 QSSQSQVP-PGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPaplsmPHIKPPPT---TPIPQLPNP-QSHKHPPH 377

                          250
                   ....*....|....*.
gi 568933163  2304 SAVRDPYDQPPVTPRP 2319
Cdd:pfam03154  378 LSGPSPFQMNSNLPPP 393
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 1001-1049 4.60e-07

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 49.26  E-value: 4.60e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163 1001 ECTVCEacgkatDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15541     1 WCAVCQ------NGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 391-435 4.80e-07

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 49.20  E-value: 4.80e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15630     3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 390-435 5.15e-07

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 49.31  E-value: 5.15e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTN---GWKCKNC 435
Cdd:cd15563     1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 344-388 9.99e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.36  E-value: 9.99e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 568933163    344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTP-LKRAGWQCPEC 388
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 344-388 1.06e-06

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 48.47  E-value: 1.06e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163  344 CAVCDSPGDLLDQF-FCTTCGQHYHGMCLDIAVTPL-KRAGWQCPEC 388
Cdd:cd15489     2 CIVCGKGGDLGGELlQCDGCGKWFHADCLGPPLSSFvPNGKWICPVC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 467-517 1.10e-06

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.36  E-value: 1.10e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 568933163    467 CPFCGKCYHPElqkDMLHCNMCKRWVHLECDKPTdqELDSQLKEDYICMYC 517
Cdd:smart00249    2 CSVCGKPDDGG---ELLQCDGCDRWYHQTCLGPP--LLEEEPDGKWYCPKC 47
PHA03378 PHA03378
EBNA-3B; Provisional
 2001-2388 1.46e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 55.07  E-value: 1.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2001 SPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSV 2080
Cdd:PHA03378  579 SPTTSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPLRMQPITFNVLVFPTPHQPPQVE 658

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2081 DPYERPALTPRPVDNFSHSQSNDPYSH-----------PPLTPHPAMTESFTHASRAFPQ--PGTISRSASQDPYSQPPG 2147
Cdd:PHA03378  659 ITPYKPTWTQIGHIPYQPSPTGANTMLpiqwapgtmqpPPRAPTPMRPPAAPPGRAQRPAaaTGRARPPAAAPGRARPPA 738

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2148 TPRPLIDSYSQTSGTAR---SNPDPYSQPPGTPRPNTIDPYSQQPPTPRPSPQTdmfVSSVANQRHTDPYTHHLGPPRPg 2224
Cdd:PHA03378  739 AAPGRARPPAAAPGRARppaAAPGRARPPAAAPGAPTPQPPPQAPPAPQQRPRG---APTPQPPPQAGPTSMQLMPRAA- 814

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2225 isvPYSQPPA--VPRPRTSEGFT--RPSSARPALMPNQDPflqAAQNRVPG-------LPGPLIRPP-DTCSQTPRPPGP 2292
Cdd:PHA03378  815 ---PGQQGPTkqILRQLLTGGVKrgRPSLKKPAALERQAA---AGPTPSPGsgtsdkiVQAPVFYPPvLQPIQVMRQLGS 888

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2293 GRIDTFTHASSSAVRDPYDQPPVTPRPHSESFGTSQVVHD-LVDRPVPGSEGNFSTSSNLPVSSQGQQfssvsqlpgPVP 2371
Cdd:PHA03378  889 VRAAAASTVTQAPTEYTGERRGVGPMHPTDIPPSKRAKTDaYVESQPPHGGQSHSFSVIWENVSQGQQ---------QTL 959

                         410
                  ....*....|....*..
gi 568933163 2372 TSGGTDTQNTVNMSQAD 2388
Cdd:PHA03378  960 ECGGTTKQERAMLGTGD 976
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 390-435 1.50e-06

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 47.79  E-value: 1.50e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVP----TNGWKCKNC 435
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPkktkNSGWQCSEC 50
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 466-517 1.57e-06

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 276983  Cd Length: 57  Bit Score: 48.21  E-value: 1.57e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163  466 LCPFCGKCYH-PELQKDMLHCNMCKRWVHLECDKPTDQ--ELDSQLKED--YICMYC 517
Cdd:cd15508     1 YCPLCEKCYDdDDYDSKMMQCSQCDHWVHAKCEGLSDEmyEILSYLPESieYTCSLC 57
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1662-1709 1.95e-06

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 47.90  E-value: 1.95e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163 1662 LYTNINFPNLKEEFPDWTTR--VKQIAKLWRKASSQERAPYVQKARDNRA 1709
Cdd:cd00084     8 LFSKEKRPKLKKENPDLSFTeiSKLLGERWKELSEEEKQPYEEKAKEDKE 57
PHA03377 PHA03377
EBNA-3C; Provisional
 2082-2523 2.13e-06

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 54.29  E-value: 2.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2082 PYERPALTP---RPVDNFSHSQSNDPYSHPPLTP--HPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSY 2156
Cdd:PHA03377  391 PYIDPNMEPvqqRPVMFVSRVPWRKPRTLPWPTPktHPVKRTLVKTSGRSDEAEQAQSTPERPGPSDQPSVPVEPAHLTP 470

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2157 SQTSGTArsnpdpYSQPPGTPRPNTIDPYSQ--------------------------------QPPTPRPSPQTDMFVSS 2204
Cdd:PHA03377  471 VEHTTVI------LHQPPQSPPTVAIKPAPPpsrrrrgacvvydddiievidvetteeeesvtQPAKPHRKVQDGFQRSG 544

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2205 VANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPalmPNQDPFLQAAQNRVPGLPGPLIRPPDtcS 2284
Cdd:PHA03377  545 RRQKRATPPKVSPSDRGPPKASPPVMAPPSTGPRVMATPSTGPRDMAP---PSTGPRQQAKCKDGPPASGPHEKQPP--S 619

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2285 QTPRPPGPGRIDTFThasssavRDPYDQPPVTPRPhsESFGTSQVVHDLVD-RPVPGSEGNFSTSSNLPVSSqgqQFSSV 2363
Cdd:PHA03377  620 SAPRDMAPSVVRMFL-------RERLLEQSTGPKP--KSFWEMRAGRDGSGiQQEPSSRRQPATQSTPPRPS---WLPSV 687

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2364 SQLPGpVPTSGGTDTQNTVNMSQADTEKLRQRQKLReiilqqqqqkkiaSRQEKGPQDTAVVPHPVPLP-HWQPESINQA 2442
Cdd:PHA03377  688 FVLPS-VDAGRAQPSEESHLSSMSPTQPISHEEQPR-------------YEDPDDPLDLSLHPDQAPPPsHQAPYSGHEE 753

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2443 FTRPPPPYPG--STRSPVIPPLGPRYAVFPKDQRGPYPPEVAGMGMRPHGFRF--------GFPGAGHGPMPSQDRF-HV 2511
Cdd:PHA03377  754 PQAQQAPYPGywEPRPPQAPYLGYQEPQAQGVQVSSYPGYAGPWGLRAQHPRYrhswaywsQYPGHGHPQGPWAPRPpHL 833

                         490
                  ....*....|..
gi 568933163 2512 PQQIQGSGIPPH 2523
Cdd:PHA03377  834 PPQWDGSAGHGQ 845
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 1004-1055 2.31e-06

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 47.49  E-value: 2.31e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568933163 1004 VCEACG--KATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKcKWcvWCRHC 1055
Cdd:cd15499     1 TCSICGgaEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGDE-KW--FCSRC 51
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1081-1131 2.46e-06

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 276983  Cd Length: 57  Bit Score: 47.44  E-value: 2.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568933163 1081 SCPVCCRNYREEDL---ILQCRQCDRWMHAVCQNLnTEEEVENVAD----IGFDCSMC 1131
Cdd:cd15508     1 YCPLCEKCYDDDDYdskMMQCSQCDHWVHAKCEGL-SDEMYEILSYlpesIEYTCSLC 57
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 467-518 2.55e-06

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 47.10  E-value: 2.55e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163   467 CPFCGKcyhPELQKDMLHCNMCKRWVHLECDKPTDQELDsQLKEDYICMYCK 518
Cdd:pfam00628    2 CAVCGK---SDDGGELVQCDGCDDWFHLACLGPPLDPAE-IPSGEWLCPECK 49
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 1005-1049 3.10e-06

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 46.64  E-value: 3.10e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 1005 CEACGKatdPGRLLLCDDCDISYHTYCLDPPL--QTVPKGGWKCKWC 1049
Cdd:cd15535     2 CSACGG---YGSFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45
SET_SpSet7-like cd10540
SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces ...
 4708-4827 3.46e-06

SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces pombe Set7 is a novel histone-lysine N-methyltransferase. The family also includes a viral histone H3 lysine 27 methyltransferase from Paramecium bursaria Chlorella virus 1 (PBCV-1).


Pssm-ID: 380938  Cd Length: 112  Bit Score: 48.79  E-value: 3.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4708 VYLARSRIQGLGLYAARDIEKHTmVIEYIGTIIrneVANRKEKLYESQNRGVYMFRMDNDHVidATLTGGPARYiNHSCA 4787
Cdd:cd10540     2 LEVKPSTLKGRGVFATRPIKKGE-VIEEAPVIV---LPKEEYQHLCKTVLDHYVFSWGDGCL--ALALGYGSMF-NHSYT 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 568933163 4788 PNcvAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFED 4827
Cdd:cd10540    75 PN--AEYEIDFENQTIVFYALRDIEAGEELTINYGDDLWD 112
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2175-2597 3.57e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 53.62  E-value: 3.57e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2175 GTPRPNTIDPYSQQPPTPRPSPQ---TDMFVSSVANQRHTDP-----YTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTR 2246
Cdd:pfam03154  130 GSSDPKDIDQDNRSTSPSIPSPQdneSDSDSSAQQQILQTQPpvlqaQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQ 209

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2247 PSSarPALMPNQDPFLQAA-----QNRVPGLPGPLIRPPDTCSQTPRPPGPGRIdtfthaSSSAVRDPYDQPPVTPRPHS 2321
Cdd:pfam03154  210 GSP--ATSQPPNQTQSTAAphtliQQTPTLHPQRLPSPHPPLQPMTQPPPPSQV------SPQPLPQPSLHGQMPPMPHS 281

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2322 ESFGTSQVVHDLVDRPVPGSegnfstssnlPVSSQGQQfssvsqLPGPVPTSGGTDTQNTvnMSQADTEKLRQRQKLREI 2401
Cdd:pfam03154  282 LQTGPSHMQHPVPPQPFPLT----------PQSSQSQV------PPGPSPAAPGQSQQRI--HTPPSQSQLQSQQPPREQ 343

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2402 ILQQQQqkkIASRQEKGPQDTAVVPHPVPLPHWQPESINQAF------TRPPPPY--PGSTRSPVIPPLG--PRYAVFPK 2471
Cdd:pfam03154  344 PLPPAP---LSMPHIKPPPTTPIPQLPNPQSHKHPPHLSGPSpfqmnsNLPPPPAlkPLSSLSTHHPPSAhpPPLQLMPQ 420

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2472 DQRGPYPPE-----VAGMGMRPHGFRFGFPGAGHgPMPSQDRFhvPQQIQGSGIPPHIRRPMSmemprpsnnPPLNNPVG 2546
Cdd:pfam03154  421 SQQLPPPPAqppvlTQSQSLPPPAASHPPTSGLH-QVPSQSPF--PQHPFVPGGPPPITPPSG---------PPTSTSSA 488

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568933163  2547 LPQHFPPQGLPVQQHNILGQAF------IELRHRAPDG----RSRLPFAASPS---SVIESPSH 2597
Cdd:pfam03154  489 MPGIQPPSSASVSSSGPVPAAVscplppVQIKEEALDEaeepESPPPPPRSPSpepTVVNTPSH 552
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 391-435 4.08e-06

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 46.29  E-value: 4.08e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15539     2 CAVCGDGGE---LLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
dnaA PRK14086
chromosomal replication initiator protein DnaA;
2038-2268 6.31e-06

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 52.52  E-value: 6.31e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2038 DPYAGPSLTPAPlgngpfktplHPPPSQDPYGSvsqTSRRLSVDPYERPALTPRPvdnfshsQSNDPYSHPPlTPHPAMT 2117
Cdd:PRK14086   89 DPSAGEPAPPPP----------HARRTSEPELP---RPGRRPYEGYGGPRADDRP-------PGLPRQDQLP-TARPAYP 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2118 eSFTHASRAFPQPGT-ISRSASQDPYSQPPGTPRPLIDSYS-------QTSGTARSNPDPYSQPPGTPRPNTIDPYSQQP 2189
Cdd:PRK14086  148 -AYQQRPEPGAWPRAaDDYGWQQQRLGFPPRAPYASPASYApeqerdrEPYDAGRPEYDQRRRDYDHPRPDWDRPRRDRT 226

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2190 PTPRPSPQTdmfvssvanqrHTDPYTHHLGPPRPGISVPYSQPPAvPRPRTSEGFTRPSSARPALMPNQ----DPFLQAA 2265
Cdd:PRK14086  227 DRPEPPPGA-----------GHVHRGGPGPPERDDAPVVPIRPSA-PGPLAAQPAPAPGPGEPTARLNPkytfDTFVIGA 294


                  ...
gi 568933163 2266 QNR 2268
Cdd:PRK14086  295 SNR 297
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 955-1002 6.76e-06

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 45.76  E-value: 6.76e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163  955 CVVCGSFGQGAEgrLLACSQCGQCYHPYCV--SIKITKVVLSkGWRCLEC 1002
Cdd:cd15509     2 CAVCDSPGDLSD--LLFCTSCGQHYHGSCLdpAVRPTPLVRA-GWQCPEC 48
PHA03379 PHA03379
EBNA-3A; Provisional
 1886-2343 7.12e-06

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 52.75  E-value: 7.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1886 QNSQPPSPQMFSPGSSHSR-----------PPSPVDPYAKMVGTPRPPPGGhsfprRNSVTPVEncVPLSSVPRPIHMNE 1954
Cdd:PHA03379  441 QVPEPPPVHDLEPGPLHDQhsmapcpvaqlPPGPLQDLEPGDQLPGVVQDG-----RPACAPVP--APAGPIVRPWEASL 513

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1955 TSATRPSPArdlcassMTNSDPYAKPPDtPRPmmtdqfSKPFSLPRSPVISEQSTKGPLTTGTSdhftkpsprtdafqrQ 2034
Cdd:PHA03379  514 SQVPGVAFA-------PVMPQPMPVEPV-PVP------TVALERPVCPAPPLIAMQGPGETSGI---------------V 564

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2035 RLPDPYAGPSLTPAPLgNGPFKTPLHPPPSQ-DPYGSVSQTSrrLSVDPYERPALTPRpvdnfshsqsnDPYSHpPLTPH 2113
Cdd:PHA03379  565 RVRERWRPAPWTPNPP-RSPSQMSVRDRLARlRAEAQPYQAS--VEVQPPQLTQVSPQ-----------QPMEY-PLEPE 629

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2114 PAMtesftHASRAFPQPGTISRsASQDPYSQPPGTPRPLIDSYSQTSGTArsnPDPYSQPPGTPRPNTIDPYSQQPPTPR 2193
Cdd:PHA03379  630 QQM-----FPGSPFSQVADVMR-AGGVPAMQPQYFDLPLQQPISQGAPLA---PLRASMGPVPPVPATQPQYFDIPLTEP 700

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2194 PSPQTDMFvssvanqrhtdpythHLGPPRPgisvpySQPPAVPRPRTSEGFTRPSSARPALMPNQD---PFLQAAQNRVP 2270
Cdd:PHA03379  701 INQGASAA---------------HFLPQQP------MEGPLVPERWMFQGATLSQSVRPGVAQSQYfdlPLTQPINHGAP 759

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568933163 2271 GLPGPlirppdtcsqtPRPPGPGRIdtfthassSAVRDPYDQPPVTPR----PHS-ESFGtsQVVHDLVDRPVPGSEG 2343
Cdd:PHA03379  760 AAHFL-----------HQPPMEGPW--------VPEQWMFQGAPPSQGtdvvQHQlDALG--YVLHVLNHPGVPVSPA 816
SET_SETD5 cd19181
SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and ...
 4720-4841 8.00e-06

SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. SETD5 loss-of-function mutations are a likely cause of a familial syndromic intellectual disability with variable phenotypic expression.


Pssm-ID: 380958  Cd Length: 150  Bit Score: 48.85  E-value: 8.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4720 LYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDN--DHVIDATLTGGPARYINHSCAPNCVAEVVTF 4797
Cdd:cd19181    21 LRAARDLALDTLIIEYRGKVMLRQQFEVNGHFFKRPYPFVLFYSKFNgvEMCVDARTFGNDARFIRRSCTPNAEVRHMIA 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 4798 ERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHC--GAVNC 4841
Cdd:cd19181   101 DGMIHLCIYAVAAIAKDAEVTIAFDYEYSNCNYKVDCAChkGNRNC 146
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 1005-1049 8.72e-06

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 45.48  E-value: 8.72e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKAtdpGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15559     2 CRVCHKL---GDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1005-1049 8.81e-06

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 45.76  E-value: 8.81e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVP--KGGWKCKWC 1049
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPlvRAGWQCPEC 48
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 1004-1046 9.23e-06

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 45.42  E-value: 9.23e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 568933163 1004 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGG-WKC 1046
Cdd:cd15534     1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMC 44
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
2037-2278 9.98e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 52.19  E-value: 9.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2037 PDPYAGPSLTP------APLGNGPFKTPlhPPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPL 2110
Cdd:PRK12323  347 PDEYAGFTMTLlrmlafRPGQSGGGAGP--ATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPA 424

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2111 TPHPAMTESFTHASRAFPQPGTISRSASQdPYSQPPGTPRPLIDSysqtsgtARSNPDPYSQPP--------GTPRPNTI 2182
Cdd:PRK12323  425 RRSPAPEALAAARQASARGPGGAPAPAPA-PAAAPAAAARPAAAG-------PRPVAAAAAAAParaapaaaPAPADDDP 496

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2183 DPYSQQPPT-PRPSP-QTDMFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGF---TRPSSARPALMPN 2257
Cdd:PRK12323  497 PPWEELPPEfASPAPaQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVvapRPPRASASGLPDM 576

                         250       260
                  ....*....|....*....|....
gi 568933163 2258 QD---PFLqAAQNRVPGLPGPLIR 2278
Cdd:PRK12323  577 FDgdwPAL-AARLPVRGLAQQLAR 599
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 391-435 1.02e-05

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 45.34  E-value: 1.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPT-NGWKCKNC 435
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDdEDWYCPEC 47
SET_AtSUVH-like cd10545
SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar ...
 4732-4821 1.17e-05

SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins; Arabidopsis thaliana SUVH protein (also termed suppressor of variegation 3-9 homolog protein) is a histone-lysine N-methyltransferase that methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Some family members contain a post-SET domain which binds a Zn2+ ion. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380943 [Multi-domain]  Cd Length: 232  Bit Score: 50.09  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4732 VIEYIGTIIRNEVANRKEKlyesqnRGVYMFRMDN-------------------------------DHVIDATLTGGPAR 4780
Cdd:cd10545   112 ICEYVGELLDTSEADTRSG------NDDYLFDIDNrqtnrgwdggqrldvgmsdgerssaedeessEFTIDAGSFGNVAR 185

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 4781 YINHSCAPNCVAEVVTFE----RGHKIIISSNRRIQKGEELCYDY 4821
Cdd:cd10545   186 FINHSCSPNLFVQCVLYDhndlRLPRVMLFAADNIPPLQELTYDY 230
HMG_box pfam00505
HMG (high mobility group) box;
1661-1712 1.22e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 45.68  E-value: 1.22e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 568933163  1661 VLYTNINFPNLKEEFPDWTTR--VKQIAKLWRKASSQERAPYVQKARDNRAALR 1712
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
HMG smart00398
high mobility group;
1659-1712 1.34e-05

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 45.77  E-value: 1.34e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 568933163   1659 APVLYTNINFPNLKEEFPDWTT--RVKQIAKLWRKASSQERAPYVQKARDNRAALR 1712
Cdd:smart00398    8 AFMLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
250-330 1.50e-05

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 46.95  E-value: 1.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163   250 WAHHRCVEWSLGIC-----QMEeplLVNVDKAVVSGSTERCAFCKHL-GATIKCCEEKCTQMYHYPCAAGAG---TFQDF 320
Cdd:pfam13832   21 WVHVLCAIFVPEVRfgnvaTME---PIDVSRIPPERWKLKCVFCKKRsGACIQCSKGRCTTAFHVTCAQAAGvymEPEDW 97

                           90
                   ....*....|..
gi 568933163   321 SHF--FLLCPEH 330
Cdd:pfam13832   98 PNVvvIAYCQKH 109
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 4368-4431 1.73e-05

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 46.88  E-value: 1.73e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 4368 HLNCALWSTEVYETQAG-------ALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCA--TKAQ 4431
Cdd:cd15710    26 HHKCMLFSSALVSSHSDsenlggfSIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCAlhDKAQ 98
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 251-330 2.39e-05

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277182 [Multi-domain]  Cd Length: 115  Bit Score: 46.43  E-value: 2.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  251 AHHRCVEWSLGICQMEEPLLVNVD---------KAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA----AGAGTF 317
Cdd:cd15712    23 AHQNCLLYSSGFVESEEYNPLNLDrrfdvesvlNEIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCAlcddAAIETD 102

                          90
                  ....*....|...
gi 568933163  318 QDFSHFFLLCPEH 330
Cdd:cd15712   103 EVRGIYRVFCQKH 115
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1814-2257 2.70e-05

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 50.84  E-value: 2.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1814 DTPSSGAQSPLTPQAGNGNVSPAQTFHKDLFSKHLP---GTPASTPSDGVFVKPQPPPPPSTPSRIPV-------QESLS 1883
Cdd:PTZ00449  508 DEPPEGPEASGLPPKAPGDKEGEEGEHEDSKESDEPkegGKPGETKEGEVGKKPGPAKEHKPSKIPTLskkpefpKDPKH 587

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1884 QSQNSQPPSPQMFSPGSSHSRPPSPVDP-YAKMVGTPRPPPGGHSfPRRnsvtPVencvplssvprpihmnetSATRP-S 1961
Cdd:PTZ00449  588 PKDPEEPKKPKRPRSAQRPTRPKSPKLPeLLDIPKSPKRPESPKS-PKR----PP------------------PPQRPsS 644

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1962 PARDLCASSMTNSdpyaKPPDTPRPMMTDQFSKPFSLPRSPVISEqsTKGPLTTGTSDHftkpspRTDAFQRQRLPDPYA 2041
Cdd:PTZ00449  645 PERPEGPKIIKSP----KPPKSPKPPFDPKFKEKFYDDYLDAAAK--SKETKTTVVLDE------SFESILKETLPETPG 712

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2042 GPSLTPAPLgngPFKTPLHPPPSQDPygsvsqtsrrlsvdPYERPALTPRPVDNFSHSQSNDPYSH--PPLTPHPAMT-- 2117
Cdd:PTZ00449  713 TPFTTPRPL---PPKLPRDEEFPFEP--------------IGDPDAEQPDDIEFFTPPEEERTFFHetPADTPLPDILae 775

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2118 ---ESFTHASRAFPQPgTISRSASQDPYS-QPPGT------PRPLIDSYSQTSGTARSNP-----DPYSQPPGTPRPNTI 2182
Cdd:PTZ00449  776 efkEEDIHAETGEPDE-AMKRPDSPSEHEdKPPGDhpslpkKRHRLDGLALSTTDLESDAgriakDASGKIVKLKRSKSF 854

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568933163 2183 DPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHhlgPP--RPGISVPYSQPPAVP-RPRTSEGFTRPSSARPALMPN 2257
Cdd:PTZ00449  855 DDLTTVEEAEEMGAEARKIVVDDDGTEADDEDTH---PPeeKHKSEVRRRRPPKKPsKPKKPSKPKKPKKPDSAFIPS 929
SET_SETD7 cd10530
SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins; SETD7 (EC 2. ...
 4708-4821 2.81e-05

SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins; SETD7 (EC 2.1.1.43; also termed histone H3-K4 methyltransferase SETD7, H3-K4-HMTase SETD7, lysine N-methyltransferase 7 (KMT7) or SET7/9) is a histone-lysine N-methyltransferase that specifically monomethylates 'Lys-4' of histone H3. It plays a central role in the transcriptional activation of genes such as collagenase or insulin. Set7/9 also methylates non-histone proteins, including estrogen receptor alpha (ERa), suggesting it has a role in diverse biological processes. ERa methylation by Set7/9 stabilizes ERa and activates its transcriptional activities, which are involved in the carcinogenesis of breast cancer. In a high-throughput screen, treatment of human breast cancer cells (MCF7 cells) with cyproheptadine, a Set7/9 inhibitor, decreased the expression and transcriptional activity of ERa, thereby inhibiting estrogen-dependent cell growth.


Pssm-ID: 380928  Cd Length: 130  Bit Score: 46.91  E-value: 2.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4708 VYLARSRIQ--GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESqnrgvYMFRMDNDHVID------------AT 4773
Cdd:cd10530     9 VYVAESLIPsaGEGLFAKVAVGPNTVMSFYNGVRITHQEVDSRDWSLNG-----NTISLDEETVIDvpepynsvskycAS 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163 4774 LtGGPAryiNHSCAPNCVAEVVTFER-GHKIIISSNRRIQKGEELCYDY 4821
Cdd:cd10530    84 L-GHKA---NHSFTPNCIYDPFVHPRfGPIKCIRTLRAVEAGEELTVAY 128
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 1005-1049 2.89e-05

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 44.11  E-value: 2.89e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKAtdpGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15524     2 CAACKRG---GNLQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
 968-1002 3.12e-05

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 gene family proteins; MOZ is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity and to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF) is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphoma genesis and bone development, and its homologs. This family also includes three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes via changing the condensed/decondensed state of chromatin in nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro specific gene clusters. All family members contain two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277001  Cd Length: 56  Bit Score: 44.27  E-value: 3.12e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 568933163  968 RLLACSQCGQCYHPYCV--SIKITKVVLSKGWRCLEC 1002
Cdd:cd15526    20 ELISCADCGSSGHPSCLkfSPGLTDAVKSYRWQCIEC 56
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 1005-1049 3.28e-05

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 43.84  E-value: 3.28e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163 1005 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGG--WKCKWC 1049
Cdd:cd15497     2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2099-2323 3.31e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.37  E-value: 3.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2099 SQSNDPYSHPPLTPHPAmtesfthaSRAFPQPGTISRSASQDPYSQPPGTPrplidsYSQTSGTARSNPDPYSQPPGTPR 2178
Cdd:PRK07764  606 SGPPEEAARPAAPAAPA--------APAAPAPAGAAAAPAEASAAPAPGVA------APEHHPKHVAVPDASDGGDGWPA 671

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2179 PNTIDPYSQQPPTPRPSPQtdmfvssVANQRHTDPYTHHLGPPRPGiSVPYSQPPAVPRPRTSEGFTRPSSARPALMPNQ 2258
Cdd:PRK07764  672 KAGGAAPAAPPPAPAPAAP-------AAPAGAAPAQPAPAPAATPP-AGQADDPAAQPPQAAQGASAPSPAADDPVPLPP 743

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568933163 2259 DPFLQAAQNRVPGLPGPlIRPPDTCSQTPRPPGPgridtfTHASSSAVRDPYDQPPVTPRPHSES 2323
Cdd:PRK07764  744 EPDDPPDPAGAPAQPPP-PPAPAPAAAPAAAPPP------SPPSEEEEMAEDDAPSMDDEDRRDA 801
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 4341-4437 3.73e-05

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4.


Pssm-ID: 277181  Cd Length: 118  Bit Score: 46.23  E-value: 3.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHE-EGDGLTDGPARLLNLDlDLWVHLNCALWST---EVYETQAGALINVELA-----LRRGLQMKCVFCHKTGATS 4411
Cdd:cd15711     1 CGFCHAgEEENETRGKLHIFNAK-KAAAHYKCMLFSSgtvQLTTTSRAEFGDFDIKtviqeIKRGKRMKCTLCSQLGATI 79

                          90       100
                  ....*....|....*....|....*.
gi 568933163 4412 GCHRFRCTNIYHFTCATKAQCMFFKD 4437
Cdd:cd15711    80 GCEIKACVKTYHYHCGVQDKAKYIEN 105
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 246-330 3.75e-05

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 45.90  E-value: 3.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  246 TGTCWAHHRCVEW----SLGICQMEEPLlVNVDKAVVSGSTERCAFCK-HLGATIKCCEEKCTQMYHYPCAAGAG----- 315
Cdd:cd15671    16 SGTKWVHVSCALWipevSIGCPEKMEPI-TKISHIPMSRWALVCVLCKeKTGACIQCSVKSCKTAFHVTCAFQHGlemkt 94

                          90
                  ....*....|....*...
gi 568933163  316 ---TFQDFSHFFLLCPEH 330
Cdd:cd15671    95 ileDEDDEVKFKSYCPKH 112
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 390-434 4.03e-05

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 43.87  E-value: 4.03e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNG-WKCKN 434
Cdd:cd15534     1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMCPN 46
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 1004-1049 4.63e-05

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 43.58  E-value: 4.63e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568933163 1004 VCEACGKAT--DPGRLLLCD-DCDISYHTYCLDPPLQT--VPKG--GWKCKWC 1049
Cdd:cd15504     1 FCAKCQSGEasPDNDILLCDgGCNRAYHQKCLEPPLLTedIPPEdeGWLCPLC 53
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 1002-1049 4.65e-05

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 43.58  E-value: 4.65e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568933163 1002 CTVCEaCGKATDPGRLLLCDDCDISYHTYCLDPPLQT----VPKGGWKCKWC 1049
Cdd:cd15502     2 CIVCQ-RGHSPKSNRIVFCDGCNTPYHQLCHDPSIDDevveDPDAEWFCKKC 52
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 2003-2290 4.89e-05

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 49.54  E-value: 4.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2003 VISEqsTKGPLTTgTSDHFTK-PSprtdafQRQRLPDPYAGPSLTPAPLGNGPFKTPLhPPPSQDPYGSVSQTSRRLSvd 2081
Cdd:PLN03209  305 VIAE--TTAPLTP-MEELLAKiPS------QRVPPKESDAADGPKPVPTKPVTPEAPS-PPIEEEPPQPKAVVPRPLS-- 372

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2082 PYE-----RPALTPRPVdnfshsqsndPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLidsy 2156
Cdd:PLN03209  373 PYTayedlKPPTSPIPT----------PPSSSPASSKSVDAVAKPAEPDVVPSPGSASNVPEVEPAQVEAKKTRPL---- 438

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2157 sqtsgtarsnpDPYS-----QPPGTPRPNTIDPY----------SQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPP 2221
Cdd:PLN03209  439 -----------SPYAryedlKPPTSPSPTAPTGVspsvsstssvPAVPDTAPATAATDAAAPPPANMRPLSPYAVYDDLK 507

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568933163 2222 RPGISVPYSQPPAVPRPRTSEGFTRPSSARP-ALMPNQDpflQAAQNRVPGLPGPL---IRPPdtCSQTPRPP 2290
Cdd:PLN03209  508 PPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPtALADEQH---HAQPKPRPLSPYTMyedLKPP--TSPTPSPV 575
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2061-2253 5.59e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 49.60  E-value: 5.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2061 PPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDnfshsqsnDPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQD 2140
Cdd:PRK07764  590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAA--------PAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPD 661

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2141 PYSQPPGTPRPLID-----------SYSQTSGTARSNPDPYSQPPGTPRPntiDPYSQQPPTPRPSPQTDMFVSSVANQR 2209
Cdd:PRK07764  662 ASDGGDGWPAKAGGaapaapppapaPAAPAAPAGAAPAQPAPAPAATPPA---GQADDPAAQPPQAAQGASAPSPAADDP 738

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 568933163 2210 HTDPYTHHLgPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPA 2253
Cdd:PRK07764  739 VPLPPEPDD-PPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSE 781
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 4341-4434 5.74e-05

Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2 proteins. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 277145 [Multi-domain]  Cd Length: 112  Bit Score: 45.43  E-value: 5.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGL---TDGparllnldldLWVHLNCALWSTEVY--ETQAGALINVELALRRGLQMKCVFCHK-------TG 4408
Cdd:cd15675     1 CCLCCLRGGALkptTDG----------RWAHVVCAIAIPEVRfsNVPERGPIDISKIPPARLKLKCIYCSKitksmshMG 70

                          90       100
                  ....*....|....*....|....*.
gi 568933163 4409 ATSGCHRFRCTNIYHFTCATKAQCMF 4434
Cdd:cd15675    71 ACIQCSTGKCTTSFHVTCAHAAGVQM 96
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1002-1049 5.86e-05

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 43.23  E-value: 5.86e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163 1002 CTVCEACGKATDPgrLLLCDDCDISYHTYCLDPPLQTVP---KGGWKCKWC 1049
Cdd:cd15507     2 CHVCGRKGQAQKQ--LLECEKCQRGYHVDCLGPSYPTKPtrkKKTWICSKC 50
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 387-435 5.92e-05

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 43.10  E-value: 5.92e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  387 ECKVCQNckqsGEDSkmLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15541     1 WCAVCQN----GGEL--LCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 388-435 6.01e-05

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 43.64  E-value: 6.01e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163  388 CKVCQNcKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNG---WKCKNC 435
Cdd:cd15499     2 CSICGG-AEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGdekWFCSRC 51
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1999-2240 6.05e-05

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 49.54  E-value: 6.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 1999 PRSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLP---DPYAG-------PSLTPAPLGNGPFKTP----LHPPPS 2064
Cdd:PLN03209  330 PKESDAADGPKPVPTKPVTPEAPSPPIEEEPPQPKAVVPrplSPYTAyedlkppTSPIPTPPSSSPASSKsvdaVAKPAE 409

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2065 QDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQ 2144
Cdd:PLN03209  410 PDVVPSPGSASNVPEVEPAQVEAKKTRPLSPYARYEDLKPPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAATDAAAP 489

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2145 PPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTidpySQQPPTPRPSPQTdmfvSSVANQRHTDPythhlgPPRPg 2224
Cdd:PLN03209  490 PPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAPSST----NEVVKVGNSAPPT----ALADEQHHAQP------KPRP- 554

                         250       260
                  ....*....|....*....|.
gi 568933163 2225 ISvPYS-----QPPAVPRPRT 2240
Cdd:PLN03209  555 LS-PYTmyedlKPPTSPTPSP 574
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1082-1131 6.49e-05

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277067  Cd Length: 57  Bit Score: 43.44  E-value: 6.49e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568933163 1082 CPVCCRNYREEDL---ILQCRQCDRWMHAVCQNLNTE--EEVENVAD-IGFDCSMC 1131
Cdd:cd15592     2 CPLCDKCYDDDDYeskMMQCGKCDRWVHSKCENLSDEmyEILSNLPEsVAYTCINC 57
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 388-435 6.68e-05

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 43.19  E-value: 6.68e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  388 CKVCQnCKQSGEDSKMLVCDTCDKGYHTFCLQPVMK----SVPTNGWKCKNC 435
Cdd:cd15502     2 CIVCQ-RGHSPKSNRIVFCDGCNTPYHQLCHDPSIDdevvEDPDAEWFCKKC 52
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 4341-4437 7.00e-05

Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277183  Cd Length: 110  Bit Score: 44.96  E-value: 7.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGparllnlDLDLWVHLNCALWSTEVYETQAGALINVELA---LRRgLQMKCVFCHK-----TGATSG 4412
Cdd:cd15713     1 CCLCSLRGGALQRA-------NDDKWVHVMCAVAVLEARFVNIAERSPVDVSkipLQR-FKLKCIFCKKrrkrtAGCCVQ 72

                          90       100
                  ....*....|....*....|....*
gi 568933163 4413 CHRFRCTNIYHFTCATKAQCMFFKD 4437
Cdd:cd15713    73 CSHGRCPTSFHASCAQAAGVMMQPD 97
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1082-1133 8.93e-05

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 42.86  E-value: 8.93e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 568933163  1082 CPVCcRNYREEDLILQCRQCDRWMHAVCqnLNTEEEVENVADIGFDCSMCRP 1133
Cdd:pfam00628    2 CAVC-GKSDDGGELVQCDGCDDWFHLAC--LGPPLDPAEIPSGEWLCPECKP 50
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 1661-1715 9.33e-05

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 43.46  E-value: 9.33e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568933163 1661 VLYTNINFPNLKEEFPDWTTRV--KQIAKLWRKASSQERAPYVQKARD-NRAALRINK 1715
Cdd:cd21977     9 IMFCRLNRKNYIDKHPGLASTEltKELGQLWRELSAEEKKPYCVRARElSQLHNRKVK 66
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 344-388 1.03e-04

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 42.78  E-value: 1.03e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163  344 CAVCDSPGD--LLDQffCTTCGQHYHGMCLDIAVT--PLKRA--GWQCPEC 388
Cdd:cd15562     2 CGICKKSNDqhLLAL--CDTCKLYYHLGCLDPPLTrmPKKTKnsGWQCSEC 50
SET_KMT2E cd19182
SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar ...
 4720-4825 1.06e-04

SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; KMT2E (also termed inactive lysine N-methyltransferase 2E, myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. Lack of key residues in the SET domain as well as the presence of an unusually large loop in the SET-I subdomain preclude the interaction of MLL5 SET with its cofactor and substrate thus making MLL5 devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptide.


Pssm-ID: 380959  Cd Length: 129  Bit Score: 45.27  E-value: 1.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4720 LYAARDIEKHTMVIEYIGTIIRNEV--AN-----RKEK--LYESQNRGVYMfrmdndhVIDATLTGGPARYINHSCAPNC 4790
Cdd:cd19182    21 LKAAKDLPPDTLIIEYRGKFMLREQfeANgyffkRPYPfvLFYSKFHGLEM-------CVDARTFGNEARFIRRSCTPNA 93

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 568933163 4791 VAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDF 4825
Cdd:cd19182    94 EVRHVIEDGTIHLYIYSIRSIPKGTEITIAFDFDY 128
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 343-388 1.21e-04

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 42.38  E-value: 1.21e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  343 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLD--IAVTPLKRA-GWQCPEC 388
Cdd:cd15563     1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDppLKKSPKQRGyGWVCEEC 49
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 4341-4430 1.36e-04

Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277184  Cd Length: 110  Bit Score: 44.16  E-value: 1.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGL---TDgparllnldlDLWVHLNCALWSTEVYETQAGAL--INVELALRRGLQMKCVFCHKT-----GAT 4410
Cdd:cd15714     1 CCLCNLRGGALqmtTD----------ERWVHVICAIAVPEARFLNVIERhpVDVSAIPEQRWKLKCVYCRKRmkkvsGAC 70

                          90       100
                  ....*....|....*....|
gi 568933163 4411 SGCHRFRCTNIYHFTCATKA 4430
Cdd:cd15714    71 IQCSYDHCSTSFHVTCAHAA 90
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 467-517 1.54e-04

PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277068  Cd Length: 57  Bit Score: 42.53  E-value: 1.54e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568933163  467 CPFCGKCYHP-ELQKDMLHCNMCKRWVHLECDKPTDQ--ELDSQLKED--YICMYC 517
Cdd:cd15593     2 CPICLKCYEDnDYESKMMQCAKCDHWVHAKCEGLSDElyEILSSLPDSvvYSCAPC 57
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1082-1115 1.85e-04

PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277068  Cd Length: 57  Bit Score: 42.14  E-value: 1.85e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 568933163 1082 CPVCCRNYREEDL---ILQCRQCDRWMHAVCQNLNTE 1115
Cdd:cd15593     2 CPICLKCYEDNDYeskMMQCAKCDHWVHAKCEGLSDE 38
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 1005-1049 2.11e-04

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 41.71  E-value: 2.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKatdPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1049
Cdd:cd15623     2 CRVCQK---AGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
dnaA PRK14086
chromosomal replication initiator protein DnaA;
2181-2379 2.13e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 47.51  E-value: 2.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2181 TIDPYSQQPPTPRPSPQtdmfvssvanqRHTDPYTHHLGP-PRPGisvpYSQPPAVPRPRTSEGFTRPSSARPALMPNQD 2259
Cdd:PRK14086   87 TVDPSAGEPAPPPPHAR-----------RTSEPELPRPGRrPYEG----YGGPRADDRPPGLPRQDQLPTARPAYPAYQQ 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2260 PflqaaqnrvpGLPGPLIRPPDTCSQTPRPPGPGRIDTFTHASSSA-----VRDPYD----------QPPVTPRPHSEsf 2324
Cdd:PRK14086  152 R----------PEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYApeqerDREPYDagrpeydqrrRDYDHPRPDWD-- 219

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568933163 2325 gtsQVVHDLVDRPV--PGSEGNFSTSSNLPVSSQGQQFSSVSQLPG-------PVPTSGGTDTQ 2379
Cdd:PRK14086  220 ---RPRRDRTDRPEppPGAGHVHRGGPGPPERDDAPVVPIRPSAPGplaaqpaPAPGPGEPTAR 280
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 390-435 2.43e-04

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 41.58  E-value: 2.43e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163  390 VCQNCKQSGEDsKMLVCDTCDKGYHTFCLQPVMKSVPTNG--WKCKNC 435
Cdd:cd15506     1 LCFLCGSAGLN-ELLYCSVCCEPYHTFCLEEAERPLNINKdnWCCRRC 47
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 391-435 2.85e-04

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 41.53  E-value: 2.85e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNG--WKCKNC 435
Cdd:cd15497     2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 391-435 3.11e-04

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 41.25  E-value: 3.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15559     2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 966-1002 3.52e-04

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 40.77  E-value: 3.52e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 568933163  966 EGRLLACSQCGQCYHPYCVSIKITkvvLSKGWRCLEC 1002
Cdd:cd15538     8 EGQVLCCSLCPRVYHKKCLKLTSE---PDEDWVCPEC 41
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2114-2338 3.63e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 47.09  E-value: 3.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2114 PAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLidsysqtSGTARSNPDPYSQPPGT----PRPNTIDPYSQQP 2189
Cdd:PHA03307  761 PSLVPAKLAEALALLEPAEPQRGAGSSPPVRAEAAFRRP-------GRLRRSGPAADAASRTAskrkSRSHTPDGGSESS 833

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2190 PTPRPSPQTdmFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPAlmpnqdpflqaaqnRV 2269
Cdd:PHA03307  834 GPARPPGAA--ARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAA--------------PP 897

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568933163 2270 PGLPGPLIRPPDTCSQTPRPPGpGRidtfthASSSAVRDPYDQPPVTPRP---HSESFGTSQVVHDLVDRPV 2338
Cdd:PHA03307  898 AGAPAPRPRPAPRVKLGPMPPG-GP------DPRGGFRRVPPGDLHTPAPsaaALAAYCPPEVVAELVDHPL 962
PHA03379 PHA03379
EBNA-3A; Provisional
 2416-2719 3.69e-04

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 46.98  E-value: 3.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2416 EKGPQDTAVVPHP-VPLPHWQ-PESINQAFTRPPP--PYPGSTRSPVIPPLGPRYAVFP----KDQRGPYPPEVAGmGMR 2487
Cdd:PHA03379  406 EKASEPTYGTPRPpVEKPRPEvPQSLETATSHGSAqvPEPPPVHDLEPGPLHDQHSMAPcpvaQLPPGPLQDLEPG-DQL 484

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2488 PHGFRFGFPGAGHGPMPSQDRFH----VPQQIQGSGIPPHIRRPMSMEMPRPSNNPPLNNPVGLPQHFPPQGlPVQQHNI 2563
Cdd:PHA03379  485 PGVVQDGRPACAPVPAPAGPIVRpweaSLSQVPGVAFAPVMPQPMPVEPVPVPTVALERPVCPAPPLIAMQG-PGETSGI 563

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2564 LGqafIELRHRAPDGRSRLPFAASPSSVIESPSHPR-------HGNFLPRPDFPGPRHTDPIRQPSQCLSNQLPVHPnLE 2636
Cdd:PHA03379  564 VR---VRERWRPAPWTPNPPRSPSQMSVRDRLARLRaeaqpyqASVEVQPPQLTQVSPQQPMEYPLEPEQQMFPGSP-FS 639

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2637 QVPPSQQEQGHPAHQSSIVMRPLNHPLSGEFSEAPLSTST-----PAETSPDNLEIAgqssagLEEKLDSDDPSVKELDV 2711
Cdd:PHA03379  640 QVADVMRAGGVPAMQPQYFDLPLQQPISQGAPLAPLRASMgpvppVPATQPQYFDIP------LTEPINQGASAAHFLPQ 713


                  ....*...
gi 568933163 2712 KDLEGVEV 2719
Cdd:PHA03379  714 QPMEGPLV 721
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 391-435 3.71e-04

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 41.09  E-value: 3.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTN-GWKCKNC 435
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 2024-2341 3.77e-04

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 46.60  E-value: 3.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2024 PSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQ--DPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQS 2101
Cdd:COG5180   138 TREATSASAGVALAAALLQRSDPILAKDPDGDSASTLPPPAEklDKVLTEPRDALKDSPEKLDRPKVEVKDEAQEEPPDL 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2102 NDPYSHPPLtphPAMTESFthasraFPQPGTiSRSASQDPYSQPPGTPRPLIDSysqtsgtARSNPDPYSQPPGTPRPNt 2181
Cdd:COG5180   218 TGGADHPRP---EAASSPK------VDPPST-SEARSRPATVDAQPEMRPPADA-------KERRRAAIGDTPAAEPPG- 279

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2182 idpysQQPPTPRPSPQTDMfvSSVANQRHTDPYTHHLGPP--RPGISVPYSQPPAVPRPRTSEGftRPSSA-RPALMPNQ 2258
Cdd:COG5180   280 -----LPVLEAGSEPQSDA--PEAETARPIDVKGVASAPPatRPVRPPGGARDPGTPRPGQPTE--RPAGVpEAASDAGQ 350

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2259 DP-FLQAAQNRVPGLPGPLIRPPDTCSQTPRPPGpgridtfthasssavrDPYDQPPVTPRPHSESFGTSQVVHDLVDRP 2337
Cdd:COG5180   351 PPsAYPPAEEAVPGKPLEQGAPRPGSSGGDGAPF----------------QPPNGAPQPGLGRRGAPGPPMGAGDLVQAA 414


                  ....
gi 568933163 2338 VPGS 2341
Cdd:COG5180   415 LDGG 418
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 344-388 3.85e-04

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 41.15  E-value: 3.85e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163  344 CAVCDS-----PGDLLDqffCTTCGQHYHGMCLDIAVTP-LKRAGWQCPEC 388
Cdd:cd15596     9 CVVCGSfgqgaEGRLLA---CSQCGQCYHPYCVSIKITKvVLSKGWRCLEC 56
PHD_Int12 cd15501
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...
 955-1002 4.14e-04

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation.


Pssm-ID: 276976  Cd Length: 52  Bit Score: 41.18  E-value: 4.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163  955 CVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLS---KGWRCLEC 1002
Cdd:cd15501     2 CVVCKQMDVTSGNQLVECQECHNLYHQECHKPPVTDKDVNdprLVWYCSRC 52
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 388-435 4.44e-04

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 40.88  E-value: 4.44e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568933163  388 CKVCQNcKQSGEDSKMLVCD-TCDKGYHTFCLQPVMKSV----PTNGWKCKNC 435
Cdd:cd15504     2 CAKCQS-GEASPDNDILLCDgGCNRAYHQKCLEPPLLTEdippEDEGWLCPLC 53
PostSET smart00508
Cysteine-rich motif following a subset of SET domains;
4830-4846 4.53e-04

Cysteine-rich motif following a subset of SET domains;


Pssm-ID: 214703  Cd Length: 17  Bit Score: 40.08  E-value: 4.53e-04
                            10
                    ....*....|....*..
gi 568933163   4830 HKIPCHCGAVNCRKWMN 4846
Cdd:smart00508    1 KKQPCLCGAPNCRGFLG 17
SET_SMYD4 cd10536
SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing ...
 4782-4838 4.54e-04

SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 4 (SMYD4) and similar proteins; SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. In zebrafish, SMYD4 is ubiquitously expressed in early embryos and becomes enriched in the developing heart; mutants show a strong defect in cardiomyocyte proliferation, which lead to a severe cardiac malformation.


Pssm-ID: 380934 [Multi-domain]  Cd Length: 218  Bit Score: 44.98  E-value: 4.54e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568933163 4782 INHSCAPNCvaeVVTFErGHKIIISSNRRIQKGEEL--CYDYKF---DFED------DQHKIPCHCGA 4838
Cdd:cd10536   154 LNHSCDPNT---IRSFY-GNTIVVRATRPIKKGEEItiCYGPHFsrmKRSErqrllkEQYFFDCSCEA 217
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 4366-4429 4.67e-04

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 42.82  E-value: 4.67e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568933163 4366 WVHLNCALWSTEV-------YEtqagALINVELALRRGLQMKCVFCH-KTGATSGCHRFRCTNIYHFTCATK 4429
Cdd:cd15671    20 WVHVSCALWIPEVsigcpekME----PITKISHIPMSRWALVCVLCKeKTGACIQCSVKSCKTAFHVTCAFQ 87
PTZ00395 PTZ00395
Sec24-related protein; Provisional
 2039-2178 4.99e-04

Sec24-related protein; Provisional


Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 46.61  E-value: 4.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2039 PYAGPSLTPAPLGNGPFKtplHPPPSQDPYgsvsqtsrrlSVDPYERPALTPRPVDNFSHsqSNDPYSHPP---LTPHPA 2115
Cdd:PTZ00395  418 GNSNPGYNNAPNSNTPYN---NPPNSNTPY----------SNPPNSNPPYSNLPYSNTPY--SNAPLSNAPpssAKDHHS 482

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163 2116 MTESfTHASRAFPQPG----TISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPR 2178
Cdd:PTZ00395  483 AYHA-AYQHRAANQPAanlpTANQPAANNFHGAAGNSVGNPFASRPFGSAPYGGNAATTADPNGIAK 548
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 240-311 5.50e-04

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 42.64  E-value: 5.50e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163  240 QALFDSTGTCWAHHRCVEWSLGICQME---EPL----LVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA 311
Cdd:cd15710    14 QLLISENQKVAAHHKCMLFSSALVSSHsdsENLggfsIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCA 92
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 4341-4430 6.85e-04

Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2C. JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277185  Cd Length: 110  Bit Score: 42.25  E-value: 6.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4341 CCFCHEEGDGLTDGPArllnldlDLWVHLNCALWSTEVYETQAGALINVELA---LRRgLQMKCVFCHK-----TGATSG 4412
Cdd:cd15715     1 CCLCNLRGGALKQTSD-------DKWAHVMCAVALPEVRFINVVERTPIDISripLQR-LKLKCIFCRNrikrvSGACIQ 72

                          90
                  ....*....|....*...
gi 568933163 4413 CHRFRCTNIYHFTCATKA 4430
Cdd:cd15715    73 CSYGRCPASFHVTCAHAA 90
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 344-388 7.14e-04

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 40.07  E-value: 7.14e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  344 CAVCDSPGDLLdqfFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15523     2 CSVCRKSGELL---MCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 388-435 7.60e-04

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 40.14  E-value: 7.60e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  388 CKVCQNCKQsGEDSKMLVCDTCDKGYHTFCLQ-PVMKSVPTNGWKCKNC 435
Cdd:cd15512     2 CVSCGSFGR-GAEGRLIACSQCGQCYHPYCVNvKVTKVILSKGWRCLDC 49
SET_SMYD3 cd19203
SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 ...
 4783-4821 8.54e-04

SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins; SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. It is overexpressed in colorectal, breast, prostate, and hepatocellular tumors, and has been implicated as an oncogene in human malignancies. Methylation of MEKK2 by SMYD3 is important for regulation of the MEK/ERK pathway, suggesting the possibility of selectively targeting SMYD3 in RAS-driven cancers.


Pssm-ID: 380980 [Multi-domain]  Cd Length: 210  Bit Score: 43.89  E-value: 8.54e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 568933163 4783 NHSCAPNCVAevvTFErGHKIIISSNRRIQKGEELCYDY 4821
Cdd:cd19203   147 NHSCDPNCVI---VFN-GPHLLLRAIREIEVGEELTISY 181
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2022-2216 8.64e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.75  E-value: 8.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2022 TKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQS 2101
Cdd:PRK07764  600 PPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPA 679

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2102 NDPYSHPPLTPHPAMTESFT---HASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPR 2178
Cdd:PRK07764  680 APPPAPAPAAPAAPAGAAPAqpaPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPP 759

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 568933163 2179 PNTID-PYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTH 2216
Cdd:PRK07764  760 PPPAPaPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDR 798
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2041-2266 9.16e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.75  E-value: 9.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2041 AGPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQtsrrlsvdPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTESF 2120
Cdd:PRK07764  595 AGGEGPPAPASSGPPEEAARPAAPAAPAAPAAP--------APAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGG 666

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2121 THASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNP--DPYSQPPGTPRPNTIDPYS---QQPPTPRPS 2195
Cdd:PRK07764  667 DGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQadDPAAQPPQAAQGASAPSPAaddPVPLPPEPD 746

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568933163 2196 PQTDmfvssvanqrhtdPYTHHLGPPRPGISVPYSQPPAvpRPRTSEGFTRPSSARPALMPNQDPFLQAAQ 2266
Cdd:PRK07764  747 DPPD-------------PAGAPAQPPPPPAPAPAAAPAA--APPPSPPSEEEEMAEDDAPSMDDEDRRDAE 802
DUF3824 pfam12868
Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It ...
 2084-2196 9.26e-04

Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It is proline-rich, and the function is not known.


Pssm-ID: 372351 [Multi-domain]  Cd Length: 145  Bit Score: 42.81  E-value: 9.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2084 ERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTESFTHaSRAFPQPgtisrsasqdpysqPPGTPRPLIDsYSQTSGTA 2163
Cdd:pfam12868   40 ERRRYEDDYRDYYEDPYSPSPYPPSPAGPYASQGQYYPE-TNYFPPP--------------PGSTPQPPVD-PQPNAPPP 103

                           90       100       110
                   ....*....|....*....|....*....|...
gi 568933163  2164 RSNPDPYSQPPGTPRPNtidPYSQQPPTPRPSP 2196
Cdd:pfam12868  104 PYNPADYPPPPGAAPPP---QPYQYPPPPGPDP 133
PHD1_PHF10 cd15528
PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 954-1002 9.41e-04

PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277003  Cd Length: 54  Bit Score: 40.09  E-value: 9.41e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568933163  954 MCVVC---GSFGQGAEGRLLACSQCGQCYHPYCVSI--KITKVVLSKGWRCLEC 1002
Cdd:cd15528     1 VCGICekgGKSNKGEPEELIHCSQCGNSGHPSCLEMsdEMVAVIKTYPWQCMEC 54
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 467-517 9.60e-04

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D.


Pssm-ID: 276989  Cd Length: 51  Bit Score: 39.96  E-value: 9.60e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568933163  467 CPFCGKCYHPElqkDML-HCNMCKRWVHLECDK-PTDQELDSQLKEDYICMYC 517
Cdd:cd15514     2 CPVCSRSYNEG---ELIiQCSQCERWLHGACDSlRTEEEAERAADNGYRCLLC 51
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 3192-3274 9.81e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 45.55  E-value: 9.81e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3192 EEWLQETQQLLQmqqkylEEQigahrKSKKALSAKQRT--AKKAG-REFPEEDAEQLKHVTEQQSMVQKQLEQIRKQQKE 3268
Cdd:pfam01576  467 ESQLQDTQELLQ------EET-----RQKLNLSTRLRQleDERNSlQEQLEEEEEAKRNVERQLSTLQAQLSDMKKKLEE 535


                   ....*.
gi 568933163  3269 HAELIE 3274
Cdd:pfam01576  536 DAGTLE 541
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 344-388 1.01e-03

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 39.67  E-value: 1.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 1005-1048 1.01e-03

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277131  Cd Length: 43  Bit Score: 39.57  E-value: 1.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163 1005 CEACGkatDPGRLLLCD--DCDISYHTYCLDppLQTVPKGGWKCKW 1048
Cdd:cd15661     2 CFQCG---DGGELVMCDkkDCPKAYHLLCLN--LTQPPYGKWECPW 42
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 954-1002 1.03e-03

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 39.65  E-value: 1.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163  954 MCVVCGSFGQGaegRLLACSQCGQCYHPYCVSIKITKVVLSKG-WRCLEC 1002
Cdd:cd15506     1 LCFLCGSAGLN---ELLYCSVCCEPYHTFCLEEAERPLNINKDnWCCRRC 47
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 1002-1049 1.15e-03

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 39.53  E-value: 1.15e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163 1002 CTVCEAcGKATDPGRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1049
Cdd:cd15492     2 CDVCLD-GESEDDNEIVFCDGCNVAVHQSCYG--IPLIPEGDWFCRKC 46
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 251-311 1.16e-03

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4.


Pssm-ID: 277181  Cd Length: 118  Bit Score: 41.99  E-value: 1.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568933163  251 AHHRCVEWSLGICQMEEPL--------LVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA 311
Cdd:cd15711    27 AHYKCMLFSSGTVQLTTTSraefgdfdIKTVIQEIKRGKRMKCTLCSQLGATIGCEIKACVKTYHYHCG 95
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 2129-2386 1.21e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 45.41  E-value: 1.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2129 QPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPpgTPRPN----------TIDPYSQQPPTPRPSPQT 2198
Cdd:pfam09770  106 QPAARAAQSSAQPPASSLPQYQYASQQSQQPSKPVRTGYEKYKEP--EPIPDlqvdaslwgvAPKKAAAPAPAPQPAAQP 183

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2199 DMFVSSV----------ANQRHTDPythhlGPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPALMPNQDPfLQAAQNR 2268
Cdd:pfam09770  184 ASLPAPSrkmmsleeveAAMRAQAK-----KPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQP-QQPQQHP 257

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2269 VPGLP-GPLIRPPdtcSQTPRPPGPgridtftHASSSAVRDPYDQPPVTPRPhsesfgtSQVVHD---LVDRPVPGSEGN 2344
Cdd:pfam09770  258 GQGHPvTILQRPQ---SPQPDPAQP-------SIQPQAQQFHQQPPPVPVQP-------TQILQNpnrLSAARVGYPQNP 320

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 568933163  2345 FSTSSNLPVSSQGQQFSSVSQLPGPVptsggTDTQNTVNMSQ 2386
Cdd:pfam09770  321 QPGVQPAPAHQAHRQQGSFGRQAPII-----THPQQLAQLSE 357
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
4366-4449 1.32e-03

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.97  E-value: 1.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4366 WVHLNCALWSTEVY--ETQAGALINVELALRRGL-QMKCVFCHKTGATS-GCHRFRCTNIYHFTCATKAqCMFFK----- 4436
Cdd:COG5141   268 WGHVICAMFNPELSfgHLLSKDPIDNIASVSSSRwKLGCLICKEFGGTCiQCSYFNCTRAYHVTCARRA-GYFDLniysh 346

                          90       100
                  ....*....|....*....|
gi 568933163 4437 -------DKTMLCPMHKPKG 4449
Cdd:COG5141   347 ngisyciDHEPLCRKHYPLG 366
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 4366-4430 1.35e-03

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 277140  Cd Length: 116  Bit Score: 41.55  E-value: 1.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568933163 4366 WVHLNCALWSTEVYetqagaLIN-VELALRRGLQ--------MKCVFC-HKTGATSGCHRFRCTNIYHFTCATKA 4430
Cdd:cd15670    19 WAHVVCALWIPEVS------FANtVFLEPIDGIQnipkarwkLTCYICkKRMGACIQCHKKNCYTAFHVTCAQQA 87
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
 241-319 1.42e-03

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain.


Pssm-ID: 277132  Cd Length: 115  Bit Score: 41.31  E-value: 1.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  241 ALFDSTGTCWAHHRCVEW-----SLGICQMEeplLVNVDKAVvsgSTER----CAFCKH-LGATIKCCEEKCTQMYHYPC 310
Cdd:cd15662    10 ALKPTTDGRWAHLACAIWipetcLLDVKTME---PVDGINAI---SKERwelsCTICKQrYGACIQCSNNSCRVAYHPLC 83


                  ....*....
gi 568933163  311 AAGAGTFQD 319
Cdd:cd15662    84 ARAAGLCME 92
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 388-435 1.48e-03

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 39.61  E-value: 1.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  388 CKVCQNCKQsGEDSKMLVCDTCDKGYHTFCLQ-PVMKSVPTNGWKCKNC 435
Cdd:cd15596     9 CVVCGSFGQ-GAEGRLLACSQCGQCYHPYCVSiKITKVVLSKGWRCLEC 56
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 3187-3279 1.60e-03

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 44.14  E-value: 1.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3187 QRKQ--YEEWLQETQQLLQMQQKYLEEQigahrksKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQLEQIRK 3264
Cdd:pfam13868   87 QKRQeeYEEKLQEREQMDEIVERIQEED-------QAEAEEKLEKQRQLREEIDEFNEEQAEWKELEKEEEREEDERILE 159

                           90
                   ....*....|....*
gi 568933163  3265 QQKEHAELIEDYRIK 3279
Cdd:pfam13868  160 YLKEKAEREEEREAE 174
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 955-1002 1.91e-03

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 38.95  E-value: 1.91e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163  955 CVVCGSfgQGAEGRLLACSQCGQCYHPYCVSIKITKVVlSKGWRCLEC 1002
Cdd:cd15510     2 CQACRQ--PGDDTKMLVCETCDKGYHTSCLRPVMSSIP-KYGWKCKNC 46
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 955-1002 2.03e-03

PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277066  Cd Length: 50  Bit Score: 39.15  E-value: 2.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163  955 CVVCGSFGQGAEgRLLACSQCGQCYHPYCVSIKITKVVLSK--GWRCLEC 1002
Cdd:cd15591     2 CHVCGRKNKESK-PLLECERCRNCYHPACLGPNYPKPANRKkrPWICSAC 50
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 4401-4445 2.17e-03

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 38.73  E-value: 2.17e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 568933163   4401 CVFCHKTGATS---GCHRfrCTNIYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2146-2343 2.17e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.59  E-value: 2.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2146 PGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTidpysQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPPRPGI 2225
Cdd:PRK07764  588 VGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAA-----PAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDA 662

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2226 SVPYSQPPAVPRPRTSEGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPliRPPDTCSQTPRPPgpgridtftHASSSA 2305
Cdd:PRK07764  663 SDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAG--QADDPAAQPPQAA---------QGASAP 731

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 568933163 2306 VRDPYDQPPVTPRPHSESFGtSQVVHDLVDRPVPGSEG 2343
Cdd:PRK07764  732 SPAADDPVPLPPEPDDPPDP-AGAPAQPPPPPAPAPAA 768
PHA03418 PHA03418
hypothetical E4 protein; Provisional
 2141-2321 2.23e-03

hypothetical E4 protein; Provisional


Pssm-ID: 177646 [Multi-domain]  Cd Length: 230  Bit Score: 43.19  E-value: 2.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2141 PYSQPPGTPRPLIDSysqtsgtaRSNPDPYSQPPGTPRPNTIDPYSQQPP-TPRPSPQTdmfvssvANQRHTDPYTHHL- 2218
Cdd:PHA03418   34 PLLPAPHHPNPQEDP--------DKNPSPPPDPPLTPRPPAQPNGHNKPPvTKQPGGEG-------TEEDHQAPLAADAd 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 2219 GPPRPGisvpysqppavprPRTSEGFTRPSSARPALMP-----NQDPfLQAAQNRVPGLPGPL-IRPPDTCSQTPRPPGP 2292
Cdd:PHA03418   99 DDPRPG-------------KRSKADEHGPAPGRAALAPfkldlDQDP-LHGDPDPPPGATGGQgEEPPEGGEESQPPLGE 164

                         170       180
                  ....*....|....*....|....*....
gi 568933163 2293 GRIDTFTHAsssavrdPYDQPPVTPRPHS 2321
Cdd:PHA03418  165 GEGAVEGHP-------PPLPPAPEPKPHN 186
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
999-1135 2.31e-03

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.20  E-value: 2.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  999 CLECTVCEACgKATDPGRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWCVWCRHcgatsaglrcewqnNYTQCAPCAS 1078
Cdd:COG5141   193 DDICTKCTST-HNENSNAIVFCDGCEICVHQSCYG--IQFLPEGFWLCRKCIYGEY--------------QIRCCSFCPS 255

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568933163 1079 lsscpvccrnyreEDLILQCRQCDRWMHAVC---------QNLNTEEEVENVADIG-----FDCSMCRPYM 1135
Cdd:COG5141   256 -------------SDGAFKQTSDGRWGHVICamfnpelsfGHLLSKDPIDNIASVSssrwkLGCLICKEFG 313
PHD5_NSD2 cd15660
PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
 1008-1048 2.32e-03

PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger.


Pssm-ID: 277130  Cd Length: 43  Bit Score: 38.76  E-value: 2.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 568933163 1008 CGKATDPGRLLLCDD--CDISYHTYCLDppLQTVPKGGWKCKW 1048
Cdd:cd15660     2 CFRCGDGGQLVLCDRksCTKAYHLSCLG--LTKRPFGKWECPW 42
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1082-1131 2.32e-03

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 38.73  E-value: 2.32e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 568933163   1082 CPVCcRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVadiGFDCSMC 1131
Cdd:smart00249    2 CSVC-GKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDG---KWYCPKC 47
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 388-435 2.35e-03

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 38.63  E-value: 2.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568933163  388 CKVCQnckqsgEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15623     2 CRVCQ------KAGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 344-388 2.45e-03

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 38.59  E-value: 2.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  344 CAVCDSPGDLLdqfFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15539     2 CAVCGDGGELL---CCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD2_NSD cd15565
PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 954-999 2.62e-03

PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the second PHD finger.


Pssm-ID: 277040  Cd Length: 51  Bit Score: 38.95  E-value: 2.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  954 MCVVCGSFGQGAEGrLLACSQ--CGQCYHPYCVS-IKITKVVLSKGWRC 999
Cdd:cd15565     1 SCFVCKKLGSVGGE-VFKCSVasCGKFYHEECLKkWPLTTISDSKKFRC 48
PHD_PHF13 cd15632
PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated ...
 473-518 2.79e-03

PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer.


Pssm-ID: 277102  Cd Length: 47  Bit Score: 38.48  E-value: 2.79e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  473 CYHPELQKDMLHCNMCKRWVHLECDKPTdqelDSQLKEDYICMYCK 518
Cdd:cd15632     6 CMKPFAGRPMIECNECHTWIHLSCAKIR----KSNVPEVYVCQKCR 47
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1668-1704 2.92e-03

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 39.32  E-value: 2.92e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 568933163 1668 FPNLKEEFPDWTtrVKQIAK----LWRKASSQERAPYVQKA 1704
Cdd:cd21979    18 RPKIKGEHPGLS--IGDVAKklgeMWNNTSAKDKQPYEKKA 56
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 388-435 2.99e-03

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 38.60  E-value: 2.99e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163  388 CKVCQNCKQSgeDSKMLVCDTCDKGYHTFCLQPVMKSVPT---NGWKCKNC 435
Cdd:cd15507     2 CHVCGRKGQA--QKQLLECEKCQRGYHVDCLGPSYPTKPTrkkKTWICSKC 50
DUF4200 pfam13863
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ...
 3185-3278 3.31e-03

Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.


Pssm-ID: 464003 [Multi-domain]  Cd Length: 119  Bit Score: 40.63  E-value: 3.31e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3185 DSQRKQYEEW---LQETQQLLQMQQKYLEEQIGAHRKSKKALSAKQRTA-KKAgrefpEEDAEQLKHVTEQQSMVQKQLE 3260
Cdd:pfam13863   16 DAKREEIERLeelLKQREEELEKKEQELKEDLIKFDKFLKENDAKRRRAlKKA-----EEETKLKKEKEKEIKKLTAQIE 90

                           90
                   ....*....|....*...
gi 568933163  3261 QIRKQQKEHAELIEDYRI 3278
Cdd:pfam13863   91 ELKSEISKLEEKLEEYKP 108
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 4366-4430 3.51e-03

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277173 [Multi-domain]  Cd Length: 118  Bit Score: 40.42  E-value: 3.51e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568933163 4366 WVHLNCALWSTEVYETQAGALINVE----LALRRgLQMKCVFCHKTG--ATSGCHRFRCTNIYHFTCATKA 4430
Cdd:cd15703    19 WAHVVCAIWIPEVCFANTVFLEPVEgvnnIPPAR-WKLTCYLCKQKGrgAAIQCHKVNCYTAFHVTCAQRA 88
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3289-3601 3.65e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.60  E-value: 3.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3289 LAPPILM----PGVQPQPPLV-------PGATSLTMSQPNFPMVPQQLQHQQHTAVISGHTSPARMPSLPgwQSNSASAH 3357
Cdd:pfam03154  169 TQPPVLQaqsgAASPPSPPPPgttqaatAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLH--PQRLPSPH 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3358 LPLNPPRIQPPIAQLSLKTcTPAPGTVSSANP-----QNGPPPRVEFDDNNPFSESFQERERKERLREQQE--RQRVQLM 3430
Cdd:pfam03154  247 PPLQPMTQPPPPSQVSPQP-LPQPSLHGQMPPmphslQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAapGQSQQRI 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3431 QEVDRQRALQQRMEMEQHCLMGAELA-------NRTPVSQMPFYGSDRPCDFLQPPRP--LQQSPQHQQQIGPVLQQQNV 3501
Cdd:pfam03154  326 HTPPSQSQLQSQQPPREQPLPPAPLSmphikppPTTPIPQLPNPQSHKHPPHLSGPSPfqMNSNLPPPPALKPLSSLSTH 405

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  3502 QQGSVNSPPNQTFMQTneqRQVGPPsfvPDSPSASGGSPNFHSvkPGHGNLPGSSFQQSPLRPPFT--PILPGTSP--VA 3577
Cdd:pfam03154  406 HPPSAHPPPLQLMPQS---QQLPPP---PAQPPVLTQSQSLPP--PAASHPPTSGLHQVPSQSPFPqhPFVPGGPPpiTP 477

                          330       340
                   ....*....|....*....|....
gi 568933163  3578 NSNVPCGQDPAVTQGQNYSGSSQS 3601
Cdd:pfam03154  478 PSGPPTSTSSAMPGIQPPSSASVS 501
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 388-435 3.98e-03

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 38.14  E-value: 3.98e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163  388 CKVCQNcKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSV---PTNGWKCKNC 435
Cdd:cd15578     2 CTVCQD-GSSESPNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQC 51
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 246-311 4.35e-03

Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Drosophila melanogaster RNO. RNO is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating the transcription of key EGFR/Ras pathway regulators in the Drosophila eye. RNO contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277177 [Multi-domain]  Cd Length: 113  Bit Score: 39.88  E-value: 4.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568933163  246 TGTCWAHHRCVEW----SLGICQMEEPLlVNVDKAVVSGSTERCAFCKH-LGATIKCCEEKCTQMYHYPCA 311
Cdd:cd15707    16 SGTKWAHVSCALWipevSIGCVEKMEPI-TKISSIPASRWALICVLCRErTGACIQCSVKTCKTAYHVTCG 85
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
 391-436 4.37e-03

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 38.02  E-value: 4.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568933163  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCR 436
Cdd:cd15625     5 CAVCLNGGE---LLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCR 47
PHD1_DPF3 cd15692
PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed ...
 964-1002 4.38e-03

PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed BRG1-associated factor 45C (BAF45C), or zinc finger protein cer-d4, is encoded by a neuro-specific gene, cer-d4. It functions as a new epigenetic key factor for heart and muscle development and may be involved in the transcription regulation of neuro-specific gene clusters. It interacts with the BAF chromatin remodeling complex and binds methylated and acetylated lysine residues of histone 3 and 4. DPF3 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central region, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the first PHD finger.


Pssm-ID: 277162  Cd Length: 57  Bit Score: 38.51  E-value: 4.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 568933163  964 GAEGRLLACSQCGQCYHPYCV--SIKITKVVLSKGWRCLEC 1002
Cdd:cd15692    16 GRPEELVSCADCGRSGHPTCLqfTVNMTEAVKTYQWQCIEC 56
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 1005-1049 4.71e-03

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 37.61  E-value: 4.71e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163 1005 CEACGKAtdpGRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1049
Cdd:cd15567     2 CFICSEG---GSLICCESCPASFHPECLG--LEPPPEGKFYCEDC 41
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2334-2691 4.99e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.22  E-value: 4.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2334 VDRPVPGSEGNFSTSSNLPVSSQGQ---------QFSSVSQLPGPVPtsggtdtqntvNMSQADTEKLRQRQKLREIILQ 2404
Cdd:pfam03154  107 ISRPNSPSEGEGESSDGRSVNDEGSsdpkdidqdNRSTSPSIPSPQD-----------NESDSDSSAQQQILQTQPPVLQ 175

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2405 QQQQKKIASRQEKGPQDTAVVPHPVPLPHWQPESINQAfTRPPPPYPGSTRSPVI-----PPLGPRYAVFPKD--QRGPY 2477
Cdd:pfam03154  176 AQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPA-TSQPPNQTQSTAAPHTliqqtPTLHPQRLPSPHPplQPMTQ 254

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2478 PPEVAGMGMRPHGfrfgfPGAGHGPMPSqdrfhVPQQIQGSgiPPHIRRPMsmemprpsnnpplnnpvglpqhfPPQGLP 2557
Cdd:pfam03154  255 PPPPSQVSPQPLP-----QPSLHGQMPP-----MPHSLQTG--PSHMQHPV-----------------------PPQPFP 299

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163  2558 VQQHNILGQAFIELRHRAPDGRSRLPFAASPSSVIESPSHPRHgnflpRPDFPGPRHTDPIRQPSQCLSNQLpvhpnleq 2637
Cdd:pfam03154  300 LTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPRE-----QPLPPAPLSMPHIKPPPTTPIPQL-------- 366

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 568933163  2638 vpPSQQEQGHPAHQSSIVMRPLNHPLSGEFSEAPLS---TSTPAETSPDNLEIAGQS 2691
Cdd:pfam03154  367 --PNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSslsTHHPPSAHPPPLQLMPQS 421
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 954-1002 5.33e-03

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 37.82  E-value: 5.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  954 MCVVCGsfgqgAEGRLLACSQCGQCYHPYCVSIKITKVVlSKGWRCLEC 1002
Cdd:cd15539     1 ECAVCG-----DGGELLCCDGCPRAFHLACLVPPLTLIP-SGTWRCSSC 43
mukB PRK04863
chromosome partition protein MukB;
3189-3279 5.41e-03

chromosome partition protein MukB;


Pssm-ID: 235316 [Multi-domain]  Cd Length: 1486  Bit Score: 43.41  E-value: 5.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 3189 KQYEEWLQETQQLLQMQQKY--LEEQIGAHRKSKKALsakQRTAKKAGREFPEEDA---------EQLKHVTEQQSMVQK 3257
Cdd:PRK04863  503 RRLREQRHLAEQLQQLRMRLseLEQRLRQQQRAERLL---AEFCKRLGKNLDDEDEleqlqeeleARLESLSESVSEARE 579

                          90       100
                  ....*....|....*....|..
gi 568933163 3258 QLEQIRKQQKEHAELIEDYRIK 3279
Cdd:PRK04863  580 RRMALRQQLEQLQARIQRLAAR 601
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 3183-3274 5.71e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 42.44  E-value: 5.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 3183 VNDSQRKQYEEwLQETQQLLQMQQKYLEEQigahRKSKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQLEQI 3262
Cdd:COG4942   144 LAPARREQAEE-LRADLAELAALRAELEAE----RAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAEL 218

                          90
                  ....*....|..
gi 568933163 3263 RKQQKEHAELIE 3274
Cdd:COG4942   219 QQEAEELEALIA 230
SET_SMYD1 cd10526
SET domain (including post-SET domain) found in SET and MYND domain-containing protein 1 ...
 4782-4836 6.37e-03

SET domain (including post-SET domain) found in SET and MYND domain-containing protein 1 (SMYD1) and similar proteins; SMYD1 (EC 2.1.1.43), also termed BOP, is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD1 plays a critical role in cardiomyocyte differentiation, cardiac morphogenesis and myofibril organization, as well as in the regulation of endothelial cells (ECs). It is expressed in vascular endothelial cells, it has beenshown that knockdown of SMYD1 in endothelial cells impairs EC migration and tube formation.


Pssm-ID: 380924 [Multi-domain]  Cd Length: 210  Bit Score: 41.25  E-value: 6.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568933163 4782 INHSCAPNCvaeVVTFERGhKIIISSNRRIQKGEELCYDYkFDF----ED------DQHKIPCHC 4836
Cdd:cd10526   146 VNHDCWPNC---TVIFNNG-RIELRALGKISEGDELTVSY-IDFlntsEDrkeqlkKQYYFDCTC 205
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 344-388 6.54e-03

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 37.71  E-value: 6.54e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568933163  344 CAVCDS-----PGDLLDqffCTTCGQHYHGMCLDIAVTPLK-RAGWQCPEC 388
Cdd:cd15597     3 CVVCGSfgrgsEGHLLA---CSQCSQCYHPYCVNSKITKVMlLKGWRCVEC 50
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
 388-436 6.63e-03

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 37.33  E-value: 6.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  388 CKVCQNckqsGEDskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCR 436
Cdd:cd15624     2 CAVCQN----GGD--LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCR 44
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 344-388 6.65e-03

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 37.32  E-value: 6.65e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  344 CAVCDSPGDLLdqfFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15541     2 CAVCQNGGELL---CCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 955-1002 6.70e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 37.29  E-value: 6.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163  955 CVVCGSFGQgaEGRLLACSQCGQCYHPYCVSIKITKVvlSKG-WRCLEC 1002
Cdd:cd15545     2 CQICRSGDN--EDQLLLCDGCDRGYHTYCFKPKMTNV--PEGdWFCPEC 46
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 390-435 7.11e-03

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 37.53  E-value: 7.11e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163  390 VCQNCKQSGEDSKML--VCDTCDKGYHTFC--LQPVMKSVPTNgWKCKNC 435
Cdd:cd15517     1 VCGICNLETAAVDELwvQCDGCDKWFHQFClgLSNERYADEDK-FKCPNC 49
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 470-517 7.37e-03

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 37.58  E-value: 7.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568933163  470 CGKCYHPELQKDML-HCNMCKRWVHLECDKP-TDQELDSQLKEDYICMYC 517
Cdd:cd15601     2 CPVCRAKYVEEDLLiQCRHCDRWVHAVCESLfTEDEVEQAADEGFDCSSC 51
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 344-388 7.40e-03

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 37.20  E-value: 7.40e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  344 CAVCDSPGDLLdqfFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15531     2 CEVCQQGGEII---LCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 4401-4445 7.81e-03

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 37.30  E-value: 7.81e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568933163 4401 CVFCHKTGATSG----CHRfrCTNIYHFTCATKAQCMFFKDKTMLCPMH 4445
Cdd:cd15489     2 CIVCGKGGDLGGellqCDG--CGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD_ASH1L cd15548
PHD finger found in histone-lysine N-methyltransferase ASH1L; ASH1L, also termed ASH1-like ...
 1086-1117 7.82e-03

PHD finger found in histone-lysine N-methyltransferase ASH1L; ASH1L, also termed ASH1-like protein, or absent small and homeotic disks protein 1 homolog, or lysine N-methyltransferase 2H, is a protein belonging to the Trithorax family. It methylates Lys36 of histone H3 independently of transcriptional elongation to promote the establishment of Hox gene expression by counteracting Polycomb silencing. It can suppress interleukin-6 (IL-6), and tumor necrosis factor (TNF) production in Toll-like receptor (TLR)-triggered macrophages, and inflammatory autoimmune diseases by inducing the ubiquitin-editing enzyme A20. ASH1L contains an associated with SET domain (AWS), a SET domain, a post-SET domain, a bromodomain, a bromo-adjacent homology domain (BAH), and a plant homeodomain (PHD) finger.


Pssm-ID: 277023  Cd Length: 43  Bit Score: 37.06  E-value: 7.82e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 568933163 1086 CRNYREEDLILQCRQCDRWMHAVCQNLNTEEE 1117
Cdd:cd15548     5 CGLYKDEGLMIQCEKCMVWQHCDCMGVNDDVE 36
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 1002-1050 8.02e-03

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 37.37  E-value: 8.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568933163 1002 CTVCEAcGKATDPGRLLLCDDCDISYHTYCLDPPLQTV---PKGGWKCKWCV 1050
Cdd:cd15578     2 CTVCQD-GSSESPNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQCV 52
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 4366-4447 8.18e-03

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling.


Pssm-ID: 277171 [Multi-domain]  Cd Length: 121  Bit Score: 39.29  E-value: 8.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 4366 WVHLNCALWSTEVYETQAGAL---INVELALRRGLQMKCVFCHK--TGATSGCHRFRCTNIYHFTCATKAQcMFFK---- 4436
Cdd:cd15701    19 WAHVVCALWIPEVCFANTVFLepiDSIEHIPPARWKLTCYICKQrgSGACIQCHKANCYTAFHVTCAQQAG-LYMKmepv 97

                          90       100
                  ....*....|....*....|...
gi 568933163 4437 ------------DKTMLCPMHKP 4447
Cdd:cd15701    98 retgangtsfsvRKTAYCDIHTP 120
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 3186-3274 8.20e-03

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 42.51  E-value: 8.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568933163 3186 SQRKQYEEWLQETQQLLQMQQKY---LEEQIGAHRKSKKALSAKQ-RTAKKAGREFPEEDAEQLKHVTEQQSMVQ----- 3256
Cdd:PRK00409  527 ELERELEQKAEEAEALLKEAEKLkeeLEEKKEKLQEEEDKLLEEAeKEAQQAIKEAKKEADEIIKELRQLQKGGYasvka 606

                          90
                  ....*....|....*...
gi 568933163 3257 KQLEQIRKQQKEHAELIE 3274
Cdd:PRK00409  607 HELIEARKRLNKANEKKE 624
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 391-435 9.30e-03

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 37.18  E-value: 9.30e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568933163  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15524     2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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