NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|240120087|ref|NP_759014|]
View 

lysine-specific demethylase 4A isoform 2 [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 775-884 3.89e-76

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: 244.88  E-value: 3.89e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRKRNAGCCVQCSHGRCPT 854
Cdd:cd15713     1 CCLCSLRGGALQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSKIPLQRFKLKCIFCKKRRKRTAGCCVQCSHGRCPT 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 240120087  855 AFHVSCAQAAGVMMQPDDWPFVVFITCFRH 884
Cdd:cd15713    81 SFHASCAQAAGVMMQPDDWPFVVFITCFRH 110
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 667-766 3.18e-55

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.


The actual alignment was detected with superfamily member cd15575:

Pssm-ID: 473978  Cd Length: 100  Bit Score: 186.26  E-value: 3.18e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  667 HCAVCMIFQTYHQVEFGAFSQSCGDASEPAAQTQRTKPLIPEMCFTTTGCSTDINLSTPYLEEDGTSMLVSCKKCSVRVH 746
Cdd:cd15575     1 HCAVCMLFQTYQVDCWGGHNSSSGVAASEARIKKKTKPLIPEMCFTSTGCNTDLNLSTPYLEEDGTSILVTCKKCCVCVH 80

                          90       100
                  ....*....|....*....|
gi 240120087  747 ASCYGVPPAKASEEWMCSRC 766
Cdd:cd15575    81 ASCYGVSPEKAAEDWMCSRC 100
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 175-291 1.29e-49

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


:

Pssm-ID: 396791  Cd Length: 114  Bit Score: 170.94  E-value: 1.29e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087   175 YLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSaqsCEAFLRHKMTLISPLMLKKYG 254
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGE---QPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 240120087   255 IPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNF 291
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
Tudor_SF super family cl02573
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 899-947 3.23e-29

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


The actual alignment was detected with superfamily member cd20463:

Pssm-ID: 470623  Cd Length: 55  Bit Score: 110.75  E-value: 3.23e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 240120087  899 ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIV 947
Cdd:cd20463     1 ITAGQKVISKHKNGRFYQCEVVRLTKETFYEVNFDDGSFSDNLYPEDIV 49
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 13-55 4.89e-16

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


:

Pssm-ID: 128818  Cd Length: 42  Bit Score: 72.68  E-value: 4.89e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 240120087     13 RIMTFYPTMEEFRNFSRYIAYIESQgAHRAGLAKVVPPKEWKP 55
Cdd:smart00545    1 EIPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
 
Name Accession Description Interval E-value
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 775-884 3.89e-76

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: 244.88  E-value: 3.89e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRKRNAGCCVQCSHGRCPT 854
Cdd:cd15713     1 CCLCSLRGGALQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSKIPLQRFKLKCIFCKKRRKRTAGCCVQCSHGRCPT 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 240120087  855 AFHVSCAQAAGVMMQPDDWPFVVFITCFRH 884
Cdd:cd15713    81 SFHASCAQAAGVMMQPDDWPFVVFITCFRH 110
PHD_JMJD2A cd15575
PHD finger found in Jumonji domain-containing protein 2A (JMJD2A); JMJD2A, also termed ...
 667-766 3.18e-55

PHD finger found in Jumonji domain-containing protein 2A (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 Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277050  Cd Length: 100  Bit Score: 186.26  E-value: 3.18e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  667 HCAVCMIFQTYHQVEFGAFSQSCGDASEPAAQTQRTKPLIPEMCFTTTGCSTDINLSTPYLEEDGTSMLVSCKKCSVRVH 746
Cdd:cd15575     1 HCAVCMLFQTYQVDCWGGHNSSSGVAASEARIKKKTKPLIPEMCFTSTGCNTDLNLSTPYLEEDGTSILVTCKKCCVCVH 80

                          90       100
                  ....*....|....*....|
gi 240120087  747 ASCYGVPPAKASEEWMCSRC 766
Cdd:cd15575    81 ASCYGVSPEKAAEDWMCSRC 100
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
774-884 2.42e-50

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 172.91  E-value: 2.42e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087   774 DCCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRkrnaGCCVQCSHGRCP 853
Cdd:pfam13832    2 RCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIDVSRIPPERWKLKCVFCKKRS----GACIQCSKGRCT 77

                           90       100       110
                   ....*....|....*....|....*....|..
gi 240120087   854 TAFHVSCAQAAGVMMQPDDWP-FVVFITCFRH 884
Cdd:pfam13832   78 TAFHVTCAQAAGVYMEPEDWPnVVVIAYCQKH 109
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 175-291 1.29e-49

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 170.94  E-value: 1.29e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087   175 YLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSaqsCEAFLRHKMTLISPLMLKKYG 254
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGE---QPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 240120087   255 IPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNF 291
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
Tudor_JMJD2A_rpt1 cd20463
first Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins; ...
 899-947 3.23e-29

first Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins; JMJD2A, also called 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 corepressor 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 plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410534  Cd Length: 55  Bit Score: 110.75  E-value: 3.23e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 240120087  899 ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIV 947
Cdd:cd20463     1 ITAGQKVISKHKNGRFYQCEVVRLTKETFYEVNFDDGSFSDNLYPEDIV 49
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
728-868 1.79e-26

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


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 116.24  E-value: 1.79e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  728 EEDGTSMLVSCKKCSVRVHASCYGVPPAkASEEWMCSRCSANALEEDCCL-CSLRGGALQRANDDRWVHVSCAVAILEAR 806
Cdd:COG5141   203 HNENSNAIVFCDGCEICVHQSCYGIQFL-PEGFWLCRKCIYGEYQIRCCSfCPSSDGAFKQTSDGRWGHVICAMFNPELS 281

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 240120087  807 FVNIAERSPVD-VSKIPLPRFKLKCVFCKKRrkrnAGCCVQCSHGRCPTAFHVSCAQAAGVMM 868
Cdd:COG5141   282 FGHLLSKDPIDnIASVSSSRWKLGCLICKEF----GGTCIQCSYFNCTRAYHVTCARRAGYFD 340
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 13-55 4.89e-16

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 72.68  E-value: 4.89e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 240120087     13 RIMTFYPTMEEFRNFSRYIAYIESQgAHRAGLAKVVPPKEWKP 55
Cdd:smart00545    1 EIPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
Tudor_2 pfam18104
Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone ...
 902-936 2.48e-13

Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD).


Pssm-ID: 465651  Cd Length: 35  Bit Score: 64.75  E-value: 2.48e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 240120087   902 GQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGS 936
Cdd:pfam18104    1 GQDVIARWTDGRYYLGKFIGIHTQTFYEVEFEDGS 35
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 146-205 2.74e-13

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 65.35  E-value: 2.74e-13
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 240120087    146 DEWNIGRLKTILDLVEKESGItIEGVNT-PYLYFGMWKTSFAWHTEDMDLysINYLHFGEP 205
Cdd:smart00558    1 QLWNLAKLPFKLNLLSDLPED-IPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
JmjN pfam02375
jmjN domain;
15-49 3.91e-12

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 61.15  E-value: 3.91e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 240120087    15 MTFYPTMEEFRNFSRYIAYIESQGAhRAGLAKVVP 49
Cdd:pfam02375    1 PVFYPTEEEFKDPLKYIEKIRPLGE-KYGICKIVP 34
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 732-766 8.21e-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: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 60.43  E-value: 8.21e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 240120087   732 TSMLVSCKKCSVRVHASCYGVPPAKASEEWMCSRC 766
Cdd:pfam13831    1 TSPLVYCSKCSVQVHASCYGVPPIPDGDGWKCRRC 35
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 899-946 1.08e-09

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 54.97  E-value: 1.08e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 240120087    899 ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDI 946
Cdd:smart00333    3 FKVGDKVAARWEDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDL 50
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 735-766 5.28e-04

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: 5.28e-04
                            10        20        30
                    ....*....|....*....|....*....|....
gi 240120087    735 LVSCKKCSVRVHASCYGVPPAKA--SEEWMCSRC 766
Cdd:smart00249   14 LLQCDGCDRWYHQTCLGPPLLEEepDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 830-872 7.10e-04

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: 38.35  E-value: 7.10e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 240120087    830 CVFCKKrrKRNAGCCVQCSHgrCPTAFHVSCAQAAGVMMQPDD 872
Cdd:smart00249    2 CSVCGK--PDDGGELLQCDG--CDRWYHQTCLGPPLLEEEPDG 40
 
Name Accession Description Interval E-value
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 775-884 3.89e-76

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: 244.88  E-value: 3.89e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRKRNAGCCVQCSHGRCPT 854
Cdd:cd15713     1 CCLCSLRGGALQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSKIPLQRFKLKCIFCKKRRKRTAGCCVQCSHGRCPT 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 240120087  855 AFHVSCAQAAGVMMQPDDWPFVVFITCFRH 884
Cdd:cd15713    81 SFHASCAQAAGVMMQPDDWPFVVFITCFRH 110
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 775-884 1.45e-64

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: 212.99  E-value: 1.45e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRK--RNAGCCVQCSHGRC 852
Cdd:cd15675     1 CCLCCLRGGALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPIDISKIPPARLKLKCIYCSKITKsmSHMGACIQCSTGKC 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 240120087  853 PTAFHVSCAQAAGVMMQPDDWPFVVFITCFRH 884
Cdd:cd15675    81 TTSFHVTCAHAAGVQMEPDDWPYPVYVTCTKH 112
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 775-884 5.53e-59

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: 197.49  E-value: 5.53e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRKRNAGCCVQCSHGRCPT 854
Cdd:cd15715     1 CCLCNLRGGALKQTSDDKWAHVMCAVALPEVRFINVVERTPIDISRIPLQRLKLKCIFCRNRIKRVSGACIQCSYGRCPA 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 240120087  855 AFHVSCAQAAGVMMQPDDWPFVVFITCFRH 884
Cdd:cd15715    81 SFHVTCAHAAGVLMEPDDWPYVVFITCFRH 110
PHD_JMJD2A cd15575
PHD finger found in Jumonji domain-containing protein 2A (JMJD2A); JMJD2A, also termed ...
 667-766 3.18e-55

PHD finger found in Jumonji domain-containing protein 2A (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 Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277050  Cd Length: 100  Bit Score: 186.26  E-value: 3.18e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  667 HCAVCMIFQTYHQVEFGAFSQSCGDASEPAAQTQRTKPLIPEMCFTTTGCSTDINLSTPYLEEDGTSMLVSCKKCSVRVH 746
Cdd:cd15575     1 HCAVCMLFQTYQVDCWGGHNSSSGVAASEARIKKKTKPLIPEMCFTSTGCNTDLNLSTPYLEEDGTSILVTCKKCCVCVH 80

                          90       100
                  ....*....|....*....|
gi 240120087  747 ASCYGVPPAKASEEWMCSRC 766
Cdd:cd15575    81 ASCYGVSPEKAAEDWMCSRC 100
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 775-884 3.17e-54

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: 183.99  E-value: 3.17e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRKRNAGCCVQCSHGRCPT 854
Cdd:cd15714     1 CCLCNLRGGALQMTTDERWVHVICAIAVPEARFLNVIERHPVDVSAIPEQRWKLKCVYCRKRMKKVSGACIQCSYDHCST 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 240120087  855 AFHVSCAQAAGVMMQPDDWPFVVFITCFRH 884
Cdd:cd15714    81 SFHVTCAHAAGVVMEPDDWPYVVSITCFKH 110
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
774-884 2.42e-50

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 172.91  E-value: 2.42e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087   774 DCCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRkrnaGCCVQCSHGRCP 853
Cdd:pfam13832    2 RCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIDVSRIPPERWKLKCVFCKKRS----GACIQCSKGRCT 77

                           90       100       110
                   ....*....|....*....|....*....|..
gi 240120087   854 TAFHVSCAQAAGVMMQPDDWP-FVVFITCFRH 884
Cdd:pfam13832   78 TAFHVTCAQAAGVYMEPEDWPnVVVIAYCQKH 109
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 175-291 1.29e-49

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 170.94  E-value: 1.29e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087   175 YLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSaqsCEAFLRHKMTLISPLMLKKYG 254
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGE---QPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 240120087   255 IPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNF 291
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
Tudor_JMJD2A_rpt1 cd20463
first Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins; ...
 899-947 3.23e-29

first Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins; JMJD2A, also called 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 corepressor 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 plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410534  Cd Length: 55  Bit Score: 110.75  E-value: 3.23e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 240120087  899 ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIV 947
Cdd:cd20463     1 ITAGQKVISKHKNGRFYQCEVVRLTKETFYEVNFDDGSFSDNLYPEDIV 49
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 775-884 1.65e-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: 1.65e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGAL------QRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRRkrnaGCCVQCS 848
Cdd:cd15571     1 CALCPRSGGALkgggalKTTSDGLWVHVVCALWSPEVYFDDGTLLEVEGVSKIPKRRKKLKCSICGKRG----GACIQCS 76

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 240120087  849 HGRCPTAFHVSCAQAAGVMMQPDDWPFVVFITCFRH 884
Cdd:cd15571    77 YPGCPRSFHVSCAIRAGCLFEFEDGPGNFVVYCPKH 112
PHD_JMJD2B cd15576
PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed ...
 667-766 3.22e-28

PHD finger found in Jumonji domain-containing protein 2B (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 Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277051  Cd Length: 99  Bit Score: 109.23  E-value: 3.22e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  667 HCAVCMIFQTYHQvEFGAFSQSCGDASEPAAQTQRTKPLIPEMCFTTTGCSTDINLSTPYLEEDGTSMLVSCKKCSVRVH 746
Cdd:cd15576     1 YCAICTLFYPYTQ-SLQDPKEISDMSGLVSKVGQKTRPLIPEMCFTAGGENTEPLPSNSYIGDDGTSVLLSCAKCCLQVH 79

                          90       100
                  ....*....|....*....|
gi 240120087  747 ASCYGVPPAKASEEWMCSRC 766
Cdd:cd15576    80 ASCYGVNPDLVNEGWTCSRC 99
PHD_JMJD2C cd15577
PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed ...
 667-766 3.57e-27

PHD finger found in Jumonji domain-containing protein 2C (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 through 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 Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277052  Cd Length: 104  Bit Score: 106.45  E-value: 3.57e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  667 HCAVCMIFQTYHQVE-FGAFSQSCGDA---SEPAAQTQRTKPLIPEMCFTTTGCSTDINLSTPYLEEDGTSMLVSCKKCS 742
Cdd:cd15577     1 HCAICTLFMPYYKPDaLNEENSAQWEMelpAAPCISMRKTKPLIPEMCFIYREENCEPSPPNALLQEDGTSLLISCAKCC 80

                          90       100
                  ....*....|....*....|....
gi 240120087  743 VRVHASCYGVPPAKASEEWMCSRC 766
Cdd:cd15577    81 VQVHASCYGVPSHEIHDGWLCARC 104
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 775-868 1.42e-26

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: 105.11  E-value: 1.42e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVD-VSKIPLPRFKLKCVFCKKRrkrnAGCCVQCSHGRCP 853
Cdd:cd15670     1 CVLCPNKGGAFKQTDDGRWAHVVCALWIPEVSFANTVFLEPIDgIQNIPKARWKLTCYICKKR----MGACIQCHKKNCY 76

                          90
                  ....*....|....*
gi 240120087  854 TAFHVSCAQAAGVMM 868
Cdd:cd15670    77 TAFHVTCAQQAGLYM 91
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
728-868 1.79e-26

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


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 116.24  E-value: 1.79e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  728 EEDGTSMLVSCKKCSVRVHASCYGVPPAkASEEWMCSRCSANALEEDCCL-CSLRGGALQRANDDRWVHVSCAVAILEAR 806
Cdd:COG5141   203 HNENSNAIVFCDGCEICVHQSCYGIQFL-PEGFWLCRKCIYGEYQIRCCSfCPSSDGAFKQTSDGRWGHVICAMFNPELS 281

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 240120087  807 FVNIAERSPVD-VSKIPLPRFKLKCVFCKKRrkrnAGCCVQCSHGRCPTAFHVSCAQAAGVMM 868
Cdd:COG5141   282 FGHLLSKDPIDnIASVSSSRWKLGCLICKEF----GGTCIQCSYFNCTRAYHVTCARRAGYFD 340
Tudor_JMJD2_rpt1 cd20391
first Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 899-947 2.87e-25

first Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; JMJD2 proteins, also called 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 only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. JMJD2D is not included in this model, since it lacks both the PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 410462  Cd Length: 53  Bit Score: 99.20  E-value: 2.87e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 240120087  899 ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIV 947
Cdd:cd20391     1 ISVGQRVIAKHKNGRYYEAEVVDLTTQTFYEVNFDDGSFSDDLPPEDIV 49
ePHD_BRPF2 cd15702
Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and ...
 775-869 7.12e-24

Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277172  Cd Length: 118  Bit Score: 97.42  E-value: 7.12e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVD-VSKIPLPRFKLKCVFCKkrrKRNAGCCVQCSHGRCP 853
Cdd:cd15702     1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKLTCYLCK---QKGVGACIQCHKANCY 77

                          90
                  ....*....|....*.
gi 240120087  854 TAFHVSCAQAAGVMMQ 869
Cdd:cd15702    78 TAFHVTCAQKAGLYMK 93
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 775-869 1.62e-23

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: 96.69  E-value: 1.62e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVD-VSKIPLPRFKLKCVFCKKRrkrNAGCCVQCSHGRCP 853
Cdd:cd15701     1 CALCPNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIDsIEHIPPARWKLTCYICKQR---GSGACIQCHKANCY 77

                          90
                  ....*....|....*.
gi 240120087  854 TAFHVSCAQAAGVMMQ 869
Cdd:cd15701    78 TAFHVTCAQQAGLYMK 93
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 775-871 5.92e-22

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: 92.04  E-value: 5.92e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVD-VSKIPLPRFKLKCVFCKKRRKrnaGCCVQCSHGRCP 853
Cdd:cd15703     1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEgVNNIPPARWKLTCYLCKQKGR---GAAIQCHKVNCY 77

                          90
                  ....*....|....*...
gi 240120087  854 TAFHVSCAQAAGVMMQPD 871
Cdd:cd15703    78 TAFHVTCAQRAGLFMKIE 95
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 775-868 1.54e-21

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: 90.58  E-value: 1.54e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRAND-DRWVHVSCAVAILEARFVNIAERSPVD-VSKIPLPRFKLKCVFCKKRrkrnAGCCVQCSHGRC 852
Cdd:cd15671     1 CVLCPKKGGAMKSTKSgTKWVHVSCALWIPEVSIGCPEKMEPITkISHIPMSRWALVCVLCKEK----TGACIQCSVKSC 76

                          90
                  ....*....|....*.
gi 240120087  853 PTAFHVSCAQAAGVMM 868
Cdd:cd15671    77 KTAFHVTCAFQHGLEM 92
Tudor_JMJD2C_rpt1 cd20465
first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins; ...
 899-947 4.37e-21

first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins; JMJD2C, also called lysine-specific demethylase 4C (KDM4C), 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) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410536  Cd Length: 54  Bit Score: 87.22  E-value: 4.37e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 240120087  899 ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIV 947
Cdd:cd20465     1 ISVGQTVISKHRNTRYYSCRVTEVTSQTFYEVMFDDGSFSRDTFPEDIV 49
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
 775-869 1.63e-19

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: 84.83  E-value: 1.63e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVD-VSKIPLPRFKLKCVFCKKRrkrnAGCCVQCSHGRCP 853
Cdd:cd15662     1 CCLCPVVGGALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDgINAISKERWELSCTICKQR----YGACIQCSNNSCR 76

                          90
                  ....*....|....*.
gi 240120087  854 TAFHVSCAQAAGVMMQ 869
Cdd:cd15662    77 VAYHPLCARAAGLCME 92
ePHD_AF10_like cd15672
Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) ...
 775-867 1.88e-19

Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 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. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription.


Pssm-ID: 277142  Cd Length: 116  Bit Score: 84.82  E-value: 1.88e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKRR---KRNAGCCVQCSHGR 851
Cdd:cd15672     1 CELCPHKDGALKRTDNGGWAHVVCALYIPEVRFGNVATMEPIILQDVPQDRFNKTCYICEEQGresKASTGACMQCNKSG 80

                          90
                  ....*....|....*.
gi 240120087  852 CPTAFHVSCAQAAGVM 867
Cdd:cd15672    81 CKQSFHVTCAQMAGLL 96
Tudor_JMJD2B_rpt1 cd20464
first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; ...
 899-949 1.97e-19

first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; JMJD2B, also called lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the tri-methyl 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 plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410535  Cd Length: 54  Bit Score: 82.55  E-value: 1.97e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 240120087  899 ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVVM 949
Cdd:cd20464     1 VSLGQVVITKNRNGLYYRCRVIGTATQTFYEVNFDDGSYSDNVYPESITSR 51
ePHD_PHF14 cd15674
Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended ...
 775-884 4.50e-18

Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF14. 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 this non-canonical ePHD finger. It can interact with histones through its PHD fingers.


Pssm-ID: 277144  Cd Length: 114  Bit Score: 80.89  E-value: 4.50e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLK-CVFCKKRRKRNAGCCVQCSHGRCP 853
Cdd:cd15674     1 CELCPNRGGIFKETDTGRWVHLVCALYTPGVAFGDVDKLSPVTLTEMNYSKWGAReCSLCEDPRFARTGVCISCDAGMCK 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 240120087  854 TAFHVSCAQAAGVMMQPDDW-----PFvvFITCFRH 884
Cdd:cd15674    81 SYFHVTCAQREGLLSEATDEediadPF--YAYCKQH 114
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 795-869 5.47e-17

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: 76.98  E-value: 5.47e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 240120087   795 HVSCAVAILEARFVNIAER--SPVDVSKIPLPRFKLKCVFCKKRRkrnaGCCVQCSHGRCPTAFHVSCAQAAGVMMQ 869
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSMgfPIEDIEKIPKRRWKLKCYLCKKKG----GACIQCSKKNCRRAFHVTCALEAGLLMQ 73
ePHD_ATX3_4_5_like cd15663
Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The ...
 775-869 1.10e-16

Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, 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 ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. These proteins show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain proteins that consist of an N-terminal PWWP domain, a canonical PHD finger, this non-canonical extended PHD finger, and a C-terminal SET domain.


Pssm-ID: 277133  Cd Length: 112  Bit Score: 76.79  E-value: 1.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRAN-DDRWVHVSCAVAILEARFVNIAERSP-VDVSKIPLPRFKLKCVFCKKRRkrnaGCCVQCShgRC 852
Cdd:cd15663     1 CCLCPVKGGALKPTDvEGLWVHVTCAWFRPEVCFKNEEKMEPaVGLLRIPLSTFLKACVICKQIH----GSCTQCC--KC 74

                          90
                  ....*....|....*..
gi 240120087  853 PTAFHVSCAQAAGVMMQ 869
Cdd:cd15663    75 ATYFHAMCASRAGYHME 91
ePHD_AF10 cd15708
Extended PHD finger found in protein AF-10 and similar proteins; The extended plant ...
 775-869 1.60e-16

Extended PHD finger found in protein AF-10 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 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. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-10 contains an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger.


Pssm-ID: 277178  Cd Length: 129  Bit Score: 77.04  E-value: 1.60e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCK---KRRKRNAGCCVQCSHGR 851
Cdd:cd15708     5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVSTMEPIVLQSVPHERYNKTCYICDeqgRESKAATGACMTCNKHG 84

                          90
                  ....*....|....*...
gi 240120087  852 CPTAFHVSCAQAAGVMMQ 869
Cdd:cd15708    85 CRQAFHVTCAQLAGLLCE 102
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 13-55 4.89e-16

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 72.68  E-value: 4.89e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 240120087     13 RIMTFYPTMEEFRNFSRYIAYIESQgAHRAGLAKVVPPKEWKP 55
Cdd:smart00545    1 EIPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
ePHD_JADE2 cd15705
Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant ...
 775-869 7.41e-16

Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-2. Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 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, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277175  Cd Length: 111  Bit Score: 74.36  E-value: 7.41e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRAND-DRWVHVSCAVAILEARFVNIAERSPV-DVSKIPLPRFKLKCVFCKKrrkrNAGCCVQCSHGRC 852
Cdd:cd15705     1 CLLCPKRGGALKPTRSgTKWVHVSCALWIPEVSIGCPEKMEPItKISHIPASRWALSCSLCKE----CTGTCIQCSMPSC 76

                          90
                  ....*....|....*..
gi 240120087  853 PTAFHVSCAQAAGVMMQ 869
Cdd:cd15705    77 ITAFHVTCAFDHGLEMR 93
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 775-869 1.20e-15

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: 73.78  E-value: 1.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRAND-DRWVHVSCAVAILEARFVNIAERSPV-DVSKIPLPRFKLKCVFCKKRrkrnAGCCVQCSHGRC 852
Cdd:cd15707     1 CILCPNKGGAMKSTRSgTKWAHVSCALWIPEVSIGCVEKMEPItKISSIPASRWALICVLCRER----TGACIQCSVKTC 76

                          90
                  ....*....|....*..
gi 240120087  853 PTAFHVSCAQAAGVMMQ 869
Cdd:cd15707    77 KTAYHVTCGFQHGLEMK 93
ePHD_AF17 cd15709
Extended PHD finger found in protein AF-17 and similar proteins; The extended plant ...
 775-871 6.56e-15

Extended PHD finger found in protein AF-17 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-17. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as a translocation partner of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. AF-17 contains an N-terminal plant homeodomain (PHD) finger followed by a non-canonical ePHD finger.


Pssm-ID: 277179  Cd Length: 125  Bit Score: 72.40  E-value: 6.56e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCVFCK---KRRKRNAGCCVQCSHGR 851
Cdd:cd15709     5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVLTMEPIVLQYVPHDRFNKTCYICEeqgRESKAASGACMTCNRHG 84

                          90       100
                  ....*....|....*....|
gi 240120087  852 CPTAFHVSCAQAAGVMMQPD 871
Cdd:cd15709    85 CRQAFHVTCAQMAGLLCEEE 104
ePHD_JADE3 cd15706
Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...
 775-884 2.76e-14

Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-3. Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is close related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (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. Jade-3 contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277176  Cd Length: 111  Bit Score: 70.14  E-value: 2.76e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRAND-DRWVHVSCAVAILEARFVNIAERSPV-DVSKIPLPRFKLKCVFCKKRrkrnAGCCVQCSHGRC 852
Cdd:cd15706     1 CLLCPKTGGAMKATRTgTKWAHVSCALWIPEVSIACPERMEPItKVSHIPPSRWALVCSLCKLK----TGACIQCSVKSC 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 240120087  853 PTAFHVSCAQAAGVMMQP--DDWPFVVFIT-CFRH 884
Cdd:cd15706    77 ITAFHVTCAFEHSLEMKTilDEGDEVKFKSyCLKH 111
Tudor_2 pfam18104
Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone ...
 902-936 2.48e-13

Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD).


Pssm-ID: 465651  Cd Length: 35  Bit Score: 64.75  E-value: 2.48e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 240120087   902 GQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGS 936
Cdd:pfam18104    1 GQDVIARWTDGRYYLGKFIGIHTQTFYEVEFEDGS 35
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 146-205 2.74e-13

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 65.35  E-value: 2.74e-13
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 240120087    146 DEWNIGRLKTILDLVEKESGItIEGVNT-PYLYFGMWKTSFAWHTEDMDLysINYLHFGEP 205
Cdd:smart00558    1 QLWNLAKLPFKLNLLSDLPED-IPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
ePHD_JADE1 cd15704
Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant ...
 775-869 8.09e-13

Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1. Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the Serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation and ASA transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277174  Cd Length: 118  Bit Score: 65.86  E-value: 8.09e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRAND-DRWVHVSCAVAILEARFVNIAERSPV-DVSKIPLPRFKLKCVFCKKRrkrnAGCCVQCSHGRC 852
Cdd:cd15704     4 CLLCPKKGGAMKPTRSgTKWVHVSCALWIPEVSIGSPEKMEPItKVSHIPSSRWALVCSLCNEK----VGASIQCSVKNC 79

                          90
                  ....*....|....*..
gi 240120087  853 PTAFHVSCAQAAGVMMQ 869
Cdd:cd15704    80 RTAFHVTCAFDRGLEMK 96
JmjN pfam02375
jmjN domain;
15-49 3.91e-12

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 61.15  E-value: 3.91e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 240120087    15 MTFYPTMEEFRNFSRYIAYIESQGAhRAGLAKVVP 49
Cdd:pfam02375    1 PVFYPTEEEFKDPLKYIEKIRPLGE-KYGICKIVP 34
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 732-766 8.21e-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: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 60.43  E-value: 8.21e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 240120087   732 TSMLVSCKKCSVRVHASCYGVPPAKASEEWMCSRC 766
Cdd:pfam13831    1 TSPLVYCSKCSVQVHASCYGVPPIPDGDGWKCRRC 35
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 899-946 1.08e-09

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 54.97  E-value: 1.08e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 240120087    899 ITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDI 946
Cdd:smart00333    3 FKVGDKVAARWEDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDL 50
PHD_JMJD2 cd15493
PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; ...
 735-766 3.80e-09

PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; 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 only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a Cys4HisCys3 canonical PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, 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. This model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276968  Cd Length: 42  Bit Score: 53.09  E-value: 3.80e-09
                          10        20        30
                  ....*....|....*....|....*....|...
gi 240120087  735 LVSCKKCSVRVHASCYGVPPAK-ASEEWMCSRC 766
Cdd:cd15493    10 LLVCSRCCVCVHASCYGVPDIPgDGEGWKCDRC 42
ePHD_Snt2p_like cd15667
Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) ...
 775-862 5.21e-07

Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Snt2p. Sntp2 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 PHD fingers, a non-canonical ePHD finger, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain.


Pssm-ID: 277137  Cd Length: 141  Bit Score: 50.07  E-value: 5.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGG---------------ALQRANDDRWVHVSCAVAILEARFVNIAERSP-VDVSKIPLPRFKLKCVFCKKrrk 838
Cdd:cd15667     1 CSLCNAKESnyelakkqsprtrpdALKCTSNGTWCHVLCALFNEDIKFGNSKSLQPiLNTESVLLKGSRQKCEICKV--- 77

                          90       100
                  ....*....|....*....|....
gi 240120087  839 rNAGCCVQCShgRCPTAFHVSCAQ 862
Cdd:cd15667    78 -SGGGLVKCE--VCDDRFHVSCAQ 98
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 775-871 1.22e-06

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: 47.79  E-value: 1.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRG-------GALQRANDDRWVHVSCAVAILEArFVNIAERSPVDVSKIPLPRfKLKCVFCKKrrkrnAGCCVQC 847
Cdd:cd15664     1 CALCGVYGddepndaGRLLYCGQDEWVHINCALWSAEV-FEEDDGSLQNVHSAVSRGR-MMKCELCGK-----PGATVGC 73

                          90       100
                  ....*....|....*....|....
gi 240120087  848 SHGRCPTAFHVSCAQAAGVMMQPD 871
Cdd:cd15664    74 CLKSCPANYHFMCARKAECVFQDD 97
PHD_ATX3_4_5_like cd15495
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
 728-766 9.08e-06

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276970 [Multi-domain]  Cd Length: 47  Bit Score: 43.52  E-value: 9.08e-06
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 240120087  728 EEDGTSMLVSCKKCSVRVHASCYGVPPAKASEEWMCSRC 766
Cdd:cd15495     9 EDDDNNPLITCNRCQISVHQKCYGIREVDPDGSWVCRAC 47
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 775-867 1.52e-05

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: 44.99  E-value: 1.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRG-------GALQRANDDRWVHVSCAVAILE------ARFVNIAErspvdvskiPLPR-FKLKCVFCKKRrkrn 840
Cdd:cd15666     1 CVLCGGEGdgdtdgpGRLLNLDVDKWVHLNCALWSYEvyetqnGALMNVEE---------ALRRaLTTTCSHCGRT---- 67

                          90       100
                  ....*....|....*....|....*..
gi 240120087  841 aGCCVQCSHGRCPTAFHVSCAQAAGVM 867
Cdd:cd15666    68 -GATVPCFKPRCANVYHLPCAIKDGCM 93
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 734-766 3.33e-05

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: 41.84  E-value: 3.33e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 240120087  734 MLVSCKKCSVRVHASCYGVpPAKASEEWMCSRC 766
Cdd:cd15492    15 EIVFCDGCNVAVHQSCYGI-PLIPEGDWFCRKC 46
Tudor_SF cd04508
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 902-947 5.08e-05

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


Pssm-ID: 410449 [Multi-domain]  Cd Length: 47  Bit Score: 41.42  E-value: 5.08e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 240120087  902 GQKVISKHKN-GRFYQCEVVRLTTETFYEVNFDDGSfSDNLYPEDIV 947
Cdd:cd04508     1 GDRVEAKWSDdGQWYPATVVAVNDDGKYTVLFDDGN-EEEVSEDDIR 46
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 775-886 5.32e-05

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: 43.50  E-value: 5.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRG-------GALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSkipLPR-FKLKCVFCKKrrkrnAGCCVQ 846
Cdd:cd15698     1 CCFCHEEGdgatdgpARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVA---LHRgLLTKCSLCQK-----TGATNS 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 240120087  847 CSHGRCPTAFHVSCAQAAGVMMQPDDwpfvvFITCFRHKI 886
Cdd:cd15698    73 CNRLRCPNVYHFACAIRAKCMFFKDK-----TMLCPMHKL 107
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
 729-766 3.87e-04

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 38.84  E-value: 3.87e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 240120087  729 EDGTSMLVSCKKCSVRVHASCYGVPPAKASEEWMCSRC 766
Cdd:cd15550     7 EHDDGFMICCDKCSVWQHGDCMGIDRENIPDSYLCEQC 44
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 735-766 5.28e-04

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: 5.28e-04
                            10        20        30
                    ....*....|....*....|....*....|....
gi 240120087    735 LVSCKKCSVRVHASCYGVPPAKA--SEEWMCSRC 766
Cdd:smart00249   14 LLQCDGCDRWYHQTCLGPPLLEEepDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 830-872 7.10e-04

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: 38.35  E-value: 7.10e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 240120087    830 CVFCKKrrKRNAGCCVQCSHgrCPTAFHVSCAQAAGVMMQPDD 872
Cdd:smart00249    2 CSVCGK--PDDGGELLQCDG--CDRWYHQTCLGPPLLEEEPDG 40
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 775-865 7.90e-04

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: 39.61  E-value: 7.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLrggalqranDDRWVHVSCAvaILEARFVNIAERSPVDVSKIPLPRFKLKCVFCKKrrkrnAGCCVQCSHGRCPT 854
Cdd:cd15665     1 CALCNL---------GEVYAHHCCA--AWSEGVCQTEDGALENVDKAVAKALSQKCSFCLR-----YGASISCRMPSCSK 64

                          90
                  ....*....|.
gi 240120087  855 AFHVSCAQAAG 865
Cdd:cd15665    65 SFHFPCAAAAG 75
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 775-871 2.56e-03

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: 38.49  E-value: 2.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240120087  775 CCLCSLRGGALQRA-------NDDRWVHVSCAVAILEARFVNIAERSPVDVSkipLPR-FKLKCVFCKKrrkrnAGCCVQ 846
Cdd:cd15697     1 CCFCHEEGDGLTDGparllnlDLDLWVHLNCALWSTEVYETQAGALINVELA---LRRgLQMKCVFCHK-----TGATSG 72

                          90       100
                  ....*....|....*....|....*
gi 240120087  847 CSHGRCPTAFHVSCAQAAGVMMQPD 871
Cdd:cd15697    73 CHRLRCTNVYHFTCAIKAQCMFFKD 97
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 730-766 2.99e-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: 36.53  E-value: 2.99e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 240120087  730 DGTSMLVSCKKCSVRVHASCYGVPPAKA--SEEWMCSRC 766
Cdd:cd15489    10 DLGGELLQCDGCGKWFHADCLGPPLSSFvpNGKWICPVC 48
PHD3_NSD cd15566
PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 830-884 3.12e-03

PHD finger 3 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 third PHD finger.


Pssm-ID: 277041  Cd Length: 48  Bit Score: 36.64  E-value: 3.12e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 240120087  830 CVFCKKRRKRNAGCCVQCShgRCPTAFHVSCAQAAGVMMQPddwpfvVFITCFRH 884
Cdd:cd15566     2 CATCEASGDGSSGKLVRCI--RCPRAYHAGCIPAGSKLLNK------KLIICPKH 48
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
 729-766 6.37e-03

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277149 [Multi-domain]  Cd Length: 46  Bit Score: 35.82  E-value: 6.37e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 240120087  729 EDGTSMlVSCKKCSVRVHASCYGVppAKASE-EWMCSRC 766
Cdd:cd15679    11 EDGNEM-VFCDKCNICVHQACYGI--LKVPEgSWLCRTC 46
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
 728-766 7.44e-03

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They 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. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 35.67  E-value: 7.44e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 240120087  728 EEDGTSMLVSCKKCSVRVHASCYGVPPAKASeEWMCSRC 766
Cdd:cd15572    11 ECQNSNVILFCDMCNLAVHQECYGVPYIPEG-QWLCRRC 48
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH