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Conserved domains on  [gi|528881361|ref|NP_001268711|]
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MYND-type zinc finger-containing chromatin reader ZMYND8 isoform p [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF3544 pfam12064
Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and ...
 417-615 1.17e-80

Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).


:

Pssm-ID: 463452  Cd Length: 195  Bit Score: 261.77  E-value: 1.17e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   417 RRISLSDMPRSPMSTNSSVHTGSDVEQD-AEK---KATSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 492
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDtAEKgqaKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   493 lsAPITTKTDKTSTTGSILNLNLDRSKAEMDLKELSESVQQ-QSTPVPLISPKRQIRSRFQLNLDKTIESCKAQLGINEI 571
Cdd:pfam12064   74 --APGTPKQEKTPTTGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGIDEI 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 528881361   572 SEDVYTAVEHSDSEDSEKSDSSDSEYISDDEQKSKNEPEDTEDK 615
Cdd:pfam12064  152 SVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 146-244 1.04e-58

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


:

Pssm-ID: 99940  Cd Length: 99  Bit Score: 196.45  E-value: 1.04e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  146 IEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 225
Cdd:cd05508     1 VDQLSKLLKFALERMKQPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGG 80

                          90
                  ....*....|....*....
gi 528881361  226 NHKLTQIAKVVIKICEHEM 244
Cdd:cd05508    81 DHKLTQAAKAIVKICEQEM 99
PWWP_PRKCBP1 cd20160
PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; ...
 267-357 3.17e-56

PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


:

Pssm-ID: 438988  Cd Length: 91  Bit Score: 188.93  E-value: 3.17e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  267 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 346
Cdd:cd20160     1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                          90
                  ....*....|.
gi 528881361  347 NIRRKFGVFNY 357
Cdd:cd20160    81 KLREKFGKFNY 91
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 85-125 5.16e-23

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


:

Pssm-ID: 277013  Cd Length: 41  Bit Score: 92.39  E-value: 5.16e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15538     1 FCWRCHKEGQVLCCSLCPRVYHKKCLKLTSEPDEDWVCPEC 41
zf-MYND pfam01753
MYND finger;
950-984 3.59e-07

MYND finger;


:

Pssm-ID: 460312  Cd Length: 39  Bit Score: 47.41  E-value: 3.59e-07
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 528881361   950 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 984
Cdd:pfam01753    1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39
TNG2 super family cl34876
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
24-128 6.67e-06

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


The actual alignment was detected with superfamily member COG5034:

Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 49.17  E-value: 6.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   24 STRSKDPGSAER-TAQKRKFPSPPHSSNGHSPQDTSTSPIKKKK---KPGLLNSNNKEQDGR-------NDFYCWvCHRE 92
Cdd:COG5034   151 SQGSRHTKLKKRkNIHNLKRRSPELSSKREVSFTLESPSVPDTAtrvKEGNNGGSTKSRGVSsednsegEELYCF-CQQV 229

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 528881361   93 --GQVLCC--ELCPRV-YHAKCLRLTSEPEGDWFCPECEKI 128
Cdd:COG5034   230 syGQMVACdnANCKREwFHLECVGLKEPPKGKWYCPECKKA 270
ATP-synt_Fo_b super family cl21478
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ...
 867-946 2.13e-04

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.


The actual alignment was detected with superfamily member cd06503:

Pssm-ID: 473877 [Multi-domain]  Cd Length: 132  Bit Score: 42.42  E-value: 2.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  867 ASADVAADIAKYTSKIRRLRIEIEKLqwlhqqeLSEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 946
Cdd:cd06503    45 AKEEAEELLAEYEEKLAEARAEAQEI-------IEEARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELRK 117
TFIIF_alpha super family cl37738
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation ...
 597-755 2.41e-03

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II.


The actual alignment was detected with superfamily member pfam05793:

Pssm-ID: 310411 [Multi-domain]  Cd Length: 528  Bit Score: 41.86  E-value: 2.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   597 YISDDEQkSKNEPEDTEDkegcqmdkepsavKKKPKPTNPVEIkeelkstspasEKADPGAVKDKASPEPEKDFSEKAKP 676
Cdd:pfam05793  285 YISDSSA-SGNDPEERED-------------KLSPEEPAKGEI-----------EQSDDSEESEEEKNEEEGKLSKKGKK 339

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528881361   677 SPHPiKDKLKGKDETDSptvhlglDSDSESELVIDLGEDHSGREGRKNKKEPKEPSPKQDVVGKTPPSttvGSHSPPET 755
Cdd:pfam05793  340 AKKL-KGKKNGKDKSES-------SDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPVDSGPSSPGNS---GPARPSPE 407
 
Name Accession Description Interval E-value
DUF3544 pfam12064
Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and ...
 417-615 1.17e-80

Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).


Pssm-ID: 463452  Cd Length: 195  Bit Score: 261.77  E-value: 1.17e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   417 RRISLSDMPRSPMSTNSSVHTGSDVEQD-AEK---KATSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 492
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDtAEKgqaKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   493 lsAPITTKTDKTSTTGSILNLNLDRSKAEMDLKELSESVQQ-QSTPVPLISPKRQIRSRFQLNLDKTIESCKAQLGINEI 571
Cdd:pfam12064   74 --APGTPKQEKTPTTGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGIDEI 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 528881361   572 SEDVYTAVEHSDSEDSEKSDSSDSEYISDDEQKSKNEPEDTEDK 615
Cdd:pfam12064  152 SVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 146-244 1.04e-58

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 196.45  E-value: 1.04e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  146 IEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 225
Cdd:cd05508     1 VDQLSKLLKFALERMKQPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGG 80

                          90
                  ....*....|....*....
gi 528881361  226 NHKLTQIAKVVIKICEHEM 244
Cdd:cd05508    81 DHKLTQAAKAIVKICEQEM 99
PWWP_PRKCBP1 cd20160
PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; ...
 267-357 3.17e-56

PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438988  Cd Length: 91  Bit Score: 188.93  E-value: 3.17e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  267 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 346
Cdd:cd20160     1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                          90
                  ....*....|.
gi 528881361  347 NIRRKFGVFNY 357
Cdd:cd20160    81 KLREKFGKFNY 91
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 85-125 5.16e-23

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 92.39  E-value: 5.16e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15538     1 FCWRCHKEGQVLCCSLCPRVYHKKCLKLTSEPDEDWVCPEC 41
BROMO smart00297
bromo domain;
147-247 8.65e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 80.02  E-value: 8.65e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361    147 EQLSYLLKFAI-QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 225
Cdd:smart00297    6 KKLQELLKAVLdKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGP 85

                            90       100
                    ....*....|....*....|..
gi 528881361    226 NHKLTQIAKVVIKICEHEMNEI 247
Cdd:smart00297   86 DSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 158-234 4.05e-16

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 74.27  E-value: 4.05e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528881361   158 QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 234
Cdd:pfam00439    7 KLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 85-125 5.83e-10

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 55.68  E-value: 5.83e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 528881361     85 YCWVCHR---EGQVLCCELCPRVYHAKCLRLT---SEPEGDWFCPEC 125
Cdd:smart00249    1 YCSVCGKpddGGELLQCDGCDRWYHQTCLGPPlleEEPDGKWYCPKC 47
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 275-346 7.30e-10

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 56.67  E-value: 7.30e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   275 LVWAKLKGFPFWPAK---------ALRDKDGQVDA---RFFGQHDRAWVPINNCYLMSKEIPFSV------KKTKSIFNS 336
Cdd:pfam00855    3 LVWAKLKGYPWWPARvvdpeelpeNVLKPKKKDGEylvRFFGDSEFAWVKPKDLKPFDEGDEFEYlkkkkkKKKKKAFKK 82

                           90
                   ....*....|
gi 528881361   337 AMQEMEVYVE 346
Cdd:pfam00855   83 ALEEAEEALK 92
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 85-125 8.58e-10

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 55.19  E-value: 8.58e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 528881361    85 YCWVCHR---EGQVLCCELCPRVYHAKCLRLTSE----PEGDWFCPEC 125
Cdd:pfam00628    1 YCAVCGKsddGGELVQCDGCDDWFHLACLGPPLDpaeiPSGEWLCPEC 48
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 271-315 1.49e-09

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 55.04  E-value: 1.49e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 528881361    271 NPHPLVWAKLKGFPFWPA-----KALRD-------KDGQVDARFFGQHDRAWVPINN 315
Cdd:smart00293    2 KPGDLVWAKMKGFPWWPAlvispKMTPDnimkrksDENLYPVLFFGDKDTAWIPSSK 58
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 143-268 3.25e-07

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 54.04  E-value: 3.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  143 MLTIEQLSYLLKFAIQKMKQ---PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNC 219
Cdd:COG5076   141 ELLYADNKAIAKFKKQLFLRdgrFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNC 220

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 528881361  220 IIYNGGNHKLTQIAKVVIKICEHEMNEIevcPECYLAACQKRDNWFCEP 268
Cdd:COG5076   221 KLYNGPDSSVYVDAKELEKYFLKLIEEI---PEEMLELSIKPGREEREE 266
zf-MYND pfam01753
MYND finger;
950-984 3.59e-07

MYND finger;


Pssm-ID: 460312  Cd Length: 39  Bit Score: 47.41  E-value: 3.59e-07
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 528881361   950 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 984
Cdd:pfam01753    1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
24-128 6.67e-06

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 49.17  E-value: 6.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   24 STRSKDPGSAER-TAQKRKFPSPPHSSNGHSPQDTSTSPIKKKK---KPGLLNSNNKEQDGR-------NDFYCWvCHRE 92
Cdd:COG5034   151 SQGSRHTKLKKRkNIHNLKRRSPELSSKREVSFTLESPSVPDTAtrvKEGNNGGSTKSRGVSsednsegEELYCF-CQQV 229

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 528881361   93 --GQVLCC--ELCPRV-YHAKCLRLTSEPEGDWFCPECEKI 128
Cdd:COG5034   230 syGQMVACdnANCKREwFHLECVGLKEPPKGKWYCPECKKA 270
ATP-synt_Fo_b cd06503
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ...
 867-946 2.13e-04

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.


Pssm-ID: 349951 [Multi-domain]  Cd Length: 132  Bit Score: 42.42  E-value: 2.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  867 ASADVAADIAKYTSKIRRLRIEIEKLqwlhqqeLSEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 946
Cdd:cd06503    45 AKEEAEELLAEYEEKLAEARAEAQEI-------IEEARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELRK 117
AtpF COG0711
FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ...
 865-946 3.32e-04

FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase


Pssm-ID: 440475 [Multi-domain]  Cd Length: 152  Bit Score: 42.08  E-value: 3.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  865 ATASADVAADIAKYTSKIRRLRIEIEKLqwlhqqeLSEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDET 944
Cdd:COG0711    44 ERAKEEAEAALAEYEEKLAEARAEAAEI-------IAEARKEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAEL 116


                  ..
gi 528881361  945 KK 946
Cdd:COG0711   117 RA 118
PRK05759 PRK05759
F0F1 ATP synthase subunit B; Validated
 863-947 9.92e-04

F0F1 ATP synthase subunit B; Validated


Pssm-ID: 180240 [Multi-domain]  Cd Length: 156  Bit Score: 40.91  E-value: 9.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  863 PIATASADVAADIAKYTSKIRRLRIEIEKLQWLHQQELSEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKK 931
Cdd:PRK05759   28 PIMKALEERQKKIADGLAAAERAKKELELAQAKYEAQLAEARAeaaeiieqakkRAAQIIEEAKAEAEAEAARIKAQAQA 107

                          90
                  ....*....|....*.
gi 528881361  932 QLELEKQQAVDETKKK 947
Cdd:PRK05759  108 EIEQERKRAREELRKQ 123
TFIIF_alpha pfam05793
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation ...
 597-755 2.41e-03

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II.


Pssm-ID: 310411 [Multi-domain]  Cd Length: 528  Bit Score: 41.86  E-value: 2.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   597 YISDDEQkSKNEPEDTEDkegcqmdkepsavKKKPKPTNPVEIkeelkstspasEKADPGAVKDKASPEPEKDFSEKAKP 676
Cdd:pfam05793  285 YISDSSA-SGNDPEERED-------------KLSPEEPAKGEI-----------EQSDDSEESEEEKNEEEGKLSKKGKK 339

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528881361   677 SPHPiKDKLKGKDETDSptvhlglDSDSESELVIDLGEDHSGREGRKNKKEPKEPSPKQDVVGKTPPSttvGSHSPPET 755
Cdd:pfam05793  340 AKKL-KGKKNGKDKSES-------SDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPVDSGPSSPGNS---GPARPSPE 407
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 622-829 3.42e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 41.45  E-value: 3.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  622 KEPSAVKK-KPKPTNPVEikeeLKSTSPASEKADPGAVKDKASPEPEKDFSEKAKP--SPHPIKDKLKGKDETDSPTVHL 698
Cdd:PLN03209  331 KESDAADGpKPVPTKPVT----PEAPSPPIEEEPPQPKAVVPRPLSPYTAYEDLKPptSPIPTPPSSSPASSKSVDAVAK 406

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  699 GLDSD--SESELVIDLGEDHSGREGRK------------NKKEPKEPSPKQDVVGKTPPSTTVGSHSPPETPVLTRSS-- 762
Cdd:PLN03209  407 PAEPDvvPSPGSASNVPEVEPAQVEAKktrplspyaryeDLKPPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAATda 486

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528881361  763 AQTSAAGATATTSTSSTVTVTAPAPAATGSPVKKQRPLLPKETAPAVQRVVWNSSTVQQKEITQSPS 829
Cdd:PLN03209  487 AAPPPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTALADEQHHAQPKPR 553
 
Name Accession Description Interval E-value
DUF3544 pfam12064
Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and ...
 417-615 1.17e-80

Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).


Pssm-ID: 463452  Cd Length: 195  Bit Score: 261.77  E-value: 1.17e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   417 RRISLSDMPRSPMSTNSSVHTGSDVEQD-AEK---KATSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 492
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDtAEKgqaKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   493 lsAPITTKTDKTSTTGSILNLNLDRSKAEMDLKELSESVQQ-QSTPVPLISPKRQIRSRFQLNLDKTIESCKAQLGINEI 571
Cdd:pfam12064   74 --APGTPKQEKTPTTGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGIDEI 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 528881361   572 SEDVYTAVEHSDSEDSEKSDSSDSEYISDDEQKSKNEPEDTEDK 615
Cdd:pfam12064  152 SVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 146-244 1.04e-58

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 196.45  E-value: 1.04e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  146 IEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 225
Cdd:cd05508     1 VDQLSKLLKFALERMKQPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGG 80

                          90
                  ....*....|....*....
gi 528881361  226 NHKLTQIAKVVIKICEHEM 244
Cdd:cd05508    81 DHKLTQAAKAIVKICEQEM 99
PWWP_PRKCBP1 cd20160
PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; ...
 267-357 3.17e-56

PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438988  Cd Length: 91  Bit Score: 188.93  E-value: 3.17e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  267 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 346
Cdd:cd20160     1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                          90
                  ....*....|.
gi 528881361  347 NIRRKFGVFNY 357
Cdd:cd20160    81 KLREKFGKFNY 91
PWWP_BS69-like cd05841
PWWP domain found in protein BS69, protein kinase C-binding protein 1 (PRKCBP1) and similar ...
 267-350 2.42e-39

PWWP domain found in protein BS69, protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. BS69 is a multi-domain protein, containing bromo, plant homeodomain (PHD), proline-tryptophan-tryptophan-proline (PWWP), and MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a PHD finger, a bromodomain, and a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438966  Cd Length: 89  Bit Score: 140.61  E-value: 2.42e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  267 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIP-----FSVKKTKSIFNSAMQEM 341
Cdd:cd05841     1 KPCPVVHPLVWVKLDGFPFWPAKVMGTKDGQVDVRFFGDYDRAWLPSKNVTLHTREIVstlpdSSESKDKRTLKKAIKEL 80


                  ....*....
gi 528881361  342 EVYVENIRR 350
Cdd:cd05841    81 ERHIALLRQ 89
PWWP_BS69 cd20159
PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger ...
 268-350 1.97e-25

PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438987  Cd Length: 85  Bit Score: 100.75  E-value: 1.97e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  268 PCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFG-QHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 346
Cdd:cd20159     2 PCRPPHELVWAKQKGFPYWPAKVIQKEDNQYDVRFFGgHHQRAWIPKENIKPITTSPKQLKVKRTAGWNKACEELKKHQE 81


                  ....
gi 528881361  347 NIRR 350
Cdd:cd20159    82 LLEE 85
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 85-125 5.16e-23

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 92.39  E-value: 5.16e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15538     1 FCWRCHKEGQVLCCSLCPRVYHKKCLKLTSEPDEDWVCPEC 41
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 149-248 1.65e-21

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 90.79  E-value: 1.65e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  149 LSYLLKFAIQKMKQ-PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNH 227
Cdd:cd05511     1 LSFILDEIVNELKNlPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80

                          90       100
                  ....*....|....*....|.
gi 528881361  228 KLTQIAKVVIKICEHEMNEIE 248
Cdd:cd05511    81 VYTKKAKEMLELAEELLAERE 101
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 145-244 2.65e-20

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 86.66  E-value: 2.65e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  145 TIEQLSYLLKfAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 224
Cdd:cd04369     1 LKKKLRSLLD-ALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNG 79

                          90       100
                  ....*....|....*....|
gi 528881361  225 GNHKLTQIAKVVIKICEHEM 244
Cdd:cd04369    80 PGSPIYKDAKKLEKLFEKLL 99
BROMO smart00297
bromo domain;
147-247 8.65e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 80.02  E-value: 8.65e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361    147 EQLSYLLKFAI-QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 225
Cdd:smart00297    6 KKLQELLKAVLdKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGP 85

                            90       100
                    ....*....|....*....|..
gi 528881361    226 NHKLTQIAKVVIKICEHEMNEI 247
Cdd:smart00297   86 DSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 158-234 4.05e-16

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 74.27  E-value: 4.05e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528881361   158 QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 234
Cdd:pfam00439    7 KLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 85-125 4.64e-16

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


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 72.70  E-value: 4.64e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15532     1 FCRVCKDGGELLCCDGCPSSYHLHCLnpPLAEIPDGDWFCPRC 43
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 148-226 8.80e-16

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 74.13  E-value: 8.80e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  148 QLSYLLKFAIQKMKQpGTDA--FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 225
Cdd:cd05509     1 PLYTQLKKVLDSLKN-HKSAwpFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGP 79


                  .
gi 528881361  226 N 226
Cdd:cd05509    80 D 80
Bromo_ZMYND11 cd05492
Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear ...
 149-250 2.52e-14

Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99924  Cd Length: 109  Bit Score: 70.10  E-value: 2.52e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  149 LSYLLKFAIQKMKQ--PGTDAFQKPVPLE-----QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCII 221
Cdd:cd05492     1 LNCLLKFIVSRMKSwlPPDTTNRAIVLNKrgkatKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAI 80

                          90       100
                  ....*....|....*....|....*....
gi 528881361  222 YNGGNHKLTQIAKVVIKICEHEMNEIEVC 250
Cdd:cd05492    81 FHGADSEQYDAARWLYRDTCHDLRELRLC 109
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 144-244 2.20e-13

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 67.34  E-value: 2.20e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  144 LTIEQLSYLLKfAIQKMKQpGTDA--FQKPV-PLEQH-PDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNC 219
Cdd:cd05500     1 MTKHQHKFLLS-SIRSLKR-LKDArpFLVPVdPVKLNiPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNC 78

                          90       100
                  ....*....|....*....|....*
gi 528881361  220 IIYNGGNHKLTQIAKVVIKICEHEM 244
Cdd:cd05500    79 LTFNGPEHPVSQMGKRLQAAFEKHL 103
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 85-125 1.62e-12

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 62.65  E-value: 1.62e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15567     1 WCFICSEGGSLICCESCPASFHPECLGLEPPPEGKFYCEDC 41
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 159-224 6.50e-12

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 62.80  E-value: 6.50e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 528881361  159 KMKQPGtDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 224
Cdd:cd05512    14 QEKDTA-EIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNA 78
PWWP cd05162
PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, ...
 275-344 7.25e-12

PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.


Pssm-ID: 438958 [Multi-domain]  Cd Length: 86  Bit Score: 62.52  E-value: 7.25e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  275 LVWAKLKGFPFWPAKALRDKDGQVDA-----------RFFGQHDRAWVPINNCYL----MSKEIPFSVKKTKSiFNSAMQ 339
Cdd:cd05162     3 LVWAKLKGYPWWPARVVDPEELPEEVgkkkkkggvlvQFFGDNDYAWVKSKNIKPfeegFKKEFKKKKKKSKK-FKKAVE 81


                  ....*
gi 528881361  340 EMEVY 344
Cdd:cd05162    82 EAEEA 86
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 85-125 1.50e-11

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


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 60.12  E-value: 1.50e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLTSE----PEGDWFCPEC 125
Cdd:cd15535     1 FCSACGGYGSFLCCDGCPRSFHFSCLDPPLEednlPDDEWFCNEC 45
PWWP_GLYR1 cd05836
PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called ...
 275-345 1.74e-11

PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called 3-hydroxyisobutyrate dehydrogenase-like protein, cytokine-like nuclear factor N-PAC, nuclear protein NP60, or nuclear protein of 60 kDa, is a putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity. It recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). GLYR1 enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In addition to the PWWP domain, GLYR1 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438961 [Multi-domain]  Cd Length: 86  Bit Score: 61.08  E-value: 1.74e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  275 LVWAKLKGFPFWPAKALR-DKDGQVDAR--------FFGQHDRAWVPINNC--YLMSKEIPFSVKKTKSiFNSAMQEMEV 343
Cdd:cd05836     6 LVWAKMKGFPPWPGKIVNpPPDLKKPPRkkkmhcvyFFGSENYAWIEDENIkpYEEFKEEMLKSKKSAG-FKDAVEAIEE 84


                  ..
gi 528881361  344 YV 345
Cdd:cd05836    85 YI 86
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 85-125 3.25e-11

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


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 59.00  E-value: 3.25e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15539     1 ECAVCGDGGELLCCDGCPRAFHLACLVppLTLIPSGTWRCSSC 43
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 167-247 4.84e-11

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 60.92  E-value: 4.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  167 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG-NHKLTQIAKVVIKICEHEMN 245
Cdd:cd05510    28 PFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDpSHPLRRHANFMKKKAEHLLK 107


                  ..
gi 528881361  246 EI 247
Cdd:cd05510   108 LI 109
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 85-125 5.33e-11

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


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 58.58  E-value: 5.33e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15559     1 HCRVCHKLGDLLCCETCSAVYHLECVDppLEEVPEEDWQCEVC 43
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 167-249 6.53e-11

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 60.07  E-value: 6.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  167 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIkicEHEMNE 246
Cdd:cd05507    23 VFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEMQ---REVMSQ 99


                  ...
gi 528881361  247 IEV 249
Cdd:cd05507   100 IQQ 102
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 85-125 6.91e-11

PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277128  Cd Length: 40  Bit Score: 58.00  E-value: 6.91e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLtSEPEGDWFCPEC 125
Cdd:cd15658     1 FCFVCARGGRLLCCESCPASFHPECLSI-EMPEGCWNCNEC 40
PHD_BS69 cd15537
PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...
 85-125 1.15e-10

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.


Pssm-ID: 277012  Cd Length: 43  Bit Score: 57.35  E-value: 1.15e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLTSEP--EGDWFCPEC 125
Cdd:cd15537     1 YCFECHAPGEVLPCSGCFRVYHSDCLSEDFRPdsTSHWTCPVC 43
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 85-125 1.45e-10

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


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 57.32  E-value: 1.45e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   85 YCWVCHR---EGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15545     1 SCQICRSgdnEDQLLLCDGCDRGYHTYCFKpkMTNVPEGDWFCPEC 46
PWWP_HRP cd05834
PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The ...
 275-342 4.17e-10

PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The HRP family includes hepatoma-derived growth factor (HDGF), and HDGF-related proteins (HRPs). HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It is a prognostic factor in several types of cancer. HDGFL1 is also called PWWP domain-containing protein 1 (PWWP1). Its biological function remains unclear. HDGFL2, also called HDGF-related protein 2 (HRP-2), or hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. HDGFL3, also called HDGF-related protein 3 (HRP-3), enhances DNA synthesis and may play a role in cell proliferation. The family also includes PC4 and SFRS1-interacting protein (PSIP) and similar proteins. PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. Members of the HRP family contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438959 [Multi-domain]  Cd Length: 82  Bit Score: 57.18  E-value: 4.17e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528881361  275 LVWAKLKGFPFWPAKALRDKDGQVDAR------FFGQHDRAWVPINNCYLMSKE-IPFSVKKTKSIFNSAMQEME 342
Cdd:cd05834     6 LVFAKVKGYPPWPARIDEIPEGAKIPKnkypvfFYGTHETAFLKPKDLFPYEENkEKYGKPRKRKGFNEGLWEIE 80
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 85-125 5.04e-10

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: 55.79  E-value: 5.04e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528881361   85 YCWVCHREGQ----VLCCELCPRVYHAKCLRLTSE---PEGDWFCPEC 125
Cdd:cd15489     1 SCIVCGKGGDlggeLLQCDGCGKWFHADCLGPPLSsfvPNGKWICPVC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 85-125 5.83e-10

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 55.68  E-value: 5.83e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 528881361     85 YCWVCHR---EGQVLCCELCPRVYHAKCLRLT---SEPEGDWFCPEC 125
Cdd:smart00249    1 YCSVCGKpddGGELLQCDGCDRWYHQTCLGPPlleEEPDGKWYCPKC 47
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 86-125 6.07e-10

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


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 55.48  E-value: 6.07e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528881361   86 CWVCHREG---QVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15627     2 CRICRRKGdaeKMLLCDGCDRGHHMYCLRppLKKVPEGDWFCPDC 46
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 85-123 7.05e-10

PHD finger 5 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 fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 55.41  E-value: 7.05e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCC--ELCPRVYHAKCLRLTSEPEGDWFCP 123
Cdd:cd15568     1 ECFRCGDGGDLVLCdfKGCPKVYHLSCLGLEKPPGGKWICP 41
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 275-346 7.30e-10

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 56.67  E-value: 7.30e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   275 LVWAKLKGFPFWPAK---------ALRDKDGQVDA---RFFGQHDRAWVPINNCYLMSKEIPFSV------KKTKSIFNS 336
Cdd:pfam00855    3 LVWAKLKGYPWWPARvvdpeelpeNVLKPKKKDGEylvRFFGDSEFAWVKPKDLKPFDEGDEFEYlkkkkkKKKKKAFKK 82

                           90
                   ....*....|
gi 528881361   337 AMQEMEVYVE 346
Cdd:pfam00855   83 ALEEAEEALK 92
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 85-125 8.58e-10

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 55.19  E-value: 8.58e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 528881361    85 YCWVCHR---EGQVLCCELCPRVYHAKCLRLTSE----PEGDWFCPEC 125
Cdd:pfam00628    1 YCAVCGKsddGGELVQCDGCDDWFHLACLGPPLDpaeiPSGEWLCPEC 48
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 85-125 9.13e-10

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


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 55.16  E-value: 9.13e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15519     4 VCGLDDNEGEVLLCDGCDAEYHTSCLDppLGEIPPGTWFCPSC 46
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 85-125 1.04e-09

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


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 54.71  E-value: 1.04e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15523     1 FCSVCRKSGELLMCDTCSLVYHLDCLDppLKTIPKGMWICPKC 43
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 271-315 1.49e-09

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 55.04  E-value: 1.49e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 528881361    271 NPHPLVWAKLKGFPFWPA-----KALRD-------KDGQVDARFFGQHDRAWVPINN 315
Cdd:smart00293    2 KPGDLVWAKMKGFPWWPAlvispKMTPDnimkrksDENLYPVLFFGDKDTAWIPSSK 58
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 85-125 1.50e-09

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


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 54.27  E-value: 1.50e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHipPIPEFPSGEWSCSLC 43
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 85-125 1.57e-09

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


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 54.53  E-value: 1.57e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15531     1 YCEVCQQGGEIILCDTCPRAYHLVCLdpELEKAPEGKWSCPHC 43
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 148-239 2.43e-09

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 55.89  E-value: 2.43e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  148 QLSYLLKFAIQKM-KQPGTDAFQKPVPLE--QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 224
Cdd:cd05497     5 QLQYLLKVVLKALwKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK 84

                          90
                  ....*....|....*
gi 528881361  225 GNHKLTQIAKVVIKI 239
Cdd:cd05497    85 PGDDVVLMAQTLEKL 99
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 167-228 7.13e-09

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 54.67  E-value: 7.13e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528881361  167 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHK 228
Cdd:cd05528    23 AFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDP 84
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 148-239 1.28e-08

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 53.94  E-value: 1.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  148 QLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYnggNH 227
Cdd:cd05504    13 NLSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLY---NP 89

                          90
                  ....*....|..
gi 528881361  228 KLTQIAKVVIKI 239
Cdd:cd05504    90 EHTSVYKAGTRL 101
PHD4_NSD1 cd15656
PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
 85-125 2.35e-08

PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains 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). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277126  Cd Length: 40  Bit Score: 50.78  E-value: 2.35e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLtSEPEGDWFCPEC 125
Cdd:cd15656     1 WCFVCSEGGSLLCCESCPAAFHRECLNI-DMPEGSWYCNDC 40
PHD4_NSD2 cd15657
PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
 85-125 2.47e-08

PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fourth PHD finger.


Pssm-ID: 277127  Cd Length: 41  Bit Score: 50.77  E-value: 2.47e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLRLtSEPEGDWFCPEC 125
Cdd:cd15657     1 WCFVCSKGGSLLCCESCPAAFHPDCLNI-EMPDGSWFCNDC 40
PHD5_NSD1 cd15659
PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
 86-123 5.00e-08

PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains 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). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277129  Cd Length: 43  Bit Score: 49.94  E-value: 5.00e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 528881361   86 CWVCHREGQVLCCEL--CPRVYHAKCLRLTSEPEGDWFCP 123
Cdd:cd15659     2 CFSCGDGGQLVSCKKpgCPKVYHADCLNLTKRPAGKWECP 41
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
 85-125 1.08e-07

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277092  Cd Length: 43  Bit Score: 49.29  E-value: 1.08e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15622     1 WCAVCQNGGELLCCEKCPKVFHLSCHvpTLMNFPSGEWICTFC 43
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 85-125 1.30e-07

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


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 48.89  E-value: 1.30e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKC----LRLTSEPEGDWFCPEC 125
Cdd:cd15533     1 YCDSCGEGGDLLCCDRCPASFHLQCcnppLDEEDLPPGEWLCHRC 45
PWWP_NSD_rpt2 cd05838
second PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 276-346 1.36e-07

second PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein family consists 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 in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play nonredundant 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 (C5HCH). This model corresponds to the second PWWP domain. The family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438963 [Multi-domain]  Cd Length: 96  Bit Score: 50.32  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  276 VWAKLKGFPFWPAKAL------------RDKDGQVDARFFGQHDRAWVPINNCYLMSKE----IPFSVKKTKSIFNSAMQ 339
Cdd:cd05838     6 VWVKLGNYRWWPAEILhprevpdniqslPHPPGEFPVRFFGSHDYYWVHRGRVFLFEEGdkgsKEKSKKSLDKSFKRALK 85


                  ....*...
gi 528881361  340 E-MEVYVE 346
Cdd:cd05838    86 EaNEAFRE 93
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 112-236 1.40e-07

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 51.57  E-value: 1.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  112 LTSEPEGDWFC--PECEKITVAEcietqskamtmltiEQLSYLLKfAIQKMKQPG----TDAFQKPVPL-EQHPDYAEYI 184
Cdd:cd05529     1 LYNPLSSEWELfdPGWEQPHIRD--------------EERERLIS-GLDKLLLSLqleiAEYFEYPVDLrAWYPDYWNRV 65

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528881361  185 FHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVV 236
Cdd:cd05529    66 PVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRL 117
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
 82-128 1.60e-07

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 48.80  E-value: 1.60e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528881361   82 NDFYCWVCHREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPECEKI 128
Cdd:cd15625     1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHvpALLSFPVGEWVCTLCRNL 49
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 160-241 1.66e-07

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 50.41  E-value: 1.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  160 MKQPGTDAFQKPVPLEQH--PDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVI 237
Cdd:cd05506    13 MKHKWGWVFNAPVDVVALglPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELL 92


                  ....
gi 528881361  238 KICE 241
Cdd:cd05506    93 KIFE 96
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 168-223 2.13e-07

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 50.10  E-value: 2.13e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 528881361  168 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 223
Cdd:cd05513    22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 85-125 2.89e-07

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


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 48.03  E-value: 2.89e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   85 YCWVCHREGQ---VLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15543     1 PCRKCGLSDHpewILLCDRCDAGYHTACLRppLMIIPDGNWFCPPC 46
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 143-268 3.25e-07

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 54.04  E-value: 3.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  143 MLTIEQLSYLLKFAIQKMKQ---PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNC 219
Cdd:COG5076   141 ELLYADNKAIAKFKKQLFLRdgrFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNC 220

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 528881361  220 IIYNGGNHKLTQIAKVVIKICEHEMNEIevcPECYLAACQKRDNWFCEP 268
Cdd:COG5076   221 KLYNGPDSSVYVDAKELEKYFLKLIEEI---PEEMLELSIKPGREEREE 266
zf-MYND pfam01753
MYND finger;
950-984 3.59e-07

MYND finger;


Pssm-ID: 460312  Cd Length: 39  Bit Score: 47.41  E-value: 3.59e-07
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 528881361   950 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 984
Cdd:pfam01753    1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 86-125 4.66e-07

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


Pssm-ID: 277004  Cd Length: 44  Bit Score: 47.30  E-value: 4.66e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   86 CWVC---HREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15529     2 CTKCgdpHDEDKMMFCDQCDRGYHTFCVGLRSIPDGRWICPLC 44
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 168-223 6.59e-07

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 48.52  E-value: 6.59e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 528881361  168 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 223
Cdd:cd05503    21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFN 76
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 168-234 6.76e-07

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 48.81  E-value: 6.76e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528881361  168 FQKPVPLEQH--PDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 234
Cdd:cd05498    24 FYKPVDPEALglHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMAR 92
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 151-223 6.87e-07

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 48.60  E-value: 6.87e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528881361  151 YLLKFAIQKMKQPgTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 223
Cdd:cd05518    11 YVLEYREGSGRRL-CDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
 85-128 6.90e-07

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 46.96  E-value: 6.90e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPECEKI 128
Cdd:cd15624     1 WCAVCQNGGDLLCCEKCPKVFHLTCHvpTLLSFPSGDWICTFCRDI 46
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 85-125 1.12e-06

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


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 46.42  E-value: 1.12e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15524     1 HCAACKRGGNLQPCGTCPRAYHLDCLDppLKTAPKGVWVCPKC 43
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 85-123 2.25e-06

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277131  Cd Length: 43  Bit Score: 45.34  E-value: 2.25e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCEL--CPRVYHAKCLRLTSEPEGDWFCP 123
Cdd:cd15661     1 YCFQCGDGGELVMCDKkdCPKAYHLLCLNLTQPPYGKWECP 41
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
 85-125 2.83e-06

PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 276980 [Multi-domain]  Cd Length: 45  Bit Score: 44.98  E-value: 2.83e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   85 YCwVCHRE--GQVLCCE--LCPRV-YHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15505     1 YC-ICNQVsyGEMVACDnpNCPIEwFHFECVGLTAKPKGKWYCPEC 45
PWWP_AtATX3-like cd20143
PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like ...
 275-347 3.36e-06

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also called protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also called protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also called 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 family of ATX1 and ATX2. They are multi-domain containing protein that consists of an N-terminal PWWP domain, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438971 [Multi-domain]  Cd Length: 100  Bit Score: 46.59  E-value: 3.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  275 LVWAKLKGFPFWPAK-----------ALRDKDGQVDARFFG---QHDRAWVPINNCYLMSKEIP-FSVKKTK-----SIF 334
Cdd:cd20143     5 LVWAKVGTHPFWPARvvepaeqaeevRRRCVPGSLCVYFFGpggSRDYGWVRRSMIFPFTDDLArFQTQKIKnkkrpQEF 84

                          90
                  ....*....|....
gi 528881361  335 NSAMQE-MEVYVEN 347
Cdd:cd20143    85 QEALEEaKLADAGF 98
PWWP_ZCWPW2 cd20146
PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ...
 275-340 3.63e-06

PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ZCWPW2 is a histone H3K4me3 reader. In addition to the PWWP domain, ZCWPW2 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438974  Cd Length: 113  Bit Score: 46.91  E-value: 3.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  275 LVWAKLKGFPFWPA----------KALRDKDGQVD---ARFFGQ-HDRAWVPI-------NNCYLMSKEIPFSVKKTKSI 333
Cdd:cd20146    14 LVWAKMTGYPRWPAiltpdpicgeYVDYDEDGEVEkyhVEFLGKpHSHAWISAksvepynSNTKTPKCKTKKSKKRKKSY 93


                  ....*..
gi 528881361  334 fNSAMQE 340
Cdd:cd20146    94 -ESALEE 99
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 168-247 3.66e-06

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 46.90  E-value: 3.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  168 FQKPVPLEQhPDYAEYIFHPMDLCTLEKNAKKK---MYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIKICEHEM 244
Cdd:cd05502    25 FHEPVSPSV-PNYYKIIKTPMDLSLIRKKLQPKspqHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQL 103


                  ...
gi 528881361  245 NEI 247
Cdd:cd05502   104 KEI 106
PWWP_AtATX1-like cd20142
PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like ...
 275-344 4.39e-06

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like proteins ATX1, ATX2, and similar proteins; This family includes A. thaliana ATX1 and ATX2, which 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 called 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 called protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438970 [Multi-domain]  Cd Length: 97  Bit Score: 46.19  E-value: 4.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  275 LVWAKLKGFPFWPA--------------KALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEI--PFSVKKTKSIFNSAM 338
Cdd:cd20142     5 VVWAKVKGYPMWPAlvideehaercgleANRPGKKGTVPVQFFGTYEVARLNPKKVVGFSKGLdlKYHSKCKAPVFRQAL 84


                  ....*.
gi 528881361  339 QEMEVY 344
Cdd:cd20142    85 EEAERY 90
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 168-234 5.49e-06

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 45.99  E-value: 5.49e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528881361  168 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN-GGNHKLTQIAK 234
Cdd:cd05505    21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYeNGSYVLSCMRK 88
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
24-128 6.67e-06

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 49.17  E-value: 6.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   24 STRSKDPGSAER-TAQKRKFPSPPHSSNGHSPQDTSTSPIKKKK---KPGLLNSNNKEQDGR-------NDFYCWvCHRE 92
Cdd:COG5034   151 SQGSRHTKLKKRkNIHNLKRRSPELSSKREVSFTLESPSVPDTAtrvKEGNNGGSTKSRGVSsednsegEELYCF-CQQV 229

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 528881361   93 --GQVLCC--ELCPRV-YHAKCLRLTSEPEGDWFCPECEKI 128
Cdd:COG5034   230 syGQMVACdnANCKREwFHLECVGLKEPPKGKWYCPECKKA 270
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 86-125 7.10e-06

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


Pssm-ID: 277098  Cd Length: 46  Bit Score: 43.96  E-value: 7.10e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528881361   86 CWVCHREGQ---VLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15628     2 CKVCRKKGEddkLILCDECNQAFHLFCLRpaLYEVPDGEWMCPAC 46
PWWP_MSH6 cd05837
PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called ...
 275-315 8.17e-06

PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called G/T mismatch-binding protein (GTBP or GTMBP), MutS protein homolog 6, or MutS-alpha 160 kDa subunit (p160), is a mismatch repair protein homologous to bacterial MutS. It is a component of the post-replicative DNA mismatch repair system (MMR). It heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, it forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. MSH6 contains a PWWP domain, but its role in MSH6 remains unclear. MSH6 orthologs found in Saccharomyces cerevisiae, Caenorhabditis elegans, and Arabidopsis thaliana lack the PWWP domain. PWWP domains typically recognize DNA and histone methylated lysines.


Pssm-ID: 438962  Cd Length: 103  Bit Score: 45.74  E-value: 8.17e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528881361  275 LVWAKLKGFPFWPA----------KALRDKDGQVDARFFGQ-HDRAWVPINN 315
Cdd:cd05837     6 LVWAKLEGYPWWPSlvcnhpttgfHKKFGKKGEVHVQFFDDpPSRAWVKAKN 57
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 86-125 8.70e-06

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


Pssm-ID: 277019  Cd Length: 46  Bit Score: 43.94  E-value: 8.70e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528881361   86 CWVCHREG---QVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15544     2 CKVCRKKGdpdNMILCDGCDKAFHLYCLRpaLREVPSGDWFCPAC 46
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 167-224 1.13e-05

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 45.35  E-value: 1.13e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  167 AFQKPVPLE--QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 224
Cdd:cd05499    23 PFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNP 82
PHD5_NSD2 cd15660
PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
 85-123 1.30e-05

PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger.


Pssm-ID: 277130  Cd Length: 43  Bit Score: 43.38  E-value: 1.30e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   85 YCWVCHREGQVLCCE--LCPRVYHAKCLRLTSEPEGDWFCP 123
Cdd:cd15660     1 ECFRCGDGGQLVLCDrkSCTKAYHLSCLGLTKRPFGKWECP 41
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 85-125 1.35e-05

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


Pssm-ID: 277011  Cd Length: 46  Bit Score: 43.17  E-value: 1.35e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   85 YCWVCH---REGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15536     1 YCEVCGrsdREDRLLLCDGCDAGYHMECLTppLDEVPIEEWFCPEC 46
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 86-125 3.15e-05

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


Pssm-ID: 277099  Cd Length: 47  Bit Score: 42.15  E-value: 3.15e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   86 CWVChREGQ----VLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15629     2 CLVC-RKGDndeyLLLCDGCDRGCHMYCHRpkMLQVPEGDWFCPNC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 86-125 7.51e-05

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


Pssm-ID: 276990  Cd Length: 46  Bit Score: 41.22  E-value: 7.51e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528881361   86 CWVCHR---EGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15515     2 CQVCGRgddEDKLLLCDGCDDSYHTFCLipPLPDIPPGDWRCPKC 46
PWWP_HULK cd20147
PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family ...
 275-342 7.64e-05

PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family includes HUA2-like proteins 1-3 (HULK1-3), which are probable transcription factors that act with partial redundancy with each other. They may play diverse and essential roles in the control of plant development, physiology and flowering time. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438975 [Multi-domain]  Cd Length: 92  Bit Score: 42.48  E-value: 7.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  275 LVWAKLKGFPFWPAKALRDKD-------GQVDARFFGQHDRAWVPINNCYLMSKEIPFSV------KKTKSIFNSAMQEM 341
Cdd:cd20147     3 LVLAKVKGFPAWPAQVSEPEDwgsapdpKKVFVHFFGTQQIGFCNPGELSEFTEEIKQSLlartlkKKKGSDFSRAVKEI 82


                  .
gi 528881361  342 E 342
Cdd:cd20147    83 C 83
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 147-226 9.03e-05

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 46.34  E-value: 9.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  147 EQLSYLLKFAIQKmkQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGN 226
Cdd:COG5076   265 EERESVLITNSQA--HVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEV 342
PWWP_PSIP cd20151
PWWP domain found in PC4 and SFRS1-interacting protein (PSIP); PSIP, also called ...
 272-352 1.03e-04

PWWP domain found in PC4 and SFRS1-interacting protein (PSIP); PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438979 [Multi-domain]  Cd Length: 88  Bit Score: 42.28  E-value: 1.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  272 PHPLVWAKLKGFPFWPAKALRDKDGQVDAR-------FFGQHDRAwvpinncYLMSKEI-PFSVKKTK-------SIFNS 336
Cdd:cd20151     3 PGDLIFAKMKGYPHWPARVDEVPDGAVKPPtnklpifFFGTHETA-------FLGPKDIfPYSENKEKygkpnkrKGFNE 75

                          90
                  ....*....|....*.
gi 528881361  337 AMQEMEvyvENIRRKF 352
Cdd:cd20151    76 GLWEID---NNPKVKF 88
PHD1_NSD1_2 cd15648
PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; ...
 86-125 1.10e-04

PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). Both NSD1 and NSD2 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). In addition, NSD2 harbors a high mobility group (HMG) box. The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the first PHD finger.


Pssm-ID: 277118  Cd Length: 43  Bit Score: 40.53  E-value: 1.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   86 CWVCHREGQVLCCE-LCPRVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15648     2 CQVCEKPGELLLCEgQCCGAFHLDCIGLSEMPSGKFICDEC 42
PHD2_KDM5B cd15607
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 88-125 1.19e-04

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


Pssm-ID: 277080  Cd Length: 44  Bit Score: 40.59  E-value: 1.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 528881361   88 VCHRE--GQVLCCELCPRVYHAKCLRLTSEPEGD--WFCPEC 125
Cdd:cd15607     3 VCQKApmAPMIQCELCRDAFHSGCVTAPSDPQGPqaWLCPQC 44
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 85-125 1.45e-04

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


Pssm-ID: 277100  Cd Length: 49  Bit Score: 40.34  E-value: 1.45e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   85 YCWVCHR---EGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15630     2 YCQICRKgdnEELLLLCDGCDKGCHTYCHRpkITTIPEGDWFCPAC 47
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
 86-125 1.55e-04

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.


Pssm-ID: 277096  Cd Length: 42  Bit Score: 40.10  E-value: 1.55e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528881361   86 CWVCHREGQVLCCELCPRVYHAKCLRLTSEPE-GDWFCPEC 125
Cdd:cd15626     2 CEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQrSPWSCTFC 42
ATP-synt_Fo_b cd06503
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ...
 867-946 2.13e-04

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.


Pssm-ID: 349951 [Multi-domain]  Cd Length: 132  Bit Score: 42.42  E-value: 2.13e-04
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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  867 ASADVAADIAKYTSKIRRLRIEIEKLqwlhqqeLSEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 946
Cdd:cd06503    45 AKEEAEELLAEYEEKLAEARAEAQEI-------IEEARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELRK 117
PHD3_NSD cd15566
PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 85-110 2.27e-04

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: 39.72  E-value: 2.27e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 528881361   85 YCWVCHRE-----GQVLCCELCPRVYHAKCL 110
Cdd:cd15566     1 TCATCEASgdgssGKLVRCIRCPRAYHAGCI 31
PWWP_DNMT3 cd05835
PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family ...
 275-311 2.28e-04

PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family includes DNMT3A and DNMT3B, which are required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Members of this family contains a PWWP domain that is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalie) syndrome , a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA.


Pssm-ID: 438960 [Multi-domain]  Cd Length: 89  Bit Score: 41.09  E-value: 2.28e-04
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gi 528881361  275 LVWAKLKGFPFWPAKALRDKDGQVDARFFGQHdraWV 311
Cdd:cd05835     5 LVWAKLKGSPWWPGIVVSHKDCGQKPPAEGSV---WV 38
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 86-125 3.19e-04

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


Pssm-ID: 277002  Cd Length: 46  Bit Score: 39.28  E-value: 3.19e-04
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gi 528881361   86 CWVCHREGQ---VLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15527     2 CSVCQDSGNadnLLFCDACDKGFHMECHdpPLTRMPKGKWVCQIC 46
AtpF COG0711
FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ...
 865-946 3.32e-04

FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase


Pssm-ID: 440475 [Multi-domain]  Cd Length: 152  Bit Score: 42.08  E-value: 3.32e-04
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gi 528881361  865 ATASADVAADIAKYTSKIRRLRIEIEKLqwlhqqeLSEMKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDET 944
Cdd:COG0711    44 ERAKEEAEAALAEYEEKLAEARAEAAEI-------IAEARKEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAEL 116


                  ..
gi 528881361  945 KK 946
Cdd:COG0711   117 RA 118
PWWP_NSD_rpt1 cd20144
first PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 275-329 3.67e-04

first PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein family consists of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1 that are critical in maintaining the chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and play nonredundant 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, through 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 (C5HCH). This model corresponds to the first PWWP domain. This family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438972  Cd Length: 114  Bit Score: 41.15  E-value: 3.67e-04
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gi 528881361  275 LVWAKLKGFPFWPA------------KALRDKDG---QVDARFFGqhD---RAWVPINNCylmskeIPFSVKK 329
Cdd:cd20144     4 LVWAKVSGHPWWPCmvtydpesglytKIKGSGGRtyrQYHVQFFG--DngeRGWVSEKSL------MPFEGKE 68
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 97-125 3.82e-04

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 39.45  E-value: 3.82e-04
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gi 528881361   97 CCELCPRVYHAKCLRLTSEP---EGDWFCPEC 125
Cdd:cd15517    18 QCDGCDKWFHQFCLGLSNERyadEDKFKCPNC 49
PHD_ING1_2 cd15584
PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic ...
 85-125 4.06e-04

PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, belongs to the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277059 [Multi-domain]  Cd Length: 45  Bit Score: 38.97  E-value: 4.06e-04
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gi 528881361   85 YCwVCHR--EGQVLCC--ELCP-RVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15584     1 YC-LCNQvsYGEMIGCdnDECPiEWFHFSCVGLTHKPKGKWYCPKC 45
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
 85-125 4.74e-04

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 38.97  E-value: 4.74e-04
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gi 528881361   85 YCwVCHR--EGQVLCC--ELCP-RVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15585     1 YC-ICNQvsYGEMVGCdnDDCPiEWFHYGCVGLTEAPKGKWYCPQC 45
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 86-125 4.83e-04

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


Pssm-ID: 277076  Cd Length: 46  Bit Score: 38.78  E-value: 4.83e-04
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gi 528881361   86 CWVC---HREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15603     2 CLVCgsgNDEDRLLLCDGCDDSYHTFCLipPLHDVPKGDWRCPKC 46
PWWP_HDGFL2 cd20149
PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2); HDGFL2, also ...
 272-342 5.07e-04

PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2); HDGFL2, also called HDGF-related protein 2 (HRP-2), or Hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438977 [Multi-domain]  Cd Length: 84  Bit Score: 39.89  E-value: 5.07e-04
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gi 528881361  272 PHPLVWAKLKGFPFWPAKALRDKDGQVDAR-------FFGQHDRAWVPINNCYLMSK-EIPFSVKKTKSIFNSAMQEME 342
Cdd:cd20149     3 PGDLVFAKMKGYPHWPARIDDIADGAVKPPpnkypifFFGTHETAFLGPKDLFPYDKyKDKYGKPNKRKGFNEGLWEIQ 81
PHD_ING4_5 cd15586
PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed ...
 85-125 5.31e-04

PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed p29ING4, and ING5, also termed p28ING5, belong to the inhibitor of growth (ING) family of type II tumor suppressors. ING4 acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). ING5 is a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. Both ING4 and ING5 contain an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger. They associate with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further direct the MOZ/MORF and HBO1 complexes to chromatin.


Pssm-ID: 277061 [Multi-domain]  Cd Length: 45  Bit Score: 38.71  E-value: 5.31e-04
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gi 528881361   85 YCwVCHR--EGQVLCCEL--CP-RVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15586     1 YC-LCHQvsYGEMIGCDNpdCPiEWFHFACVGLTTKPKGKWFCPRC 45
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 86-125 5.32e-04

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


Pssm-ID: 277078  Cd Length: 46  Bit Score: 38.97  E-value: 5.32e-04
                          10        20        30        40
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gi 528881361   86 CWVCHR---EGQVLCCELCPRVYHAKCLR--LTSEPEGDWFCPEC 125
Cdd:cd15605     2 CHTCGRgdgEESMLLCDGCDDSYHTFCLLppLSEVPKGDWRCPKC 46
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 86-125 5.32e-04

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


Pssm-ID: 277000  Cd Length: 47  Bit Score: 38.89  E-value: 5.32e-04
                          10        20        30        40
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gi 528881361   86 CWVC----HREGQVLCCElCPRVYHAKCLR--LTSEPEGD-WFCPEC 125
Cdd:cd15525     2 CHVCggkqDPEKQLLCDE-CDMAYHLYCLDppLTSLPDDDeWYCPDC 47
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 86-125 5.42e-04

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


Pssm-ID: 277075  Cd Length: 49  Bit Score: 38.78  E-value: 5.42e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528881361   86 CWVCHR---EGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15602     2 CLFCGRgnnEDKLLLCDGCDDSYHTFCLipPLPDVPKGDWRCPKC 46
PWWP_HDGF cd20148
PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility ...
 272-334 5.59e-04

PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438976 [Multi-domain]  Cd Length: 87  Bit Score: 40.01  E-value: 5.59e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  272 PHPLVWAKLKGFPFWPAK-------ALRDKDGQVDARFFGQHDRAwvpinncYLMSKEIpFSVKKTKSIF 334
Cdd:cd20148     3 CGDLVFAKMKGYPHWPARidempeaAVKSTANKYQVFFFGTHETA-------FLGPKDL-FPYEESKEKF 64
PHD_ING5 cd15685
PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one ...
 85-125 8.44e-04

PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. In addition, ING5 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING5 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277155 [Multi-domain]  Cd Length: 49  Bit Score: 38.49  E-value: 8.44e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   85 YCwVCHR--EGQVLCCEL--CP-RVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15685     2 YC-LCHQvsYGEMIGCDNpdCPiEWFHFACVDLTTKPKGKWFCPRC 46
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 85-125 8.73e-04

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 38.04  E-value: 8.73e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528881361   85 YCWVCHRE----GQVLCCElCPRVYHAKCLRLTSEP--EGDWFCPEC 125
Cdd:cd15522     1 ICPICKKPddgsPMIGCDE-CDDWYHWECVGITDEPpeEDDWFCPKC 46
PRK05759 PRK05759
F0F1 ATP synthase subunit B; Validated
 863-947 9.92e-04

F0F1 ATP synthase subunit B; Validated


Pssm-ID: 180240 [Multi-domain]  Cd Length: 156  Bit Score: 40.91  E-value: 9.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  863 PIATASADVAADIAKYTSKIRRLRIEIEKLQWLHQQELSEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKK 931
Cdd:PRK05759   28 PIMKALEERQKKIADGLAAAERAKKELELAQAKYEAQLAEARAeaaeiieqakkRAAQIIEEAKAEAEAEAARIKAQAQA 107

                          90
                  ....*....|....*.
gi 528881361  932 QLELEKQQAVDETKKK 947
Cdd:PRK05759  108 EIEQERKRAREELRKQ 123
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 95-125 1.03e-03

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 38.18  E-value: 1.03e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 528881361   95 VLCCELCPRVYHAKCLR--LTSE----PEGDWFCPEC 125
Cdd:cd15504    17 LLCDGGCNRAYHQKCLEppLLTEdippEDEGWLCPLC 53
ADDz_ATRX cd11726
ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...
 76-127 1.48e-03

ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a PHD-like zinc finger domain of ATRX, which belongs to the SNF2 family of chromatin remodeling proteins. ATRX is a large chromatin-associated nuclear protein with two domains, ADDz_ATRX at the N-terminus, followed by a C-terminal ATPase/helicase domain. The ADDz_ATRX domain recognizes a specific methylated histone, and this interaction is required for heterochromatin localization of the ATRX protein. Missense mutations in either of the two ATRX domains lead to the X-linked alpha-thalassemia and mental retardation syndrome; however the mutations in the ADDz_ATRX domain produce a more severe disease phenotype that may also relate to disturbing unknown functions or interaction sites of this domain. The ADDz domain is also present in chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3); it is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277252 [Multi-domain]  Cd Length: 102  Bit Score: 39.21  E-value: 1.48e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528881361   76 KEQDGRnDFYC-WvCHREGQVLCCELCPRVYHAKCLR-------LTSEPEGD-WFCPECEK 127
Cdd:cd11726    44 KDEDGS-DEYCrW-CGQGGDLICCDFCPNVFCKKCIKrnlgraeLSRIEESDkWKCFVCDP 102
PHD1_NSD3 cd15649
PHD finger 1 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 86-125 1.96e-03

PHD finger 1 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the first PHD finger.


Pssm-ID: 277119  Cd Length: 44  Bit Score: 37.05  E-value: 1.96e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 528881361   86 CWVCHREGQ--VLCCELCPRVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15649     2 CQVCESFGEslVTCEGECCGLFHLECLGLTSLPDEKFICQEC 43
PHD1_NSD cd15564
PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 85-126 2.32e-03

PHD finger 1 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 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 first PHD finger.


Pssm-ID: 277039  Cd Length: 43  Bit Score: 36.93  E-value: 2.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528881361   85 YCWVCHREGQVLCCE-LCPRVYHAKCLRLTSEPEGDWFCPECE 126
Cdd:cd15564     1 VCQICEKPGKLLTCEgPCCGHFHLDCLGLSEQPDEPFKCDECT 43
TFIIF_alpha pfam05793
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation ...
 597-755 2.41e-03

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II.


Pssm-ID: 310411 [Multi-domain]  Cd Length: 528  Bit Score: 41.86  E-value: 2.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361   597 YISDDEQkSKNEPEDTEDkegcqmdkepsavKKKPKPTNPVEIkeelkstspasEKADPGAVKDKASPEPEKDFSEKAKP 676
Cdd:pfam05793  285 YISDSSA-SGNDPEERED-------------KLSPEEPAKGEI-----------EQSDDSEESEEEKNEEEGKLSKKGKK 339

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528881361   677 SPHPiKDKLKGKDETDSptvhlglDSDSESELVIDLGEDHSGREGRKNKKEPKEPSPKQDVVGKTPPSttvGSHSPPET 755
Cdd:pfam05793  340 AKKL-KGKKNGKDKSES-------SDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPVDSGPSSPGNS---GPARPSPE 407
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
 89-125 2.61e-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: 37.21  E-value: 2.61e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 528881361   89 CHREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15572    12 CQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRC 48
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 622-829 3.42e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 41.45  E-value: 3.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  622 KEPSAVKK-KPKPTNPVEikeeLKSTSPASEKADPGAVKDKASPEPEKDFSEKAKP--SPHPIKDKLKGKDETDSPTVHL 698
Cdd:PLN03209  331 KESDAADGpKPVPTKPVT----PEAPSPPIEEEPPQPKAVVPRPLSPYTAYEDLKPptSPIPTPPSSSPASSKSVDAVAK 406

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528881361  699 GLDSD--SESELVIDLGEDHSGREGRK------------NKKEPKEPSPKQDVVGKTPPSTTVGSHSPPETPVLTRSS-- 762
Cdd:PLN03209  407 PAEPDvvPSPGSASNVPEVEPAQVEAKktrplspyaryeDLKPPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAATda 486

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528881361  763 AQTSAAGATATTSTSSTVTVTAPAPAATGSPVKKQRPLLPKETAPAVQRVVWNSSTVQQKEITQSPS 829
Cdd:PLN03209  487 AAPPPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTALADEQHHAQPKPR 553
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 86-125 3.53e-03

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


Pssm-ID: 277077  Cd Length: 46  Bit Score: 36.36  E-value: 3.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528881361   86 CWVCHR---EGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15604     2 CRMCSRgdeDDKLLLCDGCDDNYHTFCLlpPLPEPPKGIWRCPKC 46
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 86-125 3.82e-03

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 36.32  E-value: 3.82e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 528881361   86 CWVCHREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHlpALQEVPGEDWKCLLC 43
PHD_ING2 cd15683
PHD finger found in inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of ...
 93-125 4.73e-03

PHD finger found in inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. ING2 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277153 [Multi-domain]  Cd Length: 49  Bit Score: 36.15  E-value: 4.73e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 528881361   93 GQVLCC--ELCP-RVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15683    11 GEMIGCdnEQCPiEWFHFSCVGLTYKPKGKWYCPKC 46
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 168-223 4.75e-03

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 38.21  E-value: 4.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 528881361  168 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 223
Cdd:cd05496    26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81
PWWP_MBD5 cd20141
PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is ...
 275-314 4.87e-03

PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is a methyl-CpG-binding protein that binds to heterochromatin. It does not interact with either methylated or unmethylated DNA. MBD5 acts as a transcriptional regulator responsible for 2q23.1 deletion syndrome. It belongs to the MBD family proteins, which play central roles in transcriptional regulation and development. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438969  Cd Length: 92  Bit Score: 37.30  E-value: 4.87e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361  275 LVWAKLKGFPFWPAKALR------DKDGQVDARFFGQHDRAWVPIN 314
Cdd:cd20141     6 LVWGQIRGFPSWPGKLVSendvgkTNEGKVWVSWFGDHSFGQVEPD 51
PWWP_PWWP2 cd20140
PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family ...
 276-289 6.45e-03

PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family includes PWWP2A and its paralog PWWP2B. PWWP2A is a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. It is also required for proper mitosis progression. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438968  Cd Length: 92  Bit Score: 37.24  E-value: 6.45e-03
                          10
                  ....*....|....
gi 528881361  276 VWAKLKGFPFWPAK 289
Cdd:cd20140    10 VWGKIHGFPWWPGR 23
PHD_ING4 cd15684
PHD finger found in inhibitor of growth protein 4 (ING4); ING4, also termed p29ING4, is one ...
 85-127 6.76e-03

PHD finger found in inhibitor of growth protein 4 (ING4); ING4, also termed p29ING4, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). In addition, ING4 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING4 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277154 [Multi-domain]  Cd Length: 48  Bit Score: 35.82  E-value: 6.76e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528881361   85 YCwVCHR--EGQVLCCE---LCPRVYHAKCLRLTSEPEGDWFCPECEK 127
Cdd:cd15684     2 YC-LCHQvsYGEMIGCDnpdCSIEWFHFACVGLTTKPRGKWFCPRCSQ 48
PHD_ING1 cd15682
PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and ...
 93-125 7.74e-03

PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for the cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind phosphorylate ING1 and further regulates its activity. ING1 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277152 [Multi-domain]  Cd Length: 49  Bit Score: 35.75  E-value: 7.74e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 528881361   93 GQVLCC--ELCP-RVYHAKCLRLTSEPEGDWFCPEC 125
Cdd:cd15682    11 GEMIGCdnDECPiEWFHFSCVGLNHKPKGKWYCPKC 46
PHD_AL_plant cd15613
PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed ...
 96-125 8.09e-03

PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed nuclear proteins existing only in plants. They are involved in chromatin regulation by binding to tri- and dimethylated histone H3 at lysine 4 (H3K4me3/2), the active histone markers, through their plant homeodomain (PHD) fingers.


Pssm-ID: 277085  Cd Length: 51  Bit Score: 35.55  E-value: 8.09e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 528881361   96 LCCELCPRVYHAKCLRLT---SEPEGDWFCPEC 125
Cdd:cd15613    16 ICCDVCEKWYHGKCVKITpakAEHIKQYKCPSC 48
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 86-123 8.29e-03

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


Pssm-ID: 277009  Cd Length: 47  Bit Score: 35.40  E-value: 8.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 528881361   86 CWVCHREGQV---LCCELCPRVYHAKCLR--LTSEPEGD-WFCP 123
Cdd:cd15534     2 CFKCNRSCRVaplIQCDYCPLLFHLDCLDppLTHPPATGrWMCP 45
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 85-125 8.96e-03

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


Pssm-ID: 277005  Cd Length: 46  Bit Score: 35.44  E-value: 8.96e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528881361   85 YCWVC---HREGQVLCCELCPRVYHAKCL--RLTSEPEGDWFCPEC 125
Cdd:cd15530     1 SCSLCgtsENDDQLLFCDDCDRGYHMYCLspPMSEPPEGSWSCHLC 46
PWWP_ZCWPW1 cd20145
PWWP domain found in zinc finger CW-type PWWP domain protein 1 (ZCWPW1) and similar proteins; ...
 275-288 9.62e-03

PWWP domain found in zinc finger CW-type PWWP domain protein 1 (ZCWPW1) and similar proteins; ZCWPW1 is a histone H3K4me3 reader. It is associated with late-onset Alzheimer's disease (LOAD). In addition to the PWWP domain, ZCWPW1 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438973  Cd Length: 115  Bit Score: 37.14  E-value: 9.62e-03
                          10
                  ....*....|....
gi 528881361  275 LVWAKLKGFPFWPA 288
Cdd:cd20145    11 LVWAKMPGYPWWPA 24
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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