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Conserved domains on  [gi|17541484|ref|NP_501475|]
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Protein lin-49 [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
COG5141 super family cl34917
PHD zinc finger-containing protein [General function prediction only];
133-548 9.50e-58

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


The actual alignment was detected with superfamily member COG5141:

Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 211.77  E-value: 9.50e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  133 VDYSVDEFDMSWMSIMNAKRTKlglEIFSVAIYEHWVDRLEK----MCIWKPKEFHKLKdENGEELDDVCNICLDGDTSN 208
Cdd:COG5141  131 VIYDLDEYDTMWLRYLNESAID---ENVSEEAFEIIVTRLEKewffFEHGLPDKHVEPI-EPSDEFDDICTKCTSTHNEN 206
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  209 CNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRCGISPAGRVNCVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTI 288
Cdd:COG5141  207 SNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGHVICAMFNPELSFGHLL 286
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  289 FMENVQNVEKALHDRRALSCLLCKNrqnaRMGACIQCSETKCTASFHVTCARDSGLVMRINETEDG---QVNRFVWCPKH 365
Cdd:COG5141  287 SKDPIDNIASVSSSRWKLGCLICKE----FGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNGisyCIDHEPLCRKH 362
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  366 APP--------LTDADREMRQLMLRNARRENER----------KGPMISMPT-------LMKSMISTICVERPFSDYSEI 420
Cdd:COG5141  363 YPLgygrmnglRYFGYEKLRYKNPPTAIPRKVRaarpratlfmKLCWKQPPAtpsvlsrVEACDLKEKDRQDLPVNIFDI 442
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  421 IYFWYEKRLNRLGAPL---------LKNFTQGASKSRRLLPKSTICGQLKNVETCEMKKQVNAVKESLA-SGLEIFDMIV 490
Cdd:COG5141  443 CKYWEMKRKSEIGGPLvilpdivysLKTLEDWMSKRRMREVAKALQDQYQLLTLVESTAKRQLLKCQLSnLRKKFLNLNY 522
                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17541484  491 RREER--KKDMLNSYIRMFErgFKPTELLCQE-----VIEALKTIDAGKVFAEPVELVGYTDIIE 548
Cdd:COG5141  523 FPAQRllQVKIIDLDVDGLF--NMPLDNELKRqvfsyQIGSISSLEKKLEPIWDVDVIQCIDDME 585
BROMO smart00297
bromo domain;
508-610 2.07e-18

bromo domain;


:

Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 81.56  E-value: 2.07e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484     508 ERGFKPTELLCQEVIEALKTIDAGKVFAEPVELV---GYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCAT 584
Cdd:smart00297    2 PKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKeapDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNART 81
                            90       100
                    ....*....|....*....|....*.
gi 17541484     585 FNKGNRVYIKYGNTYRKDSTPILEIA 610
Cdd:smart00297   82 YNGPDSEVYKDAKKLEKFFEKKLREL 107
TFIIF_alpha super family cl37738
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation ...
673-869 1.60e-04

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: 45.71  E-value: 1.60e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    673 DVQELDTDDSKDSSALSEiPGSSKKSSRKRGIQDTKMEEDEEIKPSTSGTNAVASVPLLSSSRESKNKSKSS-DADVSSP 751
Cdd:pfam05793  318 DSEESEEEKNEEEGKLSK-KGKKAKKLKGKKNGKDKSESSDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPvDSGPSSP 396
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    752 KSSWLGSPSTSQ---NLRRRVQGFSGNESSPKVHKKLSTDNPSNSNLRqttltnffgtnpKTQQQVTFADMTATPSGSG- 827
Cdd:pfam05793  397 GNSGPARPSPESgstSSKRKAAAEVSKSPASVPAKKLKTENGPKSSSG------------KSTPQTFSGSKSSSNAADGg 464
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 17541484    828 -NKNVSQRSLFDTPSTSK--ASSF----TSLSSTRPSTRSTSIIPTINK 869
Cdd:pfam05793  465 vTEEAVRRYLMRKPMTTKelLKKFkakkTGLSSEETVNVLAQILKRINP 513
 
Name Accession Description Interval E-value
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
133-548 9.50e-58

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


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 211.77  E-value: 9.50e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  133 VDYSVDEFDMSWMSIMNAKRTKlglEIFSVAIYEHWVDRLEK----MCIWKPKEFHKLKdENGEELDDVCNICLDGDTSN 208
Cdd:COG5141  131 VIYDLDEYDTMWLRYLNESAID---ENVSEEAFEIIVTRLEKewffFEHGLPDKHVEPI-EPSDEFDDICTKCTSTHNEN 206
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  209 CNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRCGISPAGRVNCVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTI 288
Cdd:COG5141  207 SNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGHVICAMFNPELSFGHLL 286
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  289 FMENVQNVEKALHDRRALSCLLCKNrqnaRMGACIQCSETKCTASFHVTCARDSGLVMRINETEDG---QVNRFVWCPKH 365
Cdd:COG5141  287 SKDPIDNIASVSSSRWKLGCLICKE----FGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNGisyCIDHEPLCRKH 362
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  366 APP--------LTDADREMRQLMLRNARRENER----------KGPMISMPT-------LMKSMISTICVERPFSDYSEI 420
Cdd:COG5141  363 YPLgygrmnglRYFGYEKLRYKNPPTAIPRKVRaarpratlfmKLCWKQPPAtpsvlsrVEACDLKEKDRQDLPVNIFDI 442
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  421 IYFWYEKRLNRLGAPL---------LKNFTQGASKSRRLLPKSTICGQLKNVETCEMKKQVNAVKESLA-SGLEIFDMIV 490
Cdd:COG5141  443 CKYWEMKRKSEIGGPLvilpdivysLKTLEDWMSKRRMREVAKALQDQYQLLTLVESTAKRQLLKCQLSnLRKKFLNLNY 522
                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17541484  491 RREER--KKDMLNSYIRMFErgFKPTELLCQE-----VIEALKTIDAGKVFAEPVELVGYTDIIE 548
Cdd:COG5141  523 FPAQRllQVKIIDLDVDGLF--NMPLDNELKRqvfsyQIGSISSLEKKLEPIWDVDVIQCIDDME 585
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
250-365 8.04e-45

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 157.12  E-value: 8.04e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    250 VNCVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVqNVEKALHDRRALSCLLCKNrqnaRMGACIQCSETK 329
Cdd:pfam13832    1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPI-DVSRIPPERWKLKCVFCKK----RSGACIQCSKGR 75
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 17541484    330 CTASFHVTCARDSGLVMRINETEdgQVNRFVWCPKH 365
Cdd:pfam13832   76 CTTAFHVTCAQAAGVYMEPEDWP--NVVVIAYCQKH 109
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
252-365 3.44e-42

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 277140  Cd Length: 116  Bit Score: 149.79  E-value: 3.44e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKNrqnaRMGACIQCSETKCT 331
Cdd:cd15670    1 CVLCPNKGGAFKQTDDGRWAHVVCALWIPEVSFANTVFLEPIDGIQNIPKARWKLTCYICKK----RMGACIQCHKKNCY 76
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 17541484  332 ASFHVTCARDSGLVMRI------NETEDGQVNRFVWCPKH 365
Cdd:cd15670   77 TAFHVTCAQQAGLYMKIepvkdpGNGTSDSVRKEAYCDKH 116
BROMO smart00297
bromo domain;
508-610 2.07e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 81.56  E-value: 2.07e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484     508 ERGFKPTELLCQEVIEALKTIDAGKVFAEPVELV---GYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCAT 584
Cdd:smart00297    2 PKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKeapDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNART 81
                            90       100
                    ....*....|....*....|....*.
gi 17541484     585 FNKGNRVYIKYGNTYRKDSTPILEIA 610
Cdd:smart00297   82 YNGPDSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
518-595 9.33e-18

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: 78.89  E-value: 9.33e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    518 CQEVIEALKTIDAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGNRVYIK 594
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVdpdEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   .
gi 17541484    595 Y 595
Cdd:pfam00439   81 A 81
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
518-613 1.13e-16

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: 76.26  E-value: 1.13e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  518 CQEVIEALKTI--DAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNkgnrvy 592
Cdd:cd04369    5 LRSLLDALKKLkrDLSEPFLEPVdpkEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYN------ 78
                         90       100
                 ....*....|....*....|.
gi 17541484  593 iKYGNTYRKDSTPILEIAEKE 613
Cdd:cd04369   79 -GPGSPIYKDAKKLEKLFEKL 98
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
197-242 2.46e-07

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 47.98  E-value: 2.46e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 17541484     197 VCNICldGDTSNCNQIVYCDRCNLSVHQDCYGIP---FIPEGCLECRRC 242
Cdd:smart00249    1 YCSVC--GKPDDGGELLQCDGCDRWYHQTCLGPPlleEEPDGKWYCPKC 47
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
467-656 1.79e-05

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 48.26  E-value: 1.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  467 EMKKQVNAVKESLA-----SGLEIFDMIVRREERKKDMLNSYIRMfergfkPTELLCQEVIEALKTIDAGKVFAEPVELV 541
Cdd:COG5076   97 ESLRFDEIVFLAIEsvtpeSGLGSLLMAHLKTSVKKRKTPKIEDE------LLYADNKAIAKFKKQLFLRDGRFLSSIFL 170
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  542 GYTD---------IIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGNRVYIKYGNTYRKDSTPILEIAEK 612
Cdd:COG5076  171 GLPSkreypdyyeIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPE 250
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 17541484  613 EEVERLALKTDEKFMTQLLNGVMVEYNG---WAQSRNeVAKEIPPPT 656
Cdd:COG5076  251 EMLELSIKPGREEREERESVLITNSQAHvgaWPFLRP-VSDEEVPDY 296
TFIIF_alpha pfam05793
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation ...
673-869 1.60e-04

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: 45.71  E-value: 1.60e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    673 DVQELDTDDSKDSSALSEiPGSSKKSSRKRGIQDTKMEEDEEIKPSTSGTNAVASVPLLSSSRESKNKSKSS-DADVSSP 751
Cdd:pfam05793  318 DSEESEEEKNEEEGKLSK-KGKKAKKLKGKKNGKDKSESSDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPvDSGPSSP 396
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    752 KSSWLGSPSTSQ---NLRRRVQGFSGNESSPKVHKKLSTDNPSNSNLRqttltnffgtnpKTQQQVTFADMTATPSGSG- 827
Cdd:pfam05793  397 GNSGPARPSPESgstSSKRKAAAEVSKSPASVPAKKLKTENGPKSSSG------------KSTPQTFSGSKSSSNAADGg 464
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 17541484    828 -NKNVSQRSLFDTPSTSK--ASSF----TSLSSTRPSTRSTSIIPTINK 869
Cdd:pfam05793  465 vTEEAVRRYLMRKPMTTKelLKKFkakkTGLSSEETVNVLAQILKRINP 513
 
Name Accession Description Interval E-value
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
133-548 9.50e-58

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


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 211.77  E-value: 9.50e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  133 VDYSVDEFDMSWMSIMNAKRTKlglEIFSVAIYEHWVDRLEK----MCIWKPKEFHKLKdENGEELDDVCNICLDGDTSN 208
Cdd:COG5141  131 VIYDLDEYDTMWLRYLNESAID---ENVSEEAFEIIVTRLEKewffFEHGLPDKHVEPI-EPSDEFDDICTKCTSTHNEN 206
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  209 CNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRCGISPAGRVNCVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTI 288
Cdd:COG5141  207 SNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGHVICAMFNPELSFGHLL 286
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  289 FMENVQNVEKALHDRRALSCLLCKNrqnaRMGACIQCSETKCTASFHVTCARDSGLVMRINETEDG---QVNRFVWCPKH 365
Cdd:COG5141  287 SKDPIDNIASVSSSRWKLGCLICKE----FGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNGisyCIDHEPLCRKH 362
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  366 APP--------LTDADREMRQLMLRNARRENER----------KGPMISMPT-------LMKSMISTICVERPFSDYSEI 420
Cdd:COG5141  363 YPLgygrmnglRYFGYEKLRYKNPPTAIPRKVRaarpratlfmKLCWKQPPAtpsvlsrVEACDLKEKDRQDLPVNIFDI 442
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  421 IYFWYEKRLNRLGAPL---------LKNFTQGASKSRRLLPKSTICGQLKNVETCEMKKQVNAVKESLA-SGLEIFDMIV 490
Cdd:COG5141  443 CKYWEMKRKSEIGGPLvilpdivysLKTLEDWMSKRRMREVAKALQDQYQLLTLVESTAKRQLLKCQLSnLRKKFLNLNY 522
                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17541484  491 RREER--KKDMLNSYIRMFErgFKPTELLCQE-----VIEALKTIDAGKVFAEPVELVGYTDIIE 548
Cdd:COG5141  523 FPAQRllQVKIIDLDVDGLF--NMPLDNELKRqvfsyQIGSISSLEKKLEPIWDVDVIQCIDDME 585
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
250-365 8.04e-45

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 157.12  E-value: 8.04e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    250 VNCVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVqNVEKALHDRRALSCLLCKNrqnaRMGACIQCSETK 329
Cdd:pfam13832    1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPI-DVSRIPPERWKLKCVFCKK----RSGACIQCSKGR 75
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 17541484    330 CTASFHVTCARDSGLVMRINETEdgQVNRFVWCPKH 365
Cdd:pfam13832   76 CTTAFHVTCAQAAGVYMEPEDWP--NVVVIAYCQKH 109
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
252-365 3.44e-42

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 277140  Cd Length: 116  Bit Score: 149.79  E-value: 3.44e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKNrqnaRMGACIQCSETKCT 331
Cdd:cd15670    1 CVLCPNKGGAFKQTDDGRWAHVVCALWIPEVSFANTVFLEPIDGIQNIPKARWKLTCYICKK----RMGACIQCHKKNCY 76
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 17541484  332 ASFHVTCARDSGLVMRI------NETEDGQVNRFVWCPKH 365
Cdd:cd15670   77 TAFHVTCAQQAGLYMKIepvkdpGNGTSDSVRKEAYCDKH 116
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
252-365 2.03e-34

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


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 127.32  E-value: 2.03e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQV------DQKRWVHVLCVIWVDETHFGNTIFMEnVQNVEKALHDRRALSCLLCKNRqnarMGACIQC 325
Cdd:cd15571    1 CALCPRSGGALKGGgalkttSDGLWVHVVCALWSPEVYFDDGTLLE-VEGVSKIPKRRKKLKCSICGKR----GGACIQC 75
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 17541484  326 SETKCTASFHVTCARDSGLVMrinETEDGQVNRFVWCPKH 365
Cdd:cd15571   76 SYPGCPRSFHVSCAIRAGCLF---EFEDGPGNFVVYCPKH 112
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
252-368 1.30e-31

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling.


Pssm-ID: 277171 [Multi-domain]  Cd Length: 121  Bit Score: 119.80  E-value: 1.30e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKNRQnarMGACIQCSETKCT 331
Cdd:cd15701    1 CALCPNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIDSIEHIPPARWKLTCYICKQRG---SGACIQCHKANCY 77
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 17541484  332 ASFHVTCARDSGLVMRINETEDGQVN-------RFVWCPKHAPP 368
Cdd:cd15701   78 TAFHVTCAQQAGLYMKMEPVRETGANgtsfsvrKTAYCDIHTPP 121
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
252-365 1.23e-30

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 116.77  E-value: 1.23e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQV-DQKRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKNRqnarMGACIQCSETKC 330
Cdd:cd15671    1 CVLCPKKGGAMKSTkSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKEK----TGACIQCSVKSC 76
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 17541484  331 TASFHVTCARDSGLVMR-INETEDGQVNRFVWCPKH 365
Cdd:cd15671   77 KTAFHVTCAFQHGLEMKtILEDEDDEVKFKSYCPKH 112
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
252-357 3.32e-29

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277173 [Multi-domain]  Cd Length: 118  Bit Score: 112.84  E-value: 3.32e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKnrQNARmGACIQCSETKCT 331
Cdd:cd15703    1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEGVNNIPPARWKLTCYLCK--QKGR-GAAIQCHKVNCY 77
                         90       100
                 ....*....|....*....|....*.
gi 17541484  332 ASFHVTCARDSGLVMRINETEDGQVN 357
Cdd:cd15703   78 TAFHVTCAQRAGLFMKIEPVRETGLN 103
ePHD_BRPF2 cd15702
Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and ...
252-365 1.25e-28

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


Pssm-ID: 277172  Cd Length: 118  Bit Score: 111.29  E-value: 1.25e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKNRQnarMGACIQCSETKCT 331
Cdd:cd15702    1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKG---VGACIQCHKANCY 77
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 17541484  332 ASFHVTCARDSGLVMR---INETEDGQ----VNRFVWCPKH 365
Cdd:cd15702   78 TAFHVTCAQKAGLYMKmepVKEVTGGGttfsVRKTAYCDAH 118
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
252-365 7.13e-26

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain.


Pssm-ID: 277132  Cd Length: 115  Bit Score: 103.32  E-value: 7.13e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKnrqnARMGACIQCSETKCT 331
Cdd:cd15662    1 CCLCPVVGGALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDGINAISKERWELSCTICK----QRYGACIQCSNNSCR 76
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 17541484  332 ASFHVTCARDSGLVMRInETEDGQVN------RFVWCPKH 365
Cdd:cd15662   77 VAYHPLCARAAGLCMEV-ADEGGEDPgdqglrLLSYCPRH 115
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
252-365 1.24e-25

Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2 proteins. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 277145 [Multi-domain]  Cd Length: 112  Bit Score: 102.44  E-value: 1.24e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVqNVEKALHDRRALSCLLCKNR--QNARMGACIQCSETK 329
Cdd:cd15675    1 CCLCCLRGGALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPI-DISKIPPARLKLKCIYCSKItkSMSHMGACIQCSTGK 79
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 17541484  330 CTASFHVTCARDSGLVMrinETEDGQVNRFVWCPKH 365
Cdd:cd15675   80 CTTSFHVTCAHAAGVQM---EPDDWPYPVYVTCTKH 112
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
272-365 7.72e-24

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


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 96.24  E-value: 7.72e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    272 HVLCVIWVDETHFGNTIF-MENVQNVEKALHDRRALSCLLCKNRqnarMGACIQCSETKCTASFHVTCARDSGLVMRINE 350
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSmGFPIEDIEKIPKRRWKLKCYLCKKK----GGACIQCSKKNCRRAFHVTCALEAGLLMQFDE 76
                           90
                   ....*....|....*
gi 17541484    351 TEdgqVNRFVWCPKH 365
Cdd:pfam13771   77 DN---GTFKSYCKKH 88
ePHD_PHF14 cd15674
Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended ...
252-365 1.45e-23

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


Pssm-ID: 277144  Cd Length: 114  Bit Score: 96.68  E-value: 1.45e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENV--QNVEKALHDRRAlsCLLCKNRQNARMGACIQCSETK 329
Cdd:cd15674    1 CELCPNRGGIFKETDTGRWVHLVCALYTPGVAFGDVDKLSPVtlTEMNYSKWGARE--CSLCEDPRFARTGVCISCDAGM 78
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 17541484  330 CTASFHVTCARDSGLVMRINETEDGQVNRFVWCPKH 365
Cdd:cd15674   79 CKSYFHVTCAQREGLLSEATDEEDIADPFYAYCKQH 114
ePHD_JADE2 cd15705
Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant ...
252-365 8.33e-23

Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-2. Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277175  Cd Length: 111  Bit Score: 94.39  E-value: 8.33e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQ-KRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKNRQnarmGACIQCSETKC 330
Cdd:cd15705    1 CLLCPKRGGALKPTRSgTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECT----GTCIQCSMPSC 76
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 17541484  331 TASFHVTCARDSGLVMRINETEDGQVNRFVWCPKH 365
Cdd:cd15705   77 ITAFHVTCAFDHGLEMRTTLADNDEVKFKSFCLEH 111
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
252-365 8.56e-23

Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2C. JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277185  Cd Length: 110  Bit Score: 94.25  E-value: 8.56e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVqNVEKALHDRRALSCLLCKNRQNARMGACIQCSETKCT 331
Cdd:cd15715    1 CCLCNLRGGALKQTSDDKWAHVMCAVALPEVRFINVVERTPI-DISRIPLQRLKLKCIFCRNRIKRVSGACIQCSYGRCP 79
                         90       100       110
                 ....*....|....*....|....*....|....
gi 17541484  332 ASFHVTCARDSGLVMrinETEDGQVNRFVWCPKH 365
Cdd:cd15715   80 ASFHVTCAHAAGVLM---EPDDWPYVVFITCFRH 110
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
252-365 1.01e-22

Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277184  Cd Length: 110  Bit Score: 93.85  E-value: 1.01e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVqNVEKALHDRRALSCLLCKNRQNARMGACIQCSETKCT 331
Cdd:cd15714    1 CCLCNLRGGALQMTTDERWVHVICAIAVPEARFLNVIERHPV-DVSAIPEQRWKLKCVYCRKRMKKVSGACIQCSYDHCS 79
                         90       100       110
                 ....*....|....*....|....*....|....
gi 17541484  332 ASFHVTCARDSGLVMrinETEDGQVNRFVWCPKH 365
Cdd:cd15714   80 TSFHVTCAHAAGVVM---EPDDWPYVVSITCFKH 110
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
252-365 1.66e-22

Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Drosophila melanogaster RNO. RNO is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating the transcription of key EGFR/Ras pathway regulators in the Drosophila eye. RNO contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277177 [Multi-domain]  Cd Length: 113  Bit Score: 93.43  E-value: 1.66e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQ-KRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKNRqnarMGACIQCSETKC 330
Cdd:cd15707    1 CILCPNKGGAMKSTRSgTKWAHVSCALWIPEVSIGCVEKMEPITKISSIPASRWALICVLCRER----TGACIQCSVKTC 76
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 17541484  331 TASFHVTCARDSGLVMR--INETEDGQVNRFVWCPKH 365
Cdd:cd15707   77 KTAYHVTCGFQHGLEMKtiLDEESEDGVKLRSYCQKH 113
ePHD_JADE1 cd15704
Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant ...
252-366 3.08e-22

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


Pssm-ID: 277174  Cd Length: 118  Bit Score: 92.83  E-value: 3.08e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQ-KRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCknrqNARMGACIQCSETKC 330
Cdd:cd15704    4 CLLCPKKGGAMKPTRSgTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLC----NEKVGASIQCSVKNC 79
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 17541484  331 TASFHVTCARDSGLVMRINETEDGQVNRFVWCPKHA 366
Cdd:cd15704   80 RTAFHVTCAFDRGLEMKTILAENDEVKFKSYCPKHS 115
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
197-242 3.22e-22

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 90.37  E-value: 3.22e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRC 242
Cdd:cd15492    1 VCDVCLDGESEDDNEIVFCDGCNVAVHQSCYGIPLIPEGDWFCRKC 46
ePHD_JADE3 cd15706
Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...
252-365 5.48e-21

Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-3. Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is close related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277176  Cd Length: 111  Bit Score: 89.01  E-value: 5.48e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQ-KRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKnrqnARMGACIQCSETKC 330
Cdd:cd15706    1 CLLCPKTGGAMKATRTgTKWAHVSCALWIPEVSIACPERMEPITKVSHIPPSRWALVCSLCK----LKTGACIQCSVKSC 76
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 17541484  331 TASFHVTCARDSGLVMRINETEDGQVNRFVWCPKH 365
Cdd:cd15706   77 ITAFHVTCAFEHSLEMKTILDEGDEVKFKSYCLKH 111
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
195-247 7.53e-21

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: 86.90  E-value: 7.53e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17541484  195 DDVCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRCGISPA 247
Cdd:cd15572    1 DAVCCICLDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRCLQSPS 53
ePHD_AF10_like cd15672
Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) ...
252-365 9.08e-20

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


Pssm-ID: 277142  Cd Length: 116  Bit Score: 85.59  E-value: 9.08e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQnVEKALHDRRALSCLLC---KNRQNARMGACIQCSET 328
Cdd:cd15672    1 CELCPHKDGALKRTDNGGWAHVVCALYIPEVRFGNVATMEPII-LQDVPQDRFNKTCYICeeqGRESKASTGACMQCNKS 79
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 17541484  329 KCTASFHVTCARDSGLVMRINETEDGQVNRFVWCPKH 365
Cdd:cd15672   80 GCKQSFHVTCAQMAGLLCEEAGNYSDNVKYCGYCSYH 116
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
195-247 1.57e-19

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 83.14  E-value: 1.57e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17541484  195 DDVCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRCGISPA 247
Cdd:cd15677    1 DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRS 53
ePHD_AF10 cd15708
Extended PHD finger found in protein AF-10 and similar proteins; The extended plant ...
248-374 1.65e-19

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


Pssm-ID: 277178  Cd Length: 129  Bit Score: 85.51  E-value: 1.65e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  248 GRVNCVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQnVEKALHDRRALSCLLCKNR---QNARMGACIQ 324
Cdd:cd15708    1 ARVRCELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVSTMEPIV-LQSVPHERYNKTCYICDEQgreSKAATGACMT 79
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 17541484  325 CSETKCTASFHVTCARDSGLVMRINETEDGQVNRFVWCPKHAPPLTDADR 374
Cdd:cd15708   80 CNKHGCRQAFHVTCAQLAGLLCEEEGNGADNVQYCGYCKYHYSKLKKSKR 129
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
252-365 5.52e-19

Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277183  Cd Length: 110  Bit Score: 83.48  E-value: 5.52e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNtIFMENVQNVEKALHDRRALSCLLCKNRQNARMGACIQCSETKCT 331
Cdd:cd15713    1 CCLCSLRGGALQRANDDKWVHVMCAVAVLEARFVN-IAERSPVDVSKIPLQRFKLKCIFCKKRRKRTAGCCVQCSHGRCP 79
                         90       100       110
                 ....*....|....*....|....*....|....
gi 17541484  332 ASFHVTCARDSGLVMrinETEDGQVNRFVWCPKH 365
Cdd:cd15713   80 TSFHASCAQAAGVMM---QPDDWPFVVFITCFRH 110
BROMO smart00297
bromo domain;
508-610 2.07e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 81.56  E-value: 2.07e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484     508 ERGFKPTELLCQEVIEALKTIDAGKVFAEPVELV---GYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCAT 584
Cdd:smart00297    2 PKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKeapDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNART 81
                            90       100
                    ....*....|....*....|....*.
gi 17541484     585 FNKGNRVYIKYGNTYRKDSTPILEIA 610
Cdd:smart00297   82 YNGPDSEVYKDAKKLEKFFEKKLREL 107
ePHD_AF17 cd15709
Extended PHD finger found in protein AF-17 and similar proteins; The extended plant ...
248-365 6.83e-18

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


Pssm-ID: 277179  Cd Length: 125  Bit Score: 80.88  E-value: 6.83e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  248 GRVNCVLCPSTTGAFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQnVEKALHDRRALSCLLCKNR---QNARMGACIQ 324
Cdd:cd15709    1 ARVRCELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVLTMEPIV-LQYVPHDRFNKTCYICEEQgreSKAASGACMT 79
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 17541484  325 CSETKCTASFHVTCARDSGLVMRINETEDGQVNRFVWCPKH 365
Cdd:cd15709   80 CNRHGCRQAFHVTCAQMAGLLCEEEVLEVDNVKYCGYCKYH 120
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
518-595 9.33e-18

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: 78.89  E-value: 9.33e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    518 CQEVIEALKTIDAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGNRVYIK 594
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVdpdEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   .
gi 17541484    595 Y 595
Cdd:pfam00439   81 A 81
PHD_BRPF1 cd15676
PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar ...
195-250 4.44e-17

PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a 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. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277146 [Multi-domain]  Cd Length: 62  Bit Score: 76.25  E-value: 4.44e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 17541484  195 DDVCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRCGISPAGRV 250
Cdd:cd15676    7 DAVCCICNDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRCLQSPSRAV 62
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
518-613 1.13e-16

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: 76.26  E-value: 1.13e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  518 CQEVIEALKTI--DAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNkgnrvy 592
Cdd:cd04369    5 LRSLLDALKKLkrDLSEPFLEPVdpkEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYN------ 78
                         90       100
                 ....*....|....*....|.
gi 17541484  593 iKYGNTYRKDSTPILEIAEKE 613
Cdd:cd04369   79 -GPGSPIYKDAKKLEKLFEKL 98
PHD_BRPF3 cd15678
PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar ...
195-247 6.54e-16

PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277148 [Multi-domain]  Cd Length: 55  Bit Score: 72.74  E-value: 6.54e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17541484  195 DDVCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRCGISPA 247
Cdd:cd15678    1 DAFCCVCLDDECHNSNVILFCDICNLAVHQECYGVPYIPEGQWLCRCCLQSPS 53
PHD_JADE cd15573
PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family ...
197-242 4.06e-13

PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277048 [Multi-domain]  Cd Length: 46  Bit Score: 64.35  E-value: 4.06e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRC 242
Cdd:cd15573    1 VCDVCRSPDSEEGNEMVFCDKCNICVHQACYGIQKIPEGSWLCRTC 46
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
534-598 6.56e-13

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: 65.65  E-value: 6.56e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17541484  534 FAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGNRVYIKYGNT 598
Cdd:cd05509   22 FLEPVdkeEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANK 89
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
513-607 1.53e-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: 64.73  E-value: 1.53e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  513 PTELLCQEVIEALKTIDAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGN 589
Cdd:cd05512    1 PLEVLLRKTLDQLQEKDTAEIFSEPVdlsEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD 80
                         90
                 ....*....|....*...
gi 17541484  590 RVYIKYGNTYRKDSTPIL 607
Cdd:cd05512   81 TIFYRAAVRLRDQGGAIL 98
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
252-365 1.63e-12

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


Pssm-ID: 277136  Cd Length: 105  Bit Score: 64.63  E-value: 1.63e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLC-------PSTTGAFKQVDQKRWVHVLCVIW---VDETHFGNTIfmenvqNVEKALHDRRALSCLLCKnrqnaRMGA 321
Cdd:cd15666    1 CVLCggegdgdTDGPGRLLNLDVDKWVHLNCALWsyeVYETQNGALM------NVEEALRRALTTTCSHCG-----RTGA 69
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 17541484  322 CIQCSETKCTASFHVTCA-RDSGLVMRinetedgqvNRFVWCPKH 365
Cdd:cd15666   70 TVPCFKPRCANVYHLPCAiKDGCMFFK---------DKTMLCPSH 105
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
197-242 5.12e-12

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


Pssm-ID: 277149 [Multi-domain]  Cd Length: 46  Bit Score: 61.24  E-value: 5.12e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRC 242
Cdd:cd15679    1 VCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPEGSWLCRTC 46
PHD_JADE3 cd15681
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ...
197-242 9.68e-12

PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277151 [Multi-domain]  Cd Length: 50  Bit Score: 60.76  E-value: 9.68e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRC 242
Cdd:cd15681    1 ICDVCRSPDSEEGNDMVFCDKCNICVHQACYGILKVPEGSWLCRTC 46
ePHD_Snt2p_like cd15667
Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) ...
252-342 1.60e-11

Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Snt2p. Sntp2 is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical PHD fingers, a non-canonical ePHD finger, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain.


Pssm-ID: 277137  Cd Length: 141  Bit Score: 63.17  E-value: 1.60e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTG---------------AFKQVDQKRWVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKnrqn 316
Cdd:cd15667    1 CSLCNAKESnyelakkqsprtrpdALKCTSNGTWCHVLCALFNEDIKFGNSKSLQPILNTESVLLKGSRQKCEICK---- 76
                         90       100
                 ....*....|....*....|....*.
gi 17541484  317 ARMGACIQCSEtkCTASFHVTCARDS 342
Cdd:cd15667   77 VSGGGLVKCEV--CDDRFHVSCAQDT 100
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
252-365 1.70e-11

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


Pssm-ID: 277134  Cd Length: 105  Bit Score: 61.65  E-value: 1.70e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLC-------PSTTGAFKQVDQKRWVHVLCVIWVDEThfgntiFMEN---VQNVEKALHDRRALSCLLCKNRqnarmGA 321
Cdd:cd15664    1 CALCgvygddePNDAGRLLYCGQDEWVHINCALWSAEV------FEEDdgsLQNVHSAVSRGRMMKCELCGKP-----GA 69
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 17541484  322 CIQCSETKCTASFHVTCARDSGLVMrinetedgQVNRFVWCPKH 365
Cdd:cd15664   70 TVGCCLKSCPANYHFMCARKAECVF--------QDDKKVFCPAH 105
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
518-586 2.41e-11

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: 61.18  E-value: 2.41e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17541484  518 CQEVIEALKTIDAGKVFAEPVELVG-----YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN 586
Cdd:cd05500    9 LLSSIRSLKRLKDARPFLVPVDPVKlniphYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
518-592 4.46e-11

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: 60.38  E-value: 4.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  518 CQEVIEAL---KTIDAGKVFAEPVELV-----GYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN-KG 588
Cdd:cd05499    5 CEEVLKELmkpKHSAYNWPFLDPVDPValnipNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNpEG 84

                 ....
gi 17541484  589 NRVY 592
Cdd:cd05499   85 TDVY 88
ePHD_ATX3_4_5_like cd15663
Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The ...
252-365 6.19e-11

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


Pssm-ID: 277133  Cd Length: 112  Bit Score: 60.61  E-value: 6.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPSTTGAFKQVDQKR-WVHVLCVIWVDETHFGNTIFMENVQNVEKALHDRRALSCLLCKNRQnarmGACIQCSetKC 330
Cdd:cd15663    1 CCLCPVKGGALKPTDVEGlWVHVTCAWFRPEVCFKNEEKMEPAVGLLRIPLSTFLKACVICKQIH----GSCTQCC--KC 74
                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 17541484  331 TASFHVTCARDSGLVMRINETEDGQVNR---FVWCPKH 365
Cdd:cd15663   75 ATYFHAMCASRAGYHMELHCLEKNGVQItrmVSYCSFH 112
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
209-242 7.11e-11

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


Pssm-ID: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 57.74  E-value: 7.11e-11
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 17541484    209 CNQIVYCDRCNLSVHQDCYGIPFIPEG-CLECRRC 242
Cdd:pfam13831    1 TSPLVYCSKCSVQVHASCYGVPPIPDGdGWKCRRC 35
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
197-242 1.85e-10

PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277150 [Multi-domain]  Cd Length: 46  Bit Score: 56.94  E-value: 1.85e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRC 242
Cdd:cd15680    1 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 46
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
517-601 2.50e-10

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: 58.15  E-value: 2.50e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  517 LCQEVIEALKTIDAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGNRVYI 593
Cdd:cd05503    4 LCETILDEMEAHEDAWPFLEPVntkLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVG 83

                 ....*...
gi 17541484  594 KYGNTYRK 601
Cdd:cd05503   84 RAGHNMRK 91
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
252-365 3.04e-10

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


Pssm-ID: 277164  Cd Length: 105  Bit Score: 58.13  E-value: 3.04e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLC-------PSTTGAFKQVDQKRWVHVLCVIWVDEthfgntIFMEN---VQNVEKALHDRRALSCLLCKnrqnaRMGA 321
Cdd:cd15694    1 CALClkygdadSKDAGRLLYIGQNEWTHVNCAIWSAE------VFEENdgsLKNVHAAVARGRQMRCEHCQ-----KIGA 69
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 17541484  322 CIQCSETKCTASFHVTCARDSGLVMrinetedgQVNRFVWCPKH 365
Cdd:cd15694   70 TVGCCLSACLSNFHFMCARASRCCF--------QDDKKVFCQKH 105
PHD_AF10_AF17 cd15574
PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. ...
198-242 2.42e-09

PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukemia) oncogene in leukemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as a Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277049 [Multi-domain]  Cd Length: 48  Bit Score: 53.67  E-value: 2.42e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 17541484  198 CNICLDGDTSNCNQIVYCD--RCNLSVHQDCYGIPFIPEGCLECRRC 242
Cdd:cd15574    2 CCVCSDERGWAENPLVYCDghGCNVAVHQACYGIVQVPTGPWFCRKC 48
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
270-365 1.41e-08

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


Pssm-ID: 277138  Cd Length: 103  Bit Score: 53.47  E-value: 1.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  270 WVHVLCVIWVDETHFGNTifmeNVQNVEKALHDRRALSCLLCKNRqnarmGACIQCSETKCTASFHVTCARDSGLVMrin 349
Cdd:cd15668   24 WVHEDCAVWAPGVYLVGG----KLYGLEEAVWVAKQSVCSSCQQT-----GATIGCLHKGCKAKYHYPCAVESGCQL--- 91
                         90
                 ....*....|....*.
gi 17541484  350 eTEDgqvNRFVWCPKH 365
Cdd:cd15668   92 -DEE---NFSLLCPKH 103
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
270-365 2.43e-08

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


Pssm-ID: 277166  Cd Length: 90  Bit Score: 52.25  E-value: 2.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  270 WVHVLCVIWVDETHFGNTifmENVQNVEKALHDRRALSCLLCKnrqnaRMGACIQCSETKCTASFHVTCARDSGlvmrin 349
Cdd:cd15696   10 WAHLRCAEWSLGVCQGEE---QLLVNVDKAVVSGSTERCAFCK-----HLGATIKCCEEKCTQMYHYPCAAGAG------ 75
                         90
                 ....*....|....*.
gi 17541484  350 eTEDGQVNRFVWCPKH 365
Cdd:cd15696   76 -TFQDFSRRLLLCPTH 90
PHD_ATX3_4_5_like cd15495
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
198-242 3.10e-08

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


Pssm-ID: 276970 [Multi-domain]  Cd Length: 47  Bit Score: 50.84  E-value: 3.10e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 17541484  198 CNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFI-PEGCLECRRC 242
Cdd:cd15495    2 CAVCNEGEDDDNNPLITCNRCQISVHQKCYGIREVdPDGSWVCRAC 47
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
515-587 3.43e-08

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: 52.68  E-value: 3.43e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17541484  515 ELLCQEviealKTIDagkvFAEPV--ELVGYTDIIENPICL---KDMSEKAASGKYSTVAALSADVQLMLSNCATFNK 587
Cdd:cd05502   15 ELYCHE-----LSLP----FHEPVspSVPNYYKIIKTPMDLsliRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNE 83
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
518-593 8.44e-08

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: 51.18  E-value: 8.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  518 CQEVIEALKTIDAGKVFAEPVELVG-----YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN-KGNRV 591
Cdd:cd05506    5 CGTLLRKLMKHKWGWVFNAPVDVVAlglpdYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNpPGNDV 84

                 ..
gi 17541484  592 YI 593
Cdd:cd05506   85 HT 86
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
517-596 8.95e-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: 51.63  E-value: 8.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  517 LCQEVIEALKTIDAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN-KGNRVY 592
Cdd:cd05504   16 ALEQLLVEIVKHKDSWPFLRPVskiEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNpEHTSVY 95

                 ....
gi 17541484  593 iKYG 596
Cdd:cd05504   96 -KAG 98
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
197-242 9.79e-08

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


Pssm-ID: 276974  Cd Length: 53  Bit Score: 49.42  E-value: 9.79e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLE-----CRRC 242
Cdd:cd15499    1 TCSICGGAEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGdekwfCSRC 51
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
252-365 9.93e-08

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


Pssm-ID: 277163  Cd Length: 113  Bit Score: 51.54  E-value: 9.93e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLC-------PSTTGAFKQVDQKRWVHVLCVIWVDEthfgntIFMEN---VQNVEKALHDRRALSCLLCKnrqnaRMGA 321
Cdd:cd15693    3 CALClkygddsANDAGRLLYIGQNEWTHVNCALWSAE------VFEDDdgsLKNVHMAVIRGKQLRCEFCQ-----KPGA 71
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 17541484  322 CIQCSETKCTASFHVTCARDSGLVMrineTEDGQvnrfVWCPKH 365
Cdd:cd15693   72 TVGCCLTSCTSNYHFMCSRAKNCVF----LEDKK----VYCQRH 107
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
543-592 1.66e-07

Bromodomain, polybromo repeat II. 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: 99948  Cd Length: 103  Bit Score: 50.52  E-value: 1.66e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17541484  543 YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNK-GNRVY 592
Cdd:cd05517   39 YYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEpGSQVY 89
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
197-242 2.46e-07

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 47.98  E-value: 2.46e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 17541484     197 VCNICldGDTSNCNQIVYCDRCNLSVHQDCYGIP---FIPEGCLECRRC 242
Cdd:smart00249    1 YCSVC--GKPDDGGELLQCDGCDRWYHQTCLGPPlleEEPDGKWYCPKC 47
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
533-586 2.95e-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: 49.58  E-value: 2.95e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 17541484  533 VFAEPVELVG-----YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN 586
Cdd:cd05498   23 PFYKPVDPEAlglhdYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYN 81
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
197-242 4.15e-07

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 47.49  E-value: 4.15e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 17541484    197 VCNICLDGDTSNcnQIVYCDRCNLSVHQDCYGIPFIPEG-------CLECRRC 242
Cdd:pfam00628    1 YCAVCGKSDDGG--ELVQCDGCDDWFHLACLGPPLDPAEipsgewlCPECKPK 51
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
518-592 5.50e-07

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: 49.38  E-value: 5.50e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  518 CQEVIEALKTIDAGKVFAEPVELVGYTD---IIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATF--NKGNRVY 592
Cdd:cd05496   10 CKELVNLMWDCEDSEPFRQPVDLLKYPDyrdIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYtpNKRSRIY 89
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
197-242 1.36e-06

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


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 46.16  E-value: 1.36e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 17541484  197 VCNICLDGDTSNcNQIVYCDRCNLSVHQDCYGIP---FIPEGCLECRRC 242
Cdd:cd15489    1 SCIVCGKGGDLG-GELLQCDGCGKWFHADCLGPPlssFVPNGKWICPVC 48
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
520-630 1.69e-06

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: 47.64  E-value: 1.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  520 EVIEALKTIDAGKVFAEPVE---LVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGNRVYIkyg 596
Cdd:cd05511    7 EIVNELKNLPDSWPFHTPVNkkkVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYT--- 83
                         90       100       110
                 ....*....|....*....|....*....|....
gi 17541484  597 ntyrKDSTPILEIAEkeevERLALKTDEkfMTQL 630
Cdd:cd05511   84 ----KKAKEMLELAE----ELLAEREEK--LTQL 107
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
252-365 1.83e-06

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


Pssm-ID: 277135  Cd Length: 90  Bit Score: 46.93  E-value: 1.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCpsTTGAFkqvdqkrWVHVLCVIWvdetHFGNTIfMENVQ--NVEKALHdrRALS--CLLCKnrqnaRMGACIQCSE 327
Cdd:cd15665    1 CALC--NLGEV-------YAHHCCAAW----SEGVCQ-TEDGAleNVDKAVA--KALSqkCSFCL-----RYGASISCRM 59
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 17541484  328 TKCTASFHVTCARDSG--LVMRinetedgqvNRFVWCPKH 365
Cdd:cd15665   60 PSCSKSFHFPCAAAAGcfQDIK---------TLTLFCPEH 90
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
543-589 2.76e-06

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 46.85  E-value: 2.76e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 17541484  543 YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGN 589
Cdd:cd05522   40 YYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNEND 86
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
197-242 5.54e-06

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 44.31  E-value: 5.54e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGiPFIPEGCLE------CRRC 242
Cdd:cd15578    1 VCTVCQDGSSESPNEIVLCDKCGQGYHQLCHN-PKIDSSVLDpdvpwlCRQC 51
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
516-586 7.22e-06

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: 45.81  E-value: 7.22e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17541484  516 LLCQEVIEALKTIDAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN 586
Cdd:cd05528    6 LFLRDVLKRLASDKRFNAFTKPVdeeEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
252-365 7.34e-06

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


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 46.09  E-value: 7.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLC------PSTTGAFKQVDQKRwVHVLCVIwvdethFGNTIFM---ENV-------QNVEKALHDRRALSCLLCKNRq 315
Cdd:cd15669    1 CVLCgrsdddPDKYGEKLQKDGIC-AHYFCLL------FSSGLPQrgeDNEgiygflpEDIRKEVRRASRLRCFYCKKK- 72
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 17541484  316 narmGACIQCSETKCTASFHVTCARDSGLvmrinetedgqVNRFV-----WCPKH 365
Cdd:cd15669   73 ----GASIGCAVKGCRRSFHFPCGLENGC-----------VTQFFgeyrsFCWEH 112
PHD1_PHF14 cd15561
PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
197-229 8.02e-06

PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the first PHD finger.


Pssm-ID: 277036  Cd Length: 56  Bit Score: 43.97  E-value: 8.02e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGI 229
Cdd:cd15561    1 ICCVCLGDRSNDADEIIECDKCGISVHEGCYGV 33
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
198-242 9.50e-06

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: 43.39  E-value: 9.50e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 17541484  198 CNICLDGDTSNCnqivyCDRCNLSVHQDCYGIPFIPEGCLECRRC 242
Cdd:cd15567    2 CFICSEGGSLIC-----CESCPASFHPECLGLEPPPEGKFYCEDC 41
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
270-365 1.17e-05

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


Pssm-ID: 277170  Cd Length: 104  Bit Score: 45.25  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  270 WVHVLCVIWVDethfGNTIFMENVQNVEKALHDRRALSCLLCKnrqnaRMGACIQCSETKCTASFHVTCARDSGLVMrin 349
Cdd:cd15700   25 WVHEACAVWTT----GVYLVAGKLFGLQEAVQKAADAKCSSCQ-----GAGATVGCCHKGCTQSYHYICAVEAGCLF--- 92
                         90
                 ....*....|....*.
gi 17541484  350 eTEDgqvNRFVWCPKH 365
Cdd:cd15700   93 -EEE---NFSLRCPKH 104
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
543-592 1.19e-05

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: 45.13  E-value: 1.19e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17541484  543 YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN-KGNRVY 592
Cdd:cd05518   39 YYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNeEGSQVY 89
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
197-242 1.58e-05

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: 43.06  E-value: 1.58e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 17541484  197 VCNICldGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCLECRRC 242
Cdd:cd15529    1 TCTKC--GDPHDEDKMMFCDQCDRGYHTFCVGLRSIPDGRWICPLC 44
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
467-656 1.79e-05

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 48.26  E-value: 1.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  467 EMKKQVNAVKESLA-----SGLEIFDMIVRREERKKDMLNSYIRMfergfkPTELLCQEVIEALKTIDAGKVFAEPVELV 541
Cdd:COG5076   97 ESLRFDEIVFLAIEsvtpeSGLGSLLMAHLKTSVKKRKTPKIEDE------LLYADNKAIAKFKKQLFLRDGRFLSSIFL 170
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  542 GYTD---------IIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGNRVYIKYGNTYRKDSTPILEIAEK 612
Cdd:COG5076  171 GLPSkreypdyyeIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPE 250
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 17541484  613 EEVERLALKTDEKFMTQLLNGVMVEYNG---WAQSRNeVAKEIPPPT 656
Cdd:COG5076  251 EMLELSIKPGREEREERESVLITNSQAHvgaWPFLRP-VSDEEVPDY 296
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
270-365 2.26e-05

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


Pssm-ID: 277169  Cd Length: 103  Bit Score: 44.14  E-value: 2.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  270 WVHVLCVIWVDETHFGNTifmeNVQNVEKALHDRRALSCLLCKnrqnaRMGACIQCSETKCTASFHVTCARDSGLVMriN 349
Cdd:cd15699   24 WVHEGCILWANGIYLVCG----RLYGLQEALDIAREMKCSHCQ-----EAGATLGCYNKGCSFRYHYPCAIDADCLL--N 92
                         90
                 ....*....|....*.
gi 17541484  350 ETedgqvNRFVWCPKH 365
Cdd:cd15699   93 EE-----NFSVRCPKH 103
PHD2_Snt2p_like cd15498
PHD finger 2 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
197-229 2.48e-05

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


Pssm-ID: 276973  Cd Length: 55  Bit Score: 42.85  E-value: 2.48e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGI 229
Cdd:cd15498    1 KCSVCSEQFASNFNTSLSCYNCGLNVHASCYGI 33
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
265-339 3.10e-05

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


Pssm-ID: 277167  Cd Length: 105  Bit Score: 43.88  E-value: 3.10e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17541484  265 VDQKRWVHVLCVIW---VDETHFGNTIfmenvqNVEKALHDRRALSCLLCKnrqnaRMGACIQCSETKCTASFHVTCA 339
Cdd:cd15697   21 LDLDLWVHLNCALWsteVYETQAGALI------NVELALRRGLQMKCVFCH-----KTGATSGCHRLRCTNVYHFTCA 87
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
518-586 3.56e-05

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: 43.68  E-value: 3.56e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17541484  518 CQEVIEALKTIDAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN 586
Cdd:cd05505    5 CEEILSKILKYRFSWPFREPVtadEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
265-339 5.74e-05

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


Pssm-ID: 277168  Cd Length: 107  Bit Score: 43.12  E-value: 5.74e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17541484  265 VDQKRWVHVLCVIW---VDETHFGNTIfmenvqNVEKALHDRRALSCLLCKnrqnaRMGACIQCSETKCTASFHVTCA 339
Cdd:cd15698   21 LDLDLWVHLNCALWsteVYETQGGALM------NVEVALHRGLLTKCSLCQ-----KTGATNSCNRLRCPNVYHFACA 87
PHD1_PHF19 cd15579
PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ...
198-242 7.37e-05

PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. It binds trimethylated histone H3 Lys36 (H3K36me3) through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the first PHD finger.


Pssm-ID: 277054  Cd Length: 53  Bit Score: 41.40  E-value: 7.37e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17541484  198 CNICLDGDTSNCNQIVYCDRCNLSVHQDCYgIPFI---PEGCLE---CRRC 242
Cdd:cd15579    2 CNVCLGKSSGPLNEILICGKCGLGYHQQCH-IPVVdssDDPPLTpwfCRRC 51
TFIIF_alpha pfam05793
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); Transcription initiation ...
673-869 1.60e-04

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: 45.71  E-value: 1.60e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    673 DVQELDTDDSKDSSALSEiPGSSKKSSRKRGIQDTKMEEDEEIKPSTSGTNAVASVPLLSSSRESKNKSKSS-DADVSSP 751
Cdd:pfam05793  318 DSEESEEEKNEEEGKLSK-KGKKAKKLKGKKNGKDKSESSDGDDSDDSDIDDEDSVPLFTAKKKKEPKKEEPvDSGPSSP 396
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484    752 KSSWLGSPSTSQ---NLRRRVQGFSGNESSPKVHKKLSTDNPSNSNLRqttltnffgtnpKTQQQVTFADMTATPSGSG- 827
Cdd:pfam05793  397 GNSGPARPSPESgstSSKRKAAAEVSKSPASVPAKKLKTENGPKSSSG------------KSTPQTFSGSKSSSNAADGg 464
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 17541484    828 -NKNVSQRSLFDTPSTSK--ASSF----TSLSSTRPSTRSTSIIPTINK 869
Cdd:pfam05793  465 vTEEAVRRYLMRKPMTTKelLKKFkakkTGLSSEETVNVLAQILKRINP 513
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
539-586 1.65e-04

Bromodomain, polybromo repeat V. 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: 99946  Cd Length: 105  Bit Score: 41.91  E-value: 1.65e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 17541484  539 ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN 586
Cdd:cd05515   35 EYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYN 82
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
513-615 1.75e-04

Bromodomain, polybromo repeat I. 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: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 41.94  E-value: 1.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  513 PTELlCQEVIEALKTI--DAGKVFAEPVELV-------GYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNca 583
Cdd:cd05524    3 PIAV-CQELYDTIRNYksEDGRILCESFIRVpkrrnepEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINN-- 79
                         90       100       110
                 ....*....|....*....|....*....|....
gi 17541484  584 tfnkgNRVYIKYGNTYRKDSTPILE--IAEKEEV 615
Cdd:cd05524   80 -----AKAYYKPDSPEHKDACKLWElfLSARNEV 108
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
197-242 3.16e-04

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 39.34  E-value: 3.16e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYgIPFI-------PEGCLECRRC 242
Cdd:cd15502    1 VCIVCQRGHSPKSNRIVFCDGCNTPYHQLCH-DPSIddevvedPDAEWFCKKC 52
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
543-593 4.12e-04

Bromodomain, polybromo repeat III. 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: 99951  Cd Length: 103  Bit Score: 40.79  E-value: 4.12e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 17541484  543 YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN-KGNRVYI 593
Cdd:cd05520   39 YYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNvPNSRIYK 90
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
529-592 5.95e-04

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 40.49  E-value: 5.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17541484  529 DAGKVFAEPV-------ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN-KGNRVY 592
Cdd:cd05516   19 SDGRQLAEVFiqlpsrkELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNlEGSLIY 90
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
270-343 6.98e-04

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


Pssm-ID: 277165  Cd Length: 90  Bit Score: 39.90  E-value: 6.98e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17541484  270 WVHVLCVIWVD--ETHFGntifmENVQNVEKALHDRRALSCLLCKnrqnaRMGACIQCSETKCTASFHVTCARDSG 343
Cdd:cd15695   10 WVHHWCAAWSAgvKQHEG-----DGLIGVDKAVFSGISQKCEHCK-----RLGATIQCHAEGCPRFYHFPCAAASG 75
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
518-586 1.04e-03

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: 39.73  E-value: 1.04e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17541484  518 CQEVIEALKTI-DAGKVFAEPV---ELVGYTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN 586
Cdd:cd05510   12 LDKVLNELKTYtEHSTPFLTKVskrEAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN 84
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
308-365 1.18e-03

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 37.58  E-value: 1.18e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 17541484     308 CLLCKNRQNArmGACIQCSetKCTASFHVTCArdsglvmriNETEDGQVNRFVW-CPKH 365
Cdd:smart00249    2 CSVCGKPDDG--GELLQCD--GCDRWYHQTCL---------GPPLLEEEPDGKWyCPKC 47
PHD_ATX1_2_like cd15494
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
197-237 1.27e-03

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX1, ATX2, and similar proteins; The family includes A. thaliana ATX1 and ATX2, both of 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 termed 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. ATX1regulates 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 termed 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 Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276969  Cd Length: 47  Bit Score: 37.81  E-value: 1.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCYGIPFIPEGCL 237
Cdd:cd15494    1 KCSVCGEDEEYEDNLLLQCDKCRMMVHMRCYGVLEPPPGAL 41
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
252-365 1.38e-03

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


Pssm-ID: 277143  Cd Length: 116  Bit Score: 39.68  E-value: 1.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541484  252 CVLCPS-----TTGAFKQVDQKRWVHVLCVIW---VDETHFGNTIFME--NVQNVEKALHDRRALSCLLCKNRqnarmGA 321
Cdd:cd15673    1 CGFCKSgeenkETGGKLASGEKIAAHHNCMLFssgLVQYVSPNENDFGgfDIEDVKKEIKRGRKLKCNLCKKT-----GA 75
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 17541484  322 CIQCSETKCTASFHVTCARDSGLVMRINETedgQVNRFVWCPKH 365
Cdd:cd15673   76 TIGCDVKQCKKTYHYHCAKKDDAKIIERNS---QGIYRVYCKNH 116
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
534-594 1.58e-03

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: 39.63  E-value: 1.58e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17541484  534 FAEPVELVG----YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGNRVYIK 594
Cdd:cd05529   48 FEYPVDLRAwypdYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAK 112
C1 cd00029
protein kinase C conserved region 1 (C1 domain) superfamily; The C1 domain is a cysteine-rich ...
197-236 3.91e-03

protein kinase C conserved region 1 (C1 domain) superfamily; The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains. It contains the motif HX12CX2CXnCX2CX4HX2CX7C, where C and H are cysteine and histidine, respectively; X represents other residues; and n is either 13 or 14. C1 has a globular fold with two separate Zn(2+)-binding sites. It was originally discovered as lipid-binding modules in protein kinase C (PKC) isoforms. C1 domains that bind and respond to phorbol esters (PE) and diacylglycerol (DAG) are referred to as typical, and those that do not respond to PE and DAG are deemed atypical. A C1 domain may also be referred to as PKC or non-PKC C1, based on the parent protein's activity. Most C1 domain-containing non-PKC proteins act as lipid kinases and scaffolds, except PKD which acts as a protein kinase. PKC C1 domains play roles in membrane translocation and activation of the enzyme.


Pssm-ID: 410341  Cd Length: 50  Bit Score: 36.34  E-value: 3.91e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 17541484  197 VCNICLDGDTSNCNQIVYCDRCNLSVHQDCygIPFIPEGC 236
Cdd:cd00029   13 FCDVCGKLIWGLFKQGLKCSDCGLVCHKKC--LDKAPSPC 50
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
543-592 4.01e-03

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 37.70  E-value: 4.01e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17541484  543 YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFN-KGNRVY 592
Cdd:cd05519   39 YYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNqEGSIVY 89
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
543-597 4.27e-03

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 37.81  E-value: 4.27e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 17541484  543 YTDIIENPICLKDMSEKAASGKYSTVAALSADVQLMLSNCATFNKGN-RVYiKYGN 597
Cdd:cd05495   39 YFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTsRVY-KYCT 93
C1 smart00109
Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol ...
198-236 5.22e-03

Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.


Pssm-ID: 197519  Cd Length: 50  Bit Score: 35.91  E-value: 5.22e-03
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 17541484     198 CNICLDGDTSNCNQIVYCDRCNLSVHQDCygIPFIPEGC 236
Cdd:smart00109   14 CCVCRKSIWGSFKQGLRCSECKVKCHKKC--ADKVPKAC 50
 
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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