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Conserved domains on  [gi|1370457973|ref|XP_011518043|]
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transcription initiation factor TFIID subunit 3 isoform X1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
HFD_TAF3 cd22916
histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and ...
3-94 3.82e-52

histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and similar proteins; TAF3, also called TATA Binding Protein (TBP) associated factor 3, 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, or transcription initiation factor TFIID 140 kDa subunit (TAF(II)140, TAF140, TAFII-140,TAFII140), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors.


:

Pssm-ID: 467041  Cd Length: 92  Bit Score: 177.03  E-value: 3.82e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973   3 ESYSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVSLHELED 82
Cdd:cd22916     1 DEFSRSLLRVVVAQICQNVGWHSIQSSPLDLLTDVLQRYLLELARSAHRYAEQYGRTEPNLDDLGLAFKDMGISLNELED 80
                          90
                  ....*....|..
gi 1370457973  83 YIHNIEPVTFPH 94
Cdd:cd22916    81 YVLNVEPVPFPH 92
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
866-911 2.12e-30

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


:

Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 113.54  E-value: 2.12e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15522     1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
PTZ00449 super family cl33186
104 kDa microneme/rhoptry antigen; Provisional
228-387 2.62e-03

104 kDa microneme/rhoptry antigen; Provisional


The actual alignment was detected with superfamily member PTZ00449:

Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 41.60  E-value: 2.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973 228 SPVHVQDSTdlAPPSPEPPMLAPVAKSQMPTAKPLETKSFTPKTKTKTSSPGQKTKSPKTAQSPAMVGSPI--------- 298
Cdd:PTZ00449  599 RPRSAQRPT--RPKSPKLPELLDIPKSPKRPESPKSPKRPPPPQRPSSPERPEGPKIIKSPKPPKSPKPPFdpkfkekfy 676
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973 299 --------RSPKTVS----KEKKSPGRSKSPKSPKSPKVTTHIPQTPVRPETPNrTPSATLSEKISKETIQVkQIQTPPD 366
Cdd:PTZ00449  677 ddyldaaaKSKETKTtvvlDESFESILKETLPETPGTPFTTPRPLPPKLPRDEE-FPFEPIGDPDAEQPDDI-EFFTPPE 754
                         170       180
                  ....*....|....*....|.
gi 1370457973 367 AGKLNSENQPKKAVVADKTIE 387
Cdd:PTZ00449  755 EERTFFHETPADTPLPDILAE 775
 
Name Accession Description Interval E-value
HFD_TAF3 cd22916
histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and ...
3-94 3.82e-52

histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and similar proteins; TAF3, also called TATA Binding Protein (TBP) associated factor 3, 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, or transcription initiation factor TFIID 140 kDa subunit (TAF(II)140, TAF140, TAFII-140,TAFII140), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors.


Pssm-ID: 467041  Cd Length: 92  Bit Score: 177.03  E-value: 3.82e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973   3 ESYSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVSLHELED 82
Cdd:cd22916     1 DEFSRSLLRVVVAQICQNVGWHSIQSSPLDLLTDVLQRYLLELARSAHRYAEQYGRTEPNLDDLGLAFKDMGISLNELED 80
                          90
                  ....*....|..
gi 1370457973  83 YIHNIEPVTFPH 94
Cdd:cd22916    81 YVLNVEPVPFPH 92
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
866-911 2.12e-30

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


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 113.54  E-value: 2.12e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15522     1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
BTP smart00576
Bromodomain transcription factors and PHD domain containing proteins; subdomain of archael ...
5-79 2.02e-29

Bromodomain transcription factors and PHD domain containing proteins; subdomain of archael histone-like transcription factors


Pssm-ID: 128846  Cd Length: 77  Bit Score: 111.65  E-value: 2.02e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370457973    5 YSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVSLHE 79
Cdd:smart00576   3 LAFALLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGISVGE 77
Bromo_TP pfam07524
Bromodomain associated; This domain is predicted to bind DNA and is often found associated ...
5-79 9.67e-18

Bromodomain associated; This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold.


Pssm-ID: 400073  Cd Length: 77  Bit Score: 78.52  E-value: 9.67e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370457973   5 YSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVSLHE 79
Cdd:pfam07524   3 LAHDLLKVAVSQILEHAGFDSAEESALETLTDIAQSYIRELGEQAKSFAEHAGRSEPTLFDVVLTLVEMGINVGE 77
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
866-911 4.79e-15

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: 69.93  E-value: 4.79e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1370457973  866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGI-MTAPPEEMQWFCPKC 911
Cdd:smart00249   1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPpLLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
866-911 1.57e-12

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 62.89  E-value: 1.57e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGI---MTAPPEEmQWFCPKC 911
Cdd:pfam00628   1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPpldPAEIPSG-EWLCPEC 48
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
870-911 5.52e-08

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


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 55.33  E-value: 5.52e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 870 CNKPDDGsPMIGCD--DCD-DWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:COG5034   226 CQQVSYG-QMVACDnaNCKrEWFHLECVGLKEPP--KGKWYCPEC 267
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
228-387 2.62e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 41.60  E-value: 2.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973 228 SPVHVQDSTdlAPPSPEPPMLAPVAKSQMPTAKPLETKSFTPKTKTKTSSPGQKTKSPKTAQSPAMVGSPI--------- 298
Cdd:PTZ00449  599 RPRSAQRPT--RPKSPKLPELLDIPKSPKRPESPKSPKRPPPPQRPSSPERPEGPKIIKSPKPPKSPKPPFdpkfkekfy 676
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973 299 --------RSPKTVS----KEKKSPGRSKSPKSPKSPKVTTHIPQTPVRPETPNrTPSATLSEKISKETIQVkQIQTPPD 366
Cdd:PTZ00449  677 ddyldaaaKSKETKTtvvlDESFESILKETLPETPGTPFTTPRPLPPKLPRDEE-FPFEPIGDPDAEQPDDI-EFFTPPE 754
                         170       180
                  ....*....|....*....|.
gi 1370457973 367 AGKLNSENQPKKAVVADKTIE 387
Cdd:PTZ00449  755 EERTFFHETPADTPLPDILAE 775
 
Name Accession Description Interval E-value
HFD_TAF3 cd22916
histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and ...
3-94 3.82e-52

histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and similar proteins; TAF3, also called TATA Binding Protein (TBP) associated factor 3, 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, or transcription initiation factor TFIID 140 kDa subunit (TAF(II)140, TAF140, TAFII-140,TAFII140), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors.


Pssm-ID: 467041  Cd Length: 92  Bit Score: 177.03  E-value: 3.82e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973   3 ESYSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVSLHELED 82
Cdd:cd22916     1 DEFSRSLLRVVVAQICQNVGWHSIQSSPLDLLTDVLQRYLLELARSAHRYAEQYGRTEPNLDDLGLAFKDMGISLNELED 80
                          90
                  ....*....|..
gi 1370457973  83 YIHNIEPVTFPH 94
Cdd:cd22916    81 YVLNVEPVPFPH 92
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
866-911 2.12e-30

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


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 113.54  E-value: 2.12e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15522     1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
BTP smart00576
Bromodomain transcription factors and PHD domain containing proteins; subdomain of archael ...
5-79 2.02e-29

Bromodomain transcription factors and PHD domain containing proteins; subdomain of archael histone-like transcription factors


Pssm-ID: 128846  Cd Length: 77  Bit Score: 111.65  E-value: 2.02e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370457973    5 YSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVSLHE 79
Cdd:smart00576   3 LAFALLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGISVGE 77
HFD_TAF8 cd22918
histone-fold domain found in transcription initiation factor TFIID subunit 8 (TAF8) and ...
7-84 5.70e-18

histone-fold domain found in transcription initiation factor TFIID subunit 8 (TAF8) and similar proteins; TAF8, also called TATA Binding Protein (TBP) associated factor 8, protein taube nuss, TBP-associated factor 43 kDa, TBP-associated factor 8, or transcription initiation factor TFIID 43 kDa subunit (TAFII-43, TAFII43), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF8 mediates both basal and activator-dependent transcription. It is involved in the differentiation of preadipocyte fibroblasts to adipocytes, however, it does not seem to play a role in differentiation of myoblasts. TAF8 is required for the integration of TAF10 in the TAF complex. It may be important for survival of cells of the inner cell mass which constitute the pluripotent cell population of the early embryo.


Pssm-ID: 467043  Cd Length: 84  Bit Score: 79.51  E-value: 5.70e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370457973   7 RSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVSLHELEDYI 84
Cdd:cd22918     3 RRVLQVAVAALCLEAGFESAEKSALETLTEMLQSYLTEIGRSSKAYCELAGRTEPTLSDVVLALIDMGINVDSLPEYA 80
Bromo_TP pfam07524
Bromodomain associated; This domain is predicted to bind DNA and is often found associated ...
5-79 9.67e-18

Bromodomain associated; This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold.


Pssm-ID: 400073  Cd Length: 77  Bit Score: 78.52  E-value: 9.67e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370457973   5 YSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGVSLHE 79
Cdd:pfam07524   3 LAHDLLKVAVSQILEHAGFDSAEESALETLTDIAQSYIRELGEQAKSFAEHAGRSEPTLFDVVLTLVEMGINVGE 77
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
9-71 2.80e-17

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 76.49  E-value: 2.80e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370457973   9 LLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQ 71
Cdd:cd00076     1 LLRSAVARILKSAGFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
866-911 4.79e-15

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: 69.93  E-value: 4.79e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1370457973  866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGI-MTAPPEEMQWFCPKC 911
Cdd:smart00249   1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPpLLEEEPDGKWYCPKC 47
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
870-911 1.21e-14

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.


Pssm-ID: 277186  Cd Length: 46  Bit Score: 68.66  E-value: 1.21e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEM-QWFCPKC 911
Cdd:cd16039     4 CQKPDDGRWMIACDGCDEWYHFTCVNIPEADVELVdSFFCPPC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
866-911 1.57e-12

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 62.89  E-value: 1.57e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGI---MTAPPEEmQWFCPKC 911
Cdd:pfam00628   1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPpldPAEIPSG-EWLCPEC 48
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
866-911 2.45e-12

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: 62.33  E-value: 2.45e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370457973 866 ICPGCNKP-DDGSPMIGCDDCDDWYHWPCVGI-MTAPPEEMQWFCPKC 911
Cdd:cd15489     1 SCIVCGKGgDLGGELLQCDGCGKWFHADCLGPpLSSFVPNGKWICPVC 48
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
870-911 7.50e-12

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


Pssm-ID: 276980 [Multi-domain]  Cd Length: 45  Bit Score: 60.78  E-value: 7.50e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 870 CNKPDDGSpMIGCD--DCD-DWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15505     4 CNQVSYGE-MVACDnpNCPiEWFHFECVGLTAKP--KGKWYCPEC 45
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
869-911 8.03e-12

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology.


Pssm-ID: 277027  Cd Length: 50  Bit Score: 60.88  E-value: 8.03e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370457973 869 GCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEM-----QWFCPKC 911
Cdd:cd15552     3 ICRKPHNNRFMICCDRCEEWFHGDCVGITEAQGKEMeenieEYVCPKC 50
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
870-911 1.19e-11

PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the second and third PHD fingers.


Pssm-ID: 277035  Cd Length: 47  Bit Score: 60.05  E-value: 1.19e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370457973 870 CNKPDDGSP-MIGCDDCDDWYHWPCVGIMTAPPEEM-QWFCPKC 911
Cdd:cd15560     4 CRTPYDESQfYIGCDRCQDWFHGRCVGILQSEAEKIdEYVCPQC 47
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
870-911 2.78e-09

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.


Pssm-ID: 277028  Cd Length: 46  Bit Score: 53.53  E-value: 2.78e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGIMtappEEM-----QWFCPKC 911
Cdd:cd15553     4 CRSSDISRFMIGCDNCEEWYHGDCINIT----EKEakaikEWYCQQC 46
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
867-911 3.07e-09

PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain.


Pssm-ID: 277108  Cd Length: 51  Bit Score: 53.39  E-value: 3.07e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEM-----QWFCPKC 911
Cdd:cd15638     2 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMeeedkEYVCVKC 51
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
870-911 1.26e-08

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


Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 51.68  E-value: 1.26e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 870 CNKPDDGSpMIGCDDCD---DWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15585     4 CNQVSYGE-MVGCDNDDcpiEWFHYGCVGLTEAP--KGKWYCPQC 45
HFD_SUPT7L cd06847
histone-fold domain found in Suppressor of Ty 7-like (SUPT7L) and similar proteins; SUPT7L, ...
7-83 3.11e-08

histone-fold domain found in Suppressor of Ty 7-like (SUPT7L) and similar proteins; SUPT7L, also called STAGA complex 65 subunit gamma, adenocarcinoma antigen ART1, SPTF-associated factor 65 gamma, or STAF65gamma, is the ortholog of yeast SPT7 in mammalian cells. It is highly similar to yeast SPT7 but lacks the N-terminal SPT7 bromodomain. SUPT7L is a protein component specific to STAGA (SPT3-TAF9-GCN5 Acetyltransferase)-type complexes. It plays an essential role for the integrity of the STAGA complex.


Pssm-ID: 467022  Cd Length: 86  Bit Score: 51.80  E-value: 3.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973   7 RSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSE---LYGRTdPILDDVGEAFQLMGV-SLHELED 82
Cdd:cd06847     6 RQLLRKSVAAILAHAGFDSASESALEVLTDVLDEFLRKFTRLLRSAVDreaLSGET-GFPDILERVLHEMGIgGISSLHE 84

                  .
gi 1370457973  83 Y 83
Cdd:cd06847    85 Y 85
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
870-911 5.52e-08

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


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 55.33  E-value: 5.52e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 870 CNKPDDGsPMIGCD--DCD-DWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:COG5034   226 CQQVSYG-QMVACDnaNCKrEWFHLECVGLKEPP--KGKWYCPEC 267
PHD_MMD1_like cd15556
PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD ...
867-911 2.82e-07

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.


Pssm-ID: 277031 [Multi-domain]  Cd Length: 46  Bit Score: 47.76  E-value: 2.82e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15556     2 CSCGTRDDDGERMIACDVCEVWQHTRCVGIADNEEPPDHFLCRRC 46
PHD_ING4 cd15684
PHD finger found in inhibitor of growth protein 4 (ING4); ING4, also termed p29ING4, is one ...
879-912 3.36e-07

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


Pssm-ID: 277154 [Multi-domain]  Cd Length: 48  Bit Score: 47.76  E-value: 3.36e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1370457973 879 MIGCDDCD---DWYHWPCVGIMTAPpeEMQWFCPKCA 912
Cdd:cd15684    13 MIGCDNPDcsiEWFHFACVGLTTKP--RGKWFCPRCS 47
PHD_ING4_5 cd15586
PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed ...
879-911 3.46e-07

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


Pssm-ID: 277061 [Multi-domain]  Cd Length: 45  Bit Score: 47.57  E-value: 3.46e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1370457973 879 MIGCDDCD---DWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15586    12 MIGCDNPDcpiEWFHFACVGLTTKP--KGKWFCPRC 45
PHD_AL_plant cd15613
PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed ...
867-913 4.07e-07

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


Pssm-ID: 277085  Cd Length: 51  Bit Score: 47.49  E-value: 4.07e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1370457973 867 CPGCNKP-DDGSPMIGCDDCDDWYHWPCVGIMTAPPEEM-QWFCPKCAN 913
Cdd:cd15613     2 CGSCGGNyTADEFWICCDVCEKWYHGKCVKITPAKAEHIkQYKCPSCSN 50
HFD_SPT7 cd22927
histone-fold domain found in protein SPT7 and similar proteins; SPT7, also called suppressor ...
1-86 4.27e-07

histone-fold domain found in protein SPT7 and similar proteins; SPT7, also called suppressor of Ty 7 homolog, is a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TATA binding protein (TBP) interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA (SAGA altered, SPT8 absent), an altered form of SAGA, may be involved in positive transcriptional regulation. Besides lacking SPT8, SALSA contains an SPT7 subunit that is truncated. SLIK (SAGA-like) is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. SPT7 is transcriptional activator of TY elements and other genes.


Pssm-ID: 467052  Cd Length: 117  Bit Score: 49.46  E-value: 4.27e-07
                          10        20        30        40        50        60        70        80
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gi 1370457973   1 MCESYSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILDDVGEAFQLMGV-SLHE 79
Cdd:cd22927     7 LSEEAARAALRRSVAKLLAHAGFEGAQPSALDVLTDIAADYLSNLGRTLRLYLDRYSKKMSPEEILLHTLFENGVeDISD 86

                  ....*..
gi 1370457973  80 LEDYIHN 86
Cdd:cd22927    87 LESYIKD 93
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
867-911 5.57e-07

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


Pssm-ID: 277004  Cd Length: 44  Bit Score: 46.92  E-value: 5.57e-07
                          10        20        30        40
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gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15529     2 CTKCGDPHDEDKMMFCDQCDRGYHTFCVGLRSIP--DGRWICPLC 44
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
867-911 6.99e-07

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


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 46.77  E-value: 6.99e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1370457973 867 CPGCNKPDDGSPM--IGCDDCDDWYHWPCVGImtaPPEE----MQWFCPKC 911
Cdd:cd15517     2 CGICNLETAAVDElwVQCDGCDKWFHQFCLGL---SNERyadeDKFKCPNC 49
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
867-911 8.40e-07

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


Pssm-ID: 277000  Cd Length: 47  Bit Score: 46.59  E-value: 8.40e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVG-IMTAPPEEMQWFCPKC 911
Cdd:cd15525     2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDpPLTSLPDDDEWYCPDC 47
PHD_Ecm5p_Lid2p_like cd15518
PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), ...
870-911 1.52e-06

PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins; The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model includes the second PHD finger of Lid2p.


Pssm-ID: 276993  Cd Length: 45  Bit Score: 45.80  E-value: 1.52e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1370457973 870 CNKPDDGSpMIGCDDCDDWYHWPCVGI-MTAPPEEMQWFCPKC 911
Cdd:cd15518     4 CRQGEGGT-MIECEICKEWYHVKCIKNgRWKLDDDDKFVCPIC 45
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
870-911 1.64e-06

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


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 45.39  E-value: 1.64e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGIMT-APPEEmqWFCPKC 911
Cdd:cd15550     4 CGFEHDDGFMICCDKCSVWQHGDCMGIDReNIPDS--YLCEQC 44
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
867-911 4.99e-06

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


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 44.18  E-value: 4.99e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVG--IMTAPPEemQWFCPKC 911
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRppLMIIPDG--NWFCPPC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
866-911 5.41e-06

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


Pssm-ID: 276990  Cd Length: 46  Bit Score: 44.31  E-value: 5.41e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCV--GIMTAPPEEmqWFCPKC 911
Cdd:cd15515     1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLipPLPDIPPGD--WRCPKC 46
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
870-911 7.21e-06

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.


Pssm-ID: 277029  Cd Length: 47  Bit Score: 43.91  E-value: 7.21e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370457973 870 CNKPDD-GSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWF-CPKC 911
Cdd:cd15554     4 CRQPYDvTRFMIECDVCKDWFHGSCVGVEEHQANDIERYhCPNC 47
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
867-911 8.33e-06

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


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 43.61  E-value: 8.33e-06
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gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVG--IMTAPPEEmqWFCPKC 911
Cdd:cd15519     2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDppLGEIPPGT--WFCPSC 46
PHD_Yng1p_like cd15587
PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the ...
870-912 1.01e-05

PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the plant homeodomain (PHD) finger-containing ING tumor suppressor family consists of chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Its PHD finger binding to H3 Trimethylated at K4 (H3K4me3) promotes NuA3 H3 HAT activity at K14 of H3 on chromatin. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays a critical role in intra-S-phase DNA damage response. Pho23p is part of the Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect. All family members contain an N-terminal ING histone-binding domain and a C-terminal PHD finger.


Pssm-ID: 277062 [Multi-domain]  Cd Length: 47  Bit Score: 43.56  E-value: 1.01e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 870 CNKPDDGsPMIGCDDCD---DWYHWPCVGIMTAPpeEMQWFCPKCA 912
Cdd:cd15587     4 CRRVSFG-EMVACDNPDckiEWFHFECVGLTETP--KGKWYCSDCK 46
PHD_DIDO1_like cd15639
PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family ...
870-911 1.05e-05

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.


Pssm-ID: 277109  Cd Length: 54  Bit Score: 43.80  E-value: 1.05e-05
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gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQ-----WFCPKC 911
Cdd:cd15639     8 CRQPHNNRFMICCDRCEEWFHGDCVGITEARGRLLErngedYICPNC 54
PHD_ING1_2 cd15584
PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic ...
870-911 1.15e-05

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


Pssm-ID: 277059 [Multi-domain]  Cd Length: 45  Bit Score: 43.20  E-value: 1.15e-05
                          10        20        30        40
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gi 1370457973 870 CNKPDDGSpMIGCDD--CD-DWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15584     4 CNQVSYGE-MIGCDNdeCPiEWFHFSCVGLTHKP--KGKWYCPKC 45
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
866-911 2.22e-05

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: 42.37  E-value: 2.22e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370457973 866 ICPGCNKPD--DGSPMIGCDDCDDWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15679     1 VCDVCQSPDgeDGNEMVFCDKCNICVHQACYGILKVP--EGSWLCRTC 46
PHD_ING5 cd15685
PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one ...
879-912 2.45e-05

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


Pssm-ID: 277155 [Multi-domain]  Cd Length: 49  Bit Score: 42.34  E-value: 2.45e-05
                          10        20        30
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gi 1370457973 879 MIGCDDCD---DWYHWPCVGIMTAPpeEMQWFCPKCA 912
Cdd:cd15685    13 MIGCDNPDcpiEWFHFACVDLTTKP--KGKWFCPRCT 47
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
867-911 2.79e-05

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


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 42.30  E-value: 2.79e-05
                          10        20        30        40
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gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGI-MTAPPEEmQWFCPKC 911
Cdd:cd15545     2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPkMTNVPEG-DWFCPEC 46
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
866-911 3.21e-05

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


Pssm-ID: 276983  Cd Length: 57  Bit Score: 42.43  E-value: 3.21e-05
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gi 1370457973 866 ICPGCNKPDD-GSPMIGCDDCDDWYHWPCVG-------IMTAPPEEMQWFCPKC 911
Cdd:cd15508     4 LCEKCYDDDDyDSKMMQCSQCDHWVHAKCEGlsdemyeILSYLPESIEYTCSLC 57
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
866-911 3.65e-05

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


Pssm-ID: 277069  Cd Length: 46  Bit Score: 41.85  E-value: 3.65e-05
                          10        20        30        40
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gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVG-IMTAPPEEmQWFCPKC 911
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQpVMTTIPKN-GWKCKNC 46
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
866-911 4.02e-05

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


Pssm-ID: 277078  Cd Length: 46  Bit Score: 41.67  E-value: 4.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCvgiMTAPPEEM---QWFCPKC 911
Cdd:cd15605     1 VCHTCGRGDGEESMLLCDGCDDSYHTFC---LLPPLSEVpkgDWRCPKC 46
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
866-911 4.35e-05

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


Pssm-ID: 277077  Cd Length: 46  Bit Score: 41.75  E-value: 4.35e-05
                          10        20        30        40
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gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15604     1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD_TCF19 cd15609
PHD finger found in Transcription factor 19 (TCF-19) and similar proteins; TCF-19, also termed ...
868-909 4.38e-05

PHD finger found in Transcription factor 19 (TCF-19) and similar proteins; TCF-19, also termed transcription factor SC1, was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It also functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. TCF-19 contains an N-terminal fork head association domain (FHA), a proline rich region, and a C-terminal plant homeodomain (PHD) finger. The FHA domain may serve as a nuclear signaling domain or as a phosphoprotein binding domain. The proline rich region is a common characteristic of trans-activating factors. The PHD finger may allow TCF-19 to interact with chromatin via methylated histone H3.


Pssm-ID: 277082  Cd Length: 50  Bit Score: 41.68  E-value: 4.38e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 868 PGCNKP-DDGSPMIGCDDCDDWYHWPCVG--IMTAPPEEMQWFCP 909
Cdd:cd15609     5 PSCCLPqDETVSWVQCDDCDQWYHVACVGcdYNAVKDPDADFHCG 49
PHD_JADE3 cd15681
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ...
866-911 4.93e-05

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: 41.50  E-value: 4.93e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370457973 866 ICPGCNKPD--DGSPMIGCDDCDDWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15681     1 ICDVCRSPDseEGNDMVFCDKCNICVHQACYGILKVP--EGSWLCRTC 46
PHD_KDM7 cd15640
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ...
870-912 5.93e-05

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.


Pssm-ID: 277110  Cd Length: 50  Bit Score: 41.51  E-value: 5.93e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 870 CNKPDDGSP-MIGCDDCDDWYHWPCVGIMTAPPEEMQWF-CPKCA 912
Cdd:cd15640     4 CRQPYDVNRfMIECDICKDWFHGSCVQVEEHHAADIDLYhCPNCE 48
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
867-911 6.16e-05

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


Pssm-ID: 277011  Cd Length: 46  Bit Score: 41.25  E-value: 6.16e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCvgiMTAPPEEM---QWFCPKC 911
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMEC---LTPPLDEVpieEWFCPEC 46
PHD3_KDM5A_like cd15610
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; ...
868-911 6.86e-05

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; The family includes KDM5A and KDM5B, both of which belong to the JARID subfamily within the JmjC proteins. KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well asTIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. The family also includes the Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.


Pssm-ID: 277083 [Multi-domain]  Cd Length: 50  Bit Score: 41.16  E-value: 6.86e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 868 PGCNKPD-DGSPMIGCDDCDDWYHWPCVGIMTAPPEEM-QWFCPKC 911
Cdd:cd15610     5 KQCLKPTgDEVNWVQCDGCEEWFHLLCVGLSPEEVAEDeDYICPSC 50
PHD3_Lid2p_like cd15520
PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
869-911 7.58e-05

PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1, and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. The family corresponds to the third PHD finger.


Pssm-ID: 276995  Cd Length: 47  Bit Score: 41.05  E-value: 7.58e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 869 GCNKPDD-GSPMIGCDDCDDWYHWPCVGIMTAPPEEM-QWFCPKC 911
Cdd:cd15520     3 GCGEGFNiADRMIFCDRCERTVHLDCVGLSDRIVDSPsEFFCPEC 47
PHD_PHF13_like cd15546
PHD finger found in PHD finger proteins PHF13 and PHF23; PHF13, also termed survival ...
870-911 9.04e-05

PHD finger found in PHD finger proteins PHF13 and PHF23; PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer. PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a PHD finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML).


Pssm-ID: 277021  Cd Length: 44  Bit Score: 40.50  E-value: 9.04e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGI-MTAPPEEmqWFCPKC 911
Cdd:cd15546     4 CGKPFAGRPMIECSECLTWIHLSCAKIrKNNVPEV--FICQKC 44
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
867-911 1.04e-04

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


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 40.45  E-value: 1.04e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVG-IMTAPPEEmQWFCPKC 911
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRpPLKKVPEG-DWFCPDC 46
PHD_ING1 cd15682
PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and ...
870-911 1.15e-04

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


Pssm-ID: 277152 [Multi-domain]  Cd Length: 49  Bit Score: 40.38  E-value: 1.15e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 870 CNKPDDGSpMIGCDDCD---DWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15682     5 CNQVSYGE-MIGCDNDEcpiEWFHFSCVGLNHKP--KGKWYCPKC 46
PHD_JADE cd15573
PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family ...
866-911 1.25e-04

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: 40.47  E-value: 1.25e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370457973 866 ICPGCNKPD--DGSPMIGCDDCDDWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15573     1 VCDVCRSPDseEGNEMVFCDKCNICVHQACYGIQKIP--EGSWLCRTC 46
PHD_Bye1p_SIZ1_like cd15570
PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo ...
867-911 1.52e-04

PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2.


Pssm-ID: 277045  Cd Length: 50  Bit Score: 40.14  E-value: 1.52e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1370457973 867 CPgCNKPDDGSPMIGCDDCDDWYHWPCVGI----MTAPPEE-MQWFCPKC 911
Cdd:cd15570     2 CP-CGSSMEDGSMIQCEGCKTWQHMDCVLIpdkpADGLPELpSKFYCELC 50
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
867-911 1.63e-04

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


Pssm-ID: 277087  Cd Length: 57  Bit Score: 40.16  E-value: 1.63e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1370457973 867 CPGCNK-----PDDGSPMIGCDDCDDWYHWPCVGI------MTAPPEEMQWFCPKC 911
Cdd:cd15615     2 CILCGQvyeenEGDEKEWVQCDSCSEWVHFECDGRtglgafKYAKSDGLQYVCPRC 57
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
866-911 1.86e-04

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


Pssm-ID: 276985  Cd Length: 46  Bit Score: 39.72  E-value: 1.86e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVG-IMTAPPEEmQWFCPKC 911
Cdd:cd15510     1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRpVMSSIPKY-GWKCKNC 46
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
870-911 1.98e-04

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


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 39.53  E-value: 1.98e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370457973 870 CNKPD--DGSPMIGCDDCDDWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15492     5 CLDGEseDDNEIVFCDGCNVAVHQSCYGIPLIP--EGDWFCRKC 46
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
866-911 2.10e-04

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: 39.61  E-value: 2.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370457973 866 ICPGCNKPD--DGSPMIGCDDCDDWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15680     1 VCDVCRSPEgeDGNEMVFCDKCNVCVHQACYGILKVP--TGSWLCRTC 46
PHD_PHF13 cd15632
PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated ...
870-911 2.39e-04

PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer.


Pssm-ID: 277102  Cd Length: 47  Bit Score: 39.64  E-value: 2.39e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMqWFCPKC 911
Cdd:cd15632     6 CMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEV-YVCQKC 46
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
867-911 2.78e-04

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


Pssm-ID: 277019  Cd Length: 46  Bit Score: 39.32  E-value: 2.78e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCV--GIMTAPPEEmqWFCPKC 911
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLrpALREVPSGD--WFCPAC 46
PHD_ING2 cd15683
PHD finger found in inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of ...
870-911 2.98e-04

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


Pssm-ID: 277153 [Multi-domain]  Cd Length: 49  Bit Score: 39.23  E-value: 2.98e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 870 CNKPDDGSpMIGCDD--CD-DWYHWPCVGIMTAPpeEMQWFCPKC 911
Cdd:cd15683     5 CNQVSYGE-MIGCDNeqCPiEWFHFSCVGLTYKP--KGKWYCPKC 46
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
866-909 7.15e-04

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


Pssm-ID: 277009  Cd Length: 47  Bit Score: 38.10  E-value: 7.15e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVG-IMTAPPEEMQWFCP 909
Cdd:cd15534     1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDpPLTHPPATGRWMCP 45
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
866-912 1.29e-03

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


Pssm-ID: 276988  Cd Length: 47  Bit Score: 37.46  E-value: 1.29e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVgimtAPPEEM----QWFCPKCA 912
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCL----DPPLQTvpkgGWKCKWCV 47
PHD_PHF8 cd15642
PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, ...
870-911 1.36e-03

PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20 (H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. PHF8 contains an N-terminal plant homeodomain (PHD) finger followed by a JmjC domain. The PHD finger mediates binding to nucleosomes at active gene promoters and the JmjC domain catalyzes the demethylation of mono- or dimethyl-lysines.


Pssm-ID: 277112  Cd Length: 52  Bit Score: 37.70  E-value: 1.36e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370457973 870 CNKPDDGSP-MIGCDDCDDWYHWPCVGIMTAPPEEMQWF-CPKC 911
Cdd:cd15642     5 CRLPYDVTRfMIECDVCQDWFHGSCVGVEEEKAAEIDLYhCPNC 48
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
865-911 1.37e-03

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


Pssm-ID: 277013  Cd Length: 41  Bit Score: 37.31  E-value: 1.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1370457973 865 WICPGCNkpddgsPMIGCDDCDDWYHWPCVGIMTAPPEEmqWFCPKC 911
Cdd:cd15538     3 WRCHKEG------QVLCCSLCPRVYHKKCLKLTSEPDED--WVCPEC 41
PHD_PHF23 cd15631
PHD finger found in PHD finger protein 23 (PHF23); PHF23, also termed PHD-containing protein ...
870-911 1.48e-03

PHD finger found in PHD finger protein 23 (PHF23); PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a plant homeodomain (PHD) finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML).


Pssm-ID: 277101  Cd Length: 44  Bit Score: 37.20  E-value: 1.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMqWFCPKC 911
Cdd:cd15631     4 CGKPFAGRPMIECSQCGTWIHLSCAKIKKSNVPDF-FYCQKC 44
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
867-911 1.77e-03

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


Pssm-ID: 277088  Cd Length: 47  Bit Score: 37.25  E-value: 1.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGI-MTAPPEEMQWFCPKC 911
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPpLSSIPDDEDWYCPEC 47
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
870-911 2.42e-03

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


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 36.49  E-value: 2.42e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
228-387 2.62e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 41.60  E-value: 2.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973 228 SPVHVQDSTdlAPPSPEPPMLAPVAKSQMPTAKPLETKSFTPKTKTKTSSPGQKTKSPKTAQSPAMVGSPI--------- 298
Cdd:PTZ00449  599 RPRSAQRPT--RPKSPKLPELLDIPKSPKRPESPKSPKRPPPPQRPSSPERPEGPKIIKSPKPPKSPKPPFdpkfkekfy 676
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370457973 299 --------RSPKTVS----KEKKSPGRSKSPKSPKSPKVTTHIPQTPVRPETPNrTPSATLSEKISKETIQVkQIQTPPD 366
Cdd:PTZ00449  677 ddyldaaaKSKETKTtvvlDESFESILKETLPETPGTPFTTPRPLPPKLPRDEE-FPFEPIGDPDAEQPDDI-EFFTPPE 754
                         170       180
                  ....*....|....*....|.
gi 1370457973 367 AGKLNSENQPKKAVVADKTIE 387
Cdd:PTZ00449  755 EERTFFHETPADTPLPDILAE 775
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
866-911 2.86e-03

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


Pssm-ID: 277067  Cd Length: 57  Bit Score: 36.89  E-value: 2.86e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1370457973 866 ICPGCNK--PDDG--SPMIGCDDCDDWYHWPC-------VGIMTAPPEEMQWFCPKC 911
Cdd:cd15592     1 FCPLCDKcyDDDDyeSKMMQCGKCDRWVHSKCenlsdemYEILSNLPESVAYTCINC 57
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
870-911 3.10e-03

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


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 36.27  E-value: 3.10e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1370457973 870 CNKPDDGSPMIGCDDCDDWYHWPCVGI-MTAPPEEmQWFCPKC 911
Cdd:cd15539     2 CAVCGDGGELLCCDGCPRAFHLACLVPpLTLIPSG-TWRCSSC 43
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
866-911 3.48e-03

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


Pssm-ID: 277070  Cd Length: 46  Bit Score: 36.13  E-value: 3.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCvgiMTAPPEEM---QWFCPKC 911
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFC---LKPAMESLptdSWKCKAC 46
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
866-911 3.75e-03

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


Pssm-ID: 277075  Cd Length: 49  Bit Score: 36.08  E-value: 3.75e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15602     1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHD_UBR7 cd15542
PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, ...
870-911 3.90e-03

PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, is a UBR box-containing protein that belongs to the E3 ubiquitin ligase family that recognizes N-degrons or structurally related molecules for ubiquitin-dependent proteolysis or related processes through the UBR box motif. In addition to the UBR box, UBR7 also harbors a plant homeodomain (PHD) finger. The biochemical properties of UBR7 remain unclear.


Pssm-ID: 277017  Cd Length: 54  Bit Score: 36.19  E-value: 3.90e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1370457973 870 CNKP----DDGSP--MIGCDDCDDWYHWPCVGIMTAPPEEMQWF---CPKC 911
Cdd:cd15542     4 CDRPypdpEDEVEdeMIQCVLCEDWFHGRHLGLTPPEPDPDEFDemiCSGC 54
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
867-911 4.00e-03

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


Pssm-ID: 277089  Cd Length: 47  Bit Score: 36.09  E-value: 4.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGI-MTAPPEEMQWFCPKC 911
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPpLDKIPEDEDWYCPSC 47
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
867-911 4.24e-03

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


Pssm-ID: 277038  Cd Length: 49  Bit Score: 36.22  E-value: 4.24e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGimtaPPEEMQ-------WFCPKC 911
Cdd:cd15563     2 CCVCKQTGDNSQLVRCDECKLCYHFGCLD----PPLKKSpkqrgygWVCEEC 49
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
866-911 4.36e-03

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


Pssm-ID: 277076  Cd Length: 46  Bit Score: 36.08  E-value: 4.36e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1370457973 866 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_PHF2 cd15641
PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger ...
870-911 5.13e-03

PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. It contains a plant homeodomain (PHD) finger and a JmjC domain and plays an important role in adipogenesis. The PHD finger domain can recognize trimethylated histone H3 lysine 4 (H3K4me3). PHF2 also has dimethylated histone H3 lysine 9(H3K9me2) demethylase activity and acts as a coactivator of several metabolism-related transcription factors. Moreover, it can demethylate ARID5B and further forms a complex with demethylated ARD5B to bind the promoter regions of target genes. The overexpression of PHF2 is involved in the progression of esophageal squamous cell carcinoma (ESCC).


Pssm-ID: 277111  Cd Length: 50  Bit Score: 35.76  E-value: 5.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370457973 870 CNKPDDGSP-MIGCDDCDDWYHWPCVGI-MTAPPEEMQWFCPKC 911
Cdd:cd15641     4 CRLPYDVTRfMIECDACKDWFHGSCVGVeEEEAPDIDIYHCPNC 47
PHD3_KDM5A cd15686
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A); KDM5A, also termed Histone ...
870-912 5.46e-03

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A); KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.


Pssm-ID: 277156  Cd Length: 52  Bit Score: 35.82  E-value: 5.46e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 870 CNKP-DDGSPMIGCDD-CDDWYHWPCVGIMTAPPEEMQWFCPKCA 912
Cdd:cd15686     8 CQRPcKDKVDWVQCDGgCDEWFHQVCVGVSPEMAENEDYICINCA 52
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
867-911 5.50e-03

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


Pssm-ID: 277099  Cd Length: 47  Bit Score: 35.60  E-value: 5.50e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
PHD_PYGO cd15551
PHD finger found in PYGO proteins; The family includes Drosophila melanogaster protein pygopus ...
867-911 5.52e-03

PHD finger found in PYGO proteins; The family includes Drosophila melanogaster protein pygopus (dPYGO) and its two homologs, PYGO1 and PYGO2. dPYGO is a fundamental Wnt signaling transcriptional component in Drosophila. PYGO1 is essential for the association with Legless (Lgs)/Bcl9 that acts an adaptor between Pygopus (Pygo) and Arm/beta-catenin. dPYGO and PYGO2 function as context-dependent beta-catenin coactivators, and they bind di- and trimethylated lysine 4 of histone H3 (H3K4me2/3). Moreover, PYGO2 acts as a histone methylation reader, and a chromatin remodeler in a testis-specific and Wnt-unrelated manner. It also mediates chromatin regulation and links Wnt signaling and Notch signaling to suppress the luminal/alveolar differentiation competence of mammary stem and basal cells. PYGO2 also plays a new role in rRNA transcription during cancer cell growth. It regulates mammary tumor initiation and heterogeneity in MMTV-Wnt1 mice. All family members contain a plant homeodomain (PHD) finger.


Pssm-ID: 277026  Cd Length: 54  Bit Score: 35.80  E-value: 5.52e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1370457973 867 CPGCNKP----DDGspmIGCDD-CDDWYHWPCVGIMTAPPEEM------QWFCPKC 911
Cdd:cd15551     2 CGICNNEvnddDDA---ILCESsCNKWFHRTCTGLTESAYDLLtseesaEWVCDSC 54
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
867-911 5.77e-03

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


Pssm-ID: 277005  Cd Length: 46  Bit Score: 35.44  E-value: 5.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370457973 867 CPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15530     2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD2_KDM5B cd15607
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
870-911 6.24e-03

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


Pssm-ID: 277080  Cd Length: 44  Bit Score: 35.58  E-value: 6.24e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370457973 870 CNKPDDGsPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15607     4 CQKAPMA-PMIQCELCRDAFHSGCVTAPSDPQGPQAWLCPQC 44
PHD2_KDM5A cd15606
PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
870-911 6.71e-03

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


Pssm-ID: 277079  Cd Length: 56  Bit Score: 35.88  E-value: 6.71e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1370457973 870 CNKPDDGSpMIGCDDCDDWYHWPCVGI------------MTAPPEEMQWFCPKC 911
Cdd:cd15606     4 CRKPFSGF-MLQCELCKDWFHSSCVPLpksssqkkggngSGQGAKELKFLCPLC 56
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
867-911 7.24e-03

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


Pssm-ID: 276979  Cd Length: 53  Bit Score: 35.49  E-value: 7.24e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1370457973 867 CPGCNKP--DDGSPMIGCD-DCDDWYHWPCVG----IMTAPPEEMQWFCPKC 911
Cdd:cd15504     2 CAKCQSGeaSPDNDILLCDgGCNRAYHQKCLEppllTEDIPPEDEGWLCPLC 53
PHD3_KDM5B cd15687
PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis ...
866-911 7.61e-03

PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.


Pssm-ID: 277157  Cd Length: 50  Bit Score: 35.31  E-value: 7.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1370457973 866 ICPG--CNKPD-DGSPMIGCD-DCDDWYHWPCVGIMTAPPEEMQWFCPKC 911
Cdd:cd15687     1 LCPAvsCLQPEgEEVDWVQCDgSCNRWFHQVCVGVSAEMAEKEDYICVSC 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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