NCBI Conserved Domain Search

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

Pssm-ID: 277144 Cd Length: 114 Bit Score: 253.46 E-value: 1.28e-79

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDPRFARTGVCISCDAGMCR 456
Cdd:cd15674     1 CELCPNRGGIFKETDTGRWVHLVCALYTPGVAFGDVDKLSPVTLTEMNYSKWGARECSLCEDPRFARTGVCISCDAGMCK 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2170955348 457 AYFHVTCAQKEGLLSEAAAEEDIADPFFAYCKQH 490
Cdd:cd15674    81 SYFHVTCAQREGLLSEATDEEDIADPFYAYCKQH 114

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

Pssm-ID: 277037 Cd Length: 50 Bit Score: 115.58 E-value: 4.96e-31

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKNSYWQCSEC 768
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTKNSGWQCSEC 50

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

Pssm-ID: 227470 [Multi-domain] Cd Length: 669 Bit Score: 123.94 E-value: 5.21e-29

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 304 SSQKMDHIliCCVCLGDNSEDADEIIQCDNCGITVHEGCYGVDGESDSImssasenstepWFCDacKCGVSP----SCEL 379
Cdd:COG5141   188 PSDEFDDI--CTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGF-----------WLCR--KCIYGEyqirCCSF 252

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 380 CPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEmNYSKYGAK-ECSFCEDprfaRTGVCISCDAGMCRAY 458
Cdd:COG5141   253 CPSSDGAFKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIA-SVSSSRWKlGCLICKE----FGGTCIQCSYFNCTRA 327

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 459 FHVTCAQKEGLL-SEAAAEEDIADPFF--AYCKQHAdrlDRKWKRKNYLALQSYCKMSLQ 515
Cdd:COG5141   328 YHVTCARRAGYFdLNIYSHNGISYCIDhePLCRKHY---PLGYGRMNGLRYFGYEKLRYK 384

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

Pssm-ID: 277142 Cd Length: 116 Bit Score: 109.09 E-value: 5.94e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYgAKECSFCED---PRFARTGVCISCDAG 453
Cdd:cd15672     1 CELCPHKDGALKRTDNGGWAHVVCALYIPEVRFGNVATMEPIILQDVPQDRF-NKTCYICEEqgrESKASTGACMQCNKS 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2170955348 454 MCRAYFHVTCAQKEGLLSEAAAEEDIADPFFAYCKQH 490
Cdd:cd15672    80 GCKQSFHVTCAQMAGLLCEEAGNYSDNVKYCGYCSYH 116

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

Pssm-ID: 277036 Cd Length: 56 Bit Score: 105.98 E-value: 1.20e-27

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGVDGESDSiMSSASENSTEPWFCDAC 369
Cdd:cd15561     1 ICCVCLGDRSNDADEIIECDKCGISVHEGCYGVIDESDS-SSSASSSSTEPWFCEPC 56

PHD-zinc-finger like domain;

Pssm-ID: 463991 [Multi-domain] Cd Length: 109 Bit Score: 107.04 E-value: 1.99e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 375 PSCELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKeCSFCEDprfaRTGVCISCDAGM 454
Cdd:pfam13832   1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIDVSRIPPERWKLK-CVFCKK----RSGACIQCSKGR 75

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2170955348 455 CRAYFHVTCAQKEGLLSEAAAEEDIadPFFAYCKQH 490
Cdd:pfam13832  76 CTTAFHVTCAQAAGVYMEPEDWPNV--VVIAYCQKH 109

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

Pssm-ID: 277178 Cd Length: 129 Bit Score: 104.77 E-value: 2.84e-26

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGaKECSFCED---PRFARTGVCISCDAG 453
Cdd:cd15708     5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVSTMEPIVLQSVPHERYN-KTCYICDEqgrESKAATGACMTCNKH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2170955348 454 MCRAYFHVTCAQKEGLLSEAAAEEDIADPFFAYCKQHADRLDRK 497
Cdd:cd15708    84 GCRQAFHVTCAQLAGLLCEEEGNGADNVQYCGYCKYHYSKLKKS 127

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: 100.93 E-value: 5.93e-26

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 862 ECSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTGYGWICQEC 910
Cdd:cd15563     1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQRGYGWVCEEC 49

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

Pssm-ID: 277046 [Multi-domain] Cd Length: 112 Bit Score: 101.89 E-value: 1.57e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKE------TDAGRWVHIVCALYVPGVAFGDiDKLRPVTLTEMNYSKYGAKECSFCEDprfaRTGVCISC 450
Cdd:cd15571     1 CALCPRSGGALKGggalktTSDGLWVHVVCALWSPEVYFDD-GTLLEVEGVSKIPKRRKKLKCSICGK----RGGACIQC 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2170955348 451 DAGMCRAYFHVTCAQKEGLLSEaaaEEDIADPFFAYCKQH 490
Cdd:cd15571    76 SYPGCPRSFHVSCAIRAGCLFE---FEDGPGNFVVYCPKH 112

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

Pssm-ID: 277179 Cd Length: 125 Bit Score: 97.06 E-value: 1.29e-23

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGaKECSFCED---PRFARTGVCISCDAG 453
Cdd:cd15709     5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVLTMEPIVLQYVPHDRFN-KTCYICEEqgrESKAASGACMTCNRH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2170955348 454 MCRAYFHVTCAQKEGLLSEAAAEEDIADPFFAYCKQHADRL 494
Cdd:cd15709    84 GCRQAFHVTCAQMAGLLCEEEVLEVDNVKYCGYCKYHFNKM 124

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

Pssm-ID: 277140 Cd Length: 116 Bit Score: 93.55 E-value: 1.38e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVtlteMNYSKYGAKE----CSFCEDprfaRTGVCISCDA 452
Cdd:cd15670     1 CVLCPNKGGAFKQTDDGRWAHVVCALWIPEVSFANTVFLEPI----DGIQNIPKARwkltCYICKK----RMGACIQCHK 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2170955348 453 GMCRAYFHVTCAQKEGL------LSEAAAEEDIADPFFAYCKQH 490
Cdd:cd15670    73 KNCYTAFHVTCAQQAGLymkiepVKDPGNGTSDSVRKEAYCDKH 116

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

Pssm-ID: 277141 Cd Length: 112 Bit Score: 91.74 E-value: 5.77e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGR-WVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDprfaRTGVCISCDAGMC 455
Cdd:cd15671     1 CVLCPKKGGAMKSTKSGTkWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKE----KTGACIQCSVKSC 76

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2170955348 456 RAYFHVTCAQKEGL-LSEAAAEEDIADPFFAYCKQH 490
Cdd:cd15671    77 KTAFHVTCAFQHGLeMKTILEDEDDEVKFKSYCPKH 112

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

Pssm-ID: 277171 [Multi-domain] Cd Length: 121 Bit Score: 86.29 E-value: 5.60e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDprfARTGVCISCDAGMCR 456
Cdd:cd15701     1 CALCPNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIDSIEHIPPARWKLTCYICKQ---RGSGACIQCHKANCY 77

                          90
                  ....*....|...
gi 2170955348 457 AYFHVTCAQKEGL 469
Cdd:cd15701    78 TAFHVTCAQQAGL 90

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

Pssm-ID: 277145 [Multi-domain] Cd Length: 112 Bit Score: 84.72 E-value: 1.73e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKeCSFCEDPR--FARTGVCISCDAGM 454
Cdd:cd15675     1 CCLCCLRGGALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPIDISKIPPARLKLK-CIYCSKITksMSHMGACIQCSTGK 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2170955348 455 CRAYFHVTCAQKEGLLSEAaaeEDIADPFFAYCKQH 490
Cdd:cd15675    80 CTTSFHVTCAHAAGVQMEP---DDWPYPVYVTCTKH 112

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

Pssm-ID: 463977 [Multi-domain] Cd Length: 88 Bit Score: 82.38 E-value: 6.27e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 397 HIVCALYVPGVAF-GDIDKLRPVTLTEMNYSKYGAKECSFCEDprfaRTGVCISCDAGMCRAYFHVTCAQKEGLLSEaaa 475
Cdd:pfam13771   1 HVVCALWSPELVQrGNDSMGFPIEDIEKIPKRRWKLKCYLCKK----KGGACIQCSKKNCRRAFHVTCALEAGLLMQ--- 73

                          90
                  ....*....|....*
gi 2170955348 476 EEDIADPFFAYCKQH 490
Cdd:pfam13771  74 FDEDNGTFKSYCKKH 88

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

Pssm-ID: 277177 [Multi-domain] Cd Length: 113 Bit Score: 81.87 E-value: 1.85e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAG-RWVHIVCALYVPGVAFGDIDKLRPVT-LTEMNYSKYgAKECSFCEDprfaRTGVCISCDAGM 454
Cdd:cd15707     1 CILCPNKGGAMKSTRSGtKWAHVSCALWIPEVSIGCVEKMEPITkISSIPASRW-ALICVLCRE----RTGACIQCSVKT 75

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2170955348 455 CRAYFHVTCAQKEGLLSEAAAEEDIAD--PFFAYCKQH 490
Cdd:cd15707    76 CKTAYHVTCGFQHGLEMKTILDEESEDgvKLRSYCQKH 113

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

Pssm-ID: 277174 Cd Length: 118 Bit Score: 80.50 E-value: 5.68e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 375 PSCELCPNQDGIFKETDAG-RWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDprfaRTGVCISCDAG 453
Cdd:cd15704     2 PKCLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNE----KVGASIQCSVK 77

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2170955348 454 MCRAYFHVTCAQKEGLLSEAAAEEDIADPFFAYCKQHA 491
Cdd:cd15704    78 NCRTAFHVTCAFDRGLEMKTILAENDEVKFKSYCPKHS 115

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

Pssm-ID: 277173 [Multi-domain] Cd Length: 118 Bit Score: 80.48 E-value: 6.03e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDprfARTGVCISCDAGMCR 456
Cdd:cd15703     1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEGVNNIPPARWKLTCYLCKQ---KGRGAAIQCHKVNCY 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2170955348 457 AYFHVTCAQKEGLLS--EAAAEEDIADPFF-----AYCKQH 490
Cdd:cd15703    78 TAFHVTCAQRAGLFMkiEPVRETGLNGTTFtvrktAYCENH 118

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

Pssm-ID: 277175 Cd Length: 111 Bit Score: 80.14 E-value: 6.32e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAG-RWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDprfaRTGVCISCDAGMC 455
Cdd:cd15705     1 CLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKE----CTGTCIQCSMPSC 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2170955348 456 RAYFHVTCAQKEGLLSEAAAEEDIADPFFAYCKQH 490
Cdd:cd15705    77 ITAFHVTCAFDHGLEMRTTLADNDEVKFKSFCLEH 111

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

Pssm-ID: 277185 Cd Length: 110 Bit Score: 79.23 E-value: 1.36e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKeCSFCEDPRFARTGVCISCDAGMCR 456
Cdd:cd15715     1 CCLCNLRGGALKQTSDDKWAHVMCAVALPEVRFINVVERTPIDISRIPLQRLKLK-CIFCRNRIKRVSGACIQCSYGRCP 79

                          90
                  ....*....|....*.
gi 2170955348 457 AYFHVTCAQKEGLLSE 472
Cdd:cd15715    80 ASFHVTCAHAAGVLME 95

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

Pssm-ID: 277172 Cd Length: 118 Bit Score: 78.93 E-value: 2.46e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDprfARTGVCISCDAGMCR 456
Cdd:cd15702     1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQ---KGVGACIQCHKANCY 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2170955348 457 AYFHVTCAQKEGLL--SEAAAEEDIADPFF-----AYCKQH 490
Cdd:cd15702    78 TAFHVTCAQKAGLYmkMEPVKEVTGGGTTFsvrktAYCDAH 118

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

Pssm-ID: 277176 Cd Length: 111 Bit Score: 75.14 E-value: 3.97e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAG-RWVHIVCALYVPGVAFGDIDKLRPVT-LTEMNYSKYgAKECSFCEdprfARTGVCISCDAGM 454
Cdd:cd15706     1 CLLCPKTGGAMKATRTGtKWAHVSCALWIPEVSIACPERMEPITkVSHIPPSRW-ALVCSLCK----LKTGACIQCSVKS 75

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2170955348 455 CRAYFHVTCAQKEGLLSEAAAEEDIADPFFAYCKQH 490
Cdd:cd15706    76 CITAFHVTCAFEHSLEMKTILDEGDEVKFKSYCLKH 111

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

Pssm-ID: 277183 Cd Length: 110 Bit Score: 70.39 E-value: 1.95e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKeCSFCEDPRFARTGVCISCDAGMCR 456
Cdd:cd15713     1 CCLCSLRGGALQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSKIPLQRFKLK-CIFCKKRRKRTAGCCVQCSHGRCP 79

                          90
                  ....*....|....
gi 2170955348 457 AYFHVTCAQKEGLL 470
Cdd:cd15713    80 TSFHASCAQAAGVM 93

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

Pssm-ID: 277037 Cd Length: 50 Bit Score: 66.28 E-value: 1.07e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 862 ECSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTG-YGWICQEC 910
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTKnSGWQCSEC 50

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

Pssm-ID: 277132 Cd Length: 115 Bit Score: 68.27 E-value: 1.15e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVtltemNYSKYGAKE-----CSFCEdprfARTGVCISCD 451
Cdd:cd15662     1 CCLCPVVGGALKPTTDGRWAHLACAIWIPETCLLDVKTMEPV-----DGINAISKErwelsCTICK----QRYGACIQCS 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2170955348 452 AGMCRAYFHVTCAQKEGLLSEaAAEEDIADP------FFAYCKQH 490
Cdd:cd15662    72 NNSCRVAYHPLCARAAGLCME-VADEGGEDPgdqglrLLSYCPRH 115

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

Pssm-ID: 277184 Cd Length: 110 Bit Score: 67.65 E-value: 1.47e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKeCSFCEDPRFARTGVCISCDAGMCR 456
Cdd:cd15714     1 CCLCNLRGGALQMTTDERWVHVICAIAVPEARFLNVIERHPVDVSAIPEQRWKLK-CVYCRKRMKKVSGACIQCSYDHCS 79

                          90
                  ....*....|....*...
gi 2170955348 457 AYFHVTCAQKEGLLSEAA 474
Cdd:cd15714    80 TSFHVTCAHAAGVVMEPD 97

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

Pssm-ID: 277133 Cd Length: 112 Bit Score: 64.84 E-value: 1.46e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQDGIFKETD-AGRWVHIVCALYVPGVAFGDIDKLRP-VTLTEMNYSKYgAKECSFCEDPRfartGVCISCDAgm 454
Cdd:cd15663     1 CCLCPVKGGALKPTDvEGLWVHVTCAWFRPEVCFKNEEKMEPaVGLLRIPLSTF-LKACVICKQIH----GSCTQCCK-- 73

                          90
                  ....*....|....
gi 2170955348 455 CRAYFHVTCAQKEG 468
Cdd:cd15663    74 CATYFHAMCASRAG 87

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

Pssm-ID: 277137 Cd Length: 141 Bit Score: 63.17 E-value: 1.12e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 366 CDACKC----GVSPSCELCPNQdgiFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDPrf 441
Cdd:cd15667     4 CNAKESnyelAKKQSPRTRPDA---LKCTSNGTWCHVLCALFNEDIKFGNSKSLQPILNTESVLLKGSRQKCEICKVS-- 78

                          90       100
                  ....*....|....*....|....*.
gi 2170955348 442 arTGVCISCDagMCRAYFHVTCAQKE 467
Cdd:cd15667    79 --GGGLVKCE--VCDDRFHVSCAQDT 100

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

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 60.20 E-value: 1.23e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKNsyWQCSECDQA 771
Cdd:pfam00628   2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGE--WLCPECKPK 51

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: 59.31 E-value: 2.57e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPrktKNSYWQCSEC 768
Cdd:cd15525     1 ACHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLP---DDDEWYCPDC 47

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: 58.40 E-value: 5.15e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2170955348 314 CCVCLGDNSEDADEIIQCDNCGITVHEGCYGVdgesDSImssasenSTEPWFCDAC 369
Cdd:cd15492     2 CDVCLDGESEDDNEIVFCDGCNVAVHQSCYGI----PLI-------PEGDWFCRKC 46

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: 58.17 E-value: 6.98e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKNSyWQCSEC 768
Cdd:cd15563     1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQRGYG-WVCEEC 49

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: 57.66 E-value: 9.37e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPrktKNSYWQCSEC 768
Cdd:cd15617     1 SCYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIP---EDEDWYCPSC 47

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

Pssm-ID: 276972 Cd Length: 48 Bit Score: 56.55 E-value: 2.02e-10

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQtGYGWICQEC 910
Cdd:cd15497     2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNR-GFVWSCAPC 48

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: 53.81 E-value: 2.01e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGN----WFCPPC 46

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: 53.91 E-value: 2.02e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgyGWICQEC 910
Cdd:cd15525     2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDD--EWYCPDC 47

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

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 53.65 E-value: 2.39e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTGyGWICQECDSS 913
Cdd:pfam00628   2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSG-EWLCPECKPK 51

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: 53.75 E-value: 2.65e-09

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2170955348  720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPrktKNSYWQCSEC 768
Cdd:smart00249   2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEE---PDGKWYCPKC 47

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

Pssm-ID: 276998 [Multi-domain] Cd Length: 43 Bit Score: 52.40 E-value: 5.89e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGEnenLVRCDECRLCYHFGCLDPPLKKSPKqtgYGWICQEC 910
Cdd:cd15523     2 CSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPK---GMWICPKC 43

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: 52.09 E-value: 8.13e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15513     2 CEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGG----WKCKWC 46

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: 51.06 E-value: 1.79e-08

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2170955348  863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKqtGYGWICQEC 910
Cdd:smart00249   2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEP--DGKWYCPKC 47

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

Pssm-ID: 276970 [Multi-domain] Cd Length: 47 Bit Score: 51.22 E-value: 1.85e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2170955348 314 CCVCLGDNSEDADEIIQCDNCGITVHEGCYGVdgesdsimssASENSTEPWFCDAC 369
Cdd:cd15495     2 CAVCNEGEDDDNNPLITCNRCQISVHQKCYGI----------REVDPDGSWVCRAC 47

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

Pssm-ID: 276998 [Multi-domain] Cd Length: 43 Bit Score: 50.86 E-value: 2.15e-08

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                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDqhlLLLCDTCKLHYHLGCLDPPLTRMPRktknSYWQCSEC 768
Cdd:cd15523     2 CSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPK----GMWICPKC 43

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: 50.54 E-value: 2.77e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15519     2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGT----WFCPSC 46

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: 49.70 E-value: 5.25e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15515     2 CQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGD----WRCPKC 46

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: 49.65 E-value: 6.00e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKnsyWQC 765
Cdd:cd15534     2 CFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGR---WMC 44

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: 49.37 E-value: 6.76e-08

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                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKknhDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15539     2 CAVCG---DGGELLCCDGCPRAFHLACLVPPLTLIPSGT----WRCSSC 43

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

Pssm-ID: 277002 Cd Length: 46 Bit Score: 49.30 E-value: 8.49e-08

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                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGK---WVCQIC 46

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: 48.95 E-value: 9.43e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGD---WFCPAC 46

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

Pssm-ID: 276973 Cd Length: 55 Bit Score: 49.01 E-value: 1.37e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2170955348 314 CCVCLGDNSEDADEIIQCDNCGITVHEGCYGVDgeSDSIMSSASENSTEPWFCDAC 369
Cdd:cd15498     2 CSVCSEQFASNFNTSLSCYNCGLNVHASCYGIT--VPGKMNKVKNLKSYKWLCDPC 55

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

Pssm-ID: 277053 Cd Length: 53 Bit Score: 48.54 E-value: 2.00e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGVDGESDSIMSSasenstEPWFCDAC 369
Cdd:cd15578     1 VCTVCQDGSSESPNEIVLCDKCGQGYHQLCHNPKIDSSVLDPD------VPWLCRQC 51

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

Pssm-ID: 276966 [Multi-domain] Cd Length: 48 Bit Score: 48.08 E-value: 2.24e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 863 CSTCKGTGENEN-LVRCDECRLCYHFGCLDPPLKKSPKqtGYGWICQEC 910
Cdd:cd15489     2 CIVCGKGGDLGGeLLQCDGCGKWFHADCLGPPLSSFVP--NGKWICPVC 48

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: 47.77 E-value: 2.78e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGD----WFCPDC 46

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: 47.00 E-value: 5.20e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGD---WFCPDC 46

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

Pssm-ID: 277002 Cd Length: 46 Bit Score: 46.99 E-value: 5.21e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRktknSYWQCSEC 768
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPK----GKWVCQIC 46

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: 46.88 E-value: 5.39e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKnsyWQCSEC 768
Cdd:cd15616     1 ACHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDDED---WYCPEC 47

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: 46.92 E-value: 5.62e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15545     1 SCQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGD----WFCPEC 46

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

Pssm-ID: 276966 [Multi-domain] Cd Length: 48 Bit Score: 46.93 E-value: 5.63e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2170955348 719 SCGICKKNHD-QHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKnsyWQCSEC 768
Cdd:cd15489     1 SCIVCGKGGDlGGELLQCDGCGKWFHADCLGPPLSSFVPNGK---WICPVC 48

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

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 47.10 E-value: 5.88e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2170955348 313 ICCVCLGdnSEDADEIIQCDNCGITVHEGCYGVDGESDSIMSsasenstEPWFCDACKC 371
Cdd:pfam00628   1 YCAVCGK--SDDGGELVQCDGCDDWFHLACLGPPLDPAEIPS-------GEWLCPECKP 50

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

Pssm-ID: 276984 Cd Length: 48 Bit Score: 46.92 E-value: 6.20e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRktKNSYWQCSEC 768
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPL--VRAGWQCPEC 48

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: 46.64 E-value: 6.31e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGD----WFCPAC 46

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: 46.37 E-value: 8.50e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRktknSYWQCSEC 768
Cdd:cd15604     2 CRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPK----GIWRCPKC 46

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: 46.19 E-value: 1.03e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKqTGYgWIC 907
Cdd:cd15534     2 CFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPA-TGR-WMC 44

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

Pssm-ID: 276999 [Multi-domain] Cd Length: 43 Bit Score: 45.65 E-value: 1.52e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKgtgENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15524     2 CAACK---RGGNLQPCGTCPRAYHLDCLDPPLKTAPKGV---WVCPKC 43

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

Pssm-ID: 276984 Cd Length: 48 Bit Score: 45.76 E-value: 1.77e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 862 ECSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPkQTGYGWICQEC 910
Cdd:cd15509     1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTP-LVRAGWQCPEC 48

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: 45.72 E-value: 1.84e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgyGWICQEC 910
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDE--DWYCPSC 47

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: 45.12 E-value: 2.41e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKqtgYGWICQEC 910
Cdd:cd15510     2 CQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPK---YGWKCKNC 46

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: 44.94 E-value: 2.53e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15603     2 CLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGD----WRCPKC 46

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: 44.39 E-value: 4.76e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQtgyGWICQEC 910
Cdd:cd15513     2 CEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKG---GWKCKWC 46

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: 44.36 E-value: 5.07e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15605     2 CHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGD----WRCPKC 46

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: 43.98 E-value: 6.15e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 862 ECSTCKGTGEnenLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15539     1 ECAVCGDGGE---LLCCDGCPRAFHLACLVPPLTLIPSGT---WRCSSC 43

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: 44.23 E-value: 6.42e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2170955348 313 ICCVClGDNSEDADEIIQCDNCGITVHEGCYGVDGEsdsimssaSENSTEPWFCDAC 369
Cdd:cd15489     1 SCIVC-GKGGDLGGELLQCDGCGKWFHADCLGPPLS--------SFVPNGKWICPVC 48

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

Pssm-ID: 277010 [Multi-domain] Cd Length: 45 Bit Score: 43.95 E-value: 6.46e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGEnenLVRCDECRLCYHFGCLDPPLKKSPKQTGyGWICQEC 910
Cdd:cd15535     2 CSACGGYGS---FLCCDGCPRSFHFSCLDPPLEEDNLPDD-EWFCNEC 45

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: 43.77 E-value: 7.74e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQtgyGWICQEC 910
Cdd:cd15594     2 CQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKN---GWKCKNC 46

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: 43.42 E-value: 1.09e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgyGWICQEC 910
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDDE--DWYCPEC 47

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

Pssm-ID: 277098 Cd Length: 46 Bit Score: 43.19 E-value: 1.14e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRktknSYWQCSEC 768
Cdd:cd15628     2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPD----GEWMCPAC 46

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: 43.04 E-value: 1.34e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDqhlLLLCDTCKLHYHLGCLDPPLTRMPRKtknsYWQCSEC 768
Cdd:cd15532     1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDG----DWFCPRC 43

PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a Cys4HisCys3 canonical PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. This model corresponds to the Cys4HisCys3 canonical PHD finger.

Pssm-ID: 276968 Cd Length: 42 Bit Score: 42.69 E-value: 1.44e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2170955348 328 IIQCDNCGITVHEGCYGVDGEsdsimssasENSTEPWFCDAC 369
Cdd:cd15493    10 LLVCSRCCVCVHASCYGVPDI---------PGDGEGWKCDRC 42

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: 42.97 E-value: 1.48e-05

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2170955348  313 ICCVCLGdnSEDADEIIQCDNCGITVHEGCYGVDGEsdsimssaSENSTEPWFCDAC 369
Cdd:smart00249   1 YCSVCGK--PDDGGELLQCDGCDRWYHQTCLGPPLL--------EEEPDGKWYCPKC 47

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

Pssm-ID: 277049 [Multi-domain] Cd Length: 48 Bit Score: 42.89 E-value: 1.61e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2170955348 314 CCVCLGDNSEDADEIIQCD--NCGITVHEGCYGVdgesdsimssaSENSTEPWFCDAC 369
Cdd:cd15574     2 CCVCSDERGWAENPLVYCDghGCNVAVHQACYGI-----------VQVPTGPWFCRKC 48

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: 42.79 E-value: 1.61e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEE----WFCPEC 46

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: 42.78 E-value: 1.69e-05

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGV 345
Cdd:cd15573     1 VCDVCRSPDSEEGNEMVFCDKCNICVHQACYGI 33

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

Pssm-ID: 277034 [Multi-domain] Cd Length: 43 Bit Score: 42.79 E-value: 1.72e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDqhlLLLCDTCKLHYHLGCLDPPLTRMPrktkNSYWQCSEC 768
Cdd:cd15559     2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVP----EEDWQCEVC 43

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: 42.23 E-value: 2.33e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPrktKNSyWQCSEC 768
Cdd:cd15594     2 CQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIP---KNG-WKCKNC 46

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.

Pssm-ID: 277047 [Multi-domain] Cd Length: 54 Bit Score: 42.60 E-value: 2.47e-05

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGV 345
Cdd:cd15572     3 VCCICLDGECQNSNVILFCDMCNLAVHQECYGV 35

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

Pssm-ID: 276974 Cd Length: 53 Bit Score: 42.49 E-value: 2.54e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2170955348 314 CCVCLGDNSEDADEIIQCDNCGITVHEGCYgvdgesDSIMSSASENSTEPWFCDACKC 371
Cdd:cd15499     2 CSICGGAEARDGNEILICDKCDKGYHQLCH------SPKVRTSPLEGDEKWFCSRCVF 53

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

Pssm-ID: 276972 Cd Length: 48 Bit Score: 42.30 E-value: 2.96e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2170955348 719 SCGICKK--NHDQHLLllCDTCKLHYHLGCLDPPLTRMPrkTKNSYWQCSEC 768
Cdd:cd15497     1 SCKVCKEwcASDDSVR--CDECKVSYHLLCVDPPLTKKP--NRGFVWSCAPC 48

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

Pssm-ID: 277054 Cd Length: 53 Bit Score: 42.17 E-value: 3.21e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2170955348 314 CCVCLGDNSEDADEIIQCDNCGITVHEGCYgvdgesDSIMSSASENSTEPWFCDAC 369
Cdd:cd15579     2 CNVCLGKSSGPLNEILICGKCGLGYHQQCH------IPVVDSSDDPPLTPWFCRRC 51

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: 41.98 E-value: 3.40e-05

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGV 345
Cdd:cd15679     1 VCDVCQSPDGEDGNEMVFCDKCNICVHQACYGI 33

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

Pssm-ID: 277066 Cd Length: 50 Bit Score: 41.85 E-value: 3.77e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 863 CSTCKGTG-ENENLVRCDECRLCYHFGCLDPPLKKSPKQTGYGWICQEC 910
Cdd:cd15591     2 CHVCGRKNkESKPLLECERCRNCYHPACLGPNYPKPANRKKRPWICSAC 50

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: 41.47 E-value: 4.84e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15602     2 CLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGD----WRCPKC 46

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

Pssm-ID: 277147 [Multi-domain] Cd Length: 54 Bit Score: 41.54 E-value: 5.74e-05

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGV 345
Cdd:cd15677     3 VCCICMDGECQNSNVILFCDMCNLAVHQECYGV 35

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: 41.15 E-value: 6.94e-05

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGV 345
Cdd:cd15680     1 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGI 33

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: 41.10 E-value: 7.03e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGN---WFCPPC 46

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: 41.11 E-value: 8.08e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGVDGESDSimssasenstePWFCDACKCGV 373
Cdd:cd15681     1 ICDVCRSPDSEEGNDMVFCDKCNICVHQACYGILKVPEG-----------SWLCRTCVLGI 50

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: 40.44 E-value: 1.00e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 863 CSTCkGTGEN-ENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15530     2 CSLC-GTSENdDQLLFCDDCDRGYHMYCLSPPMSEPPEGS---WSCHLC 46

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: 40.44 E-value: 1.10e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15530     1 SCSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGS----WSCHLC 46

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: 40.53 E-value: 1.11e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15519     2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGT---WFCPSC 46

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: 40.49 E-value: 1.12e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPrktKNSyWQCSEC 768
Cdd:cd15510     2 CQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIP---KYG-WKCKNC 46

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

Pssm-ID: 277098 Cd Length: 46 Bit Score: 40.50 E-value: 1.18e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15628     2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGE---WMCPAC 46

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: 40.34 E-value: 1.26e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGEnenLVRCDECRLCYHFGCLDPPLKKSPkqTGYgWICQEC 910
Cdd:cd15532     2 CRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIP--DGD-WFCPRC 43

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: 40.36 E-value: 1.27e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTknsyWQCSEC 768
Cdd:cd15595     2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDS----WKCKAC 46

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

Pssm-ID: 276977 Cd Length: 52 Bit Score: 40.50 E-value: 1.43e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2170955348 720 CGICKKNH--DQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKNSYWQCSEC 768
Cdd:cd15502     2 CIVCQRGHspKSNRIVFCDGCNTPYHQLCHDPSIDDEVVEDPDAEWFCKKC 52

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

Pssm-ID: 277006 [Multi-domain] Cd Length: 43 Bit Score: 39.89 E-value: 1.47e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDqhlLLLCDTCKLHYHLGCLDPPLTRMPRktknSYWQCSEC 768
Cdd:cd15531     2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPE----GKWSCPHC 43

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

Pssm-ID: 277008 [Multi-domain] Cd Length: 45 Bit Score: 39.65 E-value: 1.80e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGEnenLVRCDECRLCYHFGCLDPPLKKSPKQTGYgWICQEC 910
Cdd:cd15533     2 CDSCGEGGD---LLCCDRCPASFHLQCCNPPLDEEDLPPGE-WLCHRC 45

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: 39.98 E-value: 1.83e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15595     2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDS---WKCKAC 46

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

Pssm-ID: 277136 Cd Length: 105 Bit Score: 41.52 E-value: 1.99e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 391 DAGRWVHIVCALYVPGV------AFGDIDK--LRPVTLTemnyskygakeCSFCEdprfaRTGVCISCDAGMCRAYFHVT 462
Cdd:cd15666    22 DVDKWVHLNCALWSYEVyetqngALMNVEEalRRALTTT-----------CSHCG-----RTGATVPCFKPRCANVYHLP 85


                  ....*.
gi 2170955348 463 CAQKEG 468
Cdd:cd15666    86 CAIKDG 91

PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.

Pssm-ID: 277003 Cd Length: 54 Bit Score: 40.09 E-value: 2.02e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2170955348 719 SCGICKKNHDQH-----LLLLCDTCKLHYHLGCLDPPlTRMPRKTKNSYWQCSEC 768
Cdd:cd15528     1 VCGICEKGGKSNkgepeELIHCSQCGNSGHPSCLEMS-DEMVAVIKTYPWQCMEC 54

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

Pssm-ID: 277148 [Multi-domain] Cd Length: 55 Bit Score: 39.23 E-value: 3.51e-04

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYGV 345
Cdd:cd15678     3 FCCVCLDDECHNSNVILFCDICNLAVHQECYGV 35

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

Pssm-ID: 463990 [Multi-domain] Cd Length: 35 Bit Score: 38.48 E-value: 4.69e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2170955348 326 DEIIQCDNCGITVHEGCYGVdgesdsimssASENSTEPWFCDAC 369
Cdd:pfam13831   2 SPLVYCSKCSVQVHASCYGV----------PPIPDGDGWKCRRC 35

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

Pssm-ID: 277163 Cd Length: 113 Bit Score: 40.75 E-value: 5.04e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 377 CELCPNQdGIFKETDAGR--------WVHIVCALYVPGVAFGDIDKLRPVtltEMNYSKYGAKECSFCEDPrfartGVCI 448
Cdd:cd15693     3 CALCLKY-GDDSANDAGRllyigqneWTHVNCALWSAEVFEDDDGSLKNV---HMAVIRGKQLRCEFCQKP-----GATV 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2170955348 449 SCDAGMCRAYFHVTCAQKEgllsEAAAEEDIAdpffAYCKQHAD 492
Cdd:cd15693    74 GCCLTSCTSNYHFMCSRAK----NCVFLEDKK----VYCQRHKD 109

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

Pssm-ID: 277016 [Multi-domain] Cd Length: 43 Bit Score: 38.48 E-value: 5.05e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDqhlLLLCDTCKLHYHLGCLDPPLTRMPRktknSYWQCSEC 768
Cdd:cd15541     2 CAVCQNGGE---LLCCDKCPRVFHLDCHIPPIPEFPS----GEWSCSLC 43

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: 38.67 E-value: 5.35e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15604     2 CRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGI---WRCPKC 46

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

Pssm-ID: 277135 Cd Length: 90 Bit Score: 39.61 E-value: 6.06e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2170955348 395 WVHIVCALYVPGVAFGDIDKLrpvTLTEMNYSKYGAKECSFCedprfARTGVCISCDAGMCRAYFHVTCAqkegllSEAA 474
Cdd:cd15665    10 YAHHCCAAWSEGVCQTEDGAL---ENVDKAVAKALSQKCSFC-----LRYGASISCRMPSCSKSFHFPCA------AAAG 75

                          90
                  ....*....|....*.
gi 2170955348 475 AEEDIADpFFAYCKQH 490
Cdd:cd15665    76 CFQDIKT-LTLFCPEH 90

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: 38.14 E-value: 6.58e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15515     2 CQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGD---WRCPKC 46

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

Pssm-ID: 276982 Cd Length: 50 Bit Score: 38.22 E-value: 7.31e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 863 CSTCKGTGENEN-LVRCDECRLCYHFGCLDPPLKKSPKQTGYGWICQEC 910
Cdd:cd15507     2 CHVCGRKGQAQKqLLECEKCQRGYHVDCLGPSYPTKPTRKKKTWICSKC 50

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

Pssm-ID: 276999 [Multi-domain] Cd Length: 43 Bit Score: 37.95 E-value: 7.87e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHDqhlLLLCDTCKLHYHLGCLDPPLTRMPRktknSYWQCSEC 768
Cdd:cd15524     2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPK----GVWVCPKC 43

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: 38.16 E-value: 7.89e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEE---WFCPEC 46

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

Pssm-ID: 277010 [Multi-domain] Cd Length: 45 Bit Score: 37.78 E-value: 1.12e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 720 CGICKKNHdqhLLLLCDTCKLHYHLGCLDPPLTrmPRKTKNSYWQCSEC 768
Cdd:cd15535     2 CSACGGYG---SFLCCDGCPRSFHFSCLDPPLE--EDNLPDDEWFCNEC 45

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

Pssm-ID: 277006 [Multi-domain] Cd Length: 43 Bit Score: 37.20 E-value: 1.32e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2170955348 863 CSTCKGTGEnenLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15531     2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGK---WSCPHC 43

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: 37.52 E-value: 1.38e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2170955348 719 SCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPrktkNSYWQCSEC 768
Cdd:cd15629     1 TCLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVP----EGDWFCPNC 46

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: 37.41 E-value: 1.62e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2170955348 720 CGICKKN--HDQHLLLLCD-TCKLHYHLGCLDPPLTRMPRKTKNSYWQCSEC 768
Cdd:cd15504     2 CAKCQSGeaSPDNDILLCDgGCNRAYHQKCLEPPLLTEDIPPEDEGWLCPLC 53

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

Pssm-ID: 277016 [Multi-domain] Cd Length: 43 Bit Score: 36.94 E-value: 1.70e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2170955348 862 ECSTCKGTGEnenLVRCDECRLCYHFGCLDPPLKKSPKqtgYGWICQEC 910
Cdd:cd15541     1 WCAVCQNGGE---LLCCDKCPRVFHLDCHIPPIPEFPS---GEWSCSLC 43

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: 36.88 E-value: 1.95e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2170955348 313 ICCVCLGdnSEDADEIIQCDNCGITVHEGCYGVDGESDsimssasenSTEPWFCDAC 369
Cdd:cd15522     1 ICPICKK--PDDGSPMIGCDECDDWYHWECVGITDEPP---------EEDDWFCPKC 46

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

Pssm-ID: 276974 Cd Length: 53 Bit Score: 37.09 E-value: 2.13e-03

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gi 2170955348 863 CSTCKG---TGENENLVrCDECRLCYHFGCLDPPLKKSPKQTGYGWICQEC 910
Cdd:cd15499     2 CSICGGaeaRDGNEILI-CDKCDKGYHQLCHSPKVRTSPLEGDEKWFCSRC 51

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX1, ATX2, and similar proteins; The family includes A. thaliana ATX1 and ATX2, both of which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also termed protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also termed protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.

Pssm-ID: 276969 Cd Length: 47 Bit Score: 37.04 E-value: 2.16e-03

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gi 2170955348 314 CCVCLGDNSEDADEIIQCDNCGITVHEGCYGVDGESDSIMssasenstepWFCDAC 369
Cdd:cd15494     2 CSVCGEDEEYEDNLLLQCDKCRMMVHMRCYGVLEPPPGAL----------WLCNLC 47

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: 36.66 E-value: 2.21e-03

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gi 2170955348 863 CSTC-KGTGEnENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15605     2 CHTCgRGDGE-ESMLLCDGCDDSYHTFCLLPPLSEVPKGD---WRCPKC 46

PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger.

Pssm-ID: 277146 [Multi-domain] Cd Length: 62 Bit Score: 36.96 E-value: 2.96e-03

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gi 2170955348 305 SQKMDHILICCVCLGDNSEDADEIIQCDNCGITVHEGCYGV 345
Cdd:cd15676     1 NALIDEDAVCCICNDGECQNSNVILFCDMCNLAVHQECYGV 41

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

Pssm-ID: 277100 Cd Length: 49 Bit Score: 36.49 E-value: 3.42e-03

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gi 2170955348 720 CGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPrktkNSYWQCSEC 768
Cdd:cd15630     3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIP----EGDWFCPAC 47

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

Pssm-ID: 276977 Cd Length: 52 Bit Score: 36.26 E-value: 4.11e-03

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                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2170955348 313 ICCVCLGDNSEDADEIIQCDNCGITVHEGCYgvdgeSDSIMSSASENSTEPWFCDAC 369
Cdd:cd15502     1 VCIVCQRGHSPKSNRIVFCDGCNTPYHQLCH-----DPSIDDEVVEDPDAEWFCKKC 52

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: 36.13 E-value: 4.27e-03

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gi 2170955348 863 CSTCKgTGENEN-LVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15545     2 CQICR-SGDNEDqLLLCDGCDRGYHTYCFKPKMTNVPEGD---WFCPEC 46

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: 35.70 E-value: 5.83e-03

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gi 2170955348 863 CSTCKGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTgygWICQEC 910
Cdd:cd15603     2 CLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGD---WRCPKC 46

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

Pssm-ID: 277001 Cd Length: 56 Bit Score: 35.79 E-value: 7.06e-03

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gi 2170955348 862 ECSTCKGT-------GENENLVRCDECRLCYHFGCLDPPLKKSPKQTGYGWICQEC 910
Cdd:cd15526     1 ICDFCLGTdeknnktGEPEELISCADCGSSGHPSCLKFSPGLTDAVKSYRWQCIEC 56

PHD finger 2 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 second PHD finger.

Pssm-ID: 277065 Cd Length: 50 Bit Score: 35.39 E-value: 9.32e-03

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gi 2170955348 863 CSTC-KGTGENENLVRCDECRLCYHFGCLDPPLKKSPKQTGYGWICQEC 910
Cdd:cd15590     2 CHVCgRQHQATKQLLECNKCRNSYHPECLGPNYPTKPTKKKRVWICTKC 50