NCBI Conserved Domain Search

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...

1432-1481

6.37e-10

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

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 57.12 E-value: 6.37e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 755528517  1432 VCFLCASSG-HVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRCKFC 1481
Cdd:pfam00628    1 YCAVCGKSDdGGELVQCDGCDDWFHLACLGPPLDPAEIPSGEWLCPECKPK 51

PHD

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

1480-1529

2.91e-09

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

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 55.30 E-value: 2.91e-09

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 755528517   1480 FCHVCGRQHqATKQLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1529
Cdd:smart00249    1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEPDGK--WYCPKC 47

PHD

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...

1480-1532

6.93e-08

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 51.34 E-value: 6.93e-08

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 755528517  1480 FCHVCGRQHqATKQLLECNKCRNSYHPECLGPNyPTKPTKKKKVWICTKCVRC 1532
Cdd:pfam00628    1 YCAVCGKSD-DGGELVQCDGCDDWFHLACLGPP-LDPAEIPSGEWLCPECKPK 51

PHD

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...

1581-1629

1.18e-05

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 45.18 E-value: 1.18e-05

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 755528517  1581 ESKMMQCGKCDRWVHSKCESLSgteDEMYEILSNlpesvAYTCVNCTER 1629
Cdd:pfam00628   11 GGELVQCDGCDDWFHLACLGPP---LDPAEIPSG-----EWLCPECKPK 51

PHD

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

1432-1478

7.29e-05

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 42.58 E-value: 7.29e-05

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 755528517   1432 VCFLCASSGH-VEFVYCQVCCEPFHKFCLEENERPlEDQLENWCCRRC 1478
Cdd:smart00249    1 YCSVCGKPDDgGELLQCDGCDRWYHQTCLGPPLLE-EEPDGKWYCPKC 47

PHD

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

1934-1979

9.70e-05

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 42.58 E-value: 9.70e-05

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 755528517   1934 RCEFCQKP---GATVGCCltSCTSNYHFMCSRAKNCVFLDDKKVYCQRH 1979
Cdd:smart00249    1 YCSVCGKPddgGELLQCD--GCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47

PHD

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

1581-1626

2.19e-04

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 41.43 E-value: 2.19e-04

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 755528517   1581 ESKMMQCGKCDRWVHSKCESLSGTEDemyeilsnlPESVAYTCVNC 1626
Cdd:smart00249   11 GGELLQCDGCDRWYHQTCLGPPLLEE---------EPDGKWYCPKC 47

Herpes_BLLF1

pfam05109

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...

3152-3361

6.42e-04

Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 46.06 E-value: 6.42e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517  3152 VPHHQHLHSFPAAAQSSFP----PNISSP-PSGLLIG---VQPPPDPQLLGSE--ANQRTDLTTTVATPSSGLKK----- 3216
Cdd:pfam05109  448 LPSSTHVPTNLTAPASTGPtvstADVTSPtPAGTTSGaspVTPSPSPRDNGTEskAPDMTSPTSAVTTPTPNATSptpav 527

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517  3217 -RPISRLHTRKNKKLAPSSAPSNIAPSDVVSNMTLINFTPSQlsnhpSLLDLGSLNPSSHRTVPNIIKRSKSGIMYFEQA 3295
Cdd:pfam05109  528 tTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNA-----TIPTLGKTSPTSAVTTPTPNATSPTVGETSPQA 602

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755528517  3296 PLlPPQSVGGTAATAAGSSTISQDTSHLTSGP--VSALASGSSVLNVVSMQTTAAPTSSTSVPGHVTL 3361
Cdd:pfam05109  603 NT-TNHTLGGTSSTPVVTSPPKNATSAVTTGQhnITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPL 669

COG5141

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

1898-1975

2.91e-03

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

Pssm-ID: 227470 [Multi-domain] Cd Length: 669 Bit Score: 43.43 E-value: 2.91e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1898 NEWTHVNCALWSAEVfedddgSLKNVH-MAVIRGKQ--------LRCEFCQKPGAT-VGCCLTSCTSNYHFMCSRAKnCV 1967
Cdd:COG5141   266 GRWGHVICAMFNPEL------SFGHLLsKDPIDNIAsvsssrwkLGCLICKEFGGTcIQCSYFNCTRAYHVTCARRA-GY 338


                  ....*...
gi 755528517 1968 FldDKKVY 1975
Cdd:COG5141   339 F--DLNIY 344

Name

Accession

Description

Interval

E-value

ePHD_KMT2A

cd15693

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...

1873-1985

1.34e-82

Pssm-ID: 277163 Cd Length: 113 Bit Score: 266.87 E-value: 1.34e-82

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1873 RQCALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 1952
Cdd:cd15693     1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 755528517 1953 TSNYHFMCSRAKNCVFLDDKKVYCQRHRDLIKG 1985
Cdd:cd15693    81 TSNYHFMCSRAKNCVFLEDKKVYCQRHKDLIKG 113

ePHD_KMT2A_like

cd15664

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...

1875-1979

4.00e-72

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

Pssm-ID: 277134 Cd Length: 105 Bit Score: 236.53 E-value: 4.00e-72

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1954
Cdd:cd15664     1 CALCGVYGDDEPNDAGRLLYCGQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPA 80

                          90       100
                  ....*....|....*....|....*
gi 755528517 1955 NYHFMCSRAKNCVFLDDKKVYCQRH 1979
Cdd:cd15664    81 NYHFMCARKAECVFQDDKKVFCPAH 105

ePHD_KMT2B

cd15694

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...

1875-1979

1.09e-63

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

Pssm-ID: 277164 Cd Length: 105 Bit Score: 212.59 E-value: 1.09e-63

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1954
Cdd:cd15694     1 CALCLKYGDADSKDAGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLS 80

                          90       100
                  ....*....|....*....|....*
gi 755528517 1955 NYHFMCSRAKNCVFLDDKKVYCQRH 1979
Cdd:cd15694    81 NFHFMCARASRCCFQDDKKVFCQKH 105

Bromo_ALL-1

cd05493

Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and ...

1649-1779

2.86e-51

Pssm-ID: 99925 Cd Length: 131 Bit Score: 178.01 E-value: 2.86e-51

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1649 VLTALLNSRTTSHLLRYRqaAKPPDLNPETEESIPSRSSPEGPDPPV--LTEVSKQDEQQPLDLEGVKKRMDQGSYVSVL 1726
Cdd:cd05493     1 ELEELLDSRTKSHLLRCG--PKPPALLPETEESLPGRKSPVTPEVLQglLSSEVKQEELPPLDLEAVGKKLEAGFYTSVL 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 755528517 1727 EFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFW 1779
Cdd:cd05493    79 DFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFNSEDPKLW 131

PHD3_KMT2A

cd15592

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...

1567-1626

2.56e-36

Pssm-ID: 277067 Cd Length: 57 Bit Score: 132.42 E-value: 2.56e-36

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1567 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCESLSgteDEMYEILSNLPESVAYTCVNC 1626
Cdd:cd15592     1 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLS---DEMYEILSNLPESVAYTCINC 57

ePHD2_KMT2C_like

cd15666

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...

1875-1979

3.14e-36

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: 133.97 E-value: 3.14e-36

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1954
Cdd:cd15666     1 CVLCGGEGDGDTDGPGRLLNLDVDKWVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCAN 80

                          90       100
                  ....*....|....*....|....*
gi 755528517 1955 NYHFMCSRAKNCVFLDDKKVYCQRH 1979
Cdd:cd15666    81 VYHLPCAIKDGCMFFKDKTMLCPSH 105

PHD1_KMT2A

cd15588

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...

1432-1478

4.38e-33

Pssm-ID: 277063 Cd Length: 47 Bit Score: 123.14 E-value: 4.38e-33

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 755528517 1432 VCFLCASSGHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRC 1478
Cdd:cd15588     1 VCFLCASSGHVEFVYCQVCCEPFHKFCLEEAERPLEDQLENWCCRRC 47

FYRC

smart00542

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...

3666-3749

3.12e-32

Pssm-ID: 197781 Cd Length: 86 Bit Score: 122.02 E-value: 3.12e-32

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517   3666 LVFEISSDDGFQICAESIEDAWKSLTDKVQEARSNARLKQLSFAGVNGLRMLGILHDAVVFLIEQLAGAKHCRNYKFRFH 3745
Cdd:smart00542    2 FRVEIESDPGEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWFRYH 81


                    ....
gi 755528517   3746 KPEE 3749
Cdd:smart00542   82 RSPL 85

PHD2_KMT2A

cd15590

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...

1480-1529

5.55e-32

Pssm-ID: 277065 Cd Length: 50 Bit Score: 119.75 E-value: 5.55e-32

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 755528517 1480 FCHVCGRQHQATKQLLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1529
Cdd:cd15590     1 FCHVCGRQHQATKQLLECNKCRNSYHPECLGPNYPTKPTKKKRVWICTKC 50

ePHD

cd15571

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...

1875-1979

4.73e-30

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: 116.53 E-value: 4.73e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGDDSANdAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLK--NVHMAVIRGKQLRCEFCQKP-GATVGCCLTS 1951
Cdd:cd15571     1 CALCPRSGGALKG-GGALKTTSDGLWVHVVCALWSPEVYFDDGTLLEveGVSKIPKRRKKLKCSICGKRgGACIQCSYPG 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 755528517 1952 CTSNYHFMCSRAKNCVFL-----DDKKVYCQRH 1979
Cdd:cd15571    80 CPRSFHVSCAIRAGCLFEfedgpGNFVVYCPKH 112

ePHD2_KMT2C

cd15697

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...

1875-1979

1.17e-28

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

Pssm-ID: 277167 Cd Length: 105 Bit Score: 112.45 E-value: 1.17e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1954
Cdd:cd15697     1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                          90       100
                  ....*....|....*....|....*
gi 755528517 1955 NYHFMCSRAKNCVFLDDKKVYCQRH 1979
Cdd:cd15697    81 VYHFTCAIKAQCMFFKDKTMLCPMH 105

PHD1_KMT2A_like

cd15506

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...

1432-1478

1.77e-26

PHD finger 1 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 first PHD finger.

Pssm-ID: 276981 Cd Length: 47 Bit Score: 103.98 E-value: 1.77e-26

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 755528517 1432 VCFLCASSGHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRC 1478
Cdd:cd15506     1 LCFLCGSAGLNELLYCSVCCEPYHTFCLEEAERPLNINKDNWCCRRC 47

ePHD2_KMT2D

cd15698

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...

1875-1980

1.96e-26

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

Pssm-ID: 277168 Cd Length: 107 Bit Score: 106.29 E-value: 1.96e-26

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1954
Cdd:cd15698     1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                          90       100
                  ....*....|....*....|....*.
gi 755528517 1955 NYHFMCSRAKNCVFLDDKKVYCQRHR 1980
Cdd:cd15698    81 VYHFACAIRAKCMFFKDKTMLCPMHK 106

FYRC

pfam05965

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...

3661-3745

3.64e-24

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.

Pssm-ID: 461788 Cd Length: 83 Bit Score: 98.83 E-value: 3.64e-24

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517  3661 KPKkgLVFEISSDDGFQICAESIEDAWKSLTDKVQEARSNARLKQLSFAGVNGLRMLGILHDAVVFLIEQLAGAKHCRNY 3740
Cdd:pfam05965    1 GPL--FRVTVEEDPDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 755528517  3741 KFRFH 3745
Cdd:pfam05965   79 KFRYG 83

PHD1_KMT2B

cd15589

PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...

1432-1478

3.34e-23

PHD finger 1 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 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation 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) 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 first PHD finger.

Pssm-ID: 277064 Cd Length: 47 Bit Score: 94.92 E-value: 3.34e-23

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 755528517 1432 VCFLCASSGHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRC 1478
Cdd:cd15589     1 VCLLCASKGQHELLFCQVCCEPFHRFCLEESERPLPEQEENWCCRRC 47

PHD3_KMT2A_like

cd15508

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...

1567-1626

5.52e-23

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

Pssm-ID: 276983 Cd Length: 57 Bit Score: 94.43 E-value: 5.52e-23

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1567 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCESLSgteDEMYEILSNLPESVAYTCVNC 1626
Cdd:cd15508     1 YCPLCEKCYDDDDYDSKMMQCSQCDHWVHAKCEGLS---DEMYEILSYLPESIEYTCSLC 57

zf-CXXC

pfam02008

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...

1144-1191

9.42e-21

Pssm-ID: 366873 Cd Length: 48 Bit Score: 87.80 E-value: 9.42e-21

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 755528517  1144 KKGRRSRRCGQCPGCQVPEDCGICTNCLDKPKFGGRNIKKQCCKMRKC 1191
Cdd:pfam02008    1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48

PHD2_KMT2A_like

cd15507

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...

1480-1529

2.42e-20

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: 86.75 E-value: 2.42e-20

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 755528517 1480 FCHVCGRQHQATKQLLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1529
Cdd:cd15507     1 FCHVCGRKGQAQKQLLECEKCQRGYHVDCLGPSYPTKPTRKKKTWICSKC 50

PHD3_KMT2B

cd15593

PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...

1567-1626

2.22e-19

PHD finger 3 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 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation 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) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.

Pssm-ID: 277068 Cd Length: 57 Bit Score: 84.13 E-value: 2.22e-19

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1567 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCESLSgteDEMYEILSNLPESVAYTCVNC 1626
Cdd:cd15593     1 YCPICLKCYEDNDYESKMMQCAKCDHWVHAKCEGLS---DELYEILSSLPDSVVYSCAPC 57

ePHD_PHF6_like

cd15673

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...

1875-1979

8.10e-18

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

Pssm-ID: 277143 Cd Length: 116 Bit Score: 82.05 E-value: 8.10e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALClmYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVF------EDDDGS--LKNVHMAVIRGKQLRCEFCQKPGATVG 1946
Cdd:cd15673     1 CGFC--KSGEENKETGGKLASGEKIAAHHNCMLFSSGLVqyvspnENDFGGfdIEDVKKEIKRGRKLKCNLCKKTGATIG 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 755528517 1947 CCLTSCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1979
Cdd:cd15673    79 CDVKQCKKTYHYHCAKKDDAKIIERNsqgiyRVYCKNH 116

PHD2_KMT2B

cd15591

PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...

1480-1529

3.33e-17

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: 77.67 E-value: 3.33e-17

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 755528517 1480 FCHVCGRQHQATKQLLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1529
Cdd:cd15591     1 FCHVCGRKNKESKPLLECERCRNCYHPACLGPNYPKPANRKKRPWICSAC 50

ePHD_RAI1_like

cd15668

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...

1900-1979

3.70e-17

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

Pssm-ID: 277138 Cd Length: 103 Bit Score: 79.66 E-value: 3.70e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1900 WTHVNCALWSAEVFEDDdGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCVFLDDK-KVYCQR 1978
Cdd:cd15668    24 WVHEDCAVWAPGVYLVG-GKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHKGCKAKYHYPCAVESGCQLDEENfSLLCPK 102


                  .
gi 755528517 1979 H 1979
Cdd:cd15668   103 H 103

ePHD1_KMT2C_like

cd15665

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...

1900-1979

5.47e-17

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: 78.52 E-value: 5.47e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1900 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCvFLDDKK--VYCQ 1977
Cdd:cd15665    10 YAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSKSFHFPCAAAAGC-FQDIKTltLFCP 88


                  ..
gi 755528517 1978 RH 1979
Cdd:cd15665    89 EH 90

ePHD_PHF7_G2E3_like

cd15669

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...

1875-1979

3.88e-16

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

Pssm-ID: 277139 [Multi-domain] Cd Length: 112 Bit Score: 76.91 E-value: 3.88e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMyGDDSANDAGRLLYIGqNEWTHVNCALWSAEVF---EDDDG----SLKNVHMAVIRGKQLRCEFCQKPGATVGC 1947
Cdd:cd15669     1 CVLCGR-SDDDPDKYGEKLQKD-GICAHYFCLLFSSGLPqrgEDNEGiygfLPEDIRKEVRRASRLRCFYCKKKGASIGC 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 755528517 1948 CLTSCTSNYHFMCSRAKNCV--FLDDKKVYCQRH 1979
Cdd:cd15669    79 AVKGCRRSFHFPCGLENGCVtqFFGEYRSFCWEH 112

FYRN

pfam05964

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...

2026-2073

4.40e-16

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.

Pssm-ID: 461787 Cd Length: 51 Bit Score: 74.46 E-value: 4.40e-16

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 755528517  2026 GSMTIDCLGIL---NDLSDCEDKLFPIGYQCSRVYWSTTDARKRCVYTCKI 2073
Cdd:pfam05964    1 GSLTVLSLGEIvpdRPAFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51

zf-HC5HC2H

pfam13771

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...

1902-1979

7.68e-16

Pssm-ID: 463977 [Multi-domain] Cd Length: 88 Bit Score: 75.06 E-value: 7.68e-16

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517  1902 HVNCALWSAEVFEDDDGS----LKNVHMAVIRGKQLRCEFC-QKPGATVGCCLTSCTSNYHFMCSRAKNCVF-----LDD 1971
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqfdedNGT 80


                   ....*...
gi 755528517  1972 KKVYCQRH 1979
Cdd:pfam13771   81 FKSYCKKH 88

FYRN

smart00541

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...

2032-2075

9.88e-16

Pssm-ID: 128814 Cd Length: 44 Bit Score: 73.47 E-value: 9.88e-16

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 755528517   2032 CLGILNDLSDCEDKLFPIGYQCSRVYWSTTDARKRCVYTCKIME 2075
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44

ePHD_PHF11

cd15712

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...

1875-1979

2.80e-15

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.

Pssm-ID: 277182 [Multi-domain] Cd Length: 115 Bit Score: 74.55 E-value: 2.80e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALClmygddSANDAGRLLYIG--QNEWTHVNCALWSAEVFEDDDGSLKN---------VHMAVIRGKQLRCEFCQKPGA 1943
Cdd:cd15712     1 CAFC------PKGEEYSIMYFAqeQNIAAHQNCLLYSSGFVESEEYNPLNldrrfdvesVLNEIKRGKRLKCNFCRKKGA 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 755528517 1944 TVGCCLTSCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1979
Cdd:cd15712    75 TVGCEERACRRSYHYFCALCDDAAIETDEvrgiyRVFCQKH 115

ePHD1_KMT2C

cd15696

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...

1900-1963

6.40e-14

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

Pssm-ID: 277166 Cd Length: 90 Bit Score: 69.97 E-value: 6.40e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755528517 1900 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRA 1963
Cdd:cd15696    10 WAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAG 73

ePHD1_KMT2D

cd15695

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...

1900-1963

1.66e-12

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

Pssm-ID: 277165 Cd Length: 90 Bit Score: 65.71 E-value: 1.66e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755528517 1900 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRA 1963
Cdd:cd15695    10 WVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAA 73

ePHD_RAI1

cd15700

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...

1900-1979

1.78e-12

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

Pssm-ID: 277170 Cd Length: 104 Bit Score: 66.05 E-value: 1.78e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1900 WTHVNCALWSAEVFEDDdGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCVFLDDK-KVYCQR 1978
Cdd:cd15700    25 WVHEACAVWTTGVYLVA-GKLFGLQEAVQKAADAKCSSCQGAGATVGCCHKGCTQSYHYICAVEAGCLFEEENfSLRCPK 103


                  .
gi 755528517 1979 H 1979
Cdd:cd15700   104 H 104

BROMO

smart00297

bromo domain;

1635-1767

5.31e-11

bromo domain;

Pssm-ID: 197636 [Multi-domain] Cd Length: 107 Bit Score: 61.91 E-value: 5.31e-11

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517   1635 RLALEKELQASLKQVLTALLNSRTTSHLLryrqaaKPPDLNpeteesipsrsspEGPDppvltevSKQDEQQPLDLEGVK 1714
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFL------KPVSRK-------------EAPD-------YYDIIKKPMDLKTIK 54

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 755528517   1715 KRMDQGSYVSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERV 1767
Cdd:smart00297   55 KKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

PHD

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...

1432-1481

6.37e-10

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 57.12 E-value: 6.37e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 755528517  1432 VCFLCASSG-HVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRCKFC 1481
Cdd:pfam00628    1 YCAVCGKSDdGGELVQCDGCDDWFHLACLGPPLDPAEIPSGEWLCPECKPK 51

ePHD2_PHF6

cd15711

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...

1875-1979

1.09e-09

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4.

Pssm-ID: 277181 Cd Length: 118 Bit Score: 58.94 E-value: 1.09e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMyGDDSANDAGRL-LYIGQNEWTHVNCALWSAEVF--------EDDDGSLKNVHMAVIRGKQLRCEFCQKPGATV 1945
Cdd:cd15711     1 CGFCHA-GEEENETRGKLhIFNAKKAAAHYKCMLFSSGTVqltttsraEFGDFDIKTVIQEIKRGKRMKCTLCSQLGATI 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 755528517 1946 GCCLTSCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1979
Cdd:cd15711    80 GCEIKACVKTYHYHCGVQDKAKYIENMsrgiyKLYCKNH 118

ePHD_TCF20

cd15699

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...

1900-1979

2.28e-09

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

Pssm-ID: 277169 Cd Length: 103 Bit Score: 57.23 E-value: 2.28e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1900 WTHVNCALWSAEVFEDDdGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCVFLDDK-KVYCQR 1978
Cdd:cd15699    24 WVHEGCILWANGIYLVC-GRLYGLQEALDIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAIDADCLLNEENfSVRCPK 102


                  .
gi 755528517 1979 H 1979
Cdd:cd15699   103 H 103

PHD

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

1480-1529

2.91e-09

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 55.30 E-value: 2.91e-09

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 755528517   1480 FCHVCGRQHqATKQLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1529
Cdd:smart00249    1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEPDGK--WYCPKC 47

PHD_SF

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...

1480-1529

3.34e-09

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

Pssm-ID: 276966 [Multi-domain] Cd Length: 48 Bit Score: 55.02 E-value: 3.34e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 755528517 1480 FCHVCGRQHQATKQLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1529
Cdd:cd15489     1 SCIVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGK--WICPVC 48

zf-HC5HC2H_2

pfam13832

PHD-zinc-finger like domain;

1873-1979

3.44e-09

PHD-zinc-finger like domain;

Pssm-ID: 463991 [Multi-domain] Cd Length: 109 Bit Score: 56.97 E-value: 3.44e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517  1873 RQCALCLMYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNV---HMAVIRGKqLRCEFCQKP-GATVGCC 1948
Cdd:pfam13832    1 VRCCLCPLRG-------GALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIdvsRIPPERWK-LKCVFCKKRsGACIQCS 72

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 755528517  1949 LTSCTSNYHFMCSRAKNCVF-LDD-----KKVYCQRH 1979
Cdd:pfam13832   73 KGRCTTAFHVTCAQAAGVYMePEDwpnvvVIAYCQKH 109

ePHD1_PHF6

cd15710

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...

1875-1979

1.55e-08

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .

Pssm-ID: 277180 Cd Length: 115 Bit Score: 55.35 E-value: 1.55e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGDDsanDAGRLLyIGQNE--WTHVNCALWS-AEVFEDDDG------SLKNVHMAVIRGKQLRCEFCQKPGATV 1945
Cdd:cd15710     1 CGFCRSNREK---ECGQLL-ISENQkvAAHHKCMLFSsALVSSHSDSenlggfSIEDVQKEIKRGTKLMCSLCHCPGATI 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 755528517 1946 GCCLTSCTSNYHFMCSrakncvfLDDKK------------VYCQRH 1979
Cdd:cd15710    77 GCDVKTCHRTYHYYCA-------LHDKAqirenpsqgiymIYCRKH 115

PHD

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...

1480-1532

6.93e-08

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 51.34 E-value: 6.93e-08

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 755528517  1480 FCHVCGRQHqATKQLLECNKCRNSYHPECLGPNyPTKPTKKKKVWICTKCVRC 1532
Cdd:pfam00628    1 YCAVCGKSD-DGGELVQCDGCDDWFHLACLGPP-LDPAEIPSGEWLCPECKPK 51

ePHD_JADE

cd15671

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...

1875-1979

1.36e-06

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: 49.75 E-value: 1.36e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGDD-SANDAGRllyigqnEWTHVNCALWSAEV-FEDDDG--SLKNV-HMAVIRgKQLRCEFCQ-KPGATVGCC 1948
Cdd:cd15671     1 CVLCPKKGGAmKSTKSGT-------KWVHVSCALWIPEVsIGCPEKmePITKIsHIPMSR-WALVCVLCKeKTGACIQCS 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 755528517 1949 LTSCTSNYHFMCS-----RAKNCVFLDDKKV----YCQRH 1979
Cdd:cd15671    73 VKSCKTAFHVTCAfqhglEMKTILEDEDDEVkfksYCPKH 112

PHD

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...

1581-1629

1.18e-05

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 45.18 E-value: 1.18e-05

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 755528517  1581 ESKMMQCGKCDRWVHSKCESLSgteDEMYEILSNlpesvAYTCVNCTER 1629
Cdd:pfam00628   11 GGELVQCDGCDDWFHLACLGPP---LDPAEIPSG-----EWLCPECKPK 51

ePHD_JMJD2

cd15675

Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...

1875-1979

1.98e-05

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: 46.20 E-value: 1.98e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGK--QLRCEFCQK-------PGATV 1945
Cdd:cd15675     1 CCLCCLRG-------GALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPIDISKIPPArlKLKCIYCSKitksmshMGACI 73

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 755528517 1946 GCCLTSCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1979
Cdd:cd15675    74 QCSTGKCTTSFHVTCAHAAGVQMEPDDwpypvYVTCTKH 112

ePHD_BRPF

cd15670

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...

1898-1979

2.28e-05

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: 46.17 E-value: 2.28e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1898 NEWTHVNCALWSAEVfedddgSLKN-VHMAVIRGKQ--------LRCEFC-QKPGATVGCCLTSCTSNYHFMC------- 1960
Cdd:cd15670    17 GRWAHVVCALWIPEV------SFANtVFLEPIDGIQnipkarwkLTCYICkKRMGACIQCHKKNCYTAFHVTCaqqagly 90

                          90       100
                  ....*....|....*....|....*.
gi 755528517 1961 -----SRAKNCVFLDD--KKVYCQRH 1979
Cdd:cd15670    91 mkiepVKDPGNGTSDSvrKEAYCDKH 116

PHD

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

1432-1478

7.29e-05

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 42.58 E-value: 7.29e-05

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 755528517   1432 VCFLCASSGH-VEFVYCQVCCEPFHKFCLEENERPlEDQLENWCCRRC 1478
Cdd:smart00249    1 YCSVCGKPDDgGELLQCDGCDRWYHQTCLGPPLLE-EEPDGKWYCPKC 47

PHD

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

1934-1979

9.70e-05

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 42.58 E-value: 9.70e-05

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 755528517   1934 RCEFCQKP---GATVGCCltSCTSNYHFMCSRAKNCVFLDDKKVYCQRH 1979
Cdd:smart00249    1 YCSVCGKPddgGELLQCD--GCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47

PHD6_KMT2C_like

cd15514

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...

1583-1626

1.36e-04

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 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, 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 sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D.

Pssm-ID: 276989 Cd Length: 51 Bit Score: 41.89 E-value: 1.36e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 755528517 1583 KMMQCGKCDRWVHSKCESLSgTEDEMyEILSNlpesVAYTCVNC 1626
Cdd:cd15514    14 LIIQCSQCERWLHGACDSLR-TEEEA-ERAAD----NGYRCLLC 51

PHD_Int12

cd15501

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...

1481-1529

1.81e-04

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation.

Pssm-ID: 276976 Cd Length: 52 Bit Score: 41.95 E-value: 1.81e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 755528517 1481 CHVCGRQHQATK-QLLECNKCRNSYHPECLGPNYPTKPTK-KKKVWICTKC 1529
Cdd:cd15501     2 CVVCKQMDVTSGnQLVECQECHNLYHQECHKPPVTDKDVNdPRLVWYCSRC 52

ePHD_JADE3

cd15706

Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...

1899-1979

2.14e-04

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: 43.56 E-value: 2.14e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1899 EWTHVNCALWSAEVF----EDDDGSLKNVHMAVIRGkQLRCEFCQ-KPGATVGCCLTSCTSNYHFMCSRAKNC---VFLD 1970
Cdd:cd15706    19 KWAHVSCALWIPEVSiacpERMEPITKVSHIPPSRW-ALVCSLCKlKTGACIQCSVKSCITAFHVTCAFEHSLemkTILD 97

                          90
                  ....*....|....
gi 755528517 1971 DK-----KVYCQRH 1979
Cdd:cd15706    98 EGdevkfKSYCLKH 111

PHD

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

1581-1626

2.19e-04

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 41.43 E-value: 2.19e-04

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 755528517   1581 ESKMMQCGKCDRWVHSKCESLSGTEDemyeilsnlPESVAYTCVNC 1626
Cdd:smart00249   11 GGELLQCDGCDRWYHQTCLGPPLLEE---------EPDGKWYCPKC 47

PHD_UHRF1_2

cd15525

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...

1481-1529

3.25e-04

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

Pssm-ID: 277000 Cd Length: 47 Bit Score: 40.82 E-value: 3.25e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 755528517 1481 CHVCGRQHQATKQLLeCNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1529
Cdd:cd15525     2 CHVCGGKQDPEKQLL-CDECDMAYHLYCLDPPLTSLPDDDE--WYCPDC 47

PHD2_CHD_II

cd15532

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...

1480-1529

3.36e-04

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: 40.73 E-value: 3.36e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 755528517 1480 FCHVCGRqhqaTKQLLECNKCRNSYHPECLGPNyptKPTKKKKVWICTKC 1529
Cdd:cd15532     1 FCRVCKD----GGELLCCDGCPSSYHLHCLNPP---LAEIPDGDWFCPRC 43

PHD_UHRF2

cd15617

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...

1481-1529

4.01e-04

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: 40.71 E-value: 4.01e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 755528517 1481 CHVCGRQHQATKQLLeCNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1529
Cdd:cd15617     2 CYVCGGKQDAHMQLL-CDECNMAYHIYCLNPPLDKIPEDED--WYCPSC 47

ePHD_ATX1_2_like

cd15662

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...

1875-1979

4.04e-04

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: 42.85 E-value: 4.04e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMavIRGKQ-----LRCEFCQKP-GATVGCC 1948
Cdd:cd15662     1 CCLCPVVG-------GALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDG--INAISkerweLSCTICKQRyGACIQCS 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 755528517 1949 LTSCTSNYHFMCSRAKN-CVFLDDKKV------------YCQRH 1979
Cdd:cd15662    72 NNSCRVAYHPLCARAAGlCMEVADEGGedpgdqglrllsYCPRH 115

ePHD_BRPF1

cd15701

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...

1875-1962

4.46e-04

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: 42.76 E-value: 4.46e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALClmygddsANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNV----HMAVIRGKqLRCEFCQK--PGATVGCC 1948
Cdd:cd15701     1 CALC-------PNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIdsieHIPPARWK-LTCYICKQrgSGACIQCH 72

                          90
                  ....*....|....
gi 755528517 1949 LTSCTSNYHFMCSR 1962
Cdd:cd15701    73 KANCYTAFHVTCAQ 86

ePHD_ATX3_4_5_like

cd15663

Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The ...

1900-1979

5.36e-04

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: 42.12 E-value: 5.36e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1900 WTHVNCALWSAEV-FEDDDG-----SLKNVHMAVIRGKqlrCEFC-QKPGATVGCCltSCTSNYHFMC-SRA-------- 1963
Cdd:cd15663    20 WVHVTCAWFRPEVcFKNEEKmepavGLLRIPLSTFLKA---CVICkQIHGSCTQCC--KCATYFHAMCaSRAgyhmelhc 94

                          90
                  ....*....|....*...
gi 755528517 1964 --KNCVFLDDKKVYCQRH 1979
Cdd:cd15663    95 leKNGVQITRMVSYCSFH 112

Herpes_BLLF1

pfam05109

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...

3152-3361

6.42e-04

Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 46.06 E-value: 6.42e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517  3152 VPHHQHLHSFPAAAQSSFP----PNISSP-PSGLLIG---VQPPPDPQLLGSE--ANQRTDLTTTVATPSSGLKK----- 3216
Cdd:pfam05109  448 LPSSTHVPTNLTAPASTGPtvstADVTSPtPAGTTSGaspVTPSPSPRDNGTEskAPDMTSPTSAVTTPTPNATSptpav 527

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517  3217 -RPISRLHTRKNKKLAPSSAPSNIAPSDVVSNMTLINFTPSQlsnhpSLLDLGSLNPSSHRTVPNIIKRSKSGIMYFEQA 3295
Cdd:pfam05109  528 tTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNA-----TIPTLGKTSPTSAVTTPTPNATSPTVGETSPQA 602

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755528517  3296 PLlPPQSVGGTAATAAGSSTISQDTSHLTSGP--VSALASGSSVLNVVSMQTTAAPTSSTSVPGHVTL 3361
Cdd:pfam05109  603 NT-TNHTLGGTSSTPVVTSPPKNATSAVTTGQhnITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPL 669

PHD1_PHF1

cd15500

PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 ...

1481-1529

7.10e-04

PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with 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. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the first PHD finger.

Pssm-ID: 276975 Cd Length: 51 Bit Score: 40.20 E-value: 7.10e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 755528517 1481 CHVCGRQHQATK-QLLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1529
Cdd:cd15500     2 CCVCDSETVSPKnPLVNCEKCHHAYHQECHVPRVPLESAGDGDSWMCRQC 51

ePHD_JADE2

cd15705

Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant ...

1899-1979

7.19e-04

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: 42.00 E-value: 7.19e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1899 EWTHVNCALWSAEVF----EDDDGSLKNVHMAVIRGKqLRCEFCQK-PGATVGCCLTSCTSNYHFMCSRAKN----CVFL 1969
Cdd:cd15705    19 KWVHVSCALWIPEVSigcpEKMEPITKISHIPASRWA-LSCSLCKEcTGTCIQCSMPSCITAFHVTCAFDHGlemrTTLA 97

                          90
                  ....*....|....
gi 755528517 1970 DDKKV----YCQRH 1979
Cdd:cd15705    98 DNDEVkfksFCLEH 111

Bromodomain

cd04369

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...

1705-1759

8.18e-04

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

Pssm-ID: 99922 [Multi-domain] Cd Length: 99 Bit Score: 41.20 E-value: 8.18e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 755528517 1705 QQPLDLEGVKKRMDQGSYVSVLEFSDDIVKIIQAAINSDGGQPEI-KKANSMVKSF 1759
Cdd:cd04369    40 KNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIyKDAKKLEKLF 95

PHD_Phf1p_Phf2p_like

cd15502

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...

1480-1529

9.06e-04

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

Pssm-ID: 276977 Cd Length: 52 Bit Score: 39.73 E-value: 9.06e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 755528517 1480 FCHVCGRQHQATK-QLLECNKCRNSYHPECLGPN-YPTKPTKKKKVWICTKC 1529
Cdd:cd15502     1 VCIVCQRGHSPKSnRIVFCDGCNTPYHQLCHDPSiDDEVVEDPDAEWFCKKC 52

PHD_SF

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...

1581-1626

1.07e-03

Pssm-ID: 276966 [Multi-domain] Cd Length: 48 Bit Score: 39.61 E-value: 1.07e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 755528517 1581 ESKMMQCGKCDRWVHSKCESLSGTEdemyeilsnLPESVAYTCVNC 1626
Cdd:cd15489    12 GGELLQCDGCGKWFHADCLGPPLSS---------FVPNGKWICPVC 48

ePHD_RNO

cd15707

Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...

1875-1979

1.14e-03

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: 41.43 E-value: 1.14e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALCLMYGddSANDAGRllyiGQNEWTHVNCALWSAEV----FEDDDGSLKNVHMAVIRGkQLRCEFC-QKPGATVGCCL 1949
Cdd:cd15707     1 CILCPNKG--GAMKSTR----SGTKWAHVSCALWIPEVsigcVEKMEPITKISSIPASRW-ALICVLCrERTGACIQCSV 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 755528517 1950 TSCTSNYHFMCSRAKNC---VFLDDK-------KVYCQRH 1979
Cdd:cd15707    74 KTCKTAYHVTCGFQHGLemkTILDEEsedgvklRSYCQKH 113

PHD5_KMT2D

cd15601

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...

1581-1626

1.23e-03

PHD finger 5 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 downregulated 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 fifth PHD finger.

Pssm-ID: 277074 Cd Length: 51 Bit Score: 39.50 E-value: 1.23e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 755528517 1581 ESKMMQCGKCDRWVHSKCESLSgTEDEMYEILSNlpesvAYTCVNC 1626
Cdd:cd15601    12 EDLLIQCRHCDRWVHAVCESLF-TEDEVEQAADE-----GFDCSSC 51

PHD_TCF19_like

cd15517

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...

1585-1626

1.42e-03

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

Pssm-ID: 276992 [Multi-domain] Cd Length: 49 Bit Score: 39.07 E-value: 1.42e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 755528517 1585 MQCGKCDRWVHSKCESLSGTEDEMYEIlsnlpesvaYTCVNC 1626
Cdd:cd15517    17 VQCDGCDKWFHQFCLGLSNERYADEDK---------FKCPNC 49

PHD_SF

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...

1432-1478

1.57e-03

Pssm-ID: 276966 [Multi-domain] Cd Length: 48 Bit Score: 39.22 E-value: 1.57e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 755528517 1432 VCFLCASSGHV--EFVYCQVCCEPFHKFCLEENErPLEDQLENWCCRRC 1478
Cdd:cd15489     1 SCIVCGKGGDLggELLQCDGCGKWFHADCLGPPL-SSFVPNGKWICPVC 48

PHD_UHRF1

cd15616

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...

1481-1529

1.72e-03

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

Pssm-ID: 277088 Cd Length: 47 Bit Score: 38.80 E-value: 1.72e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 755528517 1481 CHVCGRQHQATKQLLeCNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1529
Cdd:cd15616     2 CHVCGGKQDPDKQLM-CDECDMAFHIYCLNPPLSSIPDDED--WYCPEC 47

PHD6_KMT2C

cd15600

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...

1581-1627

1.96e-03

PHD finger 6 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 sixth PHD finger.

Pssm-ID: 277073 Cd Length: 51 Bit Score: 38.76 E-value: 1.96e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 755528517 1581 ESKMMQCGKCDRWVHSKCESLSgTEDEMyeilsnlpESVAYTCVNCT 1627
Cdd:cd15600    12 EELILQCRQCDRWMHASCQNLN-TEEEV--------ENAADNGFDCT 49

ePHD_BRPF3

cd15703

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...

1875-1979

2.11e-03

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: 40.81 E-value: 2.11e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755528517 1875 CALClmygddsANDAGRLLYIGQNEWTHVNCALWSAE------VFEDDDGSLKNVHMAviRGKqLRCEFCQKP--GATVG 1946
Cdd:cd15703     1 CVLC-------PNKGGAFKQTSDGRWAHVVCAIWIPEvcfantVFLEPVEGVNNIPPA--RWK-LTCYLCKQKgrGAAIQ 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 755528517 1947 CCLTSCTSNYHFMCS-RA--------------KNCVFLDDKKVYCQRH 1979
Cdd:cd15703    71 CHKVNCYTAFHVTCAqRAglfmkiepvretglNGTTFTVRKTAYCENH 118

PHD_SF