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Conserved domains on  [gi|655860861|ref|XP_008266793|]
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lysine-specific demethylase 5B isoform X4 [Oryctolagus cuniculus]

Protein Classification

ARID_KDM5B and PLU-1 domain-containing protein( domain architecture ID 13013813)

protein containing domains ARID_KDM5B, JmjC, PLU-1, and PHD3_KDM5B

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PLU-1 pfam08429
PLU-1-like protein; Sequences in this family bear similarity to the central region of PLU-1. ...
691-1022 1.28e-118

PLU-1-like protein; Sequences in this family bear similarity to the central region of PLU-1. This is a nuclear protein that may have a role in DNA-binding and transcription, and is closely associated with the malignant phenotype of breast cancer. This region is found in various other Jumonji/ARID domain-containing proteins (see pfam02373, pfam01388).


:

Pssm-ID: 429992 [Multi-domain]  Cd Length: 336  Bit Score: 375.01  E-value: 1.28e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   691 EWALTVNEALEAkiNKKKSLVSFKALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLTGKRQTRYRSG---GGKS 767
Cdd:pfam08429    1 TWAEKVEEALEE--EPKPSLKELRALLNEAEKIKFPLPELLQDLRAFVQRANKWVEEAQQLLSRKQRTRRKNEaeeDERE 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   768 QNQLTVNELRQFVTQLYALPCVLSQTPLLKDLLDRVEDFQQHSQKLLSEEMP--SAAELQDLLDVSFEFDVELPQLAEMR 845
Cdd:pfam08429   79 REKRTVEELRKLLEEADNLPFDCPEIDQLKELLEEIEEFQKRAREALSEEPPslSIEELEELLEEGKSFNVDLPELEELE 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   846 VRLEQARWLEEVQQAcLDPGSLTLDDMRRLIDLGVGLAPYSAVEKAMARLQELLTVSEHWDDKAKSLLKaRPRHSLNSLA 925
Cdd:pfam08429  159 KVLEQLKWLEEVREF-SRKKSLTLEDVRELIEEGVELGIPPPYEDAMAELQELLTAGERWEEKAKELLS-RERVSLAQLE 236
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   926 TAVKEIEEIPAYLPNGAALKDSVQRAKDWLQDVEALQ----AGGRvPVLDTLLELVTRGRSIPVHLNSLPRLESLVAEVQ 1001
Cdd:pfam08429  237 ALSKEAQNIPVSLPNLAALDEILKKAREWQRQIEALYqrsdFGKR-PTLDELEELVAKGESLPVKPEGLSDLEKEVKRAE 315
                          330       340
                   ....*....|....*....|.
gi 655860861  1002 AWKECAANTFLTENSPYSLLE 1022
Cdd:pfam08429  316 DWKRRGKKLFLKKNAPLTLLE 336
ARID_KDM5B cd16874
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called ...
28-117 2.14e-59

ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called cancer/testis antigen 31 (CT31), histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible earlygene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers.


:

Pssm-ID: 350638  Cd Length: 90  Bit Score: 198.24  E-value: 2.14e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   28 EAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRG 107
Cdd:cd16874     1 EAQTRVKLNFLDQIAKFWELQGCTLKIPHVERKILDLFQLNKLVAEEGGFDLVCKERKWTKIATKMGFAPGKAVGSHIRA 80
                          90
                  ....*....|
gi 655860861  108 HYERILNPYN 117
Cdd:cd16874    81 HYERILYPYN 90
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
420-536 1.10e-52

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation.


:

Pssm-ID: 396791  Cd Length: 114  Bit Score: 180.19  E-value: 1.10e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   420 WLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLETVMKklaPELFVSQPDLLHQLVTIMNPNTLMTHE 499
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77
                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 655860861   500 VPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNF 536
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
PHD3_KDM5B cd15687
PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis ...
1413-1462 2.85e-30

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


:

Pssm-ID: 277157  Cd Length: 50  Bit Score: 113.89  E-value: 2.85e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 655860861 1413 LCPAASCLQPEGDEVDWVQCDGSCDQWFHQVCVGVSPEMAEKEDYICVRC 1462
Cdd:cd15687     1 LCPAVSCLQPEGEEVDWVQCDGSCNRWFHQVCVGVSAEMAEKEDYICVSC 50
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
245-290 4.87e-28

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


:

Pssm-ID: 277076  Cd Length: 46  Bit Score: 107.34  E-value: 4.87e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD2_KDM5B cd15607
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
1112-1155 2.27e-22

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


:

Pssm-ID: 277080  Cd Length: 44  Bit Score: 91.05  E-value: 2.27e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 655860861 1112 VCLCQKGPAAPMIQCELCRGAFHTGCVAVPSVSQGPQIWLCPHC 1155
Cdd:cd15607     1 VCVCQKAPMAPMIQCELCRDAFHSGCVTAPSDPQGPQAWLCPQC 44
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
626-678 2.04e-18

C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.


:

Pssm-ID: 427059  Cd Length: 54  Bit Score: 79.98  E-value: 2.04e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 655860861   626 CVKCKTTCFMSAISCSCKPGLLVCLHHVKELCS-CPPHKYKLRYRYTLDDLYPM 678
Cdd:pfam02928    1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
TNG2 super family cl34876
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
1034-1156 1.70e-03

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


The actual alignment was detected with superfamily member COG5034:

Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 41.85  E-value: 1.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861 1034 GLKRKQRKFKEPLLSGKKRSTKLESLSdlERALTESRETASAMAAlgeaRLREMEALQSLrlANEGKLLSPVQDVEMKVC 1113
Cdd:COG5034   153 GSRHTKLKKRKNIHNLKRRSPELSSKR--EVSFTLESPSVPDTAT----RVKEGNNGGST--KSRGVSSEDNSEGEELYC 224
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861 1114 LCQKGPAAPMIQC--ELC-RGAFHTGCVAVPSVSQGpqIWLCPHCR 1156
Cdd:COG5034   225 FCQQVSYGQMVACdnANCkREWFHLECVGLKEPPKG--KWYCPECK 268
 
Name Accession Description Interval E-value
PLU-1 pfam08429
PLU-1-like protein; Sequences in this family bear similarity to the central region of PLU-1. ...
691-1022 1.28e-118

PLU-1-like protein; Sequences in this family bear similarity to the central region of PLU-1. This is a nuclear protein that may have a role in DNA-binding and transcription, and is closely associated with the malignant phenotype of breast cancer. This region is found in various other Jumonji/ARID domain-containing proteins (see pfam02373, pfam01388).


Pssm-ID: 429992 [Multi-domain]  Cd Length: 336  Bit Score: 375.01  E-value: 1.28e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   691 EWALTVNEALEAkiNKKKSLVSFKALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLTGKRQTRYRSG---GGKS 767
Cdd:pfam08429    1 TWAEKVEEALEE--EPKPSLKELRALLNEAEKIKFPLPELLQDLRAFVQRANKWVEEAQQLLSRKQRTRRKNEaeeDERE 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   768 QNQLTVNELRQFVTQLYALPCVLSQTPLLKDLLDRVEDFQQHSQKLLSEEMP--SAAELQDLLDVSFEFDVELPQLAEMR 845
Cdd:pfam08429   79 REKRTVEELRKLLEEADNLPFDCPEIDQLKELLEEIEEFQKRAREALSEEPPslSIEELEELLEEGKSFNVDLPELEELE 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   846 VRLEQARWLEEVQQAcLDPGSLTLDDMRRLIDLGVGLAPYSAVEKAMARLQELLTVSEHWDDKAKSLLKaRPRHSLNSLA 925
Cdd:pfam08429  159 KVLEQLKWLEEVREF-SRKKSLTLEDVRELIEEGVELGIPPPYEDAMAELQELLTAGERWEEKAKELLS-RERVSLAQLE 236
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   926 TAVKEIEEIPAYLPNGAALKDSVQRAKDWLQDVEALQ----AGGRvPVLDTLLELVTRGRSIPVHLNSLPRLESLVAEVQ 1001
Cdd:pfam08429  237 ALSKEAQNIPVSLPNLAALDEILKKAREWQRQIEALYqrsdFGKR-PTLDELEELVAKGESLPVKPEGLSDLEKEVKRAE 315
                          330       340
                   ....*....|....*....|.
gi 655860861  1002 AWKECAANTFLTENSPYSLLE 1022
Cdd:pfam08429  316 DWKRRGKKLFLKKNAPLTLLE 336
ARID_KDM5B cd16874
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called ...
28-117 2.14e-59

ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called cancer/testis antigen 31 (CT31), histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible earlygene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers.


Pssm-ID: 350638  Cd Length: 90  Bit Score: 198.24  E-value: 2.14e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   28 EAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRG 107
Cdd:cd16874     1 EAQTRVKLNFLDQIAKFWELQGCTLKIPHVERKILDLFQLNKLVAEEGGFDLVCKERKWTKIATKMGFAPGKAVGSHIRA 80
                          90
                  ....*....|
gi 655860861  108 HYERILNPYN 117
Cdd:cd16874    81 HYERILYPYN 90
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
420-536 1.10e-52

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 180.19  E-value: 1.10e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   420 WLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLETVMKklaPELFVSQPDLLHQLVTIMNPNTLMTHE 499
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77
                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 655860861   500 VPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNF 536
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
PHD3_KDM5B cd15687
PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis ...
1413-1462 2.85e-30

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


Pssm-ID: 277157  Cd Length: 50  Bit Score: 113.89  E-value: 2.85e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 655860861 1413 LCPAASCLQPEGDEVDWVQCDGSCDQWFHQVCVGVSPEMAEKEDYICVRC 1462
Cdd:cd15687     1 LCPAVSCLQPEGEEVDWVQCDGSCNRWFHQVCVGVSAEMAEKEDYICVSC 50
BRIGHT smart00501
BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a ...
32-122 5.53e-30

BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure


Pssm-ID: 128777 [Multi-domain]  Cd Length: 93  Bit Score: 114.29  E-value: 5.53e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861     32 RVKLNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAP-GKAVGSHIRGHY 109
Cdd:smart00501    1 RERVLFLDRLYKFMEERGSPLkKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDtSTSAASSLRKHY 80
                            90
                    ....*....|...
gi 655860861    110 ERILNPYNLFLSG 122
Cdd:smart00501   81 ERYLLPYERFLRG 93
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
245-290 4.87e-28

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


Pssm-ID: 277076  Cd Length: 46  Bit Score: 107.34  E-value: 4.87e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
ARID pfam01388
ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, ...
34-116 2.55e-24

ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.


Pssm-ID: 426236  Cd Length: 87  Bit Score: 98.09  E-value: 2.55e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861    34 KLNFLDQIAKYWELQGSTLK-IPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPG-KAVGSHIRGHYER 111
Cdd:pfam01388    2 KELFLKSLRKFHEKRGTPLKnIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNKWREVAEKLGFPPGaTSAAFQLKQIYEK 81

                   ....*
gi 655860861   112 ILNPY 116
Cdd:pfam01388   82 YLLPY 86
PHD2_KDM5B cd15607
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
1112-1155 2.27e-22

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


Pssm-ID: 277080  Cd Length: 44  Bit Score: 91.05  E-value: 2.27e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 655860861 1112 VCLCQKGPAAPMIQCELCRGAFHTGCVAVPSVSQGPQIWLCPHC 1155
Cdd:cd15607     1 VCVCQKAPMAPMIQCELCRDAFHSGCVTAPSDPQGPQAWLCPQC 44
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
626-678 2.04e-18

C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.


Pssm-ID: 427059  Cd Length: 54  Bit Score: 79.98  E-value: 2.04e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 655860861   626 CVKCKTTCFMSAISCSCKPGLLVCLHHVKELCS-CPPHKYKLRYRYTLDDLYPM 678
Cdd:pfam02928    1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
393-450 5.82e-14

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 67.66  E-value: 5.82e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 655860861    393 WNLNNMPvMEQSVLAHITADICGMKL-PWLYVGMCFSSFCWHIEDHWsySINYLHWGEP 450
Cdd:smart00558    3 WNLAKLP-FKLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYD--LVNYLHQGAG 58
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
245-290 1.43e-13

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: 66.36  E-value: 1.43e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 655860861   245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPL--HDVPKGDWRCPKC 290
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLdpAEIPSGEWLCPEC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
245-290 2.95e-12

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: 62.61  E-value: 2.95e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 655860861    245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHD-VPKGDWRCPKC 290
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
1419-1462 6.03e-07

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 47.49  E-value: 6.03e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 655860861  1419 CLQPEGDEvDWVQCDGsCDQWFHQVCVGVSPEMAE--KEDYICVRC 1462
Cdd:pfam00628    5 CGKSDDGG-ELVQCDG-CDDWFHLACLGPPLDPAEipSGEWLCPEC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
1419-1462 1.08e-06

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: 46.82  E-value: 1.08e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 655860861   1419 CLQPEGDEvDWVQCDGsCDQWFHQVCVGVSPEMAEK-EDYICVRC 1462
Cdd:smart00249    5 CGKPDDGG-ELLQCDG-CDRWYHQTCLGPPLLEEEPdGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
1113-1155 1.47e-04

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: 40.66  E-value: 1.47e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 655860861   1113 CLCQK-GPAAPMIQCELCRGAFHTGCVAVPSVSQGPQ-IWLCPHC 1155
Cdd:smart00249    3 SVCGKpDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDgKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
1113-1158 2.12e-04

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: 40.17  E-value: 2.12e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 655860861  1113 CLCQKGPAA-PMIQCELCRGAFHTGCVAVPSVSQGPQI--WLCPHCRRS 1158
Cdd:pfam00628    3 AVCGKSDDGgELVQCDGCDDWFHLACLGPPLDPAEIPSgeWLCPECKPK 51
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
1034-1156 1.70e-03

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


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 41.85  E-value: 1.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861 1034 GLKRKQRKFKEPLLSGKKRSTKLESLSdlERALTESRETASAMAAlgeaRLREMEALQSLrlANEGKLLSPVQDVEMKVC 1113
Cdd:COG5034   153 GSRHTKLKKRKNIHNLKRRSPELSSKR--EVSFTLESPSVPDTAT----RVKEGNNGGST--KSRGVSSEDNSEGEELYC 224
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861 1114 LCQKGPAAPMIQC--ELC-RGAFHTGCVAVPSVSQGpqIWLCPHCR 1156
Cdd:COG5034   225 FCQQVSYGQMVACdnANCkREWFHLECVGLKEPPKG--KWYCPECK 268
 
Name Accession Description Interval E-value
PLU-1 pfam08429
PLU-1-like protein; Sequences in this family bear similarity to the central region of PLU-1. ...
691-1022 1.28e-118

PLU-1-like protein; Sequences in this family bear similarity to the central region of PLU-1. This is a nuclear protein that may have a role in DNA-binding and transcription, and is closely associated with the malignant phenotype of breast cancer. This region is found in various other Jumonji/ARID domain-containing proteins (see pfam02373, pfam01388).


Pssm-ID: 429992 [Multi-domain]  Cd Length: 336  Bit Score: 375.01  E-value: 1.28e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   691 EWALTVNEALEAkiNKKKSLVSFKALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLTGKRQTRYRSG---GGKS 767
Cdd:pfam08429    1 TWAEKVEEALEE--EPKPSLKELRALLNEAEKIKFPLPELLQDLRAFVQRANKWVEEAQQLLSRKQRTRRKNEaeeDERE 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   768 QNQLTVNELRQFVTQLYALPCVLSQTPLLKDLLDRVEDFQQHSQKLLSEEMP--SAAELQDLLDVSFEFDVELPQLAEMR 845
Cdd:pfam08429   79 REKRTVEELRKLLEEADNLPFDCPEIDQLKELLEEIEEFQKRAREALSEEPPslSIEELEELLEEGKSFNVDLPELEELE 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   846 VRLEQARWLEEVQQAcLDPGSLTLDDMRRLIDLGVGLAPYSAVEKAMARLQELLTVSEHWDDKAKSLLKaRPRHSLNSLA 925
Cdd:pfam08429  159 KVLEQLKWLEEVREF-SRKKSLTLEDVRELIEEGVELGIPPPYEDAMAELQELLTAGERWEEKAKELLS-RERVSLAQLE 236
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   926 TAVKEIEEIPAYLPNGAALKDSVQRAKDWLQDVEALQ----AGGRvPVLDTLLELVTRGRSIPVHLNSLPRLESLVAEVQ 1001
Cdd:pfam08429  237 ALSKEAQNIPVSLPNLAALDEILKKAREWQRQIEALYqrsdFGKR-PTLDELEELVAKGESLPVKPEGLSDLEKEVKRAE 315
                          330       340
                   ....*....|....*....|.
gi 655860861  1002 AWKECAANTFLTENSPYSLLE 1022
Cdd:pfam08429  316 DWKRRGKKLFLKKNAPLTLLE 336
ARID_KDM5B cd16874
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called ...
28-117 2.14e-59

ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called cancer/testis antigen 31 (CT31), histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible earlygene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers.


Pssm-ID: 350638  Cd Length: 90  Bit Score: 198.24  E-value: 2.14e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   28 EAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRG 107
Cdd:cd16874     1 EAQTRVKLNFLDQIAKFWELQGCTLKIPHVERKILDLFQLNKLVAEEGGFDLVCKERKWTKIATKMGFAPGKAVGSHIRA 80
                          90
                  ....*....|
gi 655860861  108 HYERILNPYN 117
Cdd:cd16874    81 HYERILYPYN 90
ARID_JARID cd16864
ARID/BRIGHT DNA binding domain of JARID proteins; The JARID subfamily within the JmjC protein ...
31-117 9.43e-56

ARID/BRIGHT DNA binding domain of JARID proteins; The JARID subfamily within the JmjC protein family includes lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members of this subfamily contain the catalytic JmjC domain, JmjN, the AT-rich domain interacting domain (ARID)/BRIGHT domain, a C5HC2 zinc finger, as well as two or three plant homeodomain (PHD) fingers.


Pssm-ID: 350628  Cd Length: 87  Bit Score: 187.90  E-value: 9.43e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   31 TRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYE 110
Cdd:cd16864     1 TRVKLNFLDQIAKFWELQGSSLKIPNVERKALDLFTLHKIVQEEGGFEEVTKERKWSKVARRLGYPPGKGVGSLLRGHYE 80

                  ....*..
gi 655860861  111 RILNPYN 117
Cdd:cd16864    81 RILYPYD 87
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
420-536 1.10e-52

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 180.19  E-value: 1.10e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   420 WLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLETVMKklaPELFVSQPDLLHQLVTIMNPNTLMTHE 499
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77
                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 655860861   500 VPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNF 536
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
ARID_KDM5A cd16873
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A); KDM5A, also called ...
31-122 3.29e-46

ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A); KDM5A, also called histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner; its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers.


Pssm-ID: 350637  Cd Length: 92  Bit Score: 160.82  E-value: 3.29e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   31 TRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYE 110
Cdd:cd16873     1 TRVKLDFLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASEGGFEMVTKEKKWSKVGSRMGYLPGKGTGSLLKSHYE 80
                          90
                  ....*....|..
gi 655860861  111 RILNPYNLFLSG 122
Cdd:cd16873    81 RILYPYELFQSG 92
ARID_KDM5C_5D cd16875
ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D; This group ...
31-122 4.05e-44

ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D; This group includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C, also called histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, protein SmcX, or protein Xe169, is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D, also called histocompatibility Y antigen (H-Y), histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or protein SmcY, is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as two plant homeodomain (PHD) fingers.


Pssm-ID: 350639  Cd Length: 92  Bit Score: 154.69  E-value: 4.05e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   31 TRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYE 110
Cdd:cd16875     1 TRVKLNYLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVQEEGGYEAICKDRRWARVAQRLGYPPGKNIGSLLRSHYE 80
                          90
                  ....*....|..
gi 655860861  111 RILNPYNLFLSG 122
Cdd:cd16875    81 RIIYPYEMYQSG 92
PHD3_KDM5B cd15687
PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis ...
1413-1462 2.85e-30

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


Pssm-ID: 277157  Cd Length: 50  Bit Score: 113.89  E-value: 2.85e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 655860861 1413 LCPAASCLQPEGDEVDWVQCDGSCDQWFHQVCVGVSPEMAEKEDYICVRC 1462
Cdd:cd15687     1 LCPAVSCLQPEGEEVDWVQCDGSCNRWFHQVCVGVSAEMAEKEDYICVSC 50
BRIGHT smart00501
BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a ...
32-122 5.53e-30

BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure


Pssm-ID: 128777 [Multi-domain]  Cd Length: 93  Bit Score: 114.29  E-value: 5.53e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861     32 RVKLNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAP-GKAVGSHIRGHY 109
Cdd:smart00501    1 RERVLFLDRLYKFMEERGSPLkKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDtSTSAASSLRKHY 80
                            90
                    ....*....|...
gi 655860861    110 ERILNPYNLFLSG 122
Cdd:smart00501   81 ERYLLPYERFLRG 93
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
245-290 4.87e-28

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


Pssm-ID: 277076  Cd Length: 46  Bit Score: 107.34  E-value: 4.87e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
ARID smart01014
ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction ...
32-116 2.88e-27

ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.


Pssm-ID: 198082 [Multi-domain]  Cd Length: 88  Bit Score: 106.55  E-value: 2.88e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861     32 RVKLNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPG-KAVGSHIRGHY 109
Cdd:smart01014    1 RERELFLDRLRKFMEKRGTPLdKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSaTSAGTSLRKHY 80

                    ....*..
gi 655860861    110 ERILNPY 116
Cdd:smart01014   81 EKYLLPY 87
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
245-290 8.42e-27

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


Pssm-ID: 276990  Cd Length: 46  Bit Score: 103.63  E-value: 8.42e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15515     1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
245-293 2.40e-25

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


Pssm-ID: 277075  Cd Length: 49  Bit Score: 99.64  E-value: 2.40e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQ 293
Cdd:cd15602     1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAE 49
ARID pfam01388
ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, ...
34-116 2.55e-24

ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.


Pssm-ID: 426236  Cd Length: 87  Bit Score: 98.09  E-value: 2.55e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861    34 KLNFLDQIAKYWELQGSTLK-IPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPG-KAVGSHIRGHYER 111
Cdd:pfam01388    2 KELFLKSLRKFHEKRGTPLKnIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNKWREVAEKLGFPPGaTSAAFQLKQIYEK 81

                   ....*
gi 655860861   112 ILNPY 116
Cdd:pfam01388   82 YLLPY 86
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
245-290 2.04e-23

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


Pssm-ID: 277078  Cd Length: 46  Bit Score: 94.05  E-value: 2.04e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15605     1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD3_KDM5A_like cd15610
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; ...
1414-1462 3.68e-23

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


Pssm-ID: 277083 [Multi-domain]  Cd Length: 50  Bit Score: 93.55  E-value: 3.68e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 655860861 1414 CPAASCLQPEGDEVDWVQCDGsCDQWFHQVCVGVSPE-MAEKEDYICVRC 1462
Cdd:cd15610     2 CSAKQCLKPTGDEVNWVQCDG-CEEWFHLLCVGLSPEeVAEDEDYICPSC 50
PHD2_KDM5B cd15607
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
1112-1155 2.27e-22

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


Pssm-ID: 277080  Cd Length: 44  Bit Score: 91.05  E-value: 2.27e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 655860861 1112 VCLCQKGPAAPMIQCELCRGAFHTGCVAVPSVSQGPQIWLCPHC 1155
Cdd:cd15607     1 VCVCQKAPMAPMIQCELCRDAFHSGCVTAPSDPQGPQAWLCPQC 44
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
245-290 4.05e-22

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


Pssm-ID: 277077  Cd Length: 46  Bit Score: 90.29  E-value: 4.05e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15604     1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD3_KDM5A cd15686
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A); KDM5A, also termed Histone ...
1412-1463 2.86e-21

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


Pssm-ID: 277156  Cd Length: 52  Bit Score: 88.20  E-value: 2.86e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 655860861 1412 ALCPAASCLQPEGDEVDWVQCDGSCDQWFHQVCVGVSPEMAEKEDYICVRCA 1463
Cdd:cd15686     1 AVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA 52
ARID cd16100
ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of ...
34-116 5.84e-20

ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of transcription factors, found in a broad array of organisms from fungi to mammals, is characterized by a highly conserved, helix-turn-helix DNA binding domain that binds to the major groove of DNA. The ARID domain, also called BRIGHT, was first identified in the mouse B-cell-specific transcription factor Bright and in the product of the dead ringer (dri) gene of Drosophila melanogaster. ARID family members are implicated in normal development, differentiation, cell cycle regulation, transcriptional activation and chromatin remodeling. Different family members exhibit different DNA-binding properties. Drosophila Dri, mammalian ARID3A/3B/3C and ARID5A/5B, selectively bind AT-rich sites. However, ARID1A/1B, Drosophila Osa, yeast SWI1, ARID2, ARID4A/4B, JARID1A/1B/1C/1D, and JARID2, bind DNA without sequence specificity.


Pssm-ID: 350627  Cd Length: 87  Bit Score: 85.49  E-value: 5.84e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   34 KLNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGF-APGKAVGSHIRGHYER 111
Cdd:cd16100     2 REEFLEQLRAFLESRGTPLlKPPTIGGKPLDLYKLYRAVVSRGGYEKVTEKKLWKEVARKLGLpTSSTSAAQALKRIYEK 81

                  ....*
gi 655860861  112 ILNPY 116
Cdd:cd16100    82 YLLPF 86
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
626-678 2.04e-18

C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.


Pssm-ID: 427059  Cd Length: 54  Bit Score: 79.98  E-value: 2.04e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 655860861   626 CVKCKTTCFMSAISCSCKPGLLVCLHHVKELCS-CPPHKYKLRYRYTLDDLYPM 678
Cdd:pfam02928    1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
245-290 2.41e-17

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


Pssm-ID: 276988  Cd Length: 47  Bit Score: 76.75  E-value: 2.41e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
246-290 5.54e-17

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


Pssm-ID: 277020  Cd Length: 46  Bit Score: 75.81  E-value: 5.54e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15545     2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
246-290 9.74e-17

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


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 75.00  E-value: 9.74e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
246-290 6.48e-16

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


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 72.81  E-value: 6.48e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
245-290 3.63e-15

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


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 70.57  E-value: 3.63e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15519     1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD2_KDM5A_like cd15516
PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar ...
1112-1155 6.10e-15

PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog protein, little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 276991  Cd Length: 53  Bit Score: 70.42  E-value: 6.10e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 655860861 1112 VCLCQKGPAAPMIQCELCRGAFHTGCVAVPSVSQGPQ---------IWLCPHC 1155
Cdd:cd15516     1 ICLCGKALAAGMLQCELCQDWFHGSCVAVPRISSSPRplawwegdrKFLCPLC 53
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
246-290 3.29e-14

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


Pssm-ID: 277011  Cd Length: 46  Bit Score: 67.82  E-value: 3.29e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
393-450 5.82e-14

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 67.66  E-value: 5.82e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 655860861    393 WNLNNMPvMEQSVLAHITADICGMKL-PWLYVGMCFSSFCWHIEDHWsySINYLHWGEP 450
Cdd:smart00558    3 WNLAKLP-FKLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYD--LVNYLHQGAG 58
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
245-290 1.43e-13

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: 66.36  E-value: 1.43e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 655860861   245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPL--HDVPKGDWRCPKC 290
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLdpAEIPSGEWLCPEC 48
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
246-290 5.07e-13

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


Pssm-ID: 277019  Cd Length: 46  Bit Score: 64.74  E-value: 5.07e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
246-291 7.64e-13

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


Pssm-ID: 277099  Cd Length: 47  Bit Score: 64.10  E-value: 7.64e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCL 291
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNCV 47
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
246-290 9.41e-13

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: 63.93  E-value: 9.41e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGD-WRCPKC 290
Cdd:cd15525     2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
ARID_ARID1A-like cd16865
ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ...
37-116 1.14e-12

ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ARID1B and similar proteins; This subfamily contains ARID1A and its paralog ARID1B. They are mutually exclusive components of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complexes, but display different functions in development and cell-cycle control. SWI/SNF complexes containing ARID1A have an antiproliferative function, whereas the one harboring ARID1B shows a pro-proliferative function. ARID1A functions as an important tumor suppressor in various tumor types. It has been implicated in cell-cycle arrest, as well as in the interactions with p53 and BRG1/BRM and with topoisomerase II alpha. ARID1B may be considered as a potential therapeutic target for ARID1A-mutant cancers. Moreover, mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Mutations in the ARID1B gene also have been found in many cancers. Both ARID1A and ARID1B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner.


Pssm-ID: 350629  Cd Length: 93  Bit Score: 64.99  E-value: 1.14e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   37 FLDQIAKYWELQGSTLK-IPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILNP 115
Cdd:cd16865     6 FLDRLLRFMEERGSPITnCPQISKQPLDLFRLYVTVKERGGVAEVTKNKKWKEICTELNIGASSSAAFTLRKNYIKYLLA 85

                  .
gi 655860861  116 Y 116
Cdd:cd16865    86 Y 86
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
245-290 1.20e-12

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: 63.45  E-value: 1.20e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15532     1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
245-290 2.95e-12

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: 62.61  E-value: 2.95e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 655860861    245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHD-VPKGDWRCPKC 290
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
246-290 4.27e-12

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


Pssm-ID: 277098  Cd Length: 46  Bit Score: 62.07  E-value: 4.27e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15628     2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
246-290 1.46e-11

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: 60.37  E-value: 1.46e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVP-KGDWRCPKC 290
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
245-290 2.17e-11

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


Pssm-ID: 277069  Cd Length: 46  Bit Score: 59.95  E-value: 2.17e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
246-292 2.48e-11

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


Pssm-ID: 277100  Cd Length: 49  Bit Score: 59.99  E-value: 2.48e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLA 292
Cdd:cd15630     3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACIA 49
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
246-290 3.14e-11

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


Pssm-ID: 277002  Cd Length: 46  Bit Score: 59.31  E-value: 3.14e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
245-290 4.06e-11

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


Pssm-ID: 277004  Cd Length: 44  Bit Score: 59.24  E-value: 4.06e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLipPLHDVPKGDWRCPKC 290
Cdd:cd15529     1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCV--GLRSIPDGRWICPLC 44
ARID_HMGB9-like cd16872
ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, ...
37-116 4.52e-11

ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, HMGB10, HMGB11, HMGB15 and similar proteins; This subfamily includes a group of conserved plant DNA-binding proteins, including HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA. HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104.


Pssm-ID: 350636  Cd Length: 86  Bit Score: 60.36  E-value: 4.52e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   37 FLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPG-KAVGSHIRGHYERILNP 115
Cdd:cd16872     5 FWETLRKFHESLGTKFRIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTiTNASFVLRKYYLSLLHH 84

                  .
gi 655860861  116 Y 116
Cdd:cd16872    85 Y 85
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
246-290 5.00e-11

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


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 59.00  E-value: 5.00e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15539     2 CAVCGDGGE---LLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
ARID_Swi1p-like cd16871
ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and ...
36-116 9.79e-11

ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and similar proteins; Saccharomyces cerevisiae Swi1p, also called SWI/SNF chromatin-remodeling complex subunit SWI1, regulatory protein GAM3, or transcription regulatory protein ADR6, is a transcription regulatory protein that is a subunit of the SWI/SNF complex, which plays critical roles in the regulation of gene transcription and expression. It can exist as a prion, [SWI(+)], which demonstrates a link between prionogenesis and global transcriptional regulation. Swi1p contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT) that binds DNA nonspecifically. This subfamily also includes Schizosaccharomyces pombe SWI/SNF chromatin-remodeling complex subunit sol1 (sol1p, also known as switch one-like protein). sol1p is a homolog of S. cerevisiae Swi1p and is also a part of SWI/SNF chromatin-remodeling complex.


Pssm-ID: 350635  Cd Length: 90  Bit Score: 59.57  E-value: 9.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   36 NFLDQIAKYWELQGSTLK-IPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKA--VGSHIRGHYERI 112
Cdd:cd16871     5 QFMKSLREFMAKRGTPIEqQPVIGGRPVNLFRLYQLVQKLGGSRQVTQNNQWPRVAQKLGFPPEQNpqVAQQLAQIYQRY 84

                  ....
gi 655860861  113 LNPY 116
Cdd:cd16871    85 LLPY 88
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
246-290 1.25e-10

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


Pssm-ID: 277005  Cd Length: 46  Bit Score: 57.78  E-value: 1.25e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15530     2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
1416-1462 2.06e-10

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: 57.17  E-value: 2.06e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 655860861 1416 AASCLQPEGDEVDWVQCDGsCDQWFHQVCVGVSPEM-AEKEDYICVRC 1462
Cdd:cd15517     3 GICNLETAAVDELWVQCDG-CDKWFHQFCLGLSNERyADEDKFKCPNC 49
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
245-290 3.38e-10

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


Pssm-ID: 276985  Cd Length: 46  Bit Score: 56.67  E-value: 3.38e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15510     1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
245-290 4.85e-10

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


Pssm-ID: 277070  Cd Length: 46  Bit Score: 56.16  E-value: 4.85e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
246-290 7.72e-10

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: 55.73  E-value: 7.72e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKG-DWRCPKC 290
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
PHD_TCF19 cd15609
PHD finger found in Transcription factor 19 (TCF-19) and similar proteins; TCF-19, also termed ...
1414-1457 7.83e-10

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


Pssm-ID: 277082  Cd Length: 50  Bit Score: 55.55  E-value: 7.83e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 655860861 1414 CPAASCLQPEGDEVDWVQCDGsCDQWFHQVCVGVSPEMAEKEDY 1457
Cdd:cd15609     2 CASPSCCLPQDETVSWVQCDD-CDQWYHVACVGCDYNAVKDPDA 44
ARID_ARID4 cd16868
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID4A, ...
34-116 9.48e-10

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID4A, ARID4B and similar proteins; This subfamily contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (Rb)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and Rb transcriptional activity, and play important roles in the AR and Rb pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain.


Pssm-ID: 350632  Cd Length: 87  Bit Score: 56.63  E-value: 9.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   34 KLNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAP-GKAVGSHIRGHYER 111
Cdd:cd16868     2 KENFLEQLYKFMEDRGTPInKPPVLGYKDLDLFKLYKLVQELGGMERVSQGAKWRSIYQQLGIPVlNSAASHNIKQAYKK 81

                  ....*
gi 655860861  112 ILNPY 116
Cdd:cd16868    82 YLYAF 86
ARID_ARID5 cd16869
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ...
36-116 1.33e-09

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ARID5B, and similar proteins; This subfamily contains ARID5A and its paralog ARID5B. ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also plays an important role in the promotion of inflammatory processes and autoimmune diseases. ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Both ARID5A and ARID5B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT).


Pssm-ID: 350633  Cd Length: 87  Bit Score: 56.15  E-value: 1.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   36 NFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHI-RGHYERIL 113
Cdd:cd16869     4 AFLKLLYKFMKDRGTPIeRIPHLGFKQIDLYTFFKLVQKLGGYEQVTAKRLWKHVYDELGGNPSSTSAATCtRRHYEKLL 83

                  ...
gi 655860861  114 NPY 116
Cdd:cd16869    84 LPY 86
PHD2_KDM5A cd15606
PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
1113-1155 1.47e-09

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


Pssm-ID: 277079  Cd Length: 56  Bit Score: 55.14  E-value: 1.47e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 655860861 1113 CLCQKGPAAPMIQCELCRGAFHTGCVAVPSVSQGPQI------------WLCPHC 1155
Cdd:cd15606     2 CICRKPFSGFMLQCELCKDWFHSSCVPLPKSSSQKKGgngsgqgakelkFLCPLC 56
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
1419-1462 6.80e-09

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


Pssm-ID: 277035  Cd Length: 47  Bit Score: 52.73  E-value: 6.80e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861 1419 CLQPEGDEVDWVQCDGsCDQWFHQVCVGVSPEMAEK-EDYICVRC 1462
Cdd:cd15560     4 CRTPYDESQFYIGCDR-CQDWFHGRCVGILQSEAEKiDEYVCPQC 47
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
245-290 1.04e-08

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


Pssm-ID: 276979  Cd Length: 53  Bit Score: 52.44  E-value: 1.04e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 655860861  245 VCLLCGSG--SDEDRLLLCDG-CDDSYHTFCLIPPL--HDVPKGD--WRCPKC 290
Cdd:cd15504     1 FCAKCQSGeaSPDNDILLCDGgCNRAYHQKCLEPPLltEDIPPEDegWLCPLC 53
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
245-290 3.36e-08

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: 51.16  E-value: 3.36e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 655860861  245 VCLLCG-SGSDEDRLLLCDGCDDSYHTFCLIPPLHD-VPKGDWRCPKC 290
Cdd:cd15489     1 SCIVCGkGGDLGGELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
245-290 4.32e-08

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


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 50.47  E-value: 4.32e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15523     1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
1414-1462 1.12e-07

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


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 49.59  E-value: 1.12e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 655860861 1414 CPAasCLQP-EGDEvdWVQCDGsCDQWFHQVCVGVSPEMAEKEDYICVRC 1462
Cdd:cd15522     2 CPI--CKKPdDGSP--MIGCDE-CDDWYHWECVGITDEPPEEDDWFCPKC 46
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
245-290 1.57e-07

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


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 48.88  E-value: 1.57e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15541     1 WCAVCQNGGE---LLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
ARID_ARID2 cd16866
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and ...
34-116 2.51e-07

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and similar proteins; ARID2, also called BRG1-associated factor 200 (BAF200) or zinc finger protein with activation potential (Zipzap/p200), is a novel serum response factor (SRF)-binding protein with multiple conserved domains, including an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), RFX DNA-binding domain, a glutamine-rich domain, and two C2H2 zinc fingers. It binds DNA without sequence specificity. ARID2 is an intrinsic subunit of PBAF (SWI/SNF-B) remodeling complex, which needs ARID2 to play an essential role in promoting osteoblast differentiation, maintaining cellular identity and activating tissue-specific gene expression. Moreover, ARID2 may function as a tumor suppressor in many cancers. It may also serve as a transcription co-activator for the regulation of cardiac gene expression, and is required for heart morphogenesis and coronary artery development.


Pssm-ID: 350630  Cd Length: 88  Bit Score: 49.57  E-value: 2.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   34 KLNFLDQIAKYWELQGST-LKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSH-IRGHYER 111
Cdd:cd16866     2 YDAFLNELRQFHASRGTPfKKIPVVGGKELDLYLLYSKVTALGGWAKVTDKNKWEEILEDFNFPRGCSNAAFaLKQIYLR 81

                  ....*
gi 655860861  112 ILNPY 116
Cdd:cd16866    82 YLEAY 86
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
1419-1462 5.01e-07

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


Pssm-ID: 277027  Cd Length: 50  Bit Score: 47.78  E-value: 5.01e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861 1419 CLQPEGDEVdWVQCDgSCDQWFHQVCVGVSPEM-----AEKEDYICVRC 1462
Cdd:cd15552     4 CRKPHNNRF-MICCD-RCEEWFHGDCVGITEAQgkemeENIEEYVCPKC 50
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
1419-1462 6.03e-07

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 47.49  E-value: 6.03e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 655860861  1419 CLQPEGDEvDWVQCDGsCDQWFHQVCVGVSPEMAE--KEDYICVRC 1462
Cdd:pfam00628    5 CGKSDDGG-ELVQCDG-CDDWFHLACLGPPLDPAEipSGEWLCPEC 48
ARID_ARID5A cd16884
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) ...
53-116 6.04e-07

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) and similar proteins; ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also associates with thyroid receptor alpha (TR alpha) and retinoid X receptor alpha (RXR alpha) in a ligand-dependent manner, and with ER beta, androgen receptor (AR), and the retinoic acid receptor (RAR) in a ligand-independent manner. ARID5A functions as a negative regulator of RORgamma-induced Th17 cell differentiation and may be involved in the pathogenesis of rheumatoid arthritis (RA). Moreover, it is an important transcriptional partner of the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) in stimulation of chondrocyte-specific transcription. Meanwhile, ARID5A plays an important role in promotion of inflammatory processes and autoimmune diseases. It works as a unique RNA binding protein, which stabilizes interleukin-6 (IL-6) but not tumor necrosis factor-alpha (TNF-alpha) mRNA through binding to the 3' untranslated region (UTR) of IL-6 mRNA, and inhibits the destabilizing effect of regnase-1 on IL-6 mRNA. ARID5A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT).


Pssm-ID: 350648  Cd Length: 87  Bit Score: 48.84  E-value: 6.04e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 655860861   53 KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGK-AVGSHIRGHYERILNPY 116
Cdd:cd16884    22 RIPHLGFKQINLWKIYKAVEKLGGYELVTARRLWKNVYDELGGSPGStSAATCTRRHYERLVLPY 86
PHD2_KDM5C_5D cd15608
PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
1112-1155 6.34e-07

PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARIDdomain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277081  Cd Length: 58  Bit Score: 47.49  E-value: 6.34e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 655860861 1112 VCLCQKGPAAPMIQCELCRGAFHTGCVAVPSVSQGPQ-------IW-------LCPHC 1155
Cdd:cd15608     1 VCVCGQPPRPGMLRCHLCQDWFHGGCVSFPRLLSSSGphsspslAWwewdtrfLCPLC 58
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
1419-1462 1.08e-06

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: 46.82  E-value: 1.08e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 655860861   1419 CLQPEGDEvDWVQCDGsCDQWFHQVCVGVSPEMAEK-EDYICVRC 1462
Cdd:smart00249    5 CGKPDDGG-ELLQCDG-CDRWYHQTCLGPPLLEEEPdGKWYCPKC 47
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
246-290 1.34e-06

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


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 46.44  E-value: 1.34e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15531     2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
ARID_ARID5B cd16885
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) ...
37-123 1.43e-06

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) and similar proteins; ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex, which is a signal-sensing modulator of histone methylation and gene transcription. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Its polymorphism has been associated with risk for pediatric acute lymphoblastic leukemia (ALL). ARID5B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which can bind both the major and minor grooves of its target sequences.


Pssm-ID: 350649  Cd Length: 95  Bit Score: 47.76  E-value: 1.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   37 FLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGK-AVGSHIRGHYERILN 114
Cdd:cd16885     5 FLVALYKYMKERKTPIeRIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGStSAATCTRRHYERLIL 84

                  ....*....
gi 655860861  115 PYNLFLSGD 123
Cdd:cd16885    85 PYERFIKGE 93
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
245-290 2.04e-06

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: 45.81  E-value: 2.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 655860861  245 VCLLCGSgSDEDRLLLCDGCDDSYHTFCL--IPPLHDVPKGDWRCPKC 290
Cdd:cd15506     1 LCFLCGS-AGLNELLYCSVCCEPYHTFCLeeAERPLNINKDNWCCRRC 47
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
245-290 2.17e-06

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


Pssm-ID: 277037  Cd Length: 50  Bit Score: 45.86  E-value: 2.17e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGD----WRCPKC 290
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTknsgWQCSEC 50
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
245-290 3.69e-06

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


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 45.04  E-value: 3.69e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 655860861  245 VCLLCGSGSDedrLLLCDGCDDSYHTFCLIPPL--HDVPKGDWRCPKC 290
Cdd:cd15533     1 YCDSCGEGGD---LLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
ARID_ARID1B cd16877
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) ...
37-109 5.01e-06

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins; ARID1B, also called BRG1-associated factor 250b (BAF250B), BRG1-binding protein ELD/OSA1, Osa homolog 2 (Osa2), or p250R, is the largest subunit of ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, which plays a critical role in transcriptional control and gene expression. ARID1B exhibits tumour-suppressor activities in pancreatic cancer cell lines. Mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Moreover, mutations in the ARID1B gene have been found in many cancers. ARID1B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner similar to ARID1A.


Pssm-ID: 350641  Cd Length: 93  Bit Score: 46.14  E-value: 5.01e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 655860861   37 FLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHY 109
Cdd:cd16877     6 WVDRYLTFMEERGTPVaSLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTSSSAASSLKKQY 79
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
246-290 5.35e-06

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


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 44.50  E-value: 5.35e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15524     2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
245-290 9.65e-06

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: 43.96  E-value: 9.65e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 655860861  245 VCLLC--GSGSDEDRLLLCDGCDDSYHTFCLIPPLHD----VPKGDWRCPKC 290
Cdd:cd15502     1 VCIVCqrGHSPKSNRIVFCDGCNTPYHQLCHDPSIDDevveDPDAEWFCKKC 52
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
1419-1462 9.75e-06

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


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 44.23  E-value: 9.75e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861 1419 CLQPEGDEVDWVQCDGsCDQWFHQVCVGVSPEMA-EKEDYICVRC 1462
Cdd:cd15489     5 CGKGGDLGGELLQCDG-CGKWFHADCLGPPLSSFvPNGKWICPVC 48
ARID_ARID3A cd16878
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) ...
17-132 1.66e-05

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) and similar proteins; ARID3A, also called B-cell regulator of IgH transcription (Bright), dead ringer-like protein 1 (Dril1), or E2F-binding protein 1 (E2FBP1), is an ubiquitously expressed DNA-binding protein that has been implicated in embryonic patterning, cell lineage gene regulation, and cell cycle control, chromatin remodeling and transcriptional regulation. It was originally identified as a B cell-specific trans-activator of immunoglobulin heavy-chain (IgH) transcription, which increases immunoglobulin transcription in antigen-activated B cells and plays regulatory roles in hematopoiesis. It also functions as an E2F transcription regulator, inducing promyelocytic leukemia protein (PML) reduction and suppressing the formation of PML-nuclear bodies. It antagonizes the p16(INK4A)-Rb tumor suppressor machinery by regulating PML stability. ARID3A transcriptional activity can be modulated by SUMO (Small Ubiquitin-related Modifier) modification through the interaction with the SUMO-conjugating enzyme Ubc9. ARID3A also plays an important role in marginal zone B lymphocyte development and autoantibody production. Furthermore, ARID3A is a direct p53 target gene. It controls cell growth in a p53-dependent manner. ARID3A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta.


Pssm-ID: 350642  Cd Length: 133  Bit Score: 45.82  E-value: 1.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   17 FTPRIQRLNELEAQTRVKlNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGF 95
Cdd:cd16878     7 YEEQFKQLYELDGDPKRK-EFLDDLFSFMQKRGTPVnRIPIMAKQVLDLYMLYVLVTEKGGLVEVINKKLWREITKGLNL 85
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 655860861   96 APG-KAVGSHIRGHYERILNPYNLflsgdSLRCLQKPN 132
Cdd:cd16878    86 PTSiTSAAFTLRTQYMKYLYPYEC-----EKRGLSNPN 118
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
245-290 1.71e-05

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


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 43.38  E-value: 1.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861  245 VCLLCGSGS--DEDRLLLCDGCDDSYHTFCL-IPplhDVPKGDWRCPKC 290
Cdd:cd15492     1 VCDVCLDGEseDDNEIVFCDGCNVAVHQSCYgIP---LIPEGDWFCRKC 46
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
246-290 2.47e-05

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


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 42.79  E-value: 2.47e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 655860861  246 CLLCG-SGsdedRLLLCDGCDDSYHTFCLIPPL--HDVPKGDWRCPKC 290
Cdd:cd15535     2 CSACGgYG----SFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
246-290 2.65e-05

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


Pssm-ID: 276984  Cd Length: 48  Bit Score: 42.68  E-value: 2.65e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 655860861  246 CLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVP--KGDWRCPKC 290
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPlvRAGWQCPEC 48
ARID_ARID3C cd16880
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) ...
20-116 3.45e-05

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) and similar proteins; ARID3C, also called Brightlike, is a new ARID3 family transcription factor that co-activates ARID3A-mediated immunoglobulin gene transcription. It also functions as a potential regulator of early events in B cell antigen receptor (BCR) signaling. ARID3C contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta.


Pssm-ID: 350644  Cd Length: 127  Bit Score: 45.02  E-value: 3.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   20 RIQRLNELEAQTRVKlNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPG 98
Cdd:cd16880     3 QFKQLYELDDDPKRK-EFLDDLFSFMQKRGTPVnRIPIMAKQVLDLYTLYRLVTDKGGLVEVINKKIWREITKGLSLPTS 81
                          90
                  ....*....|....*....
gi 655860861   99 -KAVGSHIRGHYERILNPY 116
Cdd:cd16880    82 iTSAAFTLRTQYMKYLYPY 100
ARID_ARID3B cd16879
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3B (ARID3B) ...
23-116 3.60e-05

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3B (ARID3B) and similar proteins; ARID3B, also called Bright and dead ringer protein, or Bright-Dri-like protein (Bdp), is a DNA binding protein involved in cellular immortalization, epithelial-mesenchymal transition (EMT), and tumorigenesis. Its expression is differentially regulated in normal and malignant tissues. It is required for heart development by regulating the motility and differentiation of heart progenitors. ARID3B is overexpressed in neuroblastoma and ovarian cancer. It acts as a novel target with roles in cell motility in breast cancer cells, promotes migration of mouse embryo fibroblasts (MEFs) and breast cancer cells, and induces tumor necrosis factor alpha (TNFalpha)-mediated apoptosis. ARID3B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta.


Pssm-ID: 350643  Cd Length: 126  Bit Score: 44.62  E-value: 3.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   23 RLNELEAQTRVKlNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPG-KA 100
Cdd:cd16879     5 KLYELDNDPKRK-EFLDDLFAFMQKRGTPInRIPIMAKQVLDLYMLYKLVTEKGGLVEVINKKIWREITKGLNLPTSiTS 83
                          90
                  ....*....|....*.
gi 655860861  101 VGSHIRGHYERILNPY 116
Cdd:cd16879    84 AAFTLRTQYMKYLYPY 99
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
245-291 3.60e-05

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


Pssm-ID: 276974  Cd Length: 53  Bit Score: 42.49  E-value: 3.60e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 655860861  245 VCLLCGSG--SDEDRLLLCDGCDDSYHTFCLIPPLHDVPK---GDWRCPKCL 291
Cdd:cd15499     1 TCSICGGAeaRDGNEILICDKCDKGYHQLCHSPKVRTSPLegdEKWFCSRCV 52
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
1113-1155 3.74e-05

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: 42.30  E-value: 3.74e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861 1113 CLCQKG--PAAPMIQCELCRGAFHTGCVAVPSVSQGP-QIWLCPHC 1155
Cdd:cd15489     3 IVCGKGgdLGGELLQCDGCGKWFHADCLGPPLSSFVPnGKWICPVC 48
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
258-290 5.54e-05

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


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 41.63  E-value: 5.54e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 655860861  258 LLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15559    11 LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
ARID_ARID1A cd16876
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) ...
37-113 7.05e-05

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins; ARID1A, also called B120, BRG1-associated factor 250a (BAF250A), Osa homolog 1(OSA1), SWI-like protein, SWI/SNF complex protein p270, or SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1 (SWI1), has been identified as a novel tumor suppressor in various tumor types. It interacts with BRG1 adenosine triphosphatase to form a SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complex, which plays a critical role in transcriptional control and gene expression. ARID1A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and Eld/Osa homology domains (EHD) 1 and 2 within the C-terminus. The ARID in ARID1A binds nonspecific DNA in general and plays an important role in targeting SWI/SNF to chromatin. The EHD1 may be capable of mediating an intramolecular association with EHD2, and/or an intermolecular association resulting in homo- or hetero-dimerization. The EHD2 binds Swi2/Brahma homologue Brahma-related gene 1 (BRG1, also known as Snf2b), a human homologue of yeast Swi2.


Pssm-ID: 350640  Cd Length: 93  Bit Score: 43.11  E-value: 7.05e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 655860861   37 FLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERIL 113
Cdd:cd16876     6 WVDRYLAFTEEKAMGMtNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQCL 83
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
245-288 8.60e-05

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


Pssm-ID: 277009  Cd Length: 47  Bit Score: 41.18  E-value: 8.60e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGD-WRCP 288
Cdd:cd15534     1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMCP 45
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
1113-1155 1.47e-04

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: 40.66  E-value: 1.47e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 655860861   1113 CLCQK-GPAAPMIQCELCRGAFHTGCVAVPSVSQGPQ-IWLCPHC 1155
Cdd:smart00249    3 SVCGKpDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDgKWYCPKC 47
PHD_PYGO1 cd15635
PHD finger found in pygopus homolog 1 (PYGO1); PYGO1 is a homolog of Drosophila melanogaster ...
1415-1448 1.86e-04

PHD finger found in pygopus homolog 1 (PYGO1); PYGO1 is a homolog of Drosophila melanogaster protein pygopus (dPYGO), which is a fundamental Wnt signaling transcriptional component in Drosophila. It functions as a context-dependent beta-catenin coactivator, and binds di- and trimethylated lysine 4 of histone H3 (H3K4me2/3). PYGO1 is essential for the association with Legless (Lgs)/Bcl9 that acts as an adaptor between Pygopus (Pygo) and Arm/beta-catenin. PYGO1 contains a plant homeodomain (PHD) finger, which is important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway.


Pssm-ID: 277105  Cd Length: 57  Bit Score: 40.85  E-value: 1.86e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 655860861 1415 PAASCLQPEGDEVDWVQCDGSCDQWFHQVCVGVS 1448
Cdd:cd15635     2 PCGICTNEVNDDQDAILCEASCQKWFHRICTGMT 35
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
1113-1158 2.12e-04

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: 40.17  E-value: 2.12e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 655860861  1113 CLCQKGPAA-PMIQCELCRGAFHTGCVAVPSVSQGPQI--WLCPHCRRS 1158
Cdd:pfam00628    3 AVCGKSDDGgELVQCDGCDDWFHLACLGPPLDPAEIPSgeWLCPECKPK 51
ARID_ARID3 cd16867
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ...
22-116 2.35e-04

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ARID3B, ARID3C, dead ringer (Dri) from Drosophila melanogaster, and similar proteins; The ARID3 subfamily includes AT-rich interactive domain (ARID, also known as BRIGHT)-containing proteins ARID3A, ARID3B and ARID3C, which are the most direct mammalian counterparts of the Drosophila "dead ringer" protein Dri. They consist of an acidic N-terminal region of unknown function, the central ARID matrix association (or attachment) region (MAR)-DNA binding domain, a SUMO-I conjugation (SUMO) motif, and a multifunctional homomerization/nuclear export REKLES domain in the C-terminal third of the molecule. The ARID domain in this subfamily has been described as the "extended" or e-ARID due to additional conserved sequences at both the N and C termini of the core ARID region. The REKLES domain is found only in the ARID3 subfamily. It has co-evolved with and regulates functional properties of the ARID DNA-binding domain.


Pssm-ID: 350631  Cd Length: 118  Bit Score: 42.09  E-value: 2.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   22 QRLNELEAQTRVKlNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGF-APGK 99
Cdd:cd16867     2 KQLYELSDDPKRK-EFLDDLFSFMQKRGTPVnRIPIMAKQVLDLYELYRLVVEKGGLVEVINKKIWREITKGLNLpSSIT 80
                          90
                  ....*....|....*..
gi 655860861  100 AVGSHIRGHYERILNPY 116
Cdd:cd16867    81 SAAFTLRTQYMKYLYPY 97
PHD_HAC_like cd15614
PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar ...
1423-1462 2.50e-04

PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar proteins; This family includes A. thaliana HACs (HAC1/2/4/5/12), which are histone acetyltransferases of the p300/CREB-binding protein (CBP) co-activator family. CBP-type HAT proteins are also found in animals, but absent in fungi. The domain architecture of CBP-type HAT proteins differs between plants and animals. Members in this family contain an N-terminal partially conserved KIX domain, a Zf-TAZ domain, a Cysteine rich CBP-type HAT domain that harbors a plant homeodomain (PHD) finger, a Zf-ZZ domain, and a Zf-TAZ domain. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277086  Cd Length: 73  Bit Score: 40.80  E-value: 2.50e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 655860861 1423 EGDEVDWVQCDgSCDQWFHQVCVGVSPEMAEKED--YICVRC 1462
Cdd:cd15614    33 EEFEEAWVQCD-KCERWQHQICGLYNGRRNADETaeYVCPLC 73
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
258-290 2.68e-04

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


Pssm-ID: 277093  Cd Length: 43  Bit Score: 39.79  E-value: 2.68e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 655860861  258 LLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15623    11 LVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
245-290 3.05e-04

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


Pssm-ID: 277038  Cd Length: 49  Bit Score: 39.68  E-value: 3.05e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKG---DWRCPKC 290
Cdd:cd15563     1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
245-288 3.49e-04

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 39.62  E-value: 3.49e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861  245 VCLLCGSGSDedrLLLCD--GCDDSYHTFCLipPLHDVPKGDWRCP 288
Cdd:cd15568     1 ECFRCGDGGD---LVLCDfkGCPKVYHLSCL--GLEKPPGGKWICP 41
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
1122-1155 3.50e-04

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


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 39.58  E-value: 3.50e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 655860861 1122 PMIQCELCRGAFHTGCVAVPSVSQGPQIWLCPHC 1155
Cdd:cd15522    13 PMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
268-300 5.58e-04

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 41.80  E-value: 5.58e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 655860861  268 YHTFCLIPPLHDVPKGDWRCPKCLAQECSKPQE 300
Cdd:cd04718     2 FHLCCLRPPLKEVPEGDWICPFCEVEKSGQSAM 34
PHD_Ecm5p_Lid2p_like cd15518
PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), ...
1113-1155 6.02e-04

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


Pssm-ID: 276993  Cd Length: 45  Bit Score: 38.87  E-value: 6.02e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 655860861 1113 CLCQKGPAAPMIQCELCRGAFHTGCVAVPS-VSQGPQIWLCPHC 1155
Cdd:cd15518     2 CFCRQGEGGTMIECEICKEWYHVKCIKNGRwKLDDDDKFVCPIC 45
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
1423-1462 7.36e-04

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


Pssm-ID: 277087  Cd Length: 57  Bit Score: 39.00  E-value: 7.36e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861 1423 EGDEVDWVQCDgSCDQWFHQVCVGVSPEMAEKE------DYICVRC 1462
Cdd:cd15615    13 EGDEKEWVQCD-SCSEWVHFECDGRTGLGAFKYaksdglQYVCPRC 57
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
1419-1462 8.27e-04

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


Pssm-ID: 277108  Cd Length: 51  Bit Score: 38.75  E-value: 8.27e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861 1419 CLQPEGDEVdWVQCdGSCDQWFHQVCVGVSPEMA---EKED--YICVRC 1462
Cdd:cd15638     5 CKKPHGNRF-MVGC-GRCDDWFHGDCVGLSLSQAqqmEEEDkeYVCVKC 51
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
246-290 8.55e-04

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


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 38.38  E-value: 8.55e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDedrLLLCDGCDDSYHTFCLipPLHDVPKGDWRCPKC 290
Cdd:cd15567     2 CFICSEGGS---LICCESCPASFHPECL--GLEPPPEGKFYCEDC 41
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
245-290 1.17e-03

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


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 38.04  E-value: 1.17e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861  245 VCLLCGSGSDEDRLLLCDGCDDSYHTFCL---IPPlhdVPKGDWRCPKC 290
Cdd:cd15522     1 ICPICKKPDDGSPMIGCDECDDWYHWECVgitDEP---PEEDDWFCPKC 46
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
245-290 1.63e-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: 37.91  E-value: 1.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861  245 VCLLCGSGS--DEDRLLLCDGCDDSYHTFCL-IPPLHDVPKGDWRCPKC 290
Cdd:cd15517     1 VCGICNLETaaVDELWVQCDGCDKWFHQFCLgLSNERYADEDKFKCPNC 49
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
1034-1156 1.70e-03

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


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 41.85  E-value: 1.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861 1034 GLKRKQRKFKEPLLSGKKRSTKLESLSdlERALTESRETASAMAAlgeaRLREMEALQSLrlANEGKLLSPVQDVEMKVC 1113
Cdd:COG5034   153 GSRHTKLKKRKNIHNLKRRSPELSSKR--EVSFTLESPSVPDTAT----RVKEGNNGGST--KSRGVSSEDNSEGEELYC 224
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861 1114 LCQKGPAAPMIQC--ELC-RGAFHTGCVAVPSVSQGpqIWLCPHCR 1156
Cdd:COG5034   225 FCQQVSYGQMVACdnANCkREWFHLECVGLKEPPKG--KWYCPECK 268
ARID_Dri-like cd16881
ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar ...
17-116 2.08e-03

ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar proteins; Dri, also termed retained (retn), is a nuclear protein with a sequence-specific DNA-binding domain termed AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is a founding member of the ARID family. Sequence comparison shows that DRI belongs to the "extended" or e-ARID subfamily, which exhibits an extended region of similarity either side of the ARID. Dri plays an important role in embryogenesis. It functions as an essential transcription factor involved in aspects of dorsal/ventral and anterior/posterior axis patterning, as well as myogenesis and hindgut development.


Pssm-ID: 350645  Cd Length: 125  Bit Score: 39.49  E-value: 2.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   17 FTPRIQRLNELEAQTRVKlNFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIaTKMGF 95
Cdd:cd16881     4 FFEQFKQLYEISDDPKRK-EFLDDLFSFMQKRGTPVnRIPIMAKQVLDLYELYNLVVARGGLVEVINKKLWREI-TKGLH 81
                          90       100
                  ....*....|....*....|...
gi 655860861   96 APGKAVGSH--IRGHYERILNPY 116
Cdd:cd16881    82 LPSSITSAAftLRTQYMKYLYPY 104
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
245-291 2.15e-03

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


Pssm-ID: 277053  Cd Length: 53  Bit Score: 37.37  E-value: 2.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 655860861  245 VCLLCGSGSDE--DRLLLCDGCDDSYHTFCLIPPLHDV---PKGDWRCPKCL 291
Cdd:cd15578     1 VCTVCQDGSSEspNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQCV 52
PHD_PYGO2 cd15636
PHD finger found in pygopus homolog 2 (PYGO2); PYGO2 is a homolog of Drosophila melanogaster ...
1415-1448 2.20e-03

PHD finger found in pygopus homolog 2 (PYGO2); PYGO2 is a homolog of Drosophila melanogaster protein pygopus (dPYGO), which is a fundamental Wnt signaling transcriptional component in Drosophila. It functions as a context-dependent beta-catenin coactivator, as well as a histone methylation reader that binds di-and trimethylated lysine 4 of histone H3 (H3K4me2/3). Moreover, PYGO2 acts as a chromatin remodeler in a testis-specific and Wnt-unrelated manner. It also mediates chromatin regulation and links Wnt signaling and Notch signaling to suppress the luminal/alveolar differentiation competence of mammary stem and basal cells. Furthermore, PYGO2 plays a new role in rRNA transcription during cancer cell growth. It regulates mammary tumor initiation and heterogeneity in MMTV-Wnt1 mice. PYGO2 contains a plant homeodomain (PHD) finger, which is important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway.


Pssm-ID: 277106  Cd Length: 54  Bit Score: 37.73  E-value: 2.20e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 655860861 1415 PAASCLQPEGDEVDWVQCDGSCDQWFHQVCVGVS 1448
Cdd:cd15636     1 PCGACRSEVNDDQDAILCEASCQKWFHRECTGMT 34
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
245-290 2.94e-03

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 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, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 37.06  E-value: 2.94e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861  245 VCLLCGS-GSDED-RLLLCDGCDDSYHTFCL-IPPLHDVPKGDWRCPKC 290
Cdd:cd15512     1 MCVSCGSfGRGAEgRLIACSQCGQCYHPYCVnVKVTKVILSKGWRCLDC 49
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
246-290 3.59e-03

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: 36.68  E-value: 3.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861  246 CLLCG-SGSDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGD---WRCPKC 290
Cdd:cd15507     2 CHVCGrKGQAQKQLLECEKCQRGYHVDCLGPSYPTKPTRKkktWICSKC 50
ARID_ARID4B cd16883
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) ...
36-113 3.61e-03

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins; ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1, or RBBP1L1), is a tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating cell cycle. ARID4B contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain.


Pssm-ID: 350647  Cd Length: 92  Bit Score: 38.03  E-value: 3.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655860861   36 NFLDQIAKYWELQGSTL-KIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGF-APGKAVGSHIRGHYERIL 113
Cdd:cd16883     4 NFLQQLYKFMEDRGTPInKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIpVLNSAAGYNVKCAYRKYL 83
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
246-290 3.95e-03

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


Pssm-ID: 277094  Cd Length: 46  Bit Score: 36.56  E-value: 3.95e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15624     2 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 43
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
1113-1158 4.35e-03

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


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 36.91  E-value: 4.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861 1113 CLCQKGP---AAPMIQCELCRGAFHTGCVAVPSVSQGPqiWLCPHCRRS 1158
Cdd:cd15677     5 CICMDGEcqnSNVILFCDMCNLAVHQECYGVPYIPEGQ--WLCRHCLQS 51
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
246-290 5.22e-03

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


Pssm-ID: 277092  Cd Length: 43  Bit Score: 36.20  E-value: 5.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15622     2 CAVCQNGGE---LLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
245-290 6.12e-03

PHD finger 4 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 fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 36.53  E-value: 6.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861  245 VCLLCGS--GSDEDRLLLCDGCDDSYHTFCL-IPPLHDVPKGDWRCPKC 290
Cdd:cd15596     8 MCVVCGSfgQGAEGRLLACSQCGQCYHPYCVsIKITKVVLSKGWRCLEC 56
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
246-290 6.61e-03

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


Pssm-ID: 277096  Cd Length: 42  Bit Score: 35.87  E-value: 6.61e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGsgsDEDRLLLCDGCDDSYHTFCLIPPLhDVPKGDWRCPKC 290
Cdd:cd15626     2 CEVCG---QEGKLFCCCTCSRVFHEDCHIPPV-EAQRSPWSCTFC 42
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
1113-1155 7.14e-03

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


Pssm-ID: 277027  Cd Length: 50  Bit Score: 35.84  E-value: 7.14e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 655860861 1113 CLCQKG-PAAPMIQCELCRGAFHTGCVAVpSVSQGPQI------WLCPHC 1155
Cdd:cd15552     2 CICRKPhNNRFMICCDRCEEWFHGDCVGI-TEAQGKEMeenieeYVCPKC 50
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
246-290 7.34e-03

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


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 36.09  E-value: 7.34e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 655860861  246 CLLCGSGSDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 290
Cdd:cd15625     5 CAVCLNGGE---LLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLC 46
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
1418-1462 7.93e-03

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


Pssm-ID: 277029  Cd Length: 47  Bit Score: 35.82  E-value: 7.93e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 655860861 1418 SCLQPEGDEVDWVQCDgSCDQWFHQVCVGVSPEMAEK-EDYICVRC 1462
Cdd:cd15554     3 ICRQPYDVTRFMIECD-VCKDWFHGSCVGVEEHQANDiERYHCPNC 47
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
1113-1158 8.70e-03

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


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 36.05  E-value: 8.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 655860861 1113 CLCQKGP---AAPMIQCELCRGAFHTGCVAVPSVSQGPqiWLCPHCRRS 1158
Cdd:cd15572     5 CICLDGEcqnSNVILFCDMCNLAVHQECYGVPYIPEGQ--WLCRRCLQS 51
PHD_PYGO cd15551
PHD finger found in PYGO proteins; The family includes Drosophila melanogaster protein pygopus ...
1415-1449 9.48e-03

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


Pssm-ID: 277026  Cd Length: 54  Bit Score: 35.80  E-value: 9.48e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 655860861 1415 PAASCLQPEGDEVDWVQCDGSCDQWFHQVCVGVSP 1449
Cdd:cd15551     1 PCGICNNEVNDDDDAILCESSCNKWFHRTCTGLTE 35
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
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