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Conserved domains on  [gi|767994058|ref|XP_011522826|]
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nucleosome-remodeling factor subunit BPTF isoform X44 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 2073-2173 4.52e-57

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


:

Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 192.77  E-value: 4.52e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2073 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSD 2152
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 767994058 2153 SPFYQCAEVLESFFVQKLKGF 2173
Cdd:cd05509    81 TEYYKCANKLEKFFWKKLKEL 101
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
 2011-2057 8.47e-34

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: 124.38  E-value: 8.47e-34
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
 1953-1999 2.69e-27

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: 105.89  E-value: 2.69e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 1953 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47
Glutenin_hmw super family cl26620
High molecular weight glutenin subunit; Members of this family include high molecular weight ...
 1213-1584 2.18e-06

High molecular weight glutenin subunit; Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.


The actual alignment was detected with superfamily member pfam03157:

Pssm-ID: 367362 [Multi-domain]  Cd Length: 786  Bit Score: 53.03  E-value: 2.18e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1213 QVQQKVLGIIPSSTGTSQQTFTSfQPRTATVTIRPNTSGSGGTTSNSQVITGPQIRPGMTVIRTPLQQSTLGK------- 1285
Cdd:pfam03157  256 QGQQGYYPISPQQPRQWQQSGQG-QQGYYPTSLQQPGQGQSGYYPTSQQQAGQLQQEQQLGQEQQDQQPGQGRqgqqpgq 334

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1286 -------AIIRTPVMVQPGAPQQVMTQIIRGQPVSTAVSAPN-TVSSTPGQKSLTSATSTSNIQSSASQPPRPQQGQVKL 1357
Cdd:pfam03157  335 gqqgqqpAQGQQPGQGQPGYYPTSPQQPGQGQPGYYPTSQQQpQQGQQPEQGQQGQQQGQGQQGQQPGQGQQPGQGQPGY 414

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1358 TMAQLTQLTQGHGGNQGLTVVIQGQGQTTGQLQLIPQGVTV---LPGPGQQLMQAAMPN-----GTVQRFLFTPLATTAT 1429
Cdd:pfam03157  415 YPTSPQQSGQGQPGYYPTSPQQSGQGQQPGQGQQPGQEQPGqgqQPGQGQQGQQPGQPEqgqqpGQGQPGYYPTSPQQSG 494

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1430 TASTTTTTVSTTAAGTGEQRQSKLSP-QMQVHQDKTLPpaQSSSVGPAEAQPQTAQPSAQPQPQTQPQSPAQPEVQTQPE 1508
Cdd:pfam03157  495 QGQQLGQWQQQGQGQPGYYPTSPLQPgQGQPGYYPTSP--QQPGQGQQLGQLQQPTQGQQGQQSGQGQQGQQPGQGQQGQ 572

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767994058  1509 VQTQTTVSSHVPSEAQPTHAQsskpQVAAQSQPQSNVQGQSPVRVQSPSQTR--IRPSTPSQLSPGQQSQVQTTTSQP 1584
Cdd:pfam03157  573 QPGQGQQGQQPGQGQQPGQGQ----PGYYPTSPQQSGQGQQPGQWQQPGQGQpgYYPTSSLQLGQGQQGYYPTSPQQP 646
TNG2 super family cl34876
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
1772-2002 2.28e-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: 42.23  E-value: 2.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1772 REENQRMIVCNQVMKYI--LDKIDKEEKQAAKKRKREESVEQKRSKQNatkLSALLFKHKEQLRAEILKKralLDKDLQI 1849
Cdd:COG5034    36 CDIIKNLRQMISILKKIidLDSQTYEEVEDGLLKEIRELLLKAIYIQK---EKSDLADRAEKLLRRHRKL---LDDRIAK 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1850 EVQEEL-KRDLKIKKEKDLMQLAQATAVAAPCPPVTPAPPAPPAPPPSPPPPPAVQHTGLLSTPTLPA---ASQKRKREE 1925
Cdd:COG5034   110 RPHEKVaARIENCHDAVSRLERNSYSSAARRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSkreVSFTLESPS 189

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1926 EKDSSSKSKKKKMISTTSKET------KKDTKLYCICKTP-YDEskfYIGCD--LCT-NWYHGECVGIteKEAKKMDVYi 1995
Cdd:COG5034   190 VPDTATRVKEGNNGGSTKSRGvssednSEGEELYCFCQQVsYGQ---MVACDnaNCKrEWFHLECVGL--KEPPKGKWY- 263


                  ....*..
gi 767994058 1996 CNDCKRA 2002
Cdd:COG5034   264 CPECKKA 270
 
Name Accession Description Interval E-value
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 2073-2173 4.52e-57

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 192.77  E-value: 4.52e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2073 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSD 2152
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 767994058 2153 SPFYQCAEVLESFFVQKLKGF 2173
Cdd:cd05509    81 TEYYKCANKLEKFFWKKLKEL 101
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
 2011-2057 8.47e-34

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: 124.38  E-value: 8.47e-34
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47
BROMO smart00297
bromo domain;
2070-2171 8.77e-33

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 123.54  E-value: 8.77e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058   2070 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYN 2149
Cdd:smart00297    4 LQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|..
gi 767994058   2150 PSDSPFYQCAEVLESFFVQKLK 2171
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLR 105
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
 1953-1999 2.69e-27

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: 105.89  E-value: 2.69e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 1953 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 2078-2160 1.26e-25

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 102.39  E-value: 1.26e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  2078 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2157
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80


                   ...
gi 767994058  2158 CAE 2160
Cdd:pfam00439   81 AAE 83
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 2067-2171 7.49e-17

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 84.86  E-value: 7.49e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2067 LTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCR 2146
Cdd:COG5076   142 LLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCK 221

                          90       100
                  ....*....|....*....|....*
gi 767994058 2147 YYNPSDSPFYQCAEVLESFFVQKLK 2171
Cdd:COG5076   222 LYNGPDSSVYVDAKELEKYFLKLIE 246
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 2011-2057 1.68e-10

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: 57.99  E-value: 1.68e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 767994058   2011 YC-ICRTPYDESQFyIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:smart00249    1 YCsVCGKPDDGGEL-LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1953-1999 7.16e-10

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: 56.07  E-value: 7.16e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 767994058   1953 YC-ICKTPYDESKFyIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:smart00249    1 YCsVCGKPDDGGEL-LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1953-2002 6.15e-09

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 53.65  E-value: 6.15e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 767994058  1953 YC-ICKTPyDESKFYIGCDLCTNWYHGECVGIT-EKEAKKMDVYICNDCKRA 2002
Cdd:pfam00628    1 YCaVCGKS-DDGGELVQCDGCDDWFHLACLGPPlDPAEIPSGEWLCPECKPK 51
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 2011-2059 1.15e-07

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 50.18  E-value: 1.15e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 767994058  2011 YC-ICRTPYDESQFyIGCDRCQNWYHGRCVGILQSEAELID-EYVCPQCQS 2059
Cdd:pfam00628    1 YCaVCGKSDDGGEL-VQCDGCDDWFHLACLGPPLDPAEIPSgEWLCPECKP 50
Glutenin_hmw pfam03157
High molecular weight glutenin subunit; Members of this family include high molecular weight ...
 1213-1584 2.18e-06

High molecular weight glutenin subunit; Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.


Pssm-ID: 367362 [Multi-domain]  Cd Length: 786  Bit Score: 53.03  E-value: 2.18e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1213 QVQQKVLGIIPSSTGTSQQTFTSfQPRTATVTIRPNTSGSGGTTSNSQVITGPQIRPGMTVIRTPLQQSTLGK------- 1285
Cdd:pfam03157  256 QGQQGYYPISPQQPRQWQQSGQG-QQGYYPTSLQQPGQGQSGYYPTSQQQAGQLQQEQQLGQEQQDQQPGQGRqgqqpgq 334

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1286 -------AIIRTPVMVQPGAPQQVMTQIIRGQPVSTAVSAPN-TVSSTPGQKSLTSATSTSNIQSSASQPPRPQQGQVKL 1357
Cdd:pfam03157  335 gqqgqqpAQGQQPGQGQPGYYPTSPQQPGQGQPGYYPTSQQQpQQGQQPEQGQQGQQQGQGQQGQQPGQGQQPGQGQPGY 414

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1358 TMAQLTQLTQGHGGNQGLTVVIQGQGQTTGQLQLIPQGVTV---LPGPGQQLMQAAMPN-----GTVQRFLFTPLATTAT 1429
Cdd:pfam03157  415 YPTSPQQSGQGQPGYYPTSPQQSGQGQQPGQGQQPGQEQPGqgqQPGQGQQGQQPGQPEqgqqpGQGQPGYYPTSPQQSG 494

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1430 TASTTTTTVSTTAAGTGEQRQSKLSP-QMQVHQDKTLPpaQSSSVGPAEAQPQTAQPSAQPQPQTQPQSPAQPEVQTQPE 1508
Cdd:pfam03157  495 QGQQLGQWQQQGQGQPGYYPTSPLQPgQGQPGYYPTSP--QQPGQGQQLGQLQQPTQGQQGQQSGQGQQGQQPGQGQQGQ 572

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767994058  1509 VQTQTTVSSHVPSEAQPTHAQsskpQVAAQSQPQSNVQGQSPVRVQSPSQTR--IRPSTPSQLSPGQQSQVQTTTSQP 1584
Cdd:pfam03157  573 QPGQGQQGQQPGQGQQPGQGQ----PGYYPTSPQQSGQGQQPGQWQQPGQGQpgYYPTSSLQLGQGQQGYYPTSPQQP 646
SP2_N cd22540
N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins ...
 1193-1589 2.19e-05

N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2.


Pssm-ID: 411776 [Multi-domain]  Cd Length: 511  Bit Score: 49.54  E-value: 2.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1193 LPANSKIV-----AVNVPATQGG-VVQVQQKVLGIIPSSTG--TSQQTFTSFQPRTATVTIRPNTSGSGGTTsNSQVITG 1264
Cdd:cd22540    79 LSAKGNIIqlqgsQLSSSAPGGQqVFAIQNPTMIIKGSQTRssTNQQYQISPQIQAAGQINNSGQIQIIPGT-NQAIITP 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1265 PQIRPG-------MTVIRTPLQQSTLGKAIIRTP--VMVQPGAPQQVMT---QIIRGQPVSTAVSAPNTVSSTPGQKslt 1332
Cdd:cd22540   158 VQVLQQpqqahkpVPIKPAPLQTSNTNSASLQVPgnVIKLQSGGNVALTlpvNNLVGTQDGATQLQLAAAPSKPSKK--- 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1333 satsTSNIQSSASQPPRPQQGQVKLTMAQLTQLTQGHGGNQGLTVVIQGQGQ--TTGQLQLIP----QGVTVLPGPGQQL 1406
Cdd:cd22540   235 ----IRKKSAQAAQPAVTVAEQVETVLIETTADNIIQAGNNLLIVQSPGTGQpaVLQQVQVLQpkqeQQVVQIPQQALRV 310

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1407 MQAA-MPNGTVQRflfTPLATTATTASTTTTTVSTTAAGTGEQrqsklspQMQVHQDKTLPPAQSSSVGPAEAQPQTAQP 1485
Cdd:cd22540   311 VQAAsATLPTVPQ---KPLQNIQIQNSEPTPTQVYIKTPSGEV-------QTVLLQEAPAATATPSSSTSTVQQQVTANN 380

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1486 SAQPQPQTQPQSPAQPEVQTQPEVQTQTTVSSHVPSEAQpTHAQSSKPQVAAQSQP--QSNVQGQSPVRVQSPSQTRIrp 1563
Cdd:cd22540   381 GTGTSKPNYNVRKERTLPKIAPAGGIISLNAAQLAAAAQ-AIQTININGVQVQGVPvtITNAGGQQQLTVQTVSSNNL-- 457

                         410       420
                  ....*....|....*....|....*.
gi 767994058 1564 sTPSQLSPGQQSQVQTTTSQpIPIQP 1589
Cdd:cd22540   458 -TISGLSPTQIQLQMEQALE-IETQP 481
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
1772-2002 2.28e-03

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


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 42.23  E-value: 2.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1772 REENQRMIVCNQVMKYI--LDKIDKEEKQAAKKRKREESVEQKRSKQNatkLSALLFKHKEQLRAEILKKralLDKDLQI 1849
Cdd:COG5034    36 CDIIKNLRQMISILKKIidLDSQTYEEVEDGLLKEIRELLLKAIYIQK---EKSDLADRAEKLLRRHRKL---LDDRIAK 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1850 EVQEEL-KRDLKIKKEKDLMQLAQATAVAAPCPPVTPAPPAPPAPPPSPPPPPAVQHTGLLSTPTLPA---ASQKRKREE 1925
Cdd:COG5034   110 RPHEKVaARIENCHDAVSRLERNSYSSAARRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSkreVSFTLESPS 189

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1926 EKDSSSKSKKKKMISTTSKET------KKDTKLYCICKTP-YDEskfYIGCD--LCT-NWYHGECVGIteKEAKKMDVYi 1995
Cdd:COG5034   190 VPDTATRVKEGNNGGSTKSRGvssednSEGEELYCFCQQVsYGQ---MVACDnaNCKrEWFHLECVGL--KEPPKGKWY- 263


                  ....*..
gi 767994058 1996 CNDCKRA 2002
Cdd:COG5034   264 CPECKKA 270
 
Name Accession Description Interval E-value
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 2073-2173 4.52e-57

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 192.77  E-value: 4.52e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2073 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSD 2152
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 767994058 2153 SPFYQCAEVLESFFVQKLKGF 2173
Cdd:cd05509    81 TEYYKCANKLEKFFWKKLKEL 101
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 2078-2170 4.45e-35

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


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 129.80  E-value: 4.45e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2078 LKRVLRSLQAH--KMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPF 2155
Cdd:cd04369     5 LRSLLDALKKLkrDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPI 84

                          90
                  ....*....|....*
gi 767994058 2156 YQCAEVLESFFVQKL 2170
Cdd:cd04369    85 YKDAKKLEKLFEKLL 99
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
 2011-2057 8.47e-34

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: 124.38  E-value: 8.47e-34
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47
BROMO smart00297
bromo domain;
2070-2171 8.77e-33

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 123.54  E-value: 8.77e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058   2070 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYN 2149
Cdd:smart00297    4 LQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|..
gi 767994058   2150 PSDSPFYQCAEVLESFFVQKLK 2171
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLR 105
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
 1953-1999 2.69e-27

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: 105.89  E-value: 2.69e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 1953 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 2078-2169 6.65e-26

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 103.51  E-value: 6.65e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2078 LKRVLRSlQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPF 2155
Cdd:cd05498     9 LKELFSK-KHKAYAWPFYKPVDPEalGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPV 87

                          90
                  ....*....|....
gi 767994058 2156 YQCAEVLESFFVQK 2169
Cdd:cd05498    88 HAMARKLQDVFEDR 101
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 2078-2160 1.26e-25

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 102.39  E-value: 1.26e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  2078 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2157
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80


                   ...
gi 767994058  2158 CAE 2160
Cdd:pfam00439   81 AAE 83
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 2081-2166 4.68e-24

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 98.22  E-value: 4.68e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2081 VLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAE 2160
Cdd:cd05503     8 ILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGH 87


                  ....*.
gi 767994058 2161 VLESFF 2166
Cdd:cd05503    88 NMRKFF 93
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 2078-2171 1.30e-22

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 94.77  E-value: 1.30e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2078 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2157
Cdd:cd05504    17 LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYK 96

                          90
                  ....*....|....
gi 767994058 2158 CAEVLESFFVQKLK 2171
Cdd:cd05504    97 AGTRLQRFFIKRCR 110
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 2072-2163 6.10e-22

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 92.89  E-value: 6.10e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2072 EKDYEGLKRVLRSLQAH-KMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNP 2150
Cdd:cd05510     6 EEFYESLDKVLNELKTYtEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNS 85

                          90
                  ....*....|....
gi 767994058 2151 SDS-PFYQCAEVLE 2163
Cdd:cd05510    86 DPShPLRRHANFMK 99
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
 2011-2057 1.11e-21

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: 89.75  E-value: 1.11e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15554     1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 2082-2166 1.82e-21

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 91.19  E-value: 1.82e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2082 LRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCA 2159
Cdd:cd05499    12 LMKPKHSAYNWPFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMG 91


                  ....*..
gi 767994058 2160 EVLESFF 2166
Cdd:cd05499    92 HQLEEVF 98
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 2080-2170 3.27e-21

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 90.45  E-value: 3.27e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2080 RVLRSLQAHKMAWPFLEPVDP--NDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2157
Cdd:cd05500    11 SSIRSLKRLKDARPFLVPVDPvkLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQ 90

                          90
                  ....*....|...
gi 767994058 2158 CAEVLESFFVQKL 2170
Cdd:cd05500    91 MGKRLQAAFEKHL 103
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 2082-2166 1.41e-20

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 88.54  E-value: 1.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2082 LRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCA 2159
Cdd:cd05506     9 LRKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMA 88


                  ....*..
gi 767994058 2160 EVLESFF 2166
Cdd:cd05506    89 KELLKIF 95
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 2078-2171 1.63e-20

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 88.63  E-value: 1.63e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2078 LKRVLRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPF 2155
Cdd:cd05497    10 LKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDV 89

                          90
                  ....*....|....*.
gi 767994058 2156 YQCAEVLESFFVQKLK 2171
Cdd:cd05497    90 VLMAQTLEKLFLQKLA 105
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 2091-2163 3.05e-20

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 88.09  E-value: 3.05e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767994058 2091 AWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCA-EVLE 2163
Cdd:cd05511    18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAkEMLE 91
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 2070-2171 6.20e-20

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 86.96  E-value: 6.20e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2070 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVdPNDAPDYYGVIKEPMDLATMEERVQRR---YYEKLTEFVADMTKIFDNCR 2146
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPV-SPSVPNYYKIIKTPMDLSLIRKKLQPKspqHYSSPEEFVADVRLMFKNCY 79

                          90       100
                  ....*....|....*....|....*
gi 767994058 2147 YYNPSDSPFYQCAEVLESFFVQKLK 2171
Cdd:cd05502    80 KFNEEDSEVAQAGKELELFFEEQLK 104
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
 1953-1999 5.25e-18

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: 79.35  E-value: 5.25e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 1953 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15554     1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 2078-2159 8.10e-18

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 80.52  E-value: 8.10e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2078 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2157
Cdd:cd05512     6 LRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYR 85


                  ..
gi 767994058 2158 CA 2159
Cdd:cd05512    86 AA 87
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
 2011-2057 2.01e-17

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


Pssm-ID: 277186  Cd Length: 46  Bit Score: 77.52  E-value: 2.01e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YCICRTPYDESqFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd16039     1 YCICQKPDDGR-WMIACDGCDEWYHFTCVNIPEADVELVDSFFCPPC 46
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 2078-2154 6.04e-17

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 78.55  E-value: 6.04e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767994058 2078 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSP 2154
Cdd:cd05528     8 LRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDP 84
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 2067-2171 7.49e-17

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 84.86  E-value: 7.49e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2067 LTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCR 2146
Cdd:COG5076   142 LLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCK 221

                          90       100
                  ....*....|....*....|....*
gi 767994058 2147 YYNPSDSPFYQCAEVLESFFVQKLK 2171
Cdd:COG5076   222 LYNGPDSSVYVDAKELEKYFLKLIE 246
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
 2011-2057 7.89e-17

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


Pssm-ID: 277028  Cd Length: 46  Bit Score: 75.88  E-value: 7.89e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YCICRTPyDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15553     1 YCICRSS-DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46
PHD_PHF2 cd15641
PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger ...
 2011-2060 9.06e-17

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


Pssm-ID: 277111  Cd Length: 50  Bit Score: 75.82  E-value: 9.06e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 767994058 2011 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST 2060
Cdd:cd15641     1 YCICRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKT 50
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
 2011-2057 2.02e-16

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: 74.74  E-value: 2.02e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767994058 2011 YCICRTPYDEsQFYIGCDRCQNWYHGRCVGILQSE----AELIDEYVCPQC 2057
Cdd:cd15552     1 YCICRKPHNN-RFMICCDRCEEWFHGDCVGITEAQgkemEENIEEYVCPKC 50
PHD_KDM7 cd15640
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ...
 1953-2000 2.50e-16

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


Pssm-ID: 277110  Cd Length: 50  Bit Score: 74.64  E-value: 2.50e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767994058 1953 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDCK 2000
Cdd:cd15640     1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48
PHD_KDM7 cd15640
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ...
 2011-2058 2.63e-16

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


Pssm-ID: 277110  Cd Length: 50  Bit Score: 74.64  E-value: 2.63e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767994058 2011 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQ 2058
Cdd:cd15640     1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
 1953-1999 4.58e-16

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: 73.97  E-value: 4.58e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767994058 1953 YCICKTPYDEsKFYIGCDLCTNWYHGECVGITEKEAKKMDV----YICNDC 1999
Cdd:cd15552     1 YCICRKPHNN-RFMICCDRCEEWFHGDCVGITEAQGKEMEEnieeYVCPKC 50
PHD_PHF8 cd15642
PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, ...
 2010-2060 6.18e-16

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


Pssm-ID: 277112  Cd Length: 52  Bit Score: 73.52  E-value: 6.18e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767994058 2010 LYCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST 2060
Cdd:cd15642     1 VYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEEKAAEIDLYHCPNCQVT 51
PHD_PHF2 cd15641
PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger ...
 1953-2001 1.01e-15

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


Pssm-ID: 277111  Cd Length: 50  Bit Score: 73.13  E-value: 1.01e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 767994058 1953 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDCKR 2001
Cdd:cd15641     1 YCICRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEK 49
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 2094-2170 1.07e-15

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 74.79  E-value: 1.07e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767994058 2094 FLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKL 2170
Cdd:cd05518    27 FMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVLKEKR 103
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
 1953-1999 1.99e-15

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


Pssm-ID: 277028  Cd Length: 46  Bit Score: 72.02  E-value: 1.99e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 1953 YCICKTPyDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15553     1 YCICRSS-DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 2074-2170 2.34e-15

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 73.34  E-value: 2.34e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2074 DYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDS 2153
Cdd:cd05505     1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                          90
                  ....*....|....*..
gi 767994058 2154 PFYQCAEVLESFFVQKL 2170
Cdd:cd05505    81 YVLSCMRKTEQCCVNLL 97
PHD_PHF8 cd15642
PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, ...
 1952-2000 8.36e-15

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


Pssm-ID: 277112  Cd Length: 52  Bit Score: 70.44  E-value: 8.36e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 767994058 1952 LYCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDCK 2000
Cdd:cd15642     1 VYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEEKAAEIDLYHCPNCQ 49
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 2088-2172 3.36e-14

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 70.41  E-value: 3.36e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2088 HKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFV 2167
Cdd:cd05515    21 RRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLL 100


                  ....*
gi 767994058 2168 QKLKG 2172
Cdd:cd05515   101 ETKRE 105
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 2061-2170 5.51e-14

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


Pssm-ID: 99927  Cd Length: 108  Bit Score: 69.78  E-value: 5.51e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2061 EDAMTVLTPLTEKDYeglkrvlrslQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADM 2138
Cdd:cd05495     2 EELRQALMPTLEKLY----------KQDPESLPFRQPVDPKllGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDV 71

                          90       100       110
                  ....*....|....*....|....*....|..
gi 767994058 2139 TKIFDNCRYYNPSDSPFYQCAEVLESFFVQKL 2170
Cdd:cd05495    72 WLMFDNAWLYNRKTSRVYKYCTKLAEVFEQEI 103
PHD_DIDO1_like cd15639
PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family ...
 2008-2057 6.64e-14

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


Pssm-ID: 277109  Cd Length: 54  Bit Score: 68.07  E-value: 6.64e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767994058 2008 EELYCICRTPYDeSQFYIGCDRCQNWYHGRCVGILQSEAELI----DEYVCPQC 2057
Cdd:cd15639     2 NALYCICRQPHN-NRFMICCDRCEEWFHGDCVGITEARGRLLerngEDYICPNC 54
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
 2074-2122 3.77e-13

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


Pssm-ID: 99926 [Multi-domain]  Cd Length: 114  Bit Score: 67.85  E-value: 3.77e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767994058 2074 DYEGLKRVLRSLQAH---KMAWPFLEPVDP--NDAPDYYGVIKEPMDLATMEER 2122
Cdd:cd05494     1 DYEALERVLRELKRHrrnEDAWPFLEPVNPprRGAPDYRDVIKRPMSFGTKVNN 54
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
 1953-1999 6.49e-13

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


Pssm-ID: 277186  Cd Length: 46  Bit Score: 64.81  E-value: 6.49e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 1953 YCICKTPYDESkFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd16039     1 YCICQKPDDGR-WMIACDGCDEWYHFTCVNIPEADVELVDSFFCPPC 46
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 2094-2169 2.89e-12

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


Pssm-ID: 99950  Cd Length: 103  Bit Score: 65.05  E-value: 2.89e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767994058 2094 FLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 2169
Cdd:cd05519    27 FLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKKK 102
PHD_DIDO1_like cd15639
PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family ...
 1951-1999 4.79e-12

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


Pssm-ID: 277109  Cd Length: 54  Bit Score: 62.68  E-value: 4.79e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767994058 1951 KLYCICKTPYDeSKFYIGCDLCTNWYHGECVGITEKEAKKMDV----YICNDC 1999
Cdd:cd15639     3 ALYCICRQPHN-NRFMICCDRCEEWFHGDCVGITEARGRLLERngedYICPNC 54
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 2076-2162 4.97e-12

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 63.97  E-value: 4.97e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2076 EGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPF 2155
Cdd:cd05513     4 KALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIY 83


                  ....*..
gi 767994058 2156 YQCAEVL 2162
Cdd:cd05513    84 YKAAKKL 90
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 2011-2057 9.99e-12

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


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 61.56  E-value: 9.99e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767994058 2011 YC-ICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15489     1 SCiVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 2046-2171 1.59e-11

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 68.29  E-value: 1.59e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2046 AELIDEY----VCPQCQSTEDAMtvLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEE 2121
Cdd:COG5076   234 AKELEKYflklIEEIPEEMLELS--IKPGREEREERESVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKEL 311

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 767994058 2122 RVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 2171
Cdd:COG5076   312 KLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKKTR 361
PHD_AL_plant cd15613
PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed ...
 2014-2057 1.60e-11

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


Pssm-ID: 277085  Cd Length: 51  Bit Score: 60.97  E-value: 1.60e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767994058 2014 CRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15613     5 CGGNYTADEFWICCDVCEKWYHGKCVKITPAKAEHIKQYKCPSC 48
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 2077-2166 1.98e-11

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


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 62.64  E-value: 1.98e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2077 GLKRvLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFY 2156
Cdd:cd05522    12 GLRK-ERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEY 90

                          90
                  ....*....|
gi 767994058 2157 QCAEVLESFF 2166
Cdd:cd05522    91 KDAVLLEKEA 100
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 2093-2182 2.00e-11

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 62.86  E-value: 2.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2093 PFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSD-SPFYQCAEVLESFFVQKLK 2171
Cdd:cd05496    25 PFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNKrSRIYSMTLRLSALFEEHIK 104

                          90
                  ....*....|....*
gi 767994058 2172 ----GFKASRSHNNK 2182
Cdd:cd05496   105 kiisDWKSALKRNEK 119
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 1953-1999 8.97e-11

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: 58.84  E-value: 8.97e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767994058 1953 YC-ICKTPYDESKfYIGCDLCTNWYHGECVGITEKEAKKMDVYiCNDC 1999
Cdd:cd15522     1 ICpICKKPDDGSP-MIGCDECDDWYHWECVGITDEPPEEDDWF-CPKC 46
PHD_MMD1_like cd15556
PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD ...
 2012-2057 1.60e-10

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


Pssm-ID: 277031 [Multi-domain]  Cd Length: 46  Bit Score: 58.16  E-value: 1.60e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 2012 CICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEaELIDEYVCPQC 2057
Cdd:cd15556     2 CSCGTRDDDGERMIACDVCEVWQHTRCVGIADNE-EPPDHFLCRRC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 2011-2057 1.68e-10

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: 57.99  E-value: 1.68e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 767994058   2011 YC-ICRTPYDESQFyIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:smart00249    1 YCsVCGKPDDGGEL-LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD3_KDM5A_like cd15610
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; ...
 1956-1999 2.12e-10

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: 57.72  E-value: 2.12e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767994058 1956 CKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15610     7 CLKPTGDEVNWVQCDGCEEWFHLLCVGLSPEEVAEDEDYICPSC 50
PHD_AL_plant cd15613
PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed ...
 1956-2001 2.31e-10

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


Pssm-ID: 277085  Cd Length: 51  Bit Score: 57.89  E-value: 2.31e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 1956 CKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDCKR 2001
Cdd:cd15613     5 CGGNYTADEFWICCDVCEKWYHGKCVKITPAKAEHIKQYKCPSCSN 50
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1953-1999 3.48e-10

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: 57.33  E-value: 3.48e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767994058 1953 YC-ICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15489     1 SCiVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD3_KDM5A_like cd15610
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; ...
 2014-2057 3.71e-10

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: 56.95  E-value: 3.71e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767994058 2014 CRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15610     7 CLKPTGDEVNWVQCDGCEEWFHLLCVGLSPEEVAEDEDYICPSC 50
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1953-1999 7.16e-10

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: 56.07  E-value: 7.16e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 767994058   1953 YC-ICKTPYDESKFyIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:smart00249    1 YCsVCGKPDDGGEL-LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 2013-2057 7.27e-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: 56.40  E-value: 7.27e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 2013 ICRTP-YDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15517     4 ICNLEtAAVDELWVQCDGCDKWFHQFCLGLSNERYADEDKFKCPNC 49
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 2081-2152 9.27e-10

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 57.76  E-value: 9.27e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767994058 2081 VLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSD 2152
Cdd:cd05507    11 VYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSD 82
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 2011-2057 9.85e-10

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: 55.76  E-value: 9.85e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767994058 2011 YC-ICRTPYDESQfYIGCDRCQNWYHGRCVGILQSEAElIDEYVCPQC 2057
Cdd:cd15522     1 ICpICKKPDDGSP-MIGCDECDDWYHWECVGITDEPPE-EDDWFCPKC 46
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 2077-2163 1.55e-09

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 57.73  E-value: 1.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2077 GLKRVLRSLQAHKmAWPFLEPVD-PNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPF 2155
Cdd:cd05529    32 GLDKLLLSLQLEI-AEYFEYPVDlRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEI 110


                  ....*...
gi 767994058 2156 YQCAEVLE 2163
Cdd:cd05529   111 AKKAKRLS 118
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
 2013-2057 2.08e-09

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


Pssm-ID: 277108  Cd Length: 51  Bit Score: 54.93  E-value: 2.08e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 767994058 2013 ICRTPYDeSQFYIGCDRCQNWYHGRCVGILQSEAELID----EYVCPQC 2057
Cdd:cd15638     4 FCKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQAQQMEeedkEYVCVKC 51
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 2102-2165 2.21e-09

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


Pssm-ID: 99952  Cd Length: 106  Bit Score: 56.56  E-value: 2.21e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767994058 2102 DAPDYYGVIKEPMDLATMEERVQRryYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESF 2165
Cdd:cd05521    36 DYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKY 97
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 2090-2163 3.04e-09

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 56.19  E-value: 3.04e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767994058 2090 MAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLE 2163
Cdd:cd05520    23 LAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQ 96
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 2093-2162 5.95e-09

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 55.47  E-value: 5.95e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2093 PFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVL 2162
Cdd:cd05508    22 PFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAI 91
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1953-2002 6.15e-09

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 53.65  E-value: 6.15e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 767994058  1953 YC-ICKTPyDESKFYIGCDLCTNWYHGECVGIT-EKEAKKMDVYICNDCKRA 2002
Cdd:pfam00628    1 YCaVCGKS-DDGGELVQCDGCDDWFHLACLGPPlDPAEIPSGEWLCPECKPK 51
PHD_Ecm5p_Lid2p_like cd15518
PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), ...
 1953-1999 8.25e-09

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: 53.12  E-value: 8.25e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 1953 YCICKTPydESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15518     1 YCFCRQG--EGGTMIECEICKEWYHVKCIKNGRWKLDDDDKFVCPIC 45
PHD_Ecm5p_Lid2p_like cd15518
PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), ...
 2011-2057 8.66e-09

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: 53.12  E-value: 8.66e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YCICRTPydESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15518     1 YCFCRQG--EGGTMIECEICKEWYHVKCIKNGRWKLDDDDKFVCPIC 45
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
 2012-2057 2.83e-08

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


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 51.55  E-value: 2.83e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 2012 CICRTPYDESqFYIGCDRCQNWYHGRCVGILQSEAEliDEYVCPQC 2057
Cdd:cd15550     2 CICGFEHDDG-FMICCDKCSVWQHGDCMGIDRENIP--DSYLCEQC 44
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 2090-2167 4.18e-08

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


Pssm-ID: 99947  Cd Length: 107  Bit Score: 53.20  E-value: 4.18e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767994058 2090 MAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFV 2167
Cdd:cd05516    24 LAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFK 101
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
 1954-1999 5.29e-08

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


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 50.78  E-value: 5.29e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 1954 CICKTPYDESkFYIGCDLCTNWYHGECVGITEKEAKkmDVYICNDC 1999
Cdd:cd15550     2 CICGFEHDDG-FMICCDKCSVWQHGDCMGIDRENIP--DSYLCEQC 44
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 2011-2059 1.15e-07

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 50.18  E-value: 1.15e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 767994058  2011 YC-ICRTPYDESQFyIGCDRCQNWYHGRCVGILQSEAELID-EYVCPQCQS 2059
Cdd:pfam00628    1 YCaVCGKSDDGGEL-VQCDGCDDWFHLACLGPPLDPAEIPSgEWLCPECKP 50
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 2105-2171 1.41e-07

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 51.66  E-value: 1.41e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767994058 2105 DYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNpSDSPFYQCAEVLESFFVQKLK 2171
Cdd:cd05501    32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFY-KDDDFGQVGITLEKKFEKNFK 97
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
 1955-1999 1.69e-07

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: 49.54  E-value: 1.69e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 767994058 1955 ICKTPYDeSKFYIGCDLCTNWYHGECVGITEKEAKKMDV----YICNDC 1999
Cdd:cd15638     4 FCKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEedkeYVCVKC 51
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 2104-2169 3.87e-07

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 50.13  E-value: 3.87e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767994058 2104 PDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 2169
Cdd:cd05517    37 PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTAK 102
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 1955-1999 5.96e-07

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


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 47.93  E-value: 5.96e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 1955 ICKTP-YDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15517     4 ICNLEtAAVDELWVQCDGCDKWFHQFCLGLSNERYADEDKFKCPNC 49
PHD3_Lid2p_like cd15520
PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 2012-2057 1.03e-06

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


Pssm-ID: 276995  Cd Length: 47  Bit Score: 47.21  E-value: 1.03e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 2012 CICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2057
Cdd:cd15520     2 CGCGEGFNIADRMIFCDRCERTVHLDCVGLSDRIVDSPSEFFCPEC 47
PHD_UBR7 cd15542
PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, ...
 2011-2057 1.12e-06

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


Pssm-ID: 277017  Cd Length: 54  Bit Score: 47.36  E-value: 1.12e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767994058 2011 YCICRTPYDESQFYIG-----CDRCQNWYHGRCVGILQSEAELID--EYVCPQC 2057
Cdd:cd15542     1 YCTCDRPYPDPEDEVEdemiqCVLCEDWFHGRHLGLTPPEPDPDEfdEMICSGC 54
Glutenin_hmw pfam03157
High molecular weight glutenin subunit; Members of this family include high molecular weight ...
 1213-1584 2.18e-06

High molecular weight glutenin subunit; Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.


Pssm-ID: 367362 [Multi-domain]  Cd Length: 786  Bit Score: 53.03  E-value: 2.18e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1213 QVQQKVLGIIPSSTGTSQQTFTSfQPRTATVTIRPNTSGSGGTTSNSQVITGPQIRPGMTVIRTPLQQSTLGK------- 1285
Cdd:pfam03157  256 QGQQGYYPISPQQPRQWQQSGQG-QQGYYPTSLQQPGQGQSGYYPTSQQQAGQLQQEQQLGQEQQDQQPGQGRqgqqpgq 334

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1286 -------AIIRTPVMVQPGAPQQVMTQIIRGQPVSTAVSAPN-TVSSTPGQKSLTSATSTSNIQSSASQPPRPQQGQVKL 1357
Cdd:pfam03157  335 gqqgqqpAQGQQPGQGQPGYYPTSPQQPGQGQPGYYPTSQQQpQQGQQPEQGQQGQQQGQGQQGQQPGQGQQPGQGQPGY 414

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1358 TMAQLTQLTQGHGGNQGLTVVIQGQGQTTGQLQLIPQGVTV---LPGPGQQLMQAAMPN-----GTVQRFLFTPLATTAT 1429
Cdd:pfam03157  415 YPTSPQQSGQGQPGYYPTSPQQSGQGQQPGQGQQPGQEQPGqgqQPGQGQQGQQPGQPEqgqqpGQGQPGYYPTSPQQSG 494

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1430 TASTTTTTVSTTAAGTGEQRQSKLSP-QMQVHQDKTLPpaQSSSVGPAEAQPQTAQPSAQPQPQTQPQSPAQPEVQTQPE 1508
Cdd:pfam03157  495 QGQQLGQWQQQGQGQPGYYPTSPLQPgQGQPGYYPTSP--QQPGQGQQLGQLQQPTQGQQGQQSGQGQQGQQPGQGQQGQ 572

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767994058  1509 VQTQTTVSSHVPSEAQPTHAQsskpQVAAQSQPQSNVQGQSPVRVQSPSQTR--IRPSTPSQLSPGQQSQVQTTTSQP 1584
Cdd:pfam03157  573 QPGQGQQGQQPGQGQQPGQGQ----PGYYPTSPQQSGQGQQPGQWQQPGQGQpgYYPTSSLQLGQGQQGYYPTSPQQP 646
PHD_UBR7 cd15542
PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, ...
 1953-1999 2.23e-06

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


Pssm-ID: 277017  Cd Length: 54  Bit Score: 46.59  E-value: 2.23e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767994058 1953 YCICKTPYDESKFYIG-----CDLCTNWYHGECVGIT--EKEAKKMDVYICNDC 1999
Cdd:cd15542     1 YCTCDRPYPDPEDEVEdemiqCVLCEDWFHGRHLGLTppEPDPDEFDEMICSGC 54
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 2104-2169 2.82e-06

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 47.77  E-value: 2.82e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767994058 2104 PDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVL-ESFFVQK 2169
Cdd:cd05525    39 PDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLrKAYYQAK 105
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 2104-2168 3.58e-06

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 47.71  E-value: 3.58e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767994058 2104 PDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQ 2168
Cdd:cd05524    39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLS 103
PHD_MMD1_like cd15556
PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD ...
 1954-1999 3.64e-06

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


Pssm-ID: 277031 [Multi-domain]  Cd Length: 46  Bit Score: 45.83  E-value: 3.64e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 1954 CICKTPYDESKFYIGCDLCTNWYHGECVGITEKEaKKMDVYICNDC 1999
Cdd:cd15556     2 CSCGTRDDDGERMIACDVCEVWQHTRCVGIADNE-EPPDHFLCRRC 46
PHD2_KDM5A cd15606
PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 2011-2057 3.70e-06

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: 45.89  E-value: 3.70e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 2011 YCICRTPYdeSQFYIGCDRCQNWYHGRCV-------------GILQSEAELidEYVCPQC 2057
Cdd:cd15606     1 YCICRKPF--SGFMLQCELCKDWFHSSCVplpksssqkkggnGSGQGAKEL--KFLCPLC 56
PHD_PHF20_like cd15549
PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 ...
 2012-2057 3.85e-06

PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 (P20L1); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. Both PHF20 and PHF20L1 contain an N-terminal MBT domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277024  Cd Length: 45  Bit Score: 45.54  E-value: 3.85e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 2012 CICRTPyDESQFYIGCDRCQNWYHGRCVGILqSEAELIDEYVCPQC 2057
Cdd:cd15549     2 CICGVN-EENGLMIQCELCLCWQHGVCMGIE-EEESVPERYVCYVC 45
PHD_PHF20 cd15634
PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen ...
 2012-2057 5.75e-06

PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. PHF20 contains an N-terminal malignant brain tumor (MBT) domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277104  Cd Length: 44  Bit Score: 44.94  E-value: 5.75e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 2012 CICRTPyDESQFYIGCDRCQNWYHGRCVGILqsEAELIDEYVCPQC 2057
Cdd:cd15634     2 CICEVQ-EENDFMIQCEECLCWQHGVCMGLL--EDNVPEKYTCYIC 44
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 1205-1550 6.54e-06

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 51.55  E-value: 6.54e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1205 PATQGGVVQVQQKVLGIIP--SSTGTSQQTFTSFQPRTatvtirPNTSGSGGTTSNSQVItGPQIRPGMTVIRTPLQQst 1282
Cdd:pfam09606  133 PMGGAGFPSQMSRVGRMQPggQAGGMMQPSSGQPGSGT------PNQMGPNGGPGQGQAG-GMNGGQQGPMGGQMPPQ-- 203

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1283 LGKAIIrtPVMVQPGAPQQVMTQIIRGQPVSTAVSAPNTVsstPGQKSLTSATSTSNIQSSASQPPrpQQgqvkltMAQL 1362
Cdd:pfam09606  204 MGVPGM--PGPADAGAQMGQQAQANGGMNPQQMGGAPNQV---AMQQQQPQQQGQQSQLGMGINQM--QQ------MPQG 270

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1363 TQLTQGHGG-NQGLTVVIQGQGQTTGQLQLIPQGVTVLPG--PGQQLMQAAMPNGTvqrflftPLATTATTASTTTTTVS 1439
Cdd:pfam09606  271 VGGGAGQGGpGQPMGPPGQQPGAMPNVMSIGDQNNYQQQQtrQQQQQQGGNHPAAH-------QQQMNQSVGQGGQVVAL 343

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1440 TTAAGTGEQRQSKLSPqMQVHQDKTLPPAQSSSVGPAEAQPQTAQPSAQPQPQtqpqspaqpevQTQPEVQTQTTVSSHV 1519
Cdd:pfam09606  344 GGLNHLETWNPGNFGG-LGANPMQRGQPGMMSSPSPVPGQQVRQVTPNQFMRQ-----------SPQPSVPSPQGPGSQP 411

                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 767994058  1520 PSEA------QPTHAQSSKPQVAAQSQPQSNVQGQSP 1550
Cdd:pfam09606  412 PQSHpggmipSPALIPSPSPQMSQQPAQQRTIGQDSP 448
PHD_PHF20_like cd15549
PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 ...
 1954-1999 9.78e-06

PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 (P20L1); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. Both PHF20 and PHF20L1 contain an N-terminal MBT domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277024  Cd Length: 45  Bit Score: 44.39  E-value: 9.78e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 1954 CICKTPyDESKFYIGCDLCTNWYHGECVGITEKEAKKmDVYICNDC 1999
Cdd:cd15549     2 CICGVN-EENGLMIQCELCLCWQHGVCMGIEEEESVP-ERYVCYVC 45
SP2_N cd22540
N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins ...
 1193-1589 2.19e-05

N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2.


Pssm-ID: 411776 [Multi-domain]  Cd Length: 511  Bit Score: 49.54  E-value: 2.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1193 LPANSKIV-----AVNVPATQGG-VVQVQQKVLGIIPSSTG--TSQQTFTSFQPRTATVTIRPNTSGSGGTTsNSQVITG 1264
Cdd:cd22540    79 LSAKGNIIqlqgsQLSSSAPGGQqVFAIQNPTMIIKGSQTRssTNQQYQISPQIQAAGQINNSGQIQIIPGT-NQAIITP 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1265 PQIRPG-------MTVIRTPLQQSTLGKAIIRTP--VMVQPGAPQQVMT---QIIRGQPVSTAVSAPNTVSSTPGQKslt 1332
Cdd:cd22540   158 VQVLQQpqqahkpVPIKPAPLQTSNTNSASLQVPgnVIKLQSGGNVALTlpvNNLVGTQDGATQLQLAAAPSKPSKK--- 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1333 satsTSNIQSSASQPPRPQQGQVKLTMAQLTQLTQGHGGNQGLTVVIQGQGQ--TTGQLQLIP----QGVTVLPGPGQQL 1406
Cdd:cd22540   235 ----IRKKSAQAAQPAVTVAEQVETVLIETTADNIIQAGNNLLIVQSPGTGQpaVLQQVQVLQpkqeQQVVQIPQQALRV 310

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1407 MQAA-MPNGTVQRflfTPLATTATTASTTTTTVSTTAAGTGEQrqsklspQMQVHQDKTLPPAQSSSVGPAEAQPQTAQP 1485
Cdd:cd22540   311 VQAAsATLPTVPQ---KPLQNIQIQNSEPTPTQVYIKTPSGEV-------QTVLLQEAPAATATPSSSTSTVQQQVTANN 380

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1486 SAQPQPQTQPQSPAQPEVQTQPEVQTQTTVSSHVPSEAQpTHAQSSKPQVAAQSQP--QSNVQGQSPVRVQSPSQTRIrp 1563
Cdd:cd22540   381 GTGTSKPNYNVRKERTLPKIAPAGGIISLNAAQLAAAAQ-AIQTININGVQVQGVPvtITNAGGQQQLTVQTVSSNNL-- 457

                         410       420
                  ....*....|....*....|....*.
gi 767994058 1564 sTPSQLSPGQQSQVQTTTSQpIPIQP 1589
Cdd:cd22540   458 -TISGLSPTQIQLQMEQALE-IETQP 481
PHD_PHF20 cd15634
PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen ...
 1954-1996 5.40e-05

PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. PHF20 contains an N-terminal malignant brain tumor (MBT) domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277104  Cd Length: 44  Bit Score: 42.24  E-value: 5.40e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767994058 1954 CICKTPyDESKFYIGCDLCTNWYHGECVGITEKEA-KKMDVYIC 1996
Cdd:cd15634     2 CICEVQ-EENDFMIQCEECLCWQHGVCMGLLEDNVpEKYTCYIC 44
PHD2_KDM5A cd15606
PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 1953-1990 7.39e-05

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: 42.42  E-value: 7.39e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 767994058 1953 YCICKTPYdeSKFYIGCDLCTNWYHGECVGITEKEAKK 1990
Cdd:cd15606     1 YCICRKPF--SGFMLQCELCKDWFHSSCVPLPKSSSQK 36
PHD3_Lid2p_like cd15520
PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 1954-1999 8.66e-05

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


Pssm-ID: 276995  Cd Length: 47  Bit Score: 41.82  E-value: 8.66e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 1954 CICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 1999
Cdd:cd15520     2 CGCGEGFNIADRMIFCDRCERTVHLDCVGLSDRIVDSPSEFFCPEC 47
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
 2011-2057 1.20e-04

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


Pssm-ID: 276980 [Multi-domain]  Cd Length: 45  Bit Score: 41.52  E-value: 1.20e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 767994058 2011 YCICRTPYDESQfyIGCD--RCQ-NWYHGRCVGILqseAELIDEYVCPQC 2057
Cdd:cd15505     1 YCICNQVSYGEM--VACDnpNCPiEWFHFECVGLT---AKPKGKWYCPEC 45
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 1225-1593 1.85e-04

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 46.49  E-value: 1.85e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1225 STGTSQQTFTSFQPRTATVTIrpnTSGSGGTTSNSQVITGpQIRPGMTVIRTPLQQS----TLGKAIIRTPVMVQPGAPQ 1300
Cdd:pfam17823   52 NKSSEQ*NFCAATAAPAPVTL---TKGTSAAHLNSTEVTA-EHTPHGTDLSEPATREgaadGAASRALAAAASSSPSSAA 127

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1301 QVMTQIIRGqPVSTAVSAPNT-VSSTPGQKSLTSATSTSNIQSSASQPPRPQQGQVKLTMAQLTQLTQ-GHGGNQGLTVV 1378
Cdd:pfam17823  128 QSLPAAIAA-LPSEAFSAPRAaACRANASAAPRAAIAAASAPHAASPAPRTAASSTTAASSTTAASSApTTAASSAPATL 206

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1379 IQGQGQTTGQLQlipqgvTVLPGPGQQLmqAAMPNGTVqrflftplattattastttttvsttaagtgeqrqsklSPQMQ 1458
Cdd:pfam17823  207 TPARGISTAATA------TGHPAAGTAL--AAVGNSSP-------------------------------------AAGTV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1459 VHQDKTLPPAqssSVGPAEAQPQTAQPSAQPqpqtqpqspaqpeVQTQPEVQTQTTVSSHVPSEaqpTHAQSSKPQVAAQ 1538
Cdd:pfam17823  242 TAAVGTVTPA---ALATLAAAAGTVASAAGT-------------INMGDPHARRLSPAKHMPSD---TMARNPAAPMGAQ 302

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767994058  1539 SQ-PQSNVQGQSPVR------VQSPSQTRIRPSTPSQLSPGQQSQVQTTTSQ-------PIPIqPHTSL 1593
Cdd:pfam17823  303 AQgPIIQVSTDQPVHntagepTPSPSNTTLEPNTPKSVASTNLAVVTTTKAQakepsasPVPV-LHTSM 370
PHD_PHF20L1 cd15633
PHD finger found in PHD finger protein 20-like protein 1 (P20L1); P20L1 is an active malignant ...
 2012-2058 2.84e-04

PHD finger found in PHD finger protein 20-like protein 1 (P20L1); P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. In addition to the MBT domain, PHF20L1 also contains two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277103  Cd Length: 46  Bit Score: 40.39  E-value: 2.84e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2012 CICRTPyDESQFYIGCDRCQNWYHGRCVGILqsEAELIDEYVCPQCQ 2058
Cdd:cd15633     2 CICEMD-EENGFMIQCEECLCWQHSVCMGLL--EESIPEQYICYICR 45
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 2011-2057 3.57e-04

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


Pssm-ID: 276983  Cd Length: 57  Bit Score: 40.51  E-value: 3.57e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YC-ICRTPYDESQF---YIGCDRCQNWYHGRCVGILQSEAELID------EYVCPQC 2057
Cdd:cd15508     1 YCpLCEKCYDDDDYdskMMQCSQCDHWVHAKCEGLSDEMYEILSylpesiEYTCSLC 57
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 2012-2057 4.33e-04

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


Pssm-ID: 276989  Cd Length: 51  Bit Score: 39.96  E-value: 4.33e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 767994058 2012 CICRTPYDESQFYIGCDRCQNWYHGRCVGIL-QSEAELIDE--YVCPQC 2057
Cdd:cd15514     3 PVCSRSYNEGELIIQCSQCERWLHGACDSLRtEEEAERAADngYRCLLC 51
PHD3_KDM5B cd15687
PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis ...
 1956-1999 4.52e-04

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: 39.93  E-value: 4.52e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767994058 1956 CKTPYDESKFYIGCD-LCTNWYHGECVGITEKEAKKMDvYICNDC 1999
Cdd:cd15687     7 CLQPEGEEVDWVQCDgSCNRWFHQVCVGVSAEMAEKED-YICVSC 50
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1305-1589 4.88e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 45.53  E-value: 4.88e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1305 QIIRGQPVSTAVSAPNTVSSTPGQKSLTSATSTSNIQSSASQPPR--------PQQGQVKLTMAQLTQ---------LTQ 1367
Cdd:pfam03154  165 QILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQgspatsqpPNQTQSTAAPHTLIQqtptlhpqrLPS 244

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1368 GHGGNQGLTvviQGQGQTTGQLQLIPQGVTVLPGP--------GQQLMQAAMPNgtvQRFLFTPLATTATTASTTTTTVS 1439
Cdd:pfam03154  245 PHPPLQPMT---QPPPPSQVSPQPLPQPSLHGQMPpmphslqtGPSHMQHPVPP---QPFPLTPQSSQSQVPPGPSPAAP 318

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1440 TTAAGTGEQ--RQSKLSPQmQVHQDKTLPPAQSS-------SVGPAEAQPQTAQPSAQPQPQTQPQSPAQPEVQTQPEVQ 1510
Cdd:pfam03154  319 GQSQQRIHTppSQSQLQSQ-QPPREQPLPPAPLSmphikppPTTPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALK 397

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767994058  1511 TQTTVSSHVPSEAQPthaqsSKPQVAAQSQPQSNVQGQSPVRVQSPSqtrirpstpsqLSPGQQSQVQTTTSQPIPIQP 1589
Cdd:pfam03154  398 PLSSLSTHHPPSAHP-----PPLQLMPQSQQLPPPPAQPPVLTQSQS-----------LPPPAASHPPTSGLHQVPSQS 460
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 2011-2057 5.27e-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: 39.77  E-value: 5.27e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767994058 2011 YC-ICRTPYDESQF----YIGCDRCQNWYHGRCVGI--LQSEAELIDE---YVCPQC 2057
Cdd:cd15615     1 FCiLCGQVYEENEGdekeWVQCDSCSEWVHFECDGRtgLGAFKYAKSDglqYVCPRC 57
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 2012-2057 5.27e-04

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 39.70  E-value: 5.27e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 2012 CICRTPYDESQ-FYIGCDRCQNWYHGRCVGIlQSEAELIDEYVCPQC 2057
Cdd:cd15547     2 CICGELDEIDNkHRVQCLKCGLWQHAECVNY-DEESDKREPYLCPHC 47
PHD2_KDM5A_like cd15516
PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar ...
 2011-2057 6.94e-04

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: 39.60  E-value: 6.94e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767994058 2011 YCICR-TPydeSQFYIGCDRCQNWYHGRCVGILQSEA--------ELIDEYVCPQC 2057
Cdd:cd15516     1 ICLCGkAL---AAGMLQCELCQDWFHGSCVAVPRISSsprplawwEGDRKFLCPLC 53
PHD_Bye1p_SIZ1_like cd15570
PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo ...
 1954-1999 7.44e-04

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


Pssm-ID: 277045  Cd Length: 50  Bit Score: 39.37  E-value: 7.44e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 767994058 1954 CICKTPYDESKFyIGCDLCTNWYHGECVGITEKEA-KKMDV---YICNDC 1999
Cdd:cd15570     2 CPCGSSMEDGSM-IQCEGCKTWQHMDCVLIPDKPAdGLPELpskFYCELC 50
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
 1953-1999 7.95e-04

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


Pssm-ID: 276980 [Multi-domain]  Cd Length: 45  Bit Score: 39.20  E-value: 7.95e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 767994058 1953 YCICKTPYDESkfYIGCD--LCT-NWYHGECVGITEKEAKKmdvYICNDC 1999
Cdd:cd15505     1 YCICNQVSYGE--MVACDnpNCPiEWFHFECVGLTAKPKGK---WYCPEC 45
PHD_ASH1L cd15548
PHD finger found in histone-lysine N-methyltransferase ASH1L; ASH1L, also termed ASH1-like ...
 2012-2057 7.98e-04

PHD finger found in histone-lysine N-methyltransferase ASH1L; ASH1L, also termed ASH1-like protein, or absent small and homeotic disks protein 1 homolog, or lysine N-methyltransferase 2H, is a protein belonging to the Trithorax family. It methylates Lys36 of histone H3 independently of transcriptional elongation to promote the establishment of Hox gene expression by counteracting Polycomb silencing. It can suppress interleukin-6 (IL-6), and tumor necrosis factor (TNF) production in Toll-like receptor (TLR)-triggered macrophages, and inflammatory autoimmune diseases by inducing the ubiquitin-editing enzyme A20. ASH1L contains an associated with SET domain (AWS), a SET domain, a post-SET domain, a bromodomain, a bromo-adjacent homology domain (BAH), and a plant homeodomain (PHD) finger.


Pssm-ID: 277023  Cd Length: 43  Bit Score: 38.99  E-value: 7.98e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 2012 CICRTpYDESQFYIGCDRCQNWYHGRCVGiLQSEAElidEYVCPQC 2057
Cdd:cd15548     3 CICGL-YKDEGLMIQCEKCMVWQHCDCMG-VNDDVE---HYLCEQC 43
PHD_Yng1p_like cd15587
PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the ...
 1953-2001 9.20e-04

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


Pssm-ID: 277062 [Multi-domain]  Cd Length: 47  Bit Score: 38.94  E-value: 9.20e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767994058 1953 YCICK-TPYDEskfYIGCD--LCT-NWYHGECVGITEKEAKKmdvYICNDCKR 2001
Cdd:cd15587     1 YCYCRrVSFGE---MVACDnpDCKiEWFHFECVGLTETPKGK---WYCSDCKV 47
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 1954-1999 9.23e-04

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


Pssm-ID: 276989  Cd Length: 51  Bit Score: 39.19  E-value: 9.23e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 767994058 1954 CICKTPYDESKFYIGCDLCTNWYHGECVGI-TEKEAKKMD--VYICNDC 1999
Cdd:cd15514     3 PVCSRSYNEGELIIQCSQCERWLHGACDSLrTEEEAERAAdnGYRCLLC 51
PHD2_KMT2A cd15590
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1953-1999 9.68e-04

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


Pssm-ID: 277065  Cd Length: 50  Bit Score: 38.86  E-value: 9.68e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 767994058 1953 YC-ICKTPYDESKFYIGCDLCTNWYHGECVGIT--EKEAKKMDVYICNDC 1999
Cdd:cd15590     1 FChVCGRQHQATKQLLECNKCRNSYHPECLGPNypTKPTKKKRVWICTKC 50
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
 2011-2057 9.90e-04

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


Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 38.97  E-value: 9.90e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767994058 2011 YCICR-TPYDEsqfYIGCD--RCQ-NWYHGRCVGILQSEAeliDEYVCPQC 2057
Cdd:cd15585     1 YCICNqVSYGE---MVGCDndDCPiEWFHYGCVGLTEAPK---GKWYCPQC 45
PHD_PHF20L1 cd15633
PHD finger found in PHD finger protein 20-like protein 1 (P20L1); P20L1 is an active malignant ...
 1954-1998 9.91e-04

PHD finger found in PHD finger protein 20-like protein 1 (P20L1); P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. In addition to the MBT domain, PHF20L1 also contains two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277103  Cd Length: 46  Bit Score: 38.85  E-value: 9.91e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767994058 1954 CICKTPyDESKFYIGCDLCTNWYHGECVGITEKEAKKMDV-YICND 1998
Cdd:cd15633     2 CICEMD-EENGFMIQCEECLCWQHSVCMGLLEESIPEQYIcYICRD 46
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1447-1589 1.18e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 44.37  E-value: 1.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1447 EQRQSKLSPQMQVhQDKTLPPAQSSSVGPAEAQPQTAQPSAQPQPQTQPQSPAQPEVQTQPEVQ----TQTTVSSHVP-- 1520
Cdd:pfam03154  164 QQILQTQPPVLQA-QSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAphtlIQQTPTLHPQrl 242

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058  1521 ----SEAQPTHAQSSKPQVAAQSQPQSNVQGQ----------SPVRVQSP------------SQTRIRPStPSQLSPGQQ 1574
Cdd:pfam03154  243 psphPPLQPMTQPPPPSQVSPQPLPQPSLHGQmppmphslqtGPSHMQHPvppqpfpltpqsSQSQVPPG-PSPAAPGQS 321

                          170
                   ....*....|....*...
gi 767994058  1575 SQVQTT---TSQPIPIQP 1589
Cdd:pfam03154  322 QQRIHTppsQSQLQSQQP 339
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 1954-1999 1.56e-03

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 38.16  E-value: 1.56e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767994058 1954 CIC-KTPYDESKFYIGCDLCTNWYHGECVGITEkEAKKMDVYICNDC 1999
Cdd:cd15547     2 CICgELDEIDNKHRVQCLKCGLWQHAECVNYDE-ESDKREPYLCPHC 47
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 1953-1999 2.07e-03

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: 38.23  E-value: 2.07e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767994058 1953 YC-ICKTPYDE----SKFYIGCDLCTNWYHGECVGITEKEAKKMDV-----YICNDC 1999
Cdd:cd15615     1 FCiLCGQVYEEnegdEKEWVQCDSCSEWVHFECDGRTGLGAFKYAKsdglqYVCPRC 57
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
1772-2002 2.28e-03

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


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 42.23  E-value: 2.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1772 REENQRMIVCNQVMKYI--LDKIDKEEKQAAKKRKREESVEQKRSKQNatkLSALLFKHKEQLRAEILKKralLDKDLQI 1849
Cdd:COG5034    36 CDIIKNLRQMISILKKIidLDSQTYEEVEDGLLKEIRELLLKAIYIQK---EKSDLADRAEKLLRRHRKL---LDDRIAK 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1850 EVQEEL-KRDLKIKKEKDLMQLAQATAVAAPCPPVTPAPPAPPAPPPSPPPPPAVQHTGLLSTPTLPA---ASQKRKREE 1925
Cdd:COG5034   110 RPHEKVaARIENCHDAVSRLERNSYSSAARRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSkreVSFTLESPS 189

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767994058 1926 EKDSSSKSKKKKMISTTSKET------KKDTKLYCICKTP-YDEskfYIGCD--LCT-NWYHGECVGIteKEAKKMDVYi 1995
Cdd:COG5034   190 VPDTATRVKEGNNGGSTKSRGvssednSEGEELYCFCQQVsYGQ---MVACDnaNCKrEWFHLECVGL--KEPPKGKWY- 263


                  ....*..
gi 767994058 1996 CNDCKRA 2002
Cdd:COG5034   264 CPECKKA 270
PHD_TCF19 cd15609
PHD finger found in Transcription factor 19 (TCF-19) and similar proteins; TCF-19, also termed ...
 2014-2040 2.39e-03

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: 37.83  E-value: 2.39e-03
                          10        20
                  ....*....|....*....|....*..
gi 767994058 2014 CRTPYDESQFYIGCDRCQNWYHGRCVG 2040
Cdd:cd15609     7 CCLPQDETVSWVQCDDCDQWYHVACVG 33
Bromo_ZMYND11 cd05492
Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear ...
 2101-2162 3.80e-03

Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99924  Cd Length: 109  Bit Score: 38.90  E-value: 3.80e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767994058 2101 NDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVL 2162
Cdd:cd05492    34 TKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWL 95
PHD2_KDM5A_like cd15516
PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar ...
 1953-1983 4.05e-03

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: 37.29  E-value: 4.05e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 767994058 1953 YCIC-KTPydeSKFYIGCDLCTNWYHGECVGI 1983
Cdd:cd15516     1 ICLCgKAL---AAGMLQCELCQDWFHGSCVAV 29
PHD2_MTF2 cd15580
PHD finger 2 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 2011-2059 4.80e-03

PHD finger 2 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 plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. This model corresponds to the second PHD finger.


Pssm-ID: 277055  Cd Length: 52  Bit Score: 37.18  E-value: 4.80e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767994058 2011 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDE---YVCPQCQS 2059
Cdd:cd15580     1 YCYCGGPGDWYLKMLQCCKCKQWFHEACVQCLEKPMLFGDRfytFICSVCNS 52
PHD2_KDM5C_5D cd15608
PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 2012-2039 4.85e-03

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: 37.09  E-value: 4.85e-03
                          10        20
                  ....*....|....*....|....*...
gi 767994058 2012 CICRTPYDESQfyIGCDRCQNWYHGRCV 2039
Cdd:cd15608     2 CVCGQPPRPGM--LRCHLCQDWFHGGCV 27
PHD2_MTF2_PHF19_like cd15503
PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 2011-2043 7.48e-03

PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The PCL family includes PHD finger protein1 (PHF1) and its homologs metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are accessory components of the Polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. PCL proteins 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 finger 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 second PHD finger.


Pssm-ID: 276978  Cd Length: 52  Bit Score: 36.61  E-value: 7.48e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 767994058 2011 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQ 2043
Cdd:cd15503     1 YCYCGGPGEWNLKMLQCCKCRQWFHEACLQCLK 33
PHD3_KDM5B cd15687
PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis ...
 2014-2057 9.04e-03

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


Pssm-ID: 277157  Cd Length: 50  Bit Score: 36.46  E-value: 9.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767994058 2014 CRTPYDESQFYIGCD-RCQNWYHGRCVGILQSEAELIDeYVCPQC 2057
Cdd:cd15687     7 CLQPEGEEVDWVQCDgSCNRWFHQVCVGVSAEMAEKED-YICVSC 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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