Psyllid ID: psy16435

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------
Protein Sequence
MELEHFGWLVDSISSCQSTRIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEEEMAVEFQEELPPKPKGKRGRKKKIVLSPRSLTPTDEEEDKENEEKSGTPFDSIPSK
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHcccccccccccccccccccccccccccccccHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHcccccccccEcccccccccccHccHHHHHcccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccHHHcccccccccccHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MELEHFGWLVDSISSCQSTRIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQRRIEnrergsrsnsedrwttedtsslcsyqtstggyrsteEDLRIGMHKVMNRLkshedawpfcdpvdeatapnyyeqikrpmdlTRMEEkldagryktfgqfRADFQLIVDNCrkyngldneYTDMVRRLQQIFRDAVSRYldgerssgsedeEEMAVEFqeelppkpkgkrgrkkkivlsprsltptdeeedkeneeksgtpfdsipsk
Flexible Loop (DISEMBL)
melehfgwlvdsisscqstrieklkhskeierklqkqkeeetrrhqeeeerleeewrkhkaarerqrrienrergsrsnsedrwttedtsslcsyqtstggyrsteEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGerssgsedeeEMAVefqeelppkpkgkrgrkkkivlsprsltptdeeedkeneeksgtpfdsipsk
Low Complexity Region (SEG)
MELEHFGWLVDSISSCQSTRIEKLKHSKEIERKLQKQKeeetrrhqeeeerleeewrKHKAArerqrrienrergsrsnsedrWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLdgerssgsedeeeMAVEFQEELppkpkgkrgrkkkIVLSPRSLTPTdeeedkeneekSGTPFDSIPSK
Disordered region (IsUnstruct)
*****FGWLVDSI************************************************************************************************RIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL********************************************************************
Disordered Region (DISOPRED)
*ELEHFGWLVD***************************************************************************************************IGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV************************************************************************
Disordered Region (DISEMBL)
MELEHFGWLVDSISSCQSTRIEKLKHSKEIERK***********************************************************************TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL***********************************IVLSPR***************************
Disordered Region (DISPRO)
*****************************************************************************************************YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL********************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MELEHFGWLVDSISSCQSTRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWRKHKAARERQRRIENRERGSRSNSEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEEEMAVEFQEELPPKPKGKRGRKKKIVLSPRSLTPTDEEEDKENEEKSGTPFDSIPSK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	277	2.2.26 [Sep-21-2011]
Q9BXF3	1484	Cat eye syndrome critical	yes	N/A	0.386	0.072	0.477	3e-24
Q6CXW4	516	Histone acetyltransferase	yes	N/A	0.339	0.182	0.425	4e-18
Q756G9	452	Histone acetyltransferase	yes	N/A	0.321	0.196	0.449	4e-17
Q03330	439	Histone acetyltransferase	yes	N/A	0.339	0.214	0.382	1e-16
Q12830	3046	Nucleosome-remodeling fac	no	N/A	0.346	0.031	0.422	1e-16
Q6FTW5	546	Histone acetyltransferase	yes	N/A	0.339	0.172	0.393	2e-16
Q9JHD2	830	Histone acetyltransferase	no	N/A	0.342	0.114	0.4	1e-15
Q92830	837	Histone acetyltransferase	no	N/A	0.342	0.113	0.4	1e-15
Q9W0T1	2669	Nucleosome-remodeling fac	no	N/A	0.346	0.035	0.364	3e-15
Q8WZM0	464	Histone acetyltransferase	yes	N/A	0.317	0.189	0.409	8e-15

>sp|Q9BXF3|CECR2_HUMAN Cat eye syndrome critical region protein 2 OS=Homo sapiens GN=CECR2 PE=1 SV=2

 Score =  112 bits (280), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/109 (47%), Positives = 75/109 (68%), Gaps = 2/109 (1%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           M+KV++ +K+H+D+WPF +PVDE+ APNYY+ IK PMD++ ME+KL+ G Y T  +F  D
Sbjct: 443 MYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVND 502

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEE 221
            + +  NCRKYNG  +EYT M   L++ F  A+ ++  GE   G  DEE
Sbjct: 503 MKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMKHFPGE--DGDTDEE 549

Part of the CERF (CECR2-containing-remodeling factor) complex, which facilitates the perturbation of chromatin structure in an ATP-dependent manner. May be involved through its interaction with LRPPRC in the integration of cytoskeletal network with vesicular trafficking, nucleocytosolic shuttling, transcription, chromosome remodeling and cytokinesis.
Homo sapiens (taxid: 9606)

>sp|Q6CXW4|GCN5_KLULA Histone acetyltransferase GCN5 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=GCN5 PE=3 SV=1

 Score = 92.0 bits (227), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 40/94 (42%), Positives = 55/94 (58%)

Query: 112 GMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
            M  ++  L++H  AWPF  PV++   P+YYE IK PMDL+ ME KL+  RY+    F  
Sbjct: 412 AMQNLLTELQNHAAAWPFLQPVNKEEVPDYYEFIKEPMDLSSMEMKLNGNRYEKMENFIY 471

Query: 172 DFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           D +LI +NCR YNG +  Y     RL++ F   V
Sbjct: 472 DARLIFNNCRAYNGENTSYFKYANRLEKFFNSKV 505

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q756G9|GCN5_ASHGO Histone acetyltransferase GCN5 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=GCN5 PE=3 SV=1

 Score = 88.6 bits (218), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 40/89 (44%), Positives = 53/89 (59%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           M  V+  L++H  AWPF  PV+    P+YYE IK PMDL+ ME KL+  RY+    F  D
Sbjct: 349 MQNVLTELQNHAAAWPFLQPVNRDEVPDYYEFIKEPMDLSTMEIKLENNRYEKMEDFIYD 408

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
            +LI +NCR YNG +  Y     RL++ F
Sbjct: 409 ARLIFNNCRAYNGENTSYFKYANRLEKFF 437

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q03330|GCN5_YEAST Histone acetyltransferase GCN5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GCN5 PE=1 SV=1

 Score = 87.4 bits (215), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 57/94 (60%)

Query: 112 GMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
            +  ++  L++H  AWPF  PV++   P+YY+ IK PMDL+ ME KL++ +Y+    F  
Sbjct: 335 AIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIY 394

Query: 172 DFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           D +L+ +NCR YNG +  Y     RL++ F + V
Sbjct: 395 DARLVFNNCRMYNGENTSYYKYANRLEKFFNNKV 428

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac and H3K36ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation. Operates in concert with certain DNA-binding transcriptional activators such as GCN4 or HAP2/3/4. Its acetylteransferase activity seems to be dependent on the association in different multisubunit complexes. Functions as histone acetyltransferase component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and ADA. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. The ADA histone acetyltransferase complex preferentially acetylates nucleosomal histones H3 (to form H3K14ac and H3K18ac) and H2B, leading to transcription regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q12830|BPTF_HUMAN Nucleosome-remodeling factor subunit BPTF OS=Homo sapiens GN=BPTF PE=1 SV=3

 Score = 87.0 bits (214), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/97 (42%), Positives = 57/97 (58%), Gaps = 1/97 (1%)

Query: 105  TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
            TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct: 2929 TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 2987

Query: 165  TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
               +F AD   I DNCR YN  D+ +      L+  F
Sbjct: 2988 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 3024

Histone-binding component of NURF (nucleosome-remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. May also regulate transcription through direct binding to DNA or transcription factors.

Homo sapiens (taxid: 9606)

>sp|Q6FTW5|GCN5_CANGA Histone acetyltransferase GCN5 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=GCN5 PE=3 SV=1

 Score = 86.7 bits (213), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 57/94 (60%)

Query: 112 GMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
            +  ++  L++H  AWPF  PV++   P+YYE IK PMDL+ ME KL+  +Y+   +F  
Sbjct: 442 AIQNILVELQNHAAAWPFLRPVNKEEVPDYYEFIKEPMDLSTMELKLENNKYEKMEEFIY 501

Query: 172 DFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           D +L+ +NCR YNG +  Y     RL++ F + V
Sbjct: 502 DARLVCNNCRLYNGENTSYYKYANRLEKFFNNKV 535

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q9JHD2|KAT2A_MOUSE Histone acetyltransferase KAT2A OS=Mus musculus GN=Kat2a PE=2 SV=2

 Score = 84.0 bits (206), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 38/95 (40%), Positives = 58/95 (61%)

Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           + L   +  ++ ++KSH  AWPF +PV ++ AP+YYE I+ P+DL  M E+L +  Y T 
Sbjct: 724 DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTR 783

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
             F AD Q ++ NCR+YN  D+EY      L++ F
Sbjct: 784 KLFVADLQRVIANCREYNPPDSEYCRCASALEKFF 818

Functions as a histone acetyltransferase (HAT) to promote transcriptional activation. Acetylation of histones gives a specific tag for epigenetic transcription activation. Has significant histone acetyltransferase activity with core histones, but not with nucleosome core particles (By similarity). Component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q92830|KAT2A_HUMAN Histone acetyltransferase KAT2A OS=Homo sapiens GN=KAT2A PE=1 SV=3

 Score = 84.0 bits (206), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 38/95 (40%), Positives = 58/95 (61%)

Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           + L   +  ++ ++KSH  AWPF +PV ++ AP+YYE I+ P+DL  M E+L +  Y T 
Sbjct: 731 DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTR 790

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
             F AD Q ++ NCR+YN  D+EY      L++ F
Sbjct: 791 KLFVADLQRVIANCREYNPPDSEYCRCASALEKFF 825

Functions as a histone acetyltransferase (HAT) to promote transcriptional activation. Acetylation of histones gives a specific tag for epigenetic transcription activation. Has significant histone acetyltransferase activity with core histones, but not with nucleosome core particles. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q9W0T1|NU301_DROME Nucleosome-remodeling factor subunit NURF301 OS=Drosophila melanogaster GN=E(bx) PE=1 SV=2

 Score = 82.8 bits (203), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 54/96 (56%)

Query: 113  MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
            +  ++ +++ H+ AWPF +PVD   AP+YY+ IK PMDL RME KL++  Y    +F  D
Sbjct: 2565 LKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGD 2624

Query: 173  FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
               I DNCR YN  ++ +      L+  F   +  +
Sbjct: 2625 MTKIFDNCRYYNPKESSFYKCAEALESYFVQKIKNF 2660

Histone-binding component of NURF (nucleosome remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. Required for homeotic gene expression, proper larval blood cell development, normal male X chromosome morphology, ecdysteroid signaling and metamorphosis.

Drosophila melanogaster (taxid: 7227)

>sp|Q8WZM0|GCN5_YARLI Histone acetyltransferase GCN5 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=GCN5 PE=3 SV=1

 Score = 81.3 bits (199), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 36/88 (40%), Positives = 53/88 (60%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           M  V++ L++H  AWPF   V+    P+YYE IK PMDL+ ME++L+A  YKT  +F  D
Sbjct: 361 MQHVLSELQNHASAWPFAQAVNRDEVPDYYEVIKEPMDLSTMEQRLEADSYKTMEEFVYD 420

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQI 200
            +L+ +NCR YN     Y     +L++ 
Sbjct: 421 ARLVFNNCRAYNNETTTYYKNANKLEKF 448

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	277
242022306	1788	conserved hypothetical protein [Pediculu	0.440	0.068	0.611	6e-41
91078952	1789	PREDICTED: similar to dikar CG32393-PA [	0.624	0.096	0.5	8e-41
270003689	1867	hypothetical protein TcasGA2_TC002957 [T	0.440	0.065	0.603	4e-40
193674159	1560	PREDICTED: hypothetical protein LOC10016	0.732	0.130	0.434	4e-40
170063684	2548	conserved hypothetical protein [Culex qu	0.505	0.054	0.519	1e-38
345497179	2127	PREDICTED: hypothetical protein LOC10011	0.393	0.051	0.633	1e-37
156541982	2213	PREDICTED: hypothetical protein LOC10011	0.393	0.049	0.633	2e-37
307208900	2300	Cat eye syndrome critical region protein	0.444	0.053	0.564	7e-36
307176633	2192	Cat eye syndrome critical region protein	0.444	0.056	0.564	9e-36
403183193	2961	AAEL017575-PA [Aedes aegypti]	0.422	0.039	0.586	1e-35

>gi|242022306|ref|XP_002431581.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212516889|gb|EEB18843.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  174 bits (440), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 77/126 (61%), Positives = 99/126 (78%), Gaps = 4/126 (3%)

Query: 102 YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAG 161
           ++++ EDLR GM+K+++ +KSHE+AWPF DPVDE  AP YY  I++PMDL RMEEKLD G
Sbjct: 384 FKTSAEDLRTGMYKILDYIKSHEEAWPFVDPVDENYAPKYYSVIRKPMDLQRMEEKLDCG 443

Query: 162 RYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEE 221
            Y TF  FR DFQLIVDNCR+YNG +NEYT+MV+ LQ+ FR+A  RYL+ + SS    +E
Sbjct: 444 EYLTFNDFRNDFQLIVDNCRQYNGSENEYTEMVKNLQEAFREATDRYLESDPSS----DE 499

Query: 222 EMAVEF 227
           E+AVEF
Sbjct: 500 EVAVEF 505

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91078952|ref|XP_974145.1| PREDICTED: similar to dikar CG32393-PA [Tribolium castaneum]

 Score =  173 bits (438), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 92/184 (50%), Positives = 123/184 (66%), Gaps = 11/184 (5%)

Query: 46  QEEEERLEEEWRKHKAARERQRRIENRERGSRSNSEDRWTTEDTSSLCS--YQTSTGGYR 103
           +EE +R  +   K K A ER  R+  +E+   S SED   +E    +C+   +     +R
Sbjct: 270 EEERQRKRDLEIKRKEAYERSNRL--KEQSEDSQSED---SEVRCIICAEELKKEENRFR 324

Query: 104 STEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRY 163
            T+EDL  GMHK+++ +K+HEDAWPF DPVDE  APNYY  I++PMDL RMEE+LDAG Y
Sbjct: 325 QTDEDLITGMHKILDYVKNHEDAWPFADPVDEDYAPNYYTVIRKPMDLQRMEERLDAGYY 384

Query: 164 KTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEEEM 223
           K F +FR DFQLIVDNCR YNG++NEYT+MV  L ++F  A  ++LD   SS    ++E+
Sbjct: 385 KNFAKFRDDFQLIVDNCRLYNGVENEYTEMVDNLLKVFERATEKFLDQISSS----DDEI 440

Query: 224 AVEF 227
           AVEF
Sbjct: 441 AVEF 444

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270003689|gb|EFA00137.1| hypothetical protein TcasGA2_TC002957 [Tribolium castaneum]

 Score =  171 bits (432), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 76/126 (60%), Positives = 97/126 (76%), Gaps = 4/126 (3%)

Query: 102 YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAG 161
           +R T+EDL  GMHK+++ +K+HEDAWPF DPVDE  APNYY  I++PMDL RMEE+LDAG
Sbjct: 401 FRQTDEDLITGMHKILDYVKNHEDAWPFADPVDEDYAPNYYTVIRKPMDLQRMEERLDAG 460

Query: 162 RYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEE 221
            YK F +FR DFQLIVDNCR YNG++NEYT+MV  L ++F  A  ++LD   SS    ++
Sbjct: 461 YYKNFAKFRDDFQLIVDNCRLYNGVENEYTEMVDNLLKVFERATEKFLDQISSS----DD 516

Query: 222 EMAVEF 227
           E+AVEF
Sbjct: 517 EIAVEF 522

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193674159|ref|XP_001950556.1| PREDICTED: hypothetical protein LOC100163939 [Acyrthosiphon pisum]

 Score =  171 bits (432), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 96/221 (43%), Positives = 137/221 (61%), Gaps = 18/221 (8%)

Query: 17  QSTRIEKLKHSKEIERK----------LQKQKEEETRRHQEEEERLEEEWRKHKAARER- 65
           QSTR+EKLK  KE ERK           + +K+E  ++HQE+  +++EE +    A    
Sbjct: 264 QSTRLEKLKQQKE-ERKRYEDLCREHEEKVKKKENRKKHQEKRPKVKEEGQSDSEAESHG 322

Query: 66  ----QRRIENRE-RGSRSNSEDRWTTEDTS-SLCSYQTSTGGYRSTEEDLRIGMHKVMNR 119
                 ++  R+   S +++  +   E +        TS  G++ST EDL+IGM+K++N+
Sbjct: 323 YSSSSSKVAGRQTNNSLASATGQIVIEGSQEKPVPKATSKAGFKSTTEDLQIGMYKILNK 382

Query: 120 LKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDN 179
           LK HEDAWPF +PVDE  AP+YY  +K PMDL +ME+KL+ G Y+T  QF+ DFQLI+ N
Sbjct: 383 LKDHEDAWPFLEPVDEEIAPSYYRVVKTPMDLQQMEDKLNDGLYETLSQFKHDFQLIIAN 442

Query: 180 CRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDE 220
           C++YNG  NEYT M   LQ++F   V +YLD E S GS+DE
Sbjct: 443 CKQYNGSTNEYTVMCGNLQRVFNMGVHKYLDWEMSEGSDDE 483

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170063684|ref|XP_001867208.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167881259|gb|EDS44642.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score =  166 bits (420), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 80/154 (51%), Positives = 99/154 (64%), Gaps = 14/154 (9%)

Query: 84  WTTED----------TSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPV 133
           WTT D          T+++ S   S+  +  TEE L+IGMHKV+  +K+H+DAWPF DPV
Sbjct: 53  WTTPDISVLVGSGSFTTTISSTLISSFSFTETEEVLQIGMHKVLEYIKNHDDAWPFMDPV 112

Query: 134 DEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDM 193
           DE  AP YY  I+RPMDL +MEEKLD G Y TF  FR DF+LIV+NCR YNG  NEYT+M
Sbjct: 113 DEDIAPRYYSIIRRPMDLQKMEEKLDNGEYLTFADFRNDFKLIVNNCRLYNGQANEYTEM 172

Query: 194 VRRLQQIFRDAVSRYLDGERSSGSEDEEEMAVEF 227
           V  LQ  F  A  R+ D    S S DEE+  +E+
Sbjct: 173 VNNLQIAFEKATKRHFD----SNSSDEEQQTLEY 202

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345497179|ref|XP_003427930.1| PREDICTED: hypothetical protein LOC100114569 isoform 2 [Nasonia vitripennis]

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 69/109 (63%), Positives = 86/109 (78%)

Query: 106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKT 165
           EE+ ++GMHKV+N LK HEDAWPF DPVDE  AP YY  I+RPMDL++MEEKL+ G YKT
Sbjct: 321 EEEQQVGMHKVLNILKDHEDAWPFTDPVDEQYAPRYYSVIRRPMDLSKMEEKLEEGSYKT 380

Query: 166 FGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERS 214
            GQF+ DF+LI+DNC++YNG DNEYT+M   L+ +F  AV RYL+ E S
Sbjct: 381 IGQFKRDFRLIIDNCKQYNGSDNEYTEMAMNLKDVFDRAVDRYLESEES 429

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156541982|ref|XP_001599540.1| PREDICTED: hypothetical protein LOC100114569 isoform 1 [Nasonia vitripennis]

 Score =  161 bits (408), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 69/109 (63%), Positives = 86/109 (78%)

Query: 106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKT 165
           EE+ ++GMHKV+N LK HEDAWPF DPVDE  AP YY  I+RPMDL++MEEKL+ G YKT
Sbjct: 407 EEEQQVGMHKVLNILKDHEDAWPFTDPVDEQYAPRYYSVIRRPMDLSKMEEKLEEGSYKT 466

Query: 166 FGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERS 214
            GQF+ DF+LI+DNC++YNG DNEYT+M   L+ +F  AV RYL+ E S
Sbjct: 467 IGQFKRDFRLIIDNCKQYNGSDNEYTEMAMNLKDVFDRAVDRYLESEES 515

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307208900|gb|EFN86115.1| Cat eye syndrome critical region protein 2 [Harpegnathos saltator]

 Score =  157 bits (396), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 70/124 (56%), Positives = 89/124 (71%), Gaps = 1/124 (0%)

Query: 93  CSYQTSTG-GYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDL 151
           C+Y    G  +   EE+ R+GMHKV+  +K H DAWPF DPVDE  AP YY  ++RPMDL
Sbjct: 388 CNYGYKFGYSFGIEEEERRVGMHKVLESVKDHTDAWPFIDPVDEEYAPRYYSVVRRPMDL 447

Query: 152 TRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDG 211
           + MEEKL+ G YK+  QF+ DF+LIVDNCR+YNG DNEYT+M   L++ F  AV+RYL+ 
Sbjct: 448 STMEEKLEGGSYKSLSQFKRDFRLIVDNCRQYNGSDNEYTEMAVNLKEAFDKAVNRYLES 507

Query: 212 ERSS 215
           E SS
Sbjct: 508 ETSS 511

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307176633|gb|EFN66101.1| Cat eye syndrome critical region protein 2 [Camponotus floridanus]

 Score =  156 bits (395), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 70/124 (56%), Positives = 89/124 (71%), Gaps = 1/124 (0%)

Query: 93  CSYQTSTG-GYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDL 151
           C+Y    G  +R  EE+  +GMHKV+  +K H DAWPF DPVDE  AP YY  +++PMDL
Sbjct: 386 CNYGYKYGYSFRIEEEERCVGMHKVLESIKDHVDAWPFIDPVDEEYAPRYYSVVRKPMDL 445

Query: 152 TRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDG 211
           + MEEKL+ G YK+  QF+ DF+LIVDNCR+YNG DNEYT+M   L++ F  AVSRYL+ 
Sbjct: 446 STMEEKLEGGSYKSLSQFKHDFRLIVDNCRQYNGSDNEYTEMAINLKEAFDKAVSRYLES 505

Query: 212 ERSS 215
           E SS
Sbjct: 506 ETSS 509

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|403183193|gb|EJY57921.1| AAEL017575-PA [Aedes aegypti]

 Score =  156 bits (394), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 71/121 (58%), Positives = 86/121 (71%), Gaps = 4/121 (3%)

Query: 102 YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAG 161
           +  TEE L+IGMHK++  +K+H+DAWPF DPVDE  AP YY  I+RPMDL +ME+KLD G
Sbjct: 657 FTETEEVLQIGMHKILEYIKNHDDAWPFMDPVDEDIAPRYYSIIRRPMDLQKMEDKLDNG 716

Query: 162 RYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEE 221
            Y TFG FR DF+LIV+NCR YNG  NEYT+MV  LQ  F  A  +Y D    S S DEE
Sbjct: 717 EYLTFGDFRNDFKLIVNNCRLYNGQANEYTEMVNNLQLAFEKAKKKYFD----SNSSDEE 772

Query: 222 E 222
           +
Sbjct: 773 Q 773

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	277
FB|FBgn0261934	2465	dikar "dikar" [Drosophila mela	0.415	0.046	0.560	1.3e-30
RGD|1564182	1390	Cecr2 "cat eye syndrome chromo	0.346	0.069	0.479	3.9e-22
UNIPROTKB|Q9BXF3	1484	CECR2 "Cat eye syndrome critic	0.433	0.080	0.413	2e-21
UNIPROTKB|F1SHR4	1115	CECR2 "Uncharacterized protein	0.346	0.086	0.479	7.7e-21
UNIPROTKB|F1NJP2	1435	CECR2 "Uncharacterized protein	0.368	0.071	0.450	1.8e-20
UNIPROTKB|F1MSA7	1399	F1MSA7 "Uncharacterized protei	0.346	0.068	0.479	2.8e-20
UNIPROTKB|J3QQQ8	420	BPTF "Nucleosome-remodeling fa	0.346	0.228	0.422	1.2e-18
UNIPROTKB|E9PE19	650	BPTF "Nucleosome-remodeling fa	0.346	0.147	0.422	8.2e-18
UNIPROTKB|F1LX76	2894	F1LX76 "Uncharacterized protei	0.346	0.033	0.422	3e-16
UNIPROTKB|F1M1V5	2952	F1M1V5 "Uncharacterized protei	0.346	0.032	0.422	3.2e-16

FB|FBgn0261934 dikar "dikar" [Drosophila melanogaster (taxid:7227)]

 Score = 354 (129.7 bits), Expect = 1.3e-30, P = 1.3e-30
 Identities = 65/116 (56%), Positives = 83/116 (71%)

Query:    94 SYQTSTGG-YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLT 152
             +Y   +G  +  TEE L+IGMHKV+  +K+H DAWPF DPV+E  AP YY  I+RPMDL 
Sbjct:   119 AYSDKSGDDFTETEEVLQIGMHKVLVYVKNHRDAWPFVDPVEEDIAPRYYSIIRRPMDLL 178

Query:   153 RMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
             +ME+KLD+G Y  F +FR DF+LIV+NCR YNG +NEYT+MV  LQ  F  A  +Y
Sbjct:   179 KMEDKLDSGEYHKFSEFRNDFRLIVNNCRLYNGHNNEYTEMVNNLQDAFEKATKKY 234

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008355 "olfactory learning" evidence=IMP

GO:0007611 "learning or memory" evidence=IMP

GO:0007616 "long-term memory" evidence=IMP

RGD|1564182 Cecr2 "cat eye syndrome chromosome region, candidate 2" [Rattus norvegicus (taxid:10116)]

 Score = 257 (95.5 bits), Expect = 3.9e-22, Sum P(2) = 3.9e-22
 Identities = 46/96 (47%), Positives = 70/96 (72%)

Query:   113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
             M+KV++ +K+H+D+WPF +PVDE+ APNYY+ IK PMD++ ME+KL+ G Y T  +F  D
Sbjct:   385 MYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKIPMDISSMEKKLNGGLYCTKEEFVND 444

Query:   173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
              + +  NCRKYNG  +EYT M   L++ F  A++++
Sbjct:   445 MKTMFRNCRKYNGDSSEYTKMSENLERCFHRAMTKH 480

GO:0001842 "neural fold formation" evidence=ISO

GO:0001843 "neural tube closure" evidence=ISO

GO:0005719 "nuclear euchromatin" evidence=ISO

GO:0021915 "neural tube development" evidence=ISO

GO:0060122 "inner ear receptor stereocilium organization" evidence=ISO

GO:0090102 "cochlea development" evidence=ISO

UNIPROTKB|Q9BXF3 CECR2 "Cat eye syndrome critical region protein 2" [Homo sapiens (taxid:9606)]

 Score = 257 (95.5 bits), Expect = 2.0e-21, Sum P(2) = 2.0e-21
 Identities = 50/121 (41%), Positives = 77/121 (63%)

Query:    88 DTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKR 147
             D +S    +  T      ++D    M+KV++ +K+H+D+WPF +PVDE+ APNYY+ IK 
Sbjct:   419 DPNSPMREEKKTKDLFELDDDFT-AMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKA 477

Query:   148 PMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
             PMD++ ME+KL+ G Y T  +F  D + +  NCRKYNG  +EYT M   L++ F  A+ +
Sbjct:   478 PMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 537

Query:   208 Y 208
             +
Sbjct:   538 H 538

GO:0005719 "nuclear euchromatin" evidence=IEA

GO:0021915 "neural tube development" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=NAS

GO:0000910 "cytokinesis" evidence=NAS

GO:0016192 "vesicle-mediated transport" evidence=NAS

GO:0043044 "ATP-dependent chromatin remodeling" evidence=IDA

GO:0090537 "CERF complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0006309 "apoptotic DNA fragmentation" evidence=TAS

GO:0006915 "apoptotic process" evidence=IDA

UNIPROTKB|F1SHR4 CECR2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 258 (95.9 bits), Expect = 7.7e-21, P = 7.7e-21
 Identities = 46/96 (47%), Positives = 70/96 (72%)

Query:   113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
             M+KV++ +K+H+D+WPF +PVDE+ APNYY+ IK PMD++ ME+KL+ G Y T  +F +D
Sbjct:   132 MYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKVPMDISSMEKKLNGGLYCTKEEFVSD 191

Query:   173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
              + +  NCRKYNG  +EYT M   L++ F  A+ ++
Sbjct:   192 MKTMFRNCRKYNGESSEYTKMSENLERCFHRAMLKH 227

GO:0021915 "neural tube development" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005719 "nuclear euchromatin" evidence=IEA

UNIPROTKB|F1NJP2 CECR2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 256 (95.2 bits), Expect = 1.8e-20, P = 1.8e-20
 Identities = 46/102 (45%), Positives = 71/102 (69%)

Query:   107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
             +D    M+KV++ +K+H+D+WPF +PVDE+ APNYY+ IK PMD++ ME+KL+ G+Y T 
Sbjct:   396 DDEFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGQYCTK 455

Query:   167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
              +F  D + +  NC KYNG  +EYT M   L++ F  A+ ++
Sbjct:   456 EEFVGDMKTMFRNCLKYNGEGSEYTKMAYNLERCFHRAMMKH 497

GO:0005719 "nuclear euchromatin" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0021915 "neural tube development" evidence=IEA

UNIPROTKB|F1MSA7 F1MSA7 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 254 (94.5 bits), Expect = 2.8e-20, P = 2.8e-20
 Identities = 46/96 (47%), Positives = 69/96 (71%)

Query:   113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
             M+KV++ +K+H+D+WPF +PVDE+ APNYY+ IK PMD++ ME+KL+ G Y T  +F  D
Sbjct:   407 MYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKVPMDISSMEKKLNGGSYCTKEEFVND 466

Query:   173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
              + +  NCRKYNG  +EYT M   L++ F  A+ ++
Sbjct:   467 MKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMLKH 502

GO:0021915 "neural tube development" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0005719 "nuclear euchromatin" evidence=IEA

UNIPROTKB|J3QQQ8 BPTF "Nucleosome-remodeling factor subunit BPTF" [Homo sapiens (taxid:9606)]

 Score = 208 (78.3 bits), Expect = 1.2e-18, Sum P(2) = 1.2e-18
 Identities = 41/97 (42%), Positives = 57/97 (58%)

Query:   105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
             TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct:   313 TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 371

Query:   165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
                +F AD   I DNCR YN  D+ +      L+  F
Sbjct:   372 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 408

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E9PE19 BPTF "Nucleosome-remodeling factor subunit BPTF" [Homo sapiens (taxid:9606)]

 Score = 208 (78.3 bits), Expect = 8.2e-18, Sum P(2) = 8.2e-18
 Identities = 41/97 (42%), Positives = 57/97 (58%)

Query:   105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
             TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct:   533 TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 591

Query:   165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
                +F AD   I DNCR YN  D+ +      L+  F
Sbjct:   592 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 628

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1LX76 F1LX76 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 209 (78.6 bits), Expect = 3.0e-16, Sum P(2) = 3.0e-16
 Identities = 41/97 (42%), Positives = 57/97 (58%)

Query:   105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
             TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct:  2777 TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYE 2835

Query:   165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
                +F AD   I DNCR YN  D+ +      L+  F
Sbjct:  2836 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 2872

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1M1V5 F1M1V5 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 209 (78.6 bits), Expect = 3.2e-16, Sum P(2) = 3.2e-16
 Identities = 41/97 (42%), Positives = 57/97 (58%)

Query:   105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
             TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct:  2835 TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYE 2893

Query:   165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
                +F AD   I DNCR YN  D+ +      L+  F
Sbjct:  2894 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 2930

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	277
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	4e-41
smart00297	107	smart00297, BROMO, bromo domain	1e-28
cd04369	99	cd04369, Bromodomain, Bromodomain	1e-26
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	1e-23
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	4e-23
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	2e-22
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	2e-21
pfam00439	84	pfam00439, Bromodomain, Bromodomain	5e-21
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	2e-19
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	3e-19
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	5e-18
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	1e-17
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	1e-15
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	3e-15
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	2e-14
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	2e-13
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	2e-13
COG5076	371	COG5076, COG5076, Transcription factor involved in	2e-13
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	9e-13
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	8e-12
cd05508	99	cd05508, Bromo_RACK7, Bromodomain, RACK7_like subf	2e-11
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	3e-11
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	4e-11
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	3e-10
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	7e-10
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	2e-08
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	3e-08
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	3e-08
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	4e-08
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	2e-07
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	6e-07
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	3e-06
cd05492	109	cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like	2e-05
cd05501	102	cd05501, Bromo_SP100C_like, Bromodomain, SP100C_li	1e-04
cd05494	114	cd05494, Bromodomain_1, Bromodomain; uncharacteriz	1e-04
cd05517	103	cd05517, Bromo_polybromo_II, Bromodomain, polybrom	2e-04

>gnl|CDD|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score =  136 bits (346), Expect = 4e-41
 Identities = 48/98 (48%), Positives = 66/98 (67%)

Query: 108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFG 167
            L   + KV++ LK+H+ AWPF +PVD+  AP+YY+ IK+PMDL+ MEEKL+ G Y T  
Sbjct: 1   PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLE 60

Query: 168 QFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           +F AD +LI DNCR YNG D EY     +L++ F   +
Sbjct: 61  EFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKL 98

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. Length = 101

>gnl|CDD|197636 smart00297, BROMO, bromo domain

 Score =  105 bits (263), Expect = 1e-28
 Identities = 37/89 (41%), Positives = 58/89 (65%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           +  V+++L SH  +WPF  PV    AP+YY+ IK+PMDL  +++KL+ G+Y +  +F AD
Sbjct: 12  LKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVAD 71

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
           F L+  N R YNG D+E     ++L++ F
Sbjct: 72  FNLMFSNARTYNGPDSEVYKDAKKLEKFF 100

Length = 107

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score = 99.8 bits (249), Expect = 1e-26
 Identities = 34/91 (37%), Positives = 55/91 (60%), Gaps = 2/91 (2%)

Query: 115 KVMNRLKSH--EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
            +++ LK    + + PF +PVD   AP+YYE IK PMDL+ +++KL  G YK+  +F AD
Sbjct: 7   SLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEAD 66

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
            +LI  N + YNG  +      ++L+++F  
Sbjct: 67  VRLIFSNAKTYNGPGSPIYKDAKKLEKLFEK 97

Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. Length = 99

>gnl|CDD|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 92.0 bits (229), Expect = 1e-23
 Identities = 37/91 (40%), Positives = 53/91 (58%), Gaps = 2/91 (2%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFR 170
           +   +  LK  +DA PF  PVD  +   P+Y   IK+PMDL  +E KL +  Y +  +F 
Sbjct: 9   LLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFT 68

Query: 171 ADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
           ADF L+VDNC  +NG ++  + M +RLQ  F
Sbjct: 69  ADFNLMVDNCLTFNGPEHPVSQMGKRLQAAF 99

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. Length = 103

>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score = 90.4 bits (225), Expect = 4e-23
 Identities = 32/85 (37%), Positives = 47/85 (55%), Gaps = 2/85 (2%)

Query: 121 KSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVD 178
           K     WPF DPVD      PNY+  IK+PMDL  + +KL  G+Y++  +F  D +LI  
Sbjct: 16  KHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFK 75

Query: 179 NCRKYNGLDNEYTDMVRRLQQIFRD 203
           NC  +N    +   M  +L+++F D
Sbjct: 76  NCYTFNPEGTDVYMMGHQLEEVFND 100

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. Length = 102

>gnl|CDD|99930 cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_like subfamily, repeat II

 Score = 88.5 bits (220), Expect = 2e-22
 Identities = 38/95 (40%), Positives = 54/95 (56%), Gaps = 7/95 (7%)

Query: 115 KVMNRLKS--HED-AWPFCDPVDEATA---PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
            ++  L S  H+  AWPF  PVD   A    +Y++ IK PMDL+ +++KLD   Y    +
Sbjct: 7   GILKELFSKKHKAYAWPFYKPVD-PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQE 65

Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
           F AD +L+  NC KYN  D+    M R+LQ +F D
Sbjct: 66  FAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFED 100

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. Length = 102

>gnl|CDD|99943 cd05511, Bromo_TFIID, Bromodomain, TFIID-like subfamily

 Score = 86.5 bits (215), Expect = 2e-21
 Identities = 34/83 (40%), Positives = 54/83 (65%)

Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
           +++N LK+  D+WPF  PV++   P+YY+ IKRPMDL  + +K+   +Y++  +F  D +
Sbjct: 7   EIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIE 66

Query: 175 LIVDNCRKYNGLDNEYTDMVRRL 197
           LIVDN   YNG D+ YT   + +
Sbjct: 67  LIVDNSVLYNGPDSVYTKKAKEM 89

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. Length = 112

>gnl|CDD|215921 pfam00439, Bromodomain, Bromodomain

 Score = 84.4 bits (209), Expect = 5e-21
 Identities = 32/82 (39%), Positives = 49/82 (59%)

Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
           +++  L  H  A PF +PVD    P+YYE IK PMDL+ + +KL +G+YK+  +F  D +
Sbjct: 3   EILEDLMEHPLAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKDVE 62

Query: 175 LIVDNCRKYNGLDNEYTDMVRR 196
           LI  N   YNG D++     ++
Sbjct: 63  LIFSNAITYNGEDSDIYKDAKK 84

Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 84

>gnl|CDD|99944 cd05512, Bromo_brd1_like, Bromodomain; brd1_like subfamily

 Score = 80.5 bits (199), Expect = 2e-19
 Identities = 32/79 (40%), Positives = 51/79 (64%)

Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
           L + + K +++L+  + A  F +PVD +  P+Y + IK+PMD + M +KL++ RY+T   
Sbjct: 2   LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLED 61

Query: 169 FRADFQLIVDNCRKYNGLD 187
           F ADF LI++NC  YN  D
Sbjct: 62  FEADFNLIINNCLAYNAKD 80

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. Length = 98

>gnl|CDD|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily

 Score = 80.5 bits (199), Expect = 3e-19
 Identities = 34/89 (38%), Positives = 52/89 (58%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           + +++  +  H+D+WPF  PV +   P+YY+ IK+PMDL  ++EKL+ G YK   +F +D
Sbjct: 17  LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSD 76

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
            QL+  NC  YN           RLQ+ F
Sbjct: 77  IQLVFSNCFLYNPEHTSVYKAGTRLQRFF 105

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. Length = 115

>gnl|CDD|99935 cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BAZ2B_like subfamily

 Score = 76.6 bits (189), Expect = 5e-18
 Identities = 32/70 (45%), Positives = 49/70 (70%)

Query: 120 LKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDN 179
           +++HEDAWPF +PV+    P Y + IK+PMD + + EKL++G+YKT  +F  D +L+ DN
Sbjct: 12  MEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDN 71

Query: 180 CRKYNGLDNE 189
           C  +N  D+E
Sbjct: 72  CETFNEDDSE 81

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. Length = 97

>gnl|CDD|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 75.9 bits (187), Expect = 1e-17
 Identities = 32/87 (36%), Positives = 48/87 (55%), Gaps = 2/87 (2%)

Query: 115 KVMNRLKSH-EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADF 173
           KV+N LK++ E + PF   V +  AP+YY+ IK+PMDL  M +KL   +YK+  +F  D 
Sbjct: 14  KVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDL 73

Query: 174 QLIVDNCRKYNG-LDNEYTDMVRRLQQ 199
            LI  NC  YN    +        +++
Sbjct: 74  NLIWKNCLLYNSDPSHPLRRHANFMKK 100

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. Length = 112

>gnl|CDD|99957 cd05528, Bromo_AAA, Bromodomain; sub-family co-occurring with AAA domains

 Score = 71.2 bits (175), Expect = 1e-15
 Identities = 39/104 (37%), Positives = 54/104 (51%)

Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
           LR+ +  V+ RL S +    F  PVDE   P+YYE IK+PMDL  + +KLD  +Y T   
Sbjct: 4   LRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKD 63

Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGE 212
           F  D  LIV N  +YN   +    ++R      RD V   ++ E
Sbjct: 64  FLKDIDLIVTNALEYNPDRDPADKLIRSRACELRDEVHAMIEAE 107

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. Length = 112

>gnl|CDD|99938 cd05506, Bromo_plant1, Bromodomain, uncharacterized subfamily specific to plants

 Score = 69.7 bits (171), Expect = 3e-15
 Identities = 32/90 (35%), Positives = 51/90 (56%), Gaps = 4/90 (4%)

Query: 115 KVMNRLKSHEDAWPFCDPVDEATA---PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
            ++ +L  H+  W F  PVD   A   P+Y++ IK+PMDL  +++KL+ G Y +  +F A
Sbjct: 7   TLLRKLMKHKWGWVFNAPVD-VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAA 65

Query: 172 DFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
           D +L   N  +YN   N+   M + L +IF
Sbjct: 66  DVRLTFANAMRYNPPGNDVHTMAKELLKIF 95

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. Length = 99

>gnl|CDD|99945 cd05513, Bromo_brd7_like, Bromodomain, brd7_like subgroup

 Score = 67.1 bits (164), Expect = 2e-14
 Identities = 26/72 (36%), Positives = 39/72 (54%)

Query: 129 FCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDN 188
           F  PV +  AP Y   IK PMD + M+EK+    Y++  +F+ DF+L+ +N  KYN  D 
Sbjct: 22  FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDT 81

Query: 189 EYTDMVRRLQQI 200
            Y    ++L   
Sbjct: 82  IYYKAAKKLLHS 93

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. Length = 98

>gnl|CDD|99937 cd05505, Bromo_WSTF_like, Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like)

 Score = 64.5 bits (157), Expect = 2e-13
 Identities = 24/88 (27%), Positives = 44/88 (50%)

Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           +++++  +  +WPF +PV    A +Y + I  PMDL  M+ K   G Y +  +F  D +L
Sbjct: 8   ILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKL 67

Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
           +  N  KY    +     +R+ +Q   +
Sbjct: 68  VFSNAEKYYENGSYVLSCMRKTEQCCVN 95

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. Length = 97

>gnl|CDD|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 35/108 (32%), Positives = 56/108 (51%), Gaps = 5/108 (4%)

Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLD---AG 161
           +  D R    +++  L  HE + PF +PV   + PNYY+ IK PMDL+ + +KL      
Sbjct: 2   SPIDQRK-CERLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQ 59

Query: 162 RYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL 209
            Y +  +F AD +L+  NC K+N  D+E     + L+  F + +   L
Sbjct: 60  HYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKEIL 107

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. Length = 109

>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

 Score = 69.1 bits (169), Expect = 2e-13
 Identities = 30/81 (37%), Positives = 45/81 (55%)

Query: 121 KSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNC 180
                +  F     +   P+YYE IK PMDL  +++KL  GRYK+F +F +D  L+ DNC
Sbjct: 161 DGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNC 220

Query: 181 RKYNGLDNEYTDMVRRLQQIF 201
           + YNG D+      + L++ F
Sbjct: 221 KLYNGPDSSVYVDAKELEKYF 241

Length = 371

>gnl|CDD|99929 cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like subfamily, repeat I

 Score = 62.8 bits (153), Expect = 9e-13
 Identities = 30/94 (31%), Positives = 51/94 (54%), Gaps = 4/94 (4%)

Query: 116 VMNRLKSHEDAWPFCDPVDEATA---PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           V+  L  H+ AWPF  PVD A     P+Y++ IK PMDL  ++++L+   Y +  +   D
Sbjct: 13  VLKALWKHKFAWPFQQPVD-AVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQD 71

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
           F  +  NC  YN   ++   M + L+++F   ++
Sbjct: 72  FNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLA 105

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. Length = 107

>gnl|CDD|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily

 Score = 60.5 bits (147), Expect = 8e-12
 Identities = 31/98 (31%), Positives = 51/98 (52%), Gaps = 3/98 (3%)

Query: 107 EDLRIGMHKVMNRL-KSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLDAGRY 163
           E+LR  +   + +L K   ++ PF  PVD      P+Y++ +K PMDL+ +  KLD G+Y
Sbjct: 2   EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQY 61

Query: 164 KTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
           +   Q+  D  L+ DN   YN   +       +L ++F
Sbjct: 62  QDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVF 99

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. Length = 108

>gnl|CDD|99940 cd05508, Bromo_RACK7, Bromodomain, RACK7_like subfamily

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 117 MNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLI 176
           M +  +     PF  PVD    P+Y + + +PMDL+ +E+ +    Y +   F AD + I
Sbjct: 15  MKQPGAE----PFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWI 70

Query: 177 VDNCRKYNGLDNEYTDMVRRLQQIFR 202
           + N   YNG D++ T   + + +I  
Sbjct: 71  LHNAIIYNGGDHKLTQAAKAIVKICE 96

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. Length = 99

>gnl|CDD|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V

 Score = 58.5 bits (142), Expect = 3e-11
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 10/68 (14%)

Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           P+YY+ IK+P+D+ ++  K++  +Y++     +DF L+ DN  KYN  D+          
Sbjct: 37  PDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDS---------- 86

Query: 199 QIFRDAVS 206
           QI++DA++
Sbjct: 87  QIYKDALT 94

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. Length = 105

>gnl|CDD|99954 cd05524, Bromo_polybromo_I, Bromodomain, polybromo repeat I

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 27/106 (25%), Positives = 52/106 (49%), Gaps = 8/106 (7%)

Query: 114 HKVMNRLKSH--EDAWPFCDPVDEA----TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFG 167
            ++ + ++++  ED    C+           P YYE +  P+DL ++++KL    Y    
Sbjct: 8   QELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVD 67

Query: 168 QFRADFQLIVDNCRKYNGLDN-EYTDMVRRLQQIFRDAVSRYLDGE 212
              ADF+L+++N + Y   D+ E+ D   +L ++F  A +  L G 
Sbjct: 68  DLTADFELLINNAKAYYKPDSPEHKDAC-KLWELFLSARNEVLSGG 112

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. Length = 113

>gnl|CDD|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 27/85 (31%), Positives = 44/85 (51%)

Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
            V   L SH  A  F  PV E  AP Y+  + RPMDL+ +++ ++ G  ++  +F+ D  
Sbjct: 10  LVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVL 69

Query: 175 LIVDNCRKYNGLDNEYTDMVRRLQQ 199
           L+  N   YN  D++   M   +Q+
Sbjct: 70  LMFQNAIMYNSSDHDVYLMAVEMQR 94

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. Length = 104

>gnl|CDD|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily

 Score = 55.2 bits (133), Expect = 7e-10
 Identities = 25/70 (35%), Positives = 37/70 (52%)

Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
           +++N +   ED+ PF  PVD    P+Y + I  PMDL  ++E L  G Y    +F  D +
Sbjct: 12  ELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVR 71

Query: 175 LIVDNCRKYN 184
           LI  N + Y 
Sbjct: 72  LIFSNSKSYT 81

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. Length = 119

>gnl|CDD|99958 cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like subfamily

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 27/96 (28%), Positives = 46/96 (47%), Gaps = 2/96 (2%)

Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDE-ATAPNYYEQIKRPMDLTRMEEKLDAGRYKT 165
           E L  G+ K++  L+       F  PVD  A  P+Y+ ++  PMDL  +  +L+   Y++
Sbjct: 27  ERLISGLDKLLLSLQLEIAE-YFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRS 85

Query: 166 FGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
               R D +LI+ N   +N  ++E     +RL    
Sbjct: 86  LEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWL 121

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. Length = 128

>gnl|CDD|99953 cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 10/72 (13%)

Query: 134 DEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDM 193
           D+A  P YY++I  P+ L  +++K+   +YK+F QF  D  L+ +N + YN  D      
Sbjct: 33  DKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNEND------ 86

Query: 194 VRRLQQIFRDAV 205
                Q ++DAV
Sbjct: 87  ----SQEYKDAV 94

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. Length = 104

>gnl|CDD|99955 cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-family

 Score = 50.1 bits (120), Expect = 3e-08
 Identities = 23/66 (34%), Positives = 37/66 (56%)

Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           P+YYE+I  P+DL+ +E+++  G YKT   F +D   +  N  KY G  +     V RL+
Sbjct: 39  PDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLR 98

Query: 199 QIFRDA 204
           + +  A
Sbjct: 99  KAYYQA 104

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. Length = 106

>gnl|CDD|99947 cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like subfamily, specific to animals

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 22/101 (21%), Positives = 48/101 (47%), Gaps = 6/101 (5%)

Query: 113 MHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           M+K+++ +  ++D      A  F         P YYE I++P+D  +++E++   +Y++ 
Sbjct: 6   MNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSL 65

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
                D  L+  N + +N   +   +    LQ +F+ A  +
Sbjct: 66  EDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKSARQK 106

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. Length = 107

>gnl|CDD|99951 cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 20/64 (31%), Positives = 38/64 (59%)

Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           P+YY++IK P+ L ++  KL  G Y+T  +  AD  L+ +N ++YN  ++       +LQ
Sbjct: 37  PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQ 96

Query: 199 QIFR 202
           ++ +
Sbjct: 97  KLMQ 100

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. Length = 103

>gnl|CDD|99950 cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfamily, specific to fungi

 Score = 46.6 bits (111), Expect = 6e-07
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 129 FCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN 184
           F +   +   P+YY  IKRP+ L +++ +++   YK+  +F  DF L+  N R YN
Sbjct: 27  FLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN 82

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. Length = 103

>gnl|CDD|99949 cd05518, Bromo_polybromo_IV, Bromodomain, polybromo repeat IV

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 17/46 (36%), Positives = 26/46 (56%)

Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN 184
           P+YY+ I  P+DL  +E  +   +Y T  +   DF+L+  N R YN
Sbjct: 37  PDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82

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. Length = 103

>gnl|CDD|99924 cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like sub-family

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 17/65 (26%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 134 DEATAPNYYEQIKR-PMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTD 192
            +AT      ++    +D+  ++EK+++ +Y +  +F+AD  L++ N   ++G D+E  D
Sbjct: 31  GKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYD 90

Query: 193 MVRRL 197
             R L
Sbjct: 91  AARWL 95

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. Length = 109

>gnl|CDD|99933 cd05501, Bromo_SP100C_like, Bromodomain, SP100C_like subfamily

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 141 YYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQI 200
           Y + IK PM L +++E+L+   Y T   F  D +LI  N + +   D+++  +   L++ 
Sbjct: 33  YCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYK-DDDFGQVGITLEKK 91

Query: 201 F 201
           F
Sbjct: 92  F 92

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. Length = 102

>gnl|CDD|99926 cd05494, Bromodomain_1, Bromodomain; uncharacterized subfamily

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 2/41 (4%)

Query: 116 VMNRLKSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRM 154
            + R + +EDAWPF +PV+     AP+Y + IKRPM     
Sbjct: 11  ELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTK 51

Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. Length = 114

>gnl|CDD|99948 cd05517, Bromo_polybromo_II, Bromodomain, polybromo repeat II

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 10/68 (14%)

Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           P+YY  IK P+DL  + +++ +G YK+      D  L+V N + +N   +          
Sbjct: 37  PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGS---------- 86

Query: 199 QIFRDAVS 206
           Q+++DA +
Sbjct: 87  QVYKDANA 94

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. Length = 103

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	277
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.96
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.96
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.96
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.96
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.96
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.96
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.96
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.95
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.95
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.95
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.95
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.95
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.95
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.95
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.95
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.95
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.94
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.94
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.94
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.94
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.94
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.94
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.94
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.94
KOG1474|consensus	640		99.93
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.93
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.93
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.93
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.93
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.93
smart00297	107	BROMO bromo domain.	99.93
KOG0955|consensus	1051		99.92
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.91
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.91
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.9
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.89
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.88
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.86
COG5076	371	Transcription factor involved in chromatin remodel	99.79
KOG1245|consensus	1404		99.77
KOG1472|consensus	720		99.63
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.33
KOG1827|consensus	629		99.25
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	99.19
KOG0008|consensus	1563		99.16
KOG0386|consensus	1157		99.14
KOG0008|consensus	1563		98.97
KOG1472|consensus	720		98.9
KOG1828|consensus	418		98.77
KOG1828|consensus	418		98.65
KOG1474|consensus	640		98.49
COG5076	371	Transcription factor involved in chromatin remodel	97.45
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	96.81
KOG0644|consensus	1113		95.9
KOG0732|consensus	1080		92.13
COG5141	669	PHD zinc finger-containing protein [General functi	91.65
KOG1827|consensus	629		87.23

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.96  E-value=1.2e-29  Score=202.53  Aligned_cols=107  Identities=29%  Similarity=0.479  Sum_probs=102.6

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ...|+..|..||+.|+.++.+++|..||++..+||||++|++||||+||+.||.+|.|.++.+|.+||+|||.||++||+
T Consensus         3 ~~~w~~~c~~il~~l~~~~~s~~F~~PVd~~~~pdY~~iIk~PmDL~tIk~kL~~~~Y~~~~ef~~D~~lif~Na~~yN~   82 (119)
T cd05496           3 ESDWKKQCKELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTP   82 (119)
T ss_pred             HHHHHHHHHHHHHHHHhCCccccccCCCChhhcCcHHHHhCCcccHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C-CCHHHHHHHHHHHHHHHHHHHhhccc
Q psy16435        186 L-DNEYTDMVRRLQQIFRDAVSRYLDGE  212 (277)
Q Consensus       186 ~-~s~i~~~A~~L~~~f~~~~~~~~~~~  212 (277)
                      + +|.||.+|..|+++|+..+.+++...
T Consensus        83 ~~~s~i~~~a~~L~~~F~~~~~~l~~~~  110 (119)
T cd05496          83 NKRSRIYSMTLRLSALFEEHIKKIISDW  110 (119)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5 89999999999999999999997653

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.

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.96  E-value=2e-29  Score=198.35  Aligned_cols=103  Identities=29%  Similarity=0.585  Sum_probs=99.4

Q ss_pred             HHHHHHHHHHHHHHHcC-CCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhh
Q psy16435        107 EDLRIGMHKVMNRLKSH-EDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY  183 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~-~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~Y  183 (277)
                      ++|+..|..+++.|..+ +.|++|..||++.  .+||||++|++||||+||++||.+|.|.++.+|.+||.|||.||+.|
T Consensus         2 ~~l~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~y   81 (108)
T cd05495           2 EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLY   81 (108)
T ss_pred             HHHHHHHHHHHHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            58899999999999999 9999999999987  69999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhh
Q psy16435        184 NGLDNEYTDMVRRLQQIFRDAVSRYL  209 (277)
Q Consensus       184 N~~~s~i~~~A~~L~~~f~~~~~~~~  209 (277)
                      |+++|.+|.+|..|++.|+..+..++
T Consensus        82 N~~~s~i~~~a~~l~~~F~~~~~~~~  107 (108)
T cd05495          82 NRKTSRVYKYCTKLAEVFEQEIDPVM  107 (108)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999998765

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.

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.96  E-value=2.9e-29  Score=197.09  Aligned_cols=102  Identities=29%  Similarity=0.565  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      .++...+..||..|+.++.|++|..||++.  .+||||++|++||||+||++||.+|.|.++.+|.+||.|||.||+.||
T Consensus         4 ~q~~~~~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN   83 (107)
T cd05497           4 NQLQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYN   83 (107)
T ss_pred             HHHHHHHHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            478888899999999999999999999986  699999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHh
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      +++|.++.+|..|++.|.+.+.++
T Consensus        84 ~~~s~i~~~A~~l~~~f~~~l~~~  107 (107)
T cd05497          84 KPGDDVVLMAQTLEKLFLQKLAQM  107 (107)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHcC
Confidence            999999999999999999988753

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.

>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like)

Probab=99.96  E-value=4.4e-29  Score=192.63  Aligned_cols=94  Identities=26%  Similarity=0.488  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHH
Q psy16435        111 IGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEY  190 (277)
Q Consensus       111 ~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i  190 (277)
                      ..|..||+.|+.++.+++|..||++..+||||++|++||||+||++||++|.|.|+.+|.+||.|||.||+.||+++|.+
T Consensus         3 ~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i   82 (97)
T cd05505           3 QKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV   82 (97)
T ss_pred             HHHHHHHHHHHhCCCcccccCCCChhhcccHHHHcCCcCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q psy16435        191 TDMVRRLQQIFRDA  204 (277)
Q Consensus       191 ~~~A~~L~~~f~~~  204 (277)
                      +.+|..|++.|...
T Consensus        83 ~~~a~~le~~f~~~   96 (97)
T cd05505          83 LSCMRKTEQCCVNL   96 (97)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999875

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.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.96  E-value=1.4e-28  Score=194.58  Aligned_cols=106  Identities=32%  Similarity=0.496  Sum_probs=100.3

Q ss_pred             ChHHHHHHHHHHHHHHHcC-CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhh
Q psy16435        105 TEEDLRIGMHKVMNRLKSH-EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY  183 (277)
Q Consensus       105 ~~~~l~~~l~~il~~l~~~-~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~Y  183 (277)
                      .+++|...|..||..|+.+ +.+++|..||++..+||||++|++||||+||++||++|.|.|+.+|.+||.|||.||+.|
T Consensus         4 ~~~~~~~~~~~il~~l~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~Li~~N~~~y   83 (112)
T cd05510           4 GQEEFYESLDKVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLY   83 (112)
T ss_pred             cHHHHHHHHHHHHHHHHhcCccccchhcCCChhhcCCHHHHhcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999 899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC-HHHHHHHHHHHHHHHHHHHhhc
Q psy16435        184 NGLDN-EYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       184 N~~~s-~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      |+++| .++.+|..|++.|...+..+++
T Consensus        84 N~~~s~~~~~~A~~l~~~~~~~~~~~~~  111 (112)
T cd05510          84 NSDPSHPLRRHANFMKKKAEHLLKLIPD  111 (112)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence            99876 6889999999999999988753

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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.96  E-value=9.9e-29  Score=191.22  Aligned_cols=97  Identities=29%  Similarity=0.487  Sum_probs=93.5

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCC
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGL  186 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~  186 (277)
                      .+|...|..++..|+ ++.+++|..||++..+||||.+|++||||+||++||.+|.|.++++|.+||.|||.||+.||++
T Consensus         2 ~~l~~~L~~~~~~~~-~~~s~~F~~PV~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~Na~~YN~~   80 (99)
T cd05508           2 DQLSKLLKFALERMK-QPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGG   80 (99)
T ss_pred             hHHHHHHHHHHHHHh-CcCcchhcCCCChhhCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            478899999999999 9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHH
Q psy16435        187 DNEYTDMVRRLQQIFRDA  204 (277)
Q Consensus       187 ~s~i~~~A~~L~~~f~~~  204 (277)
                      +|.++.+|..|.+.|...
T Consensus        81 ~s~i~~~A~~l~~~~~~e   98 (99)
T cd05508          81 DHKLTQAAKAIVKICEQE   98 (99)
T ss_pred             CCHHHHHHHHHHHHHHhh
Confidence            999999999999988764

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.

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.96  E-value=1.7e-28  Score=191.87  Aligned_cols=101  Identities=27%  Similarity=0.439  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      .|+..|..+++.|..++.+++|..||+...+|+||++|++||||+||++||++|.|.++.+|.+||.|||.||+.||+++
T Consensus         3 ~~~~~~~~il~~l~~~~~a~~F~~pV~~~~~p~Y~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~   82 (104)
T cd05507           3 AWKKAILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSD   82 (104)
T ss_pred             HHHHHHHHHHHHHHcCCCCHhhcCCCCccccCCHHHHhCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHh
Q psy16435        188 NEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      |.++.+|..|+..|...+..+
T Consensus        83 s~v~~~A~~l~~~~~~~~~~~  103 (104)
T cd05507          83 HDVYLMAVEMQREVMSQIQQL  103 (104)
T ss_pred             CHHHHHHHHHHHHHHHHhhcc
Confidence            999999999999998887654

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.95  E-value=5.5e-28  Score=192.14  Aligned_cols=102  Identities=33%  Similarity=0.624  Sum_probs=98.3

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCC
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGL  186 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~  186 (277)
                      ......|..||..|+.++.+++|..||+...+||||++|++||||+||++||.+|.|.|+.+|.+||.|||.||++||++
T Consensus        11 ~~~~~~c~~il~~l~~~~~s~~F~~pvd~~~~pdY~~vI~~PmDL~tI~~kL~~~~Y~s~~~f~~Dv~LI~~Na~~yN~~   90 (115)
T cd05504          11 PLNLSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPE   90 (115)
T ss_pred             HHHHHHHHHHHHHHHhCCCchhhcCCCCccccccHHHHhcCcccHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            35577899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Q psy16435        187 DNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       187 ~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      +|.+|.+|..|+++|...++++
T Consensus        91 ~s~i~~~A~~l~~~f~~~~~~~  112 (115)
T cd05504          91 HTSVYKAGTRLQRFFIKRCRKL  112 (115)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999876

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.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.95  E-value=3.2e-28  Score=188.07  Aligned_cols=95  Identities=35%  Similarity=0.740  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHH
Q psy16435        111 IGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEY  190 (277)
Q Consensus       111 ~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i  190 (277)
                      ..|..||+.|..++.+++|+.||++..+|+||.+|++||||+||++||.+|.|.|+.+|.+||.|||.||+.||+++|.+
T Consensus         3 ~~c~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i   82 (97)
T cd05503           3 ALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEV   82 (97)
T ss_pred             HHHHHHHHHHHcCCCchhhcCCCCccccCCHHHHhCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHH
Confidence            56999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy16435        191 TDMVRRLQQIFRDAV  205 (277)
Q Consensus       191 ~~~A~~L~~~f~~~~  205 (277)
                      +.+|..|++.|+..|
T Consensus        83 ~~~a~~l~~~f~~~~   97 (97)
T cd05503          83 GRAGHNMRKFFEKRW   97 (97)
T ss_pred             HHHHHHHHHHHHHhC
Confidence            999999999999864

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.

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.95  E-value=4.4e-28  Score=188.57  Aligned_cols=100  Identities=48%  Similarity=0.913  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCC
Q psy16435        109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDN  188 (277)
Q Consensus       109 l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s  188 (277)
                      ++..|..||+.|..++.+++|..||++..+|+||++|++||||+||++||.+|.|.|+.+|..||.|||.||+.||+++|
T Consensus         2 ~~~~~~~il~~l~~~~~a~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s   81 (101)
T cd05509           2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDT   81 (101)
T ss_pred             hHHHHHHHHHHHHhCCCchhhcCCCChhhcCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHh
Q psy16435        189 EYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       189 ~i~~~A~~L~~~f~~~~~~~  208 (277)
                      .++.+|..|+..|++.++++
T Consensus        82 ~~~~~a~~l~~~f~~~~~~~  101 (101)
T cd05509          82 EYYKCANKLEKFFWKKLKEL  101 (101)
T ss_pred             HHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999988764

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.95  E-value=1.7e-27  Score=187.78  Aligned_cols=103  Identities=32%  Similarity=0.565  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhC---CCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDA---GRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~---~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      ..+..|..||..|..++.+++|..||++ .+|+||++|++||||+||++||.+   |.|.++++|.+||+|||.||+.||
T Consensus         4 ~~~~~c~~il~~l~~~~~s~~F~~pv~~-~~p~Y~~iI~~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~~yN   82 (109)
T cd05502           4 IDQRKCERLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFN   82 (109)
T ss_pred             HHHHHHHHHHHHHHhCCCChhhcCCCCC-CCCCHHHHCCCCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            4477899999999999999999999998 899999999999999999999998   699999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      +++|.++.+|..|++.|++.+.+++++
T Consensus        83 ~~~s~i~~~a~~l~~~f~~~~~~~~p~  109 (109)
T cd05502          83 EEDSEVAQAGKELELFFEEQLKEILPD  109 (109)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCcC
Confidence            999999999999999999999998763

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.

>cd05516 Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, specific to animals

Probab=99.95  E-value=7.9e-28  Score=188.98  Aligned_cols=99  Identities=23%  Similarity=0.446  Sum_probs=94.8

Q ss_pred             HHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhh
Q psy16435        109 LRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRK  182 (277)
Q Consensus       109 l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~  182 (277)
                      |...|..||+.|..+.+      +++|..||+...+||||.+|++||||+||++||.+|.|.++.+|..||.|||.||+.
T Consensus         2 l~~~~~~il~~v~~~~d~~g~~~s~~F~~~p~~~~~pdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~   81 (107)
T cd05516           2 LTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQT   81 (107)
T ss_pred             HHHHHHHHHHHHHhhhCcCCCEeeHHhhcCCCcccCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHH
Confidence            67889999999988877      899999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHH
Q psy16435        183 YNGLDNEYTDMVRRLQQIFRDAVSR  207 (277)
Q Consensus       183 YN~~~s~i~~~A~~L~~~f~~~~~~  207 (277)
                      ||+++|.+|.+|..|+++|...+.+
T Consensus        82 yN~~~s~i~~~a~~l~~~f~~~~~~  106 (107)
T cd05516          82 FNLEGSLIYEDSIVLQSVFKSARQK  106 (107)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999998875

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.

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.95  E-value=1e-27  Score=185.26  Aligned_cols=95  Identities=29%  Similarity=0.534  Sum_probs=90.4

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      +|...|..||+.|+.++.+++|..||+...+||||++|++||||+||++||.++.|.|+.+|.+||.|||.||+.||+++
T Consensus         1 ~l~~~l~~il~~l~~~~~~~~F~~PV~~~~~pdY~~vIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~   80 (98)
T cd05513           1 PLQKALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPD   80 (98)
T ss_pred             CHHHHHHHHHHHHHcCCccccccCcCCccccccHHHHHcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            36788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHH
Q psy16435        188 NEYTDMVRRLQQIFR  202 (277)
Q Consensus       188 s~i~~~A~~L~~~f~  202 (277)
                      |.+|.+|..|...-.
T Consensus        81 s~~~~~A~~L~~~~~   95 (98)
T cd05513          81 TIYYKAAKKLLHSGM   95 (98)
T ss_pred             CHHHHHHHHHHHhhh
Confidence            999999999976543

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.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.95  E-value=1.1e-27  Score=185.20  Aligned_cols=94  Identities=36%  Similarity=0.690  Sum_probs=90.4

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      +|...|+.+|+.|..++.+++|..||+...+|+||++|++||||+||++||.+|.|.|+++|..||+|||.||+.||+++
T Consensus         1 p~~~~l~~il~~l~~~~~~~~F~~pVd~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~   80 (98)
T cd05512           1 PLEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD   80 (98)
T ss_pred             CHHHHHHHHHHHHHhCCCchhhcCCCCccccCCHHHHhcCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            36778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q psy16435        188 NEYTDMVRRLQQIF  201 (277)
Q Consensus       188 s~i~~~A~~L~~~f  201 (277)
                      |.+|++|..|++.-
T Consensus        81 s~~~~~A~~l~~~~   94 (98)
T cd05512          81 TIFYRAAVRLRDQG   94 (98)
T ss_pred             CHHHHHHHHHHHhh
Confidence            99999999998764

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.

>cd05528 Bromo_AAA Bromodomain; sub-family co-occurring with AAA domains

Probab=99.95  E-value=2.6e-27  Score=187.31  Aligned_cols=105  Identities=35%  Similarity=0.524  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCC
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGL  186 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~  186 (277)
                      .+|+..|..|++.|+.++.+++|..||+...+||||++|++||||+||++||++|.|.|+.+|.+||.|||.||+.||++
T Consensus         2 ~~lr~~L~~il~~l~~~~~~~~F~~pv~~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~   81 (112)
T cd05528           2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD   81 (112)
T ss_pred             hHHHHHHHHHHHHHHhCCCchhhcCCCCccccCcHHHHHcCCCCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHCCC
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C----CHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        187 D----NEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       187 ~----s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      +    |.++.+|..|++.|...+...++.
T Consensus        82 ~s~~~s~i~~~A~~L~~~~~~~~~~~~~~  110 (112)
T cd05528          82 RDPADKLIRSRACELRDEVHAMIEAELDP  110 (112)
T ss_pred             CCccccHHHHHHHHHHHHHHHHHHhcCCC
Confidence            5    699999999999999999887653

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

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.95  E-value=3.3e-27  Score=186.92  Aligned_cols=102  Identities=33%  Similarity=0.672  Sum_probs=98.1

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCH
Q psy16435        110 RIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNE  189 (277)
Q Consensus       110 ~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~  189 (277)
                      ...+..|+..|+.++.+++|..||++..+|+||++|++||||+||++||.+|.|.|+++|.+||.|||.||+.||+++|.
T Consensus         2 ~~~l~~ii~~l~~~~~s~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~   81 (112)
T cd05511           2 SFILDEIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSV   81 (112)
T ss_pred             HHHHHHHHHHHHhCCCchhhcCCCChhhcccHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhhcc
Q psy16435        190 YTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       190 i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      ++.+|..|...|...+..+...
T Consensus        82 i~~~A~~l~~~~~~~~~~~~~~  103 (112)
T cd05511          82 YTKKAKEMLELAEELLAEREEK  103 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHH
Confidence            9999999999999999988553

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.94  E-value=4e-27  Score=182.49  Aligned_cols=96  Identities=32%  Similarity=0.593  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        110 RIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       110 ~~~l~~il~~l~~~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      ...|..||+.|+.++.+++|..||++.  .+|+||.+|++||||+||+.||++|.|.|+.+|.+||.+||.||+.||+++
T Consensus         2 ~~~c~~il~~l~~~~~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yn~~~   81 (99)
T cd05506           2 MKQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPG   81 (99)
T ss_pred             HHHHHHHHHHHHhCCCCccccCCCCccccCCCCHHHHHcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            568999999999999999999999976  699999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHH
Q psy16435        188 NEYTDMVRRLQQIFRDAV  205 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~  205 (277)
                      |.++.+|..|...|+..|
T Consensus        82 s~i~~~a~~l~~~fe~~w   99 (99)
T cd05506          82 NDVHTMAKELLKIFETRW   99 (99)
T ss_pred             CHHHHHHHHHHHHHHHhC
Confidence            999999999999999864

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.

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.94  E-value=9.4e-27  Score=180.36  Aligned_cols=97  Identities=20%  Similarity=0.312  Sum_probs=91.2

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHH
Q psy16435        111 IGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEY  190 (277)
Q Consensus       111 ~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i  190 (277)
                      ..|..||..|..++.|++|..++  ..+||||++|++||||+||++||.+|.|.|+++|.+||+|||.||++||+++ .+
T Consensus         5 ~~ce~il~~l~~~~~s~~f~~~p--~~~pdY~~iIk~PMDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~N~~~yN~~~-~~   81 (102)
T cd05501           5 LKCEFLLLKVYCMSKSGFFISKP--YYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-DF   81 (102)
T ss_pred             HHHHHHHHHHHhCcccccccCCC--CCCCchHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHcCCC-HH
Confidence            34999999999999999997643  4899999999999999999999999999999999999999999999999999 99


Q ss_pred             HHHHHHHHHHHHHHHHHhhc
Q psy16435        191 TDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       191 ~~~A~~L~~~f~~~~~~~~~  210 (277)
                      +.+|..|++.|++.+.+++.
T Consensus        82 ~~~a~~L~~~Fek~~~~~f~  101 (102)
T cd05501          82 GQVGITLEKKFEKNFKEVFA  101 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999998764

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.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.94  E-value=8.5e-27  Score=181.66  Aligned_cols=95  Identities=35%  Similarity=0.655  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHcC---CCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        111 IGMHKVMNRLKSH---EDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       111 ~~l~~il~~l~~~---~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ..|..||..|..+   +.+++|+.||++.  .+|+||++|++||||++|++||.+|.|.|+.+|.+||+|||.||+.||+
T Consensus         3 ~~c~~Il~~l~~~~~~~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I~~kl~~~~Y~s~~ef~~D~~li~~N~~~yn~   82 (102)
T cd05499           3 KFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNP   82 (102)
T ss_pred             HHHHHHHHHHHcccCCcccchhcCCCCccccCCCCHHHHhcCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            5689999999884   5699999999998  8999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHH
Q psy16435        186 LDNEYTDMVRRLQQIFRDAV  205 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~  205 (277)
                      ++|.++.+|..|++.|+..|
T Consensus        83 ~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          83 EGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             CCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999999864

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.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.94  E-value=1.4e-26  Score=180.70  Aligned_cols=97  Identities=38%  Similarity=0.636  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      .....|..||..|+.++.+++|..||++.  .+|+||++|++||||++|+.||.+|.|.++.+|..||.|||.||+.||+
T Consensus         4 ~~~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~   83 (103)
T cd05500           4 HQHKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNG   83 (103)
T ss_pred             HHHHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            45778999999999999999999999976  7999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHH
Q psy16435        186 LDNEYTDMVRRLQQIFRDA  204 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~  204 (277)
                      ++|.++.+|..|++.|++.
T Consensus        84 ~~s~~~~~A~~l~~~fe~~  102 (103)
T cd05500          84 PEHPVSQMGKRLQAAFEKH  102 (103)
T ss_pred             CCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999875

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.94  E-value=2.3e-26  Score=179.19  Aligned_cols=96  Identities=38%  Similarity=0.628  Sum_probs=91.3

Q ss_pred             HHHHHHHHHHHHcC---CCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        110 RIGMHKVMNRLKSH---EDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       110 ~~~l~~il~~l~~~---~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      ...|..||+.|+.+   +.+++|..||++.  .+|+||++|++||||++|++||.+|.|.|+.+|..||+|||.||+.||
T Consensus         2 ~~~c~~il~~l~~~~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~yn   81 (102)
T cd05498           2 LKFCSGILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYN   81 (102)
T ss_pred             hhHHHHHHHHHHhCCCccccCcccCcCCccccCCCcHHHHccCCCcHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            45799999999999   7899999999986  599999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAV  205 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~  205 (277)
                      +++|.++.+|..|++.|++.|
T Consensus        82 ~~~s~i~~~a~~l~~~fe~~~  102 (102)
T cd05498          82 PPDHPVHAMARKLQDVFEDRW  102 (102)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999864

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.

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.94  E-value=2.9e-26  Score=181.75  Aligned_cols=102  Identities=23%  Similarity=0.456  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhh
Q psy16435        110 RIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY  183 (277)
Q Consensus       110 ~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~Y  183 (277)
                      ...|..|++.|+.+..      +.+|..+|+...+|+||++|++||||+||++||.+|.|.|+.+|.+||.|||+||+.|
T Consensus         4 ~~~c~~il~~l~~~~~~~g~~l~~~F~~~p~~~~~PdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~y   83 (113)
T cd05524           4 IAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAY   83 (113)
T ss_pred             HHHHHHHHHHHHhhcccCCCchhHHHhcCCCcccCCCHHHHhCCccCHHHHHHHhCcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            5678999999986544      5689999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        184 NGLDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       184 N~~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      |+++|.+|.+|..|+++|+..+.+++.+
T Consensus        84 N~~~s~~~~~A~~L~~~f~~~~~~~~~~  111 (113)
T cd05524          84 YKPDSPEHKDACKLWELFLSARNEVLSG  111 (113)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999999998765

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.

>cd05519 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi

Probab=99.94  E-value=2e-26  Score=179.94  Aligned_cols=96  Identities=23%  Similarity=0.466  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHHHHcC------CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhh
Q psy16435        109 LRIGMHKVMNRLKSH------EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRK  182 (277)
Q Consensus       109 l~~~l~~il~~l~~~------~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~  182 (277)
                      |+..|..|++.|..+      ..+++|..||+...+|+||++|++||||++|++||++|.|.|+.+|..||+|||.||+.
T Consensus         1 ~~~~~~~i~~~v~~~~~~~~~~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~   80 (103)
T cd05519           1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANART   80 (103)
T ss_pred             CHHHHHHHHHHHHHhcCcCCCchhHHhcCCCCCCCCcCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHH
Confidence            467889999999844      44889999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHH
Q psy16435        183 YNGLDNEYTDMVRRLQQIFRDA  204 (277)
Q Consensus       183 YN~~~s~i~~~A~~L~~~f~~~  204 (277)
                      ||+++|.+|.+|..|++.|..+
T Consensus        81 yn~~~s~i~~~A~~l~~~f~~~  102 (103)
T cd05519          81 YNQEGSIVYEDAVEMEKAFKKK  102 (103)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999875

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.

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.94  E-value=2.2e-26  Score=180.26  Aligned_cols=96  Identities=24%  Similarity=0.487  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHHHcC------CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhh
Q psy16435        110 RIGMHKVMNRLKSH------EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY  183 (277)
Q Consensus       110 ~~~l~~il~~l~~~------~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~Y  183 (277)
                      ++.|..|++.|..+      ..+++|..||+...+||||++|++||||+||++||.++.|.|+++|..||.|||.||++|
T Consensus         2 ~~~~~~~~~~i~~~~d~~~~~~a~~F~~~p~~~~~pdYy~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~~y   81 (105)
T cd05515           2 QQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKY   81 (105)
T ss_pred             hHHHHHHHHHHHHhhCcCCCcccHHhccCCCcccCCcHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHH
Confidence            45677888888765      447899999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHH
Q psy16435        184 NGLDNEYTDMVRRLQQIFRDAV  205 (277)
Q Consensus       184 N~~~s~i~~~A~~L~~~f~~~~  205 (277)
                      |+++|.+|.+|..|+++|....
T Consensus        82 N~~~s~i~~~A~~L~~~~~~~~  103 (105)
T cd05515          82 NEPDSQIYKDALTLQKVLLETK  103 (105)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998764

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.

>KOG1474|consensus

Probab=99.93  E-value=2.5e-26  Score=229.42  Aligned_cols=109  Identities=34%  Similarity=0.619  Sum_probs=102.7

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhh
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY  183 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~Y  183 (277)
                      ..++...|..||..|+.|..+|||..|||+.  .+||||+||++||||+||+.||.+|.|.++.+|..||+|||.||++|
T Consensus       220 ~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~Y~~~~eF~~DVRL~F~Ncm~Y  299 (640)
T KOG1474|consen  220 TVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGEYKSAEEFAADVRLTFDNCMTY  299 (640)
T ss_pred             cHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccccCCHHHHHHHHHHHHHHHHhc
Confidence            4566778999999999999999999999997  68999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhhcccCC
Q psy16435        184 NGLDNEYTDMVRRLQQIFRDAVSRYLDGERS  214 (277)
Q Consensus       184 N~~~s~i~~~A~~L~~~f~~~~~~~~~~~~~  214 (277)
                      |++++.||.||..|+.+|+..|..++.....
T Consensus       300 Np~g~dV~~Ma~~L~~~Fe~rw~~~~~~~~~  330 (640)
T KOG1474|consen  300 NPEGSDVYAMAKKLQEVFEERWASMPLEIEE  330 (640)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhhccccccc
Confidence            9999999999999999999999998766543

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.93  E-value=2.8e-26  Score=178.91  Aligned_cols=94  Identities=21%  Similarity=0.467  Sum_probs=87.9

Q ss_pred             HHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhh
Q psy16435        110 RIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY  183 (277)
Q Consensus       110 ~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~Y  183 (277)
                      ++.|..|++.|..+.+      +++|..+|++..+||||++|++||||+||++||.++.|.++.+|..||.|||.||+.|
T Consensus         2 ~~~~~~l~~~i~~~~d~~gr~~~~~F~~lp~~~~~pdYy~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~y   81 (103)
T cd05517           2 KQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTF   81 (103)
T ss_pred             hHHHHHHHHHHHHhhCcCCCChhHHHhcCCCCCCCCCHHHHcCCCcCHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            5677888888877544      6899999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHH
Q psy16435        184 NGLDNEYTDMVRRLQQIFRD  203 (277)
Q Consensus       184 N~~~s~i~~~A~~L~~~f~~  203 (277)
                      |+++|.+|.+|..|+++|..
T Consensus        82 N~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          82 NEPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             CCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999976

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.

>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family

Probab=99.93  E-value=5.2e-26  Score=178.19  Aligned_cols=96  Identities=29%  Similarity=0.513  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhh
Q psy16435        109 LRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRK  182 (277)
Q Consensus       109 l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~  182 (277)
                      |...|..|++.|....+      +++|..+|++..+||||++|++||||++|++||.+|.|.|+.+|..||.|||.||+.
T Consensus         3 l~~~l~~i~~~i~~~kd~~g~~~s~~F~~lp~k~~~pdYy~~I~~P~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f~Na~~   82 (106)
T cd05525           3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEK   82 (106)
T ss_pred             HHHHHHHHHHHHHHhhccCCCcccHhhccCCCcccCCchhhhCCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            56778888888876544      689999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHH
Q psy16435        183 YNGLDNEYTDMVRRLQQIFRDA  204 (277)
Q Consensus       183 YN~~~s~i~~~A~~L~~~f~~~  204 (277)
                      ||+++|.+|.+|..|+++|.+.
T Consensus        83 yn~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          83 YYGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHc
Confidence            9999999999999999999874

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.

>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III

Probab=99.93  E-value=5.8e-26  Score=177.17  Aligned_cols=81  Identities=28%  Similarity=0.560  Sum_probs=78.1

Q ss_pred             CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHH
Q psy16435        124 EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD  203 (277)
Q Consensus       124 ~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f~~  203 (277)
                      ..+++|..||+...+||||++|++||||+||+.||.+|.|.++.+|+.||.|||.||+.||+++|.+|.+|..|+++|+.
T Consensus        22 ~~s~pF~~~p~~~~~PdYy~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~L~~~f~~  101 (103)
T cd05520          22 LLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKLMQA  101 (103)
T ss_pred             CccHhhhcCCCcccCCCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence            45889999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             H
Q psy16435        204 A  204 (277)
Q Consensus       204 ~  204 (277)
                      .
T Consensus       102 ~  102 (103)
T cd05520         102 K  102 (103)
T ss_pred             h
Confidence            3

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.

>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV

Probab=99.93  E-value=9.3e-26  Score=175.94  Aligned_cols=83  Identities=23%  Similarity=0.453  Sum_probs=79.0

Q ss_pred             cCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHH
Q psy16435        122 SHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF  201 (277)
Q Consensus       122 ~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f  201 (277)
                      ++..+.+|..+|+...+||||++|++||||+||+.||.+|.|.|+.+|.+||.|||.||+.||+++|.+|.+|..|+++|
T Consensus        20 gr~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le~~~   99 (103)
T cd05518          20 GRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVL   99 (103)
T ss_pred             CCcccHHHhcCCCcccCccHHHHcCCCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            34568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHH
Q psy16435        202 RDA  204 (277)
Q Consensus       202 ~~~  204 (277)
                      ...
T Consensus       100 ~~~  102 (103)
T cd05518         100 KEK  102 (103)
T ss_pred             Hhc
Confidence            763

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.

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.93  E-value=3.4e-25  Score=179.32  Aligned_cols=103  Identities=25%  Similarity=0.424  Sum_probs=97.4

Q ss_pred             CChHHHHHHHHHHHHHHH---cCCCCCCCCCCCCCC-CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHh
Q psy16435        104 STEEDLRIGMHKVMNRLK---SHEDAWPFCDPVDEA-TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDN  179 (277)
Q Consensus       104 ~~~~~l~~~l~~il~~l~---~~~~s~~F~~pv~~~-~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~N  179 (277)
                      +....++..|..+|..|.   .++.+++|..||+.. .+|+||++|++||||+||++||.+|.|.++++|..||.|||.|
T Consensus        20 ~~~~~~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~~~p~Y~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~N   99 (128)
T cd05529          20 HIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSN   99 (128)
T ss_pred             CCCHHHHHHHHHHHHHHHhcccCcccccccCCCCccccCCcHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            345677888999999999   899999999999999 9999999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCCHHHHHHHHHHHHHHHHHH
Q psy16435        180 CRKYNGLDNEYTDMVRRLQQIFRDAVS  206 (277)
Q Consensus       180 a~~YN~~~s~i~~~A~~L~~~f~~~~~  206 (277)
                      |+.||+++|.++.+|..|.+.|...+.
T Consensus       100 a~~yN~~~s~i~~~A~~l~~~~~~~l~  126 (128)
T cd05529         100 AETFNEPNSEIAKKAKRLSDWLLRILS  126 (128)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999988765

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.

>smart00297 BROMO bromo domain

Probab=99.93  E-value=4.3e-25  Score=172.70  Aligned_cols=102  Identities=37%  Similarity=0.774  Sum_probs=98.2

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ...+...|..|++.+..++.+++|..||+...+|+||.+|++||||++|++||++|.|.|+.+|.+||.+||.||+.||+
T Consensus         5 ~~~~~~~~~~i~~~~~~~~~~~~F~~~~~~~~~p~Y~~~i~~P~dl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~~n~   84 (107)
T smart00297        5 QKKLQSLLKAVLDKLDSHRLSWPFLKPVDRKEAPDYYDIIKKPMDLSTIKKKLENGKYSSVEEFVADVQLMFSNAKTYNG   84 (107)
T ss_pred             HHHHHHHHHHHHHHHHhCccchhhccCCChhhccCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            45788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q psy16435        186 LDNEYTDMVRRLQQIFRDAVSR  207 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~~~  207 (277)
                      ++|.++.+|..|...|...+.+
T Consensus        85 ~~s~~~~~a~~l~~~f~~~~~~  106 (107)
T smart00297       85 PDSEVYKDAKKLEKFFEKKLRE  106 (107)
T ss_pred             CCCHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999998875

>KOG0955|consensus

Probab=99.92  E-value=2.4e-25  Score=227.62  Aligned_cols=187  Identities=22%  Similarity=0.395  Sum_probs=164.8

Q ss_pred             CcccccchhhhhcccccchhHHhhccchHHHHHhhhhhHHHH--hhhhHHHHHHHH---HHHHhhHHHHHHH----HHHh
Q psy16435          1 MELEHFGWLVDSISSCQSTRIEKLKHSKEIERKLQKQKEEET--RRHQEEEERLEE---EWRKHKAARERQR----RIEN   71 (277)
Q Consensus         1 ~~~~~~~W~~kr~~r~g~~llkr~~~~~~~e~~~~~~~~~~~--~~~~e~~~~~~e---~~~~~r~~~er~R----~~rk   71 (277)
                      |+++|+||++||..|.|+||+++||+      +.+++++.++  ++.+.+..++.+   +|+.|++++++.+    +.++
T Consensus       470 ~~~i~~~w~~kR~~r~g~pLl~~lq~------~~~s~rn~~~~~~~~D~~~~~~~d~~k~~~~L~~~~~s~~~l~e~~r~  543 (1051)
T KOG0955|consen  470 MDRICKYWYLKRLSRNGAPLLGRLQS------LSKSSRNKEQVGREGDLKNKARVDSLKYWQALRLDLESAQLLVELTRK  543 (1051)
T ss_pred             hhhhhhhHHHHHHhhCCcchhhhhhh------hhhccccchhcccccCccchhhhHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            56899999999999999999999987      7888888887  455666666655   8999999999999    7888


Q ss_pred             hhccCCCCCccCcCCcCcccccccCCCCCCCCCChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcH
Q psy16435         72 RERGSRSNSEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDL  151 (277)
Q Consensus        72 Re~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL  151 (277)
                      |++.++.+.....               ..+..+..++...|..+++.|...+....|..||+..++|||+++|++||||
T Consensus       544 r~~lk~~~~~~~~---------------~~~~~~l~p~~kLl~~~l~~lq~kD~~gif~~pvd~~e~pdy~~iik~pmd~  608 (1051)
T KOG0955|consen  544 REKLKRILVKSQK---------------EALELGLNPFKKLLQKSLDKLQKKDSYGIFAEPVDPSELPDYIDIIKKPMDF  608 (1051)
T ss_pred             HHHHHHHHhchhh---------------hhhcccCchHHHHHHHHHHHhhcccccCceeeccChhhcccHHHHhcCccch
Confidence            9999887655431               1122244578889999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHHHHHHh
Q psy16435        152 TRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       152 ~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      .+|+.++.+|.|.++++|..|+.+|+.||+.||..++.+|++|.+++......+...
T Consensus       609 ~t~~~kl~s~~y~tle~ieed~~l~~~nc~~yn~~dtv~~r~av~~~e~~~~~~~~a  665 (1051)
T KOG0955|consen  609 FTMRLKLESGAYSTLEPIEEDVNLIVSNCMEYNAKDTVYYRAAVRLRELIKKDFRNA  665 (1051)
T ss_pred             hhhhhhccccchhhhhHHHHhHhHhHhHHHHhhccCeehHhhhHHHHhhhhhHHHhc
Confidence            999999999999999999999999999999999999999999999999888877665

>cd05521 Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi

Probab=99.91  E-value=2.4e-24  Score=168.76  Aligned_cols=95  Identities=21%  Similarity=0.308  Sum_probs=87.9

Q ss_pred             HHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhh
Q psy16435        109 LRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRK  182 (277)
Q Consensus       109 l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~  182 (277)
                      |...|..+++.|.....      +.+|..+|+...+||||++|++||||+||++||.+  |.|+.+|.+||.|||.||+.
T Consensus         2 l~~~~~~l~~~i~~~~~~~g~~~~~~F~~lp~~~~~pdYy~iI~~PmdL~tI~~kl~~--Y~s~~ef~~D~~li~~Na~~   79 (106)
T cd05521           2 LSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARL   79 (106)
T ss_pred             HHHHHHHHHHHHHhhcCcCCCCchHhhhcCCccccCccHHHHhcCCCCHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHH
Confidence            56778888888877655      46999999999999999999999999999999998  99999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHH
Q psy16435        183 YNGLDNEYTDMVRRLQQIFRDAV  205 (277)
Q Consensus       183 YN~~~s~i~~~A~~L~~~f~~~~  205 (277)
                      ||+++|.+|.+|..|+++|...+
T Consensus        80 yN~~~s~i~~~A~~le~~~~~~~  102 (106)
T cd05521          80 YNTKGSVIYKYALILEKYINDVI  102 (106)
T ss_pred             HcCCCCHHHHHHHHHHHHHHHhh
Confidence            99999999999999999998865

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.

>cd05522 Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi

Probab=99.91  E-value=2.1e-24  Score=168.69  Aligned_cols=95  Identities=25%  Similarity=0.449  Sum_probs=86.3

Q ss_pred             HHHHHHHHHHHHc------CCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhh
Q psy16435        110 RIGMHKVMNRLKS------HEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY  183 (277)
Q Consensus       110 ~~~l~~il~~l~~------~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~Y  183 (277)
                      .+.+..|++.|.+      ++.+.+|..+|+...+|+||++|++||||++|++||.+|.|.++.+|..||.|||.||+.|
T Consensus         3 ~~~~~~i~~~v~~~~d~~g~~l~~~F~~~p~~~~~pdYy~~I~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~y   82 (104)
T cd05522           3 EARIKNILKGLRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLY   82 (104)
T ss_pred             HHHHHHHHHHHHHHhCcCCCcccHHHhcCCCccccCcHHHHhCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHH
Confidence            3455666666655      4458899999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHH
Q psy16435        184 NGLDNEYTDMVRRLQQIFRDA  204 (277)
Q Consensus       184 N~~~s~i~~~A~~L~~~f~~~  204 (277)
                      |+++|.+|.+|..|++.|...
T Consensus        83 n~~~s~i~~~A~~l~~~f~~l  103 (104)
T cd05522          83 NENDSQEYKDAVLLEKEARLL  103 (104)
T ss_pred             CCCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999999863

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.

>PF00439 Bromodomain: Bromodomain; InterPro: IPR001487 Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins []

Probab=99.90  E-value=1.2e-23  Score=157.54  Aligned_cols=84  Identities=38%  Similarity=0.722  Sum_probs=80.0

Q ss_pred             HHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHH
Q psy16435        113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTD  192 (277)
Q Consensus       113 l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~  192 (277)
                      |..||+.|..++.+.+|..||+...+|+|+.+|++||||++|++||.+|.|.++.+|..||.+||.||+.||+++|.+|.
T Consensus         1 C~~il~~l~~~~~~~~F~~~~~~~~~p~y~~~i~~P~dL~~I~~kl~~~~Y~s~~~f~~Dv~~i~~Na~~yn~~~s~~~~   80 (84)
T PF00439_consen    1 CREILEELMKHPISSPFSKPVDPKEYPDYYEIIKNPMDLSTIRKKLENGKYKSIEEFEADVRLIFQNARRYNPPDSPIYK   80 (84)
T ss_dssp             HHHHHHHHHTSTTGGGGSSSTHTTTSTTHHHHSSSS--HHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHHHSCTTSHHHH
T ss_pred             CHHHHHHHHcCCCchhhcCCCChhhCCCHHHHHhhccchhhhhHHhhccchhhHHHHHHHHHHHHHHHHHHCCCcCHHHH
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHH
Q psy16435        193 MVRR  196 (277)
Q Consensus       193 ~A~~  196 (277)
                      +|.+
T Consensus        81 ~A~~   84 (84)
T PF00439_consen   81 AAEK   84 (84)
T ss_dssp             HHHH
T ss_pred             HhcC
Confidence            9963

Bromodomains can interact with acetylated lysine []. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate. The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [].; GO: 0005515 protein binding; PDB: 3P1C_A 4A9K_B 3SVH_A 3P1E_B 3P1F_A 1JSP_B 2L85_A 3P1D_B 3DWY_B 2D82_A ....

>cd04369 Bromodomain Bromodomain

Probab=99.89  E-value=3.9e-23  Score=157.64  Aligned_cols=95  Identities=36%  Similarity=0.702  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHHHcC--CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        110 RIGMHKVMNRLKSH--EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       110 ~~~l~~il~~l~~~--~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      ...|..+++.|..+  +.+.+|..||+...+|+||.+|++||||++|+.||.+|.|.++.+|..||.+||.||+.||+++
T Consensus         2 ~~~~~~i~~~l~~~~~~~~~~F~~~~~~~~~~~Y~~~i~~P~~l~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~~n~~~   81 (99)
T cd04369           2 KKKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPG   81 (99)
T ss_pred             HHHHHHHHHHHHhhcccccHHHhcCCChhcCCCHHHHHhCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            35688999999999  9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHH
Q psy16435        188 NEYTDMVRRLQQIFRDA  204 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~  204 (277)
                      |.++.+|..|...|...
T Consensus        82 ~~~~~~a~~l~~~~~~~   98 (99)
T cd04369          82 SPIYKDAKKLEKLFEKL   98 (99)
T ss_pred             CHHHHHHHHHHHHHHHh
Confidence            99999999999999875

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

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.88  E-value=1.9e-22  Score=158.37  Aligned_cols=97  Identities=22%  Similarity=0.316  Sum_probs=87.9

Q ss_pred             HHHHHHHHHHc-CCCCCCCCCCCCC-----CCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        112 GMHKVMNRLKS-HEDAWPFCDPVDE-----ATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       112 ~l~~il~~l~~-~~~s~~F~~pv~~-----~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      .|..++..++. .+.+.||..||..     ..+|+||.+|++||||+||++||++|.|.++++|..||.|||+||..||+
T Consensus         4 ~L~f~~~~~k~~lp~~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~N~~~yNg   83 (109)
T cd05492           4 LLKFIVSRMKSWLPPDTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHG   83 (109)
T ss_pred             hHHHHHHHHHhcCcccccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            46677788887 6778999999952     25999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHh
Q psy16435        186 LDNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      ++|.++.+|..|..-....+.++
T Consensus        84 ~~s~~~~~A~~l~~d~~~el~Ei  106 (109)
T cd05492          84 ADSEQYDAARWLYRDTCHDLREL  106 (109)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999888877765

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.

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.86  E-value=1.5e-21  Score=152.88  Aligned_cols=100  Identities=19%  Similarity=0.308  Sum_probs=92.2

Q ss_pred             HHHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhh
Q psy16435        108 DLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCR  181 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~  181 (277)
                      -++..+..|+..+++|.+      +.+|+++|+  ..|+||.+|+.||||++|+.||.+|.|.++++|..||.+||.||+
T Consensus         3 ~vq~~l~~l~~~V~~~~D~~Gr~~s~~f~~LP~--~~~~~~~~ik~Pi~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NAr   80 (110)
T cd05526           3 LVQELLATLFVSVMNHQDEEGRCYSDSLAELPE--LAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR   80 (110)
T ss_pred             HHHHHHHHHHHHHHhccCCCCCCchHHHHHCCC--cccCchhhhcCCccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHHH
Confidence            467788899999998865      779999998  567889999999999999999999999999999999999999999


Q ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q psy16435        182 KYNGLDNEYTDMVRRLQQIFRDAVSRYL  209 (277)
Q Consensus       182 ~YN~~~s~i~~~A~~L~~~f~~~~~~~~  209 (277)
                      .||.++|.+|.+|..|+++|.....++.
T Consensus        81 ~yN~~~S~iy~dA~eLq~~f~~~rd~~~  108 (110)
T cd05526          81 RLSRTDSEIYEDAVELQQFFIKIRDELC  108 (110)
T ss_pred             HhCcccCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999887764

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.

>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

Probab=99.79  E-value=2.2e-19  Score=169.56  Aligned_cols=89  Identities=34%  Similarity=0.574  Sum_probs=85.1

Q ss_pred             CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHH
Q psy16435        124 EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD  203 (277)
Q Consensus       124 ~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f~~  203 (277)
                      ..+.+|..+|++..+|+||.||+.||||.+|+++|+++.|.++.+|..||+|||.||.+||+++|.+|.+|..|++.|..
T Consensus       164 ~~s~~F~~~p~k~~~PdYy~iIk~Pm~L~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~~~~  243 (371)
T COG5076         164 FLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLK  243 (371)
T ss_pred             ccccccccCCccccCCChheeecchhhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHHHHHHH
Confidence            44889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccc
Q psy16435        204 AVSRYLDGE  212 (277)
Q Consensus       204 ~~~~~~~~~  212 (277)
                      .+..+....
T Consensus       244 ~i~~~~~~~  252 (371)
T COG5076         244 LIEEIPEEM  252 (371)
T ss_pred             HHHhccccc
Confidence            999886654

>KOG1245|consensus

Probab=99.77  E-value=3.3e-19  Score=188.90  Aligned_cols=97  Identities=34%  Similarity=0.693  Sum_probs=94.1

Q ss_pred             HHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHH
Q psy16435        113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTD  192 (277)
Q Consensus       113 l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~  192 (277)
                      |..||..|..|+.||||++||+...+||||+||++||||+||+.|+..|.|.++.+|..||.|||.||.+||.. |.+++
T Consensus      1306 ~e~il~e~~~~~~awPFlepVn~~~vp~Y~~IIk~Pmdl~tir~k~~~~~Y~~~eef~~Di~lvf~Nc~~yN~~-s~i~~ 1384 (1404)
T KOG1245|consen 1306 CEDILHELVVHKAAWPFLEPVNPKEVPDYYDIIKKPMDLSTIREKLSKGIYPSPEEFATDIELVFDNCETYNED-SEIGR 1384 (1404)
T ss_pred             HHHHHHHHHHhhhcchhhccCChhhcccHHHHhcChhHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHhccc-hhhhh
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHHHHHHhhc
Q psy16435        193 MVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       193 ~A~~L~~~f~~~~~~~~~  210 (277)
                      +...|.++|...|...++
T Consensus      1385 ag~~l~~ff~~~~~~~~~ 1402 (1404)
T KOG1245|consen 1385 AGTCLRRFFHKRWRKKFP 1402 (1404)
T ss_pred             hcchHHHHHHHHHHhhcC
Confidence            999999999998877654

>KOG1472|consensus

Probab=99.63  E-value=2.6e-16  Score=156.09  Aligned_cols=103  Identities=34%  Similarity=0.713  Sum_probs=98.5

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      .+...+..+|..|..|..+|||.+||+..++||||.+|++||||.||+.+|.++.|..+..|+.|+..||.||+.||+.+
T Consensus       606 ~~~s~~~~il~~l~~h~~awPf~~Pv~~~e~pdyy~~I~~pmDl~tM~~~l~~~~y~~~~~f~ad~~~vf~ncr~yn~~~  685 (720)
T KOG1472|consen  606 KLFSAIQNILDQLQNHGDAWPFLKPVNKKEVPDYYDVIKHPMDLRTMQNRLKDNQYTEVELFMADVVRVFANCRMYNGSD  685 (720)
T ss_pred             hhhHHHHhHHhhhhcCCccCCccCccccccCCcHHHHhcccccHHHHhhhccccchhhHHHHHHHHHHHHhhhhccCCcc
Confidence            56778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        188 NEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      +.+|+.|..|..+|...+...+.
T Consensus       686 ~~y~k~~~~le~~~~~k~~~~i~  708 (720)
T KOG1472|consen  686 TQYYKCAQALEKFFLFKLNELIL  708 (720)
T ss_pred             chheecccchhhhhcchhhhhhh
Confidence            99999999999999998887643

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=99.33  E-value=1.2e-12  Score=103.85  Aligned_cols=76  Identities=24%  Similarity=0.335  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCC--CCCcchhhhccCCCcHHHHHHHHhCCCCCCHH-------HHHHHHHHHHHhh
Q psy16435        110 RIGMHKVMNRLKSHEDAWPFCDPVDE--ATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFG-------QFRADFQLIVDNC  180 (277)
Q Consensus       110 ~~~l~~il~~l~~~~~s~~F~~pv~~--~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~-------~f~~Dv~lm~~Na  180 (277)
                      ...|..+|..+..++.++||..||++  ..+||||++|++||||+||+.+|.++.+++..       .+.+++..+..||
T Consensus         5 ~~~~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (114)
T cd05494           5 LERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGRR   84 (114)
T ss_pred             HHHHHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHcccccccccccccccccccccccccccc
Confidence            34566777777778899999999999  78999999999999999999999997553333       3344444444444


Q ss_pred             hhhcC
Q psy16435        181 RKYNG  185 (277)
Q Consensus       181 ~~YN~  185 (277)
                      ..+|.
T Consensus        85 ~~~~~   89 (114)
T cd05494          85 SPSNI   89 (114)
T ss_pred             Ccccc
Confidence            44443

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

>KOG1827|consensus

Probab=99.25  E-value=1.2e-11  Score=121.55  Aligned_cols=101  Identities=26%  Similarity=0.406  Sum_probs=90.0

Q ss_pred             HHHHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhh
Q psy16435        107 EDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNC  180 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na  180 (277)
                      ..+...+..+|..+..+.+      ...|.+.++....|+||.+|..||+|..|+.|+..+.|.+++.|..||.||+.||
T Consensus        51 ~~~~~~f~~il~~~~~~~d~~gk~~~d~feklp~~~~~p~yy~~i~~pisl~~ik~kv~k~~y~~~~~f~~D~~lm~ena  130 (629)
T KOG1827|consen   51 PPLIPKFKTILASLLDLKDDEGKQLFDKFEKLPSRKEFPEYYYVIQQPISLDQIKRKVKKGRYKRLSFFQLDFLLMTENA  130 (629)
T ss_pred             hHHHHHHHHHHHHHHhhccccCcccchhHhhccccccCCCcceeecCcccHHHHHHHHHhcccccHHHHHHHHHHHHHHH
Confidence            3455666677777765533      6799999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHH
Q psy16435        181 RKYNGLDNEYTDMVRRLQQIFRDAVSR  207 (277)
Q Consensus       181 ~~YN~~~s~i~~~A~~L~~~f~~~~~~  207 (277)
                      ..||.++|.+|++|..|+..|.....+
T Consensus       131 ~~~n~~ds~~~~~s~~l~~~~~~~~~~  157 (629)
T KOG1827|consen  131 RLYNRPDSLIYKDSGELEKYFISLEDE  157 (629)
T ss_pred             HHhcCcchhhhhhhhhhhcchhhhhcc
Confidence            999999999999999999999886654

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=99.19  E-value=1.6e-11  Score=96.83  Aligned_cols=42  Identities=31%  Similarity=0.432  Sum_probs=40.0

Q ss_pred             CCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCC
Q psy16435        147 RPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDN  188 (277)
Q Consensus       147 ~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s  188 (277)
                      .||||+||.+||.+|.|.++.+|++||+|||.||..||+++.
T Consensus        63 y~MDL~tIe~RL~ng~Y~tp~~F~~DiklI~~Nc~~ynd~dr  104 (119)
T cd05491          63 YNMDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKTIGDRER  104 (119)
T ss_pred             eccCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCHHH
Confidence            589999999999999999999999999999999999998754

TBP7, or TAT-binding protein homolog 7, is a yeast protein of unknown function that contains AAA-superfamily ATP-ase domains and a bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

>KOG0008|consensus

Probab=99.16  E-value=3.2e-11  Score=124.81  Aligned_cols=99  Identities=28%  Similarity=0.650  Sum_probs=90.8

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHH
Q psy16435        111 IGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEY  190 (277)
Q Consensus       111 ~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i  190 (277)
                      ..+-.++.+++..+.+|+|.+||+++.+|+||.+|++||||.+|.+++..+.|.+..+|..||++|+.||..||+..+.+
T Consensus      1385 ~~~d~~vs~~~~ipes~~f~~~v~~k~~~~yy~kik~pmdl~~i~~n~~~~~y~s~~e~l~dv~~i~~n~~~~ng~e~~y 1464 (1563)
T KOG0008|consen 1385 FILDNIVSQMKEIPESWPFHEPVNKKRVPDYYKKIKNPMDLETILKNIPPHKYDSRSEFLDDVNLIYVNSVEYNGAESAY 1464 (1563)
T ss_pred             hhhhhHHHHHHhcchhcccccccchhhchHHHHHhcChhhHHHHhhcCCccccccHHHHhhhhHhhcccceeecCccccc
Confidence            55677888888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhh
Q psy16435        191 TDMVRRLQQIFRDAVSRYL  209 (277)
Q Consensus       191 ~~~A~~L~~~f~~~~~~~~  209 (277)
                      ..-|+.+-.+....+.+.+
T Consensus      1465 ~~k~~k~~ev~~~~~~e~~ 1483 (1563)
T KOG0008|consen 1465 TKKARKIGEVGLANLLEYI 1483 (1563)
T ss_pred             cHHHHHHHHHHHHHHHHHH
Confidence            9998888877777666543

>KOG0386|consensus

Probab=99.14  E-value=8.7e-11  Score=119.20  Aligned_cols=100  Identities=22%  Similarity=0.397  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHHcC------CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        111 IGMHKVMNRLKSH------EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       111 ~~l~~il~~l~~~------~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      ..|..|+.....+      ..+..|...++...+||||.||+.||++..|.++|.++.|.+..+...||.++|.||.+||
T Consensus      1027 ~~~~~i~~~~~~~~~~~~r~~~~~~~~~~s~k~~~d~~~~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~na~~~~ 1106 (1157)
T KOG0386|consen 1027 KQALKIASTSIKYKDSAGRELSEVFLKLPSRKEYPDYYEIIKKPVAIDKIKKRIENHKYNSLKELEKDFMLLFNNARTYN 1106 (1157)
T ss_pred             HHHHHHHHHHHhcccccccccchhcccCcccccccchHHHhcchhhHHHHhhhccccccchHHHHHHHHHhhcchhhhhc
Confidence            3466677666644      4478999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      ..+|.+|.+|..|+.+|......+..
T Consensus      1107 ~egs~~y~d~~~l~~~~~~~~~~~~~ 1132 (1157)
T KOG0386|consen 1107 EEGSRVYEDAIVLQSVFKSARQEISK 1132 (1157)
T ss_pred             cCCceechhHHHHHHHHhhhHHHHhc
Confidence            99999999999999999999888865

>KOG0008|consensus

Probab=98.97  E-value=8.7e-10  Score=114.42  Aligned_cols=99  Identities=25%  Similarity=0.460  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      -+...+..|++++.......+|..||+.+.++|||.||+.||+|.++++.+....|.+-++|..|+.||+.|..+||++.
T Consensus      1261 ~~ss~l~~i~n~~~~~~~t~~f~~Pv~~k~v~dyy~vi~~P~~lq~~kk~v~kr~y~~r~~fle~~~~~~~ns~~yng~~ 1340 (1563)
T KOG0008|consen 1261 SLSSILETIINQARSSPNTYPFPTPVNAKEVKDYYRVITPPMDLQTQKKLVRKRLYESREHFLEELPLIVSNSTKYNGPL 1340 (1563)
T ss_pred             ecccchHHHHHHHhcCCCCcCCCCccchhhccchhhccCCCcchHHHHHHHHHHHHHHHHHHHHHhHHHhhchhhhcCch
Confidence            44667889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHH
Q psy16435        188 NEYTDMVRRLQQIFRDAVS  206 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~  206 (277)
                      +.+...+..+...+-..|.
T Consensus      1341 ~~~t~~~q~mls~~~~~~~ 1359 (1563)
T KOG0008|consen 1341 ASLTRQQQSMLSLCFEKLK 1359 (1563)
T ss_pred             HHHHHHHHHHHHHHHHhhc
Confidence            9999988877665544443

>KOG1472|consensus

Probab=98.90  E-value=1.8e-09  Score=107.79  Aligned_cols=82  Identities=37%  Similarity=0.558  Sum_probs=71.8

Q ss_pred             ChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       105 ~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      ..+.+...+.       .+..+++|..+|+...+|+||.||+.||||+++.+|+..+.|.+.+.|+.|+.+||.||..||
T Consensus       290 ~~~~~~~~~~-------~~~~s~~~~~kvs~~~a~~y~~i~k~pmdl~t~~~k~~~~~y~~~~~fv~d~~~~~~n~~~~n  362 (720)
T KOG1472|consen  290 GQEELYEAAE-------RTEHSTPFLEKVSKEDAPNYYQIIKAPMDLSTELKKLKSGPYCSKEEFVNDLMLIWRNCEKYN  362 (720)
T ss_pred             cCHHHHHHhc-------ccccccccccCCChhhCcchHHhhhcchHHHHHHHHhccccccchhHHHHHHHHHHhcchhhc
Confidence            3445555544       478899999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHH
Q psy16435        185 GLDNEYTDM  193 (277)
Q Consensus       185 ~~~s~i~~~  193 (277)
                      ...+.....
T Consensus       363 ~ee~~~~~~  371 (720)
T KOG1472|consen  363 SEESHGLIE  371 (720)
T ss_pred             cccchhhhh
Confidence            877654433

>KOG1828|consensus

Probab=98.77  E-value=1.2e-09  Score=101.18  Aligned_cols=99  Identities=25%  Similarity=0.285  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      ++..-...++..+-..+.-..|.-||.....|+|.+||+.|||+.||+.|++.+.|.++.+|..|..+|..||..||..+
T Consensus        19 p~~~~~ehhlrkl~sKdp~q~fafplt~~map~y~~iis~Pmd~~t~r~kidd~~yl~L~~m~~d~kl~~~na~~yn~~~   98 (418)
T KOG1828|consen   19 PDSGDAEHHLRKLPSKDPKQKFAFPLTDKMAPNYLEIISEPMDRITKRSKIDDTRYLVLSQMEFDRKLPDGNATLYNLHP   98 (418)
T ss_pred             cchhhHHHHHHhccccChhhhhccccchhhccchHhhhhcccccccccccCCCccceechhhhhhhcccccchhhhhcCC
Confidence            33444567777888888899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHH
Q psy16435        188 NEYTDMVRRLQQIFRDAVS  206 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~  206 (277)
                      +.++..|.+|..+-.....
T Consensus        99 Tv~~~aaKrL~~v~~~~~q  117 (418)
T KOG1828|consen   99 TVPIVAAKRLCPVRLGMTQ  117 (418)
T ss_pred             ccccccccccchhhcchhh
Confidence            9999999999887665554

>KOG1828|consensus

Probab=98.65  E-value=1.5e-08  Score=93.85  Aligned_cols=89  Identities=15%  Similarity=0.116  Sum_probs=81.4

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCH
Q psy16435        110 RIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNE  189 (277)
Q Consensus       110 ~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~  189 (277)
                      ...+-....++...+...+|..+|....+|.|..+|++|+++.|+..|..++.|.| -+|..|+.||+.||++||.++..
T Consensus       210 ~~l~~~q~~kl~~~~p~~~lnyg~tas~aP~YSm~Ik~~~~~~Tygdk~~andy~S-~~f~~D~kl~~l~amT~gehsk~  288 (418)
T KOG1828|consen  210 QQLQTLQEDKLNRVDPVAYLNYGPTASFAPGYSMTITEVEPPGTYGDKSSANDYES-LSFTQDRKLIALKAVTNGEHSKS  288 (418)
T ss_pred             HHHHHHHHHHhcccCchhhhcccchhhhcccccccccccCCCcchhhhhhhhhhhh-hhhhcccchhhHHHHhcCCcchH
Confidence            34455667788888899999999999999999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHHHHHH
Q psy16435        190 YTDMVRRLQQ  199 (277)
Q Consensus       190 i~~~A~~L~~  199 (277)
                      +|..|..+..
T Consensus       289 yyelank~lh  298 (418)
T KOG1828|consen  289 YYELANKQLH  298 (418)
T ss_pred             HHHHHHhhhh
Confidence            9999987765

>KOG1474|consensus

Probab=98.49  E-value=3e-08  Score=99.94  Aligned_cols=92  Identities=32%  Similarity=0.640  Sum_probs=84.0

Q ss_pred             HHcCCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHH
Q psy16435        120 LKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRL  197 (277)
Q Consensus       120 l~~~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L  197 (277)
                      +..|..+++|..||+..  ..|+||.+|.+|||+.+|..++.+.+|.+..+..+||..+|.||..||.+.-.++.++..+
T Consensus         4 ~~~~~~~~~f~~~v~~v~l~~~~~~~~~~~~~d~~~~~~~~e~n~~~~~~~~~~~f~~~~sn~~~~~~~~~~v~~~~~~~   83 (640)
T KOG1474|consen    4 ARKHKLAWPFLEPVDAVALNLPAYYEIIKRPMDIGTIEKRVENNYYFSASECIADFKTKFSNCYLFNDSGDDVVRMKQSL   83 (640)
T ss_pred             cccccccccccCccchhhccchhhhcccCCCCCchhhhhhhccCccccHhhhhhhccccccchhcccCCccchhhccccc
Confidence            45678899999999965  5799999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcc
Q psy16435        198 QQIFRDAVSRYLDG  211 (277)
Q Consensus       198 ~~~f~~~~~~~~~~  211 (277)
                      ...|.+.+..++..
T Consensus        84 ~~~~~~~~~~~~~~   97 (640)
T KOG1474|consen   84 EKLFPKKLRSMPSD   97 (640)
T ss_pred             hhhccccccccccc
Confidence            99998877766443

>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

Probab=97.45  E-value=3.7e-05  Score=72.94  Aligned_cols=93  Identities=32%  Similarity=0.607  Sum_probs=83.5

Q ss_pred             HHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHH
Q psy16435        115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMV  194 (277)
Q Consensus       115 ~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A  194 (277)
                      .++.....+-.+|+|..+++....|+|+++|..+|++++..-++..+.|.....|..|..+++.||..||+....++..+
T Consensus       270 ~~i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  349 (371)
T COG5076         270 VLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNA  349 (371)
T ss_pred             hcccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhc
Confidence            33444466677999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q psy16435        195 RRLQQIFRDAVSR  207 (277)
Q Consensus       195 ~~L~~~f~~~~~~  207 (277)
                      ..+...+...+.-
T Consensus       350 ~~~~~~~~~~~~~  362 (371)
T COG5076         350 NVLEDFVIKKTRL  362 (371)
T ss_pred             cchhhhHhhhhhh
Confidence            9888888776553

>cd05493 Bromo_ALL-1 Bromodomain, ALL-1 like proteins

Probab=96.81  E-value=0.003  Score=51.07  Aligned_cols=66  Identities=21%  Similarity=0.289  Sum_probs=54.1

Q ss_pred             CCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHHHHHHhhcccC
Q psy16435        148 PMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGER  213 (277)
Q Consensus       148 PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~  213 (277)
                      |.||..|++|+..|.|.++.+|.+||-.|+.-++.=.+....+-++-..+..+|-+.+..+++...
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~vf~Wf~  124 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFN  124 (131)
T ss_pred             cccHHHHHHHHhccceehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHhccccc
Confidence            889999999999999999999999999999988866554455555555667788888888877643

ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

>KOG0644|consensus

Probab=95.90  E-value=0.0053  Score=62.58  Aligned_cols=61  Identities=16%  Similarity=0.373  Sum_probs=53.1

Q ss_pred             ccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHHHH
Q psy16435        145 IKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV  205 (277)
Q Consensus       145 Ik~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f~~~~  205 (277)
                      ...|.+|..|+.+|++.+|++++.|.+|+..|.+||.+|.+.+--+...+..|..+|...+
T Consensus      1050 fpvpls~evi~~rlEn~yYrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~Tl 1110 (1113)
T KOG0644|consen 1050 FPVPLSLEVIRSRLENNYYRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRTL 1110 (1113)
T ss_pred             CCCcccHHHHHHHHHhhhhhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhhhc
Confidence            5678999999999999999999999999999999999999888777777777777775543

>KOG0732|consensus

Probab=92.13  E-value=0.17  Score=53.72  Aligned_cols=63  Identities=19%  Similarity=0.199  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCCC-----CcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHH--HHHHHHHhhhhhcCCC
Q psy16435        125 DAWPFCDPVDEAT-----APNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA--DFQLIVDNCRKYNGLD  187 (277)
Q Consensus       125 ~s~~F~~pv~~~~-----~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~--Dv~lm~~Na~~YN~~~  187 (277)
                      .+..|-.|++...     +++|-.+|++|||+...-.++..+.|.++.+|..  ++.|||.|++.||+..
T Consensus       532 ~~~~~s~Pl~~~~~~ll~~~~~~~~iq~~~~va~~~~k~~e~~~~~v~~~e~~~~i~lic~~~lli~~~~  601 (1080)
T KOG0732|consen  532 SSVIFSRPLSTYLKPLLPFQDALEDIQGLMDVASSMAKIEEHLKLLVRSFESNFAIRLICRPRLLINGGK  601 (1080)
T ss_pred             cccCCCCCCCcceecccchHHHHHHhhcchhHHhhhhhHHHHhHHHHHhhhcccchhhhcCcHHhcCCCc
Confidence            3678888888653     5689999999999999999999999999999999  9999999999999876

>COG5141 PHD zinc finger-containing protein [General function prediction only]

Probab=91.65  E-value=0.064  Score=51.99  Aligned_cols=21  Identities=10%  Similarity=-0.140  Sum_probs=19.0

Q ss_pred             cccccchhhhhcccccchhHH
Q psy16435          2 ELEHFGWLVDSISSCQSTRIE   22 (277)
Q Consensus         2 ~~~~~~W~~kr~~r~g~~llk   22 (277)
                      -.+|+||.+||+++-|+||++
T Consensus       440 fdIckyw~mKR~~~~g~PL~~  460 (669)
T COG5141         440 FDICKYWEMKRKSEIGGPLVI  460 (669)
T ss_pred             hHHHHHHHHhhhhcCCCCcee
Confidence            368999999999999999984

>KOG1827|consensus

Probab=87.23  E-value=0.062  Score=53.88  Aligned_cols=77  Identities=9%  Similarity=-0.096  Sum_probs=70.7

Q ss_pred             CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHHH
Q psy16435        126 AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFR  202 (277)
Q Consensus       126 s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f~  202 (277)
                      ...|...++...+|.||.+++-||.+....+++..+.|.....|..|..++|.|+..||.....++..+..|.+...
T Consensus       213 Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~q~l~g~c~v~~~~~yi~~~p~~ls~~dv  289 (629)
T KOG1827|consen  213 IERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLVQRLLGKCYVMKPTEYISGDPENLSEEDV  289 (629)
T ss_pred             ecccccCcccccccceeEeeCCccCccccccchhcccceecccccccHHHHhhcceEEeehhHhhhcCcccccccce
Confidence            45788888989999999999999999999999999999999999999999999999999999999999887766543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	277
3nxb_A	116	Crystal Structure Of The Bromodomain Of Human Cecr2		6e-23
1e6i_A	121	Bromodomain From Gcn5 Complexed With Acetylated H4		2e-17
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		6e-17
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		7e-17
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		1e-16
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		1e-16
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		1e-16
1f68_A	103	Nmr Solution Structure Of The Bromodomain From Huma		1e-16
3d7c_A	112	Crystal Structure Of The Bromodomain Of Human Gcn5,		2e-16
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		2e-15
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		3e-15
2f6j_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		3e-15
3g0l_A	117	Crystal Structure Of Human Bromodomain Adjacent To		2e-13
2e7o_A	112	Solution Structure Of The Bromodomain From Human Br		3e-13
2wp1_A	126	Structure Of Brdt Bromodomain 2 Bound To An Acetyla		9e-13
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		2e-12
2ouo_A	130	Crystal Structure Of The Bromo Domain 2 In Human Br		2e-12
2lsp_B	128	Solution Structures Of Brd4 Second Bromodomain With		3e-12
2i8n_A	114	Solution Structure Of The Second Bromodomain Of Brd		3e-12
2d9e_A	121	Solution Structure Of The Bromodomain Of Peregrin L		6e-12
3jvl_A	120	Crystal Structure Of Bromodomain 2 Of Mouse Brd4 Le		6e-12
2oo1_A	113	Crystal Structure Of The Bromo Domain 2 Of Human Br		6e-12
2e7n_A	117	Solution Structure Of The Second Bromodomain From H		7e-12
3oni_A	114	Crystal Structure Of The Second Bromodomain Of Huma		2e-11
2dvv_A	112	Crystal Structure Of The Second Bromodomain Of The		2e-11
2g4a_A	116	Solution Structure Of A Bromodomain From Ring3 Prot		2e-11
3hmh_A	155	Crystal Structure Of The Second Bromodomain Of Huma		1e-10
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		1e-10
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		2e-10
3hme_A	123	Crystal Structure Of Human Bromodomain Containing 9		2e-10
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		2e-10
3uv4_A	158	Crystal Structure Of The Second Bromodomain Of Huma		2e-10
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		8e-10
2ydw_A	153	Crystal Structure Of The First Bromodomain Of Human		8e-10
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		2e-09
2nxb_A	123	Crystal Structure Of Human Bromodomain Containing P		2e-09
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		2e-09
2dww_A	114	Crystal Structure Of Bromodomain-Containing Protein		2e-09
2wp2_A	120	Structure Of Brdt Bromodomain Bd1 Bound To A Diacet		3e-09
2yyn_A	135	Crystal Sturcture Of Human Bromodomain Protein Leng		6e-09
3o33_A	184	Crystal Structure Of Trim24 Phd-Bromo In The Free S		8e-09
3jvj_A	131	Crystal Structure Of The Bromodomain 1 In Mouse Brd		9e-09
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		9e-09
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		9e-09
2oss_A	127	Crystal Structure Of The Bromo Domain 1 In Human Br		1e-08
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		1e-08
3aqa_A	128	Crystal Structure Of The Human Brd2 Bd1 Bromodomain		1e-07
1x0j_A	122	Crystal Structure Analysis Of The N-Terminal Bromod		2e-07
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		3e-07
3dai_A	130	Crystal Structure Of The Bromodomain Of The Human A		3e-07
3i3j_A	124	Crystal Structure Of The Bromodomain Of Human Ep300		7e-07
3dwy_A	119	Crystal Structure Of The Bromodomain Of Human Crebb		8e-07
1jsp_B	121	Nmr Structure Of Cbp Bromodomain In Complex With P5		9e-07
3u5m_A	207	Crystal Structure Of Trim33 Phd-Bromo In The Free S		9e-07
2i7k_A	117	Solution Structure Of The Bromodomain Of Human Brd7		1e-06
3lxj_A	136	Crystal Structure Of The Bromodomain Of Human Aaa D		2e-06
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		3e-06
3k2j_A	130	Crystal Structure Of The 3rd Bromodomain Of Human P		3e-06
2dkw_A	131	Solution Structure Of The Bromodomain Of Human Prot		8e-06
3fkm_X	166	Plasmodium Falciparum Bromodomain-Containing Protei		3e-05
2dat_A	123	Solution Structure Of The Bromodomain Of Human SwiS		1e-04
3mqm_A	126	Crystal Structure Of The Bromodomain Of Human Ash1l		1e-04
3iu5_A	116	Crystal Structure Of The First Bromodomain Of Human		2e-04
2ktb_B	121	Solution Structure Of The Second Bromodomain Of Hum		2e-04
2r0v_A	346	Structure Of The Rsc4 Tandem Bromodomain Acetylated		2e-04
2r10_A	361	Structure Of An Acetylated Rsc4 Tandem Bromodomain		3e-04
3ljw_A	120	Crystal Structure Of The Second Bromodomain Of Huma		3e-04
3hmf_A	116	Crystal Structure Of The Second Bromodomain Of Huma		3e-04

>pdb|3NXB|A Chain A, Crystal Structure Of The Bromodomain Of Human Cecr2 Length = 116

Iteration: 1
 Score =  104 bits (259), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 46/97 (47%), Positives = 69/97 (71%)
Query: 112 GMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
            M+KV++ +K+H+D+WPF +PVDE+ APNYY+ IK PMD++ ME+KL+ G Y T  +F  
Sbjct: 20  AMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVN 79
Query: 172 DFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
           D + +  NCRKYNG  +EYT M   L++ F  A+ ++
Sbjct: 80  DMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMKH 116

>pdb|1E6I|A Chain A, Bromodomain From Gcn5 Complexed With Acetylated H4 Peptide Length = 121

Iteration: 1
 Score = 85.9 bits (211), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 57/94 (60%)
Query: 112 GMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
            +  ++  L++H  AWPF  PV++   P+YY+ IK PMDL+ ME KL++ +Y+    F  
Sbjct: 17  AIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIY 76
Query: 172 DFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           D +L+ +NCR YNG +  Y     RL++ F + V
Sbjct: 77  DARLVFNNCRMYNGENTSYYKYANRLEKFFNNKV 110

>pdb|3QZS|A Chain A, Crystal Structure Of Bptf Bromo In Complex With Histone H4k16ac - Form I Length = 115

Iteration: 1
 Score = 84.3 bits (207), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 41/97 (42%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
           TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct: 11  TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 69
Query: 165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
              +F AD   I DNCR YN  D+ +      L+  F
Sbjct: 70  KLTEFVADMTAIFDNCRYYNPSDSPFYQCAEVLESFF 106

>pdb|3UV2|A Chain A, Crystal Structure Of The Bromodomain Of Human Nucleosome-Remodeling Factor Subunit Bptf Length = 126

Iteration: 1
 Score = 84.3 bits (207), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 41/97 (42%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
           TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct: 18  TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 76
Query: 165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
              +F AD   I DNCR YN  D+ +      L+  F
Sbjct: 77  KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 113

>pdb|3QZT|A Chain A, Crystal Structure Of Bptf Bromo In Complex With Histone H4k16ac - Form Ii Length = 115

Iteration: 1
 Score = 83.6 bits (205), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/97 (42%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
           TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct: 11  TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 69
Query: 165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
              +F AD   I DNCR YN  D+ +      L+  F
Sbjct: 70  KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 106

>pdb|2RI7|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain Y17e Mutant From Human Bptf In The H3(1-9)k4me2 Bound State Length = 174

Iteration: 1
 Score = 83.6 bits (205), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/97 (42%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
           TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct: 70  TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 128
Query: 165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
              +F AD   I DNCR YN  D+ +      L+  F
Sbjct: 129 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 165

>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex With Histone H4k12ac Peptide Length = 174

Iteration: 1
 Score = 83.6 bits (205), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/97 (42%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
           TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++    Y+
Sbjct: 70  TEKDYE-GLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 128
Query: 165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
              +F AD   I DNCR YN  D+ +      L+  F
Sbjct: 129 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFF 165

>pdb|1F68|A Chain A, Nmr Solution Structure Of The Bromodomain From Human Gcn5 Length = 103

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 38/95 (40%), Positives = 58/95 (61%)
Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           + L   +  ++ ++KSH  AWPF +PV ++ AP+YYE I+ P+DL  M E+L +  Y T 
Sbjct: 2   DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTR 61
Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
             F AD Q ++ NCR+YN  D+EY      L++ F
Sbjct: 62  KLFVADLQRVIANCREYNPPDSEYCRCASALEKFF 96

>pdb|3D7C|A Chain A, Crystal Structure Of The Bromodomain Of Human Gcn5, The General Control Of Amino-Acid Synthesis Protein 5-Like 2 Length = 112

Iteration: 1
 Score = 82.8 bits (203), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/95 (40%), Positives = 58/95 (61%)
Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           + L   +  ++ ++KSH  AWPF +PV ++ AP+YYE I+ P+DL  M E+L +  Y T 
Sbjct: 6   DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTR 65
Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
             F AD Q ++ NCR+YN  D+EY      L++ F
Sbjct: 66  KLFVADLQRVIANCREYNPPDSEYCRCASALEKFF 100

>pdb|3GG3|A Chain A, Crystal Structure Of The Bromodomain Of Human Pcaf Length = 119

Iteration: 1
 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 40/108 (37%), Positives = 59/108 (54%), Gaps = 4/108 (3%)
Query: 98  STGGYRSTE----EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTR 153
           S G  +S E    + L   +  ++ ++KSH+ AWPF +PV    AP YYE I+ PMDL  
Sbjct: 1   SMGKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKT 60
Query: 154 MEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
           M E+L    Y +   F AD Q +  NC++YN  ++EY      L++ F
Sbjct: 61  MSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFF 108

>pdb|1N72|A Chain A, Structure And Ligand Of A Histone Acetyltransferase Bromodomain Length = 118

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 52/89 (58%)
Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           +  ++ ++KSH+ AWPF +PV    AP YYE I+ PMDL  M E+L    Y +   F AD
Sbjct: 18  LKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMAD 77
Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
            Q +  NC++YN  ++EY      L++ F
Sbjct: 78  LQRVFTNCKEYNPPESEYYKCANILEKFF 106

>pdb|2F6J|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain Fragment Of Human Bptf In The H3(1-15)k4me3 Bound State Length = 174

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 39/97 (40%), Positives = 55/97 (56%), Gaps = 1/97 (1%)
Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
           TE+D   G+ +V+  L++H+ AWPF +PVD   AP+YY  IK P DL   EE++    Y+
Sbjct: 70  TEKDYE-GLKRVLRSLQAHKXAWPFLEPVDPNDAPDYYGVIKEPXDLATXEERVQRRYYE 128
Query: 165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
              +F AD   I DNCR YN  D+ +      L+  F
Sbjct: 129 KLTEFVADXTKIFDNCRYYNPSDSPFYQCAEVLESFF 165

>pdb|3G0L|A Chain A, Crystal Structure Of Human Bromodomain Adjacent To Zinc Finger Domain 2b (Baz2b) Length = 117

Iteration: 1
 Score = 72.4 bits (176), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 50/86 (58%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           ++  +++HEDAWPF  PV+    P Y + IK+PMD + + EKL +G+Y     F  D +L
Sbjct: 21  ILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRL 80
Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIF 201
           + DNC  +N  D++       +++ F
Sbjct: 81  VFDNCETFNEDDSDIGRAGHNMRKYF 106

>pdb|2E7O|A Chain A, Solution Structure Of The Bromodomain From Human Bromodomain Adjacent To Zinc Finger Domain 2b Length = 112

Iteration: 1
 Score = 72.0 bits (175), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 50/86 (58%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           ++  +++HEDAWPF  PV+    P Y + IK+PMD + + EKL +G+Y     F  D +L
Sbjct: 18  ILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRL 77
Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIF 201
           + DNC  +N  D++       +++ F
Sbjct: 78  VFDNCETFNEDDSDIGRAGHNMRKYF 103

>pdb|2WP1|A Chain A, Structure Of Brdt Bromodomain 2 Bound To An Acetylated Histone H3 Peptide Length = 126

Iteration: 1
 Score = 70.5 bits (171), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 35/78 (44%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 126 AWPFCDPVDEATAP--NYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
           AWPF +PVD       NYY+ +K PMDL  ++ K+D   YK   +F AD +L+  NC KY
Sbjct: 35  AWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKY 94
Query: 184 NGLDNEYTDMVRRLQQIF 201
           N  D+E   M R LQ +F
Sbjct: 95  NPPDHEVVAMARTLQDVF 112

>pdb|3RCW|A Chain A, Crystal Structure Of The Bromodomain Of Human Brd1 Length = 135

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 49/90 (54%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
           L + +  V+++L+  + A  F  PV     P+Y + IK PMD   M ++L+A  YK   +
Sbjct: 14  LTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHE 73
Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           F  DF LI+DNC KYN  D  +     RL+
Sbjct: 74  FEEDFDLIIDNCMKYNARDTVFYRAAVRLR 103

>pdb|2OUO|A Chain A, Crystal Structure Of The Bromo Domain 2 In Human Bromodomain Containing Protein 4 (Brd4) Length = 130

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 39/92 (42%), Positives = 54/92 (58%), Gaps = 2/92 (2%)
Query: 112 GMHKVMNRLKSHEDAWPFCDPVD-EATA-PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQF 169
           G+ K M   K    AWPF  PVD EA    +Y + IK PMD++ ++ KL+A  Y+   +F
Sbjct: 29  GILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEF 88
Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
            AD +L+  NC KYN  D+E   M R+LQ +F
Sbjct: 89  GADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 120

>pdb|2LSP|B Chain B, Solution Structures Of Brd4 Second Bromodomain With Nf-Kb-K310ac Peptide Length = 128

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 39/92 (42%), Positives = 54/92 (58%), Gaps = 2/92 (2%)
Query: 112 GMHKVMNRLKSHEDAWPFCDPVD-EATA-PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQF 169
           G+ K M   K    AWPF  PVD EA    +Y + IK PMD++ ++ KL+A  Y+   +F
Sbjct: 27  GILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEF 86
Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
            AD +L+  NC KYN  D+E   M R+LQ +F
Sbjct: 87  GADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 118

>pdb|2I8N|A Chain A, Solution Structure Of The Second Bromodomain Of Brd4 Length = 114

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 40/100 (40%), Positives = 57/100 (57%), Gaps = 2/100 (2%)
Query: 112 GMHKVMNRLKSHEDAWPFCDPVD-EATA-PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQF 169
           G+ K M   K    AWPF  PVD EA    +Y + IK PMD++ ++ KL+A  Y+   +F
Sbjct: 8   GILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEF 67
Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL 209
            AD +L+  NC KYN  D+E   M R+LQ +F    ++ L
Sbjct: 68  GADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKML 107

>pdb|2D9E|A Chain A, Solution Structure Of The Bromodomain Of Peregrin Length = 121

Iteration: 1
 Score = 67.8 bits (164), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 49/89 (55%)
Query: 111 IGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFR 170
           I + K + +L+  +    F +PV  +  P+Y + IK+PMD   M++ L+A RY  F  F 
Sbjct: 10  ILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFE 69
Query: 171 ADFQLIVDNCRKYNGLDNEYTDMVRRLQQ 199
            DF LIV NC KYN  D  +     RL++
Sbjct: 70  EDFNLIVSNCLKYNAKDTIFYRAAVRLRE 98

>pdb|3JVL|A Chain A, Crystal Structure Of Bromodomain 2 Of Mouse Brd4 Length = 120

Iteration: 1
 Score = 67.8 bits (164), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 38/92 (41%), Positives = 54/92 (58%), Gaps = 2/92 (2%)
Query: 112 GMHKVMNRLKSHEDAWPFCDPVD-EATA-PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQF 169
           G+ K M   K    AWPF  PVD EA    +Y + IK PMD++ ++ KL++  Y+   +F
Sbjct: 16  GILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEF 75
Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
            AD +L+  NC KYN  D+E   M R+LQ +F
Sbjct: 76  GADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 107

>pdb|2OO1|A Chain A, Crystal Structure Of The Bromo Domain 2 Of Human Bromodomain Containing Protein 3 (Brd3) Length = 113

Iteration: 1
 Score = 67.8 bits (164), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 126 AWPFCDPVDEATAP--NYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
           AWPF  PVD       +Y++ IK PMDL+ ++ K+D   Y     F AD +L+  NC KY
Sbjct: 28  AWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKY 87
Query: 184 NGLDNEYTDMVRRLQQIF 201
           N  D+E   M R+LQ +F
Sbjct: 88  NPPDHEVVAMARKLQDVF 105

>pdb|2E7N|A Chain A, Solution Structure Of The Second Bromodomain From Human Bromodomain-Containing Protein 3 Length = 117

Iteration: 1
 Score = 67.4 bits (163), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 126 AWPFCDPVDEATAP--NYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
           AWPF  PVD       +Y++ IK PMDL+ ++ K+D   Y     F AD +L+  NC KY
Sbjct: 33  AWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKY 92
Query: 184 NGLDNEYTDMVRRLQQIF 201
           N  D+E   M R+LQ +F
Sbjct: 93  NPPDHEVVAMARKLQDVF 110

>pdb|3ONI|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Brd2 In Complex With The Inhibitor Jq1 Length = 114

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%), Gaps = 2/78 (2%)
Query: 126 AWPFCDPVDEATAP--NYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
           AWPF  PVD +     +Y++ IK PMDL+ ++ K++   Y+   +F AD +L+  NC KY
Sbjct: 28  AWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKY 87
Query: 184 NGLDNEYTDMVRRLQQIF 201
           N  D++   M R+LQ +F
Sbjct: 88  NPPDHDVVAMARKLQDVF 105

>pdb|2DVV|A Chain A, Crystal Structure Of The Second Bromodomain Of The Human Brd2 Protein Length = 112

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%), Gaps = 2/78 (2%)
Query: 126 AWPFCDPVDEATAP--NYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
           AWPF  PVD +     +Y++ IK PMDL+ ++ K++   Y+   +F AD +L+  NC KY
Sbjct: 26  AWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKY 85
Query: 184 NGLDNEYTDMVRRLQQIF 201
           N  D++   M R+LQ +F
Sbjct: 86  NPPDHDVVAMARKLQDVF 103

>pdb|2G4A|A Chain A, Solution Structure Of A Bromodomain From Ring3 Protein Length = 116

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%), Gaps = 2/78 (2%)
Query: 126 AWPFCDPVDEATAP--NYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
           AWPF  PVD +     +Y++ IK PMDL+ ++ K++   Y+   +F AD +L+  NC KY
Sbjct: 22  AWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKY 81
Query: 184 NGLDNEYTDMVRRLQQIF 201
           N  D++   M R+LQ +F
Sbjct: 82  NPPDHDVVAMARKLQDVF 99

>pdb|3HMH|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Tbp-Associated Factor Rna Polymerase 1-Like (Taf1l) Length = 155

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 51/93 (54%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           V  ++ +  D+WPF  PV++   P+YY+ I  P+DL  + + +   +Y++   F  D  L
Sbjct: 35  VTQKMMAVPDSWPFHHPVNKKFVPDYYKMIVNPVDLETIRKNISKHKYQSRESFLDDVNL 94
Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
           I+ N  KYNG +++YT   + +  I    ++ Y
Sbjct: 95  ILANSVKYNGPESQYTKTAQEIVNICYQTITEY 127

>pdb|3AAD|A Chain A, Structure Of The Histone Chaperone Cia/asf1-double Bromodomain Complex Linking Histone Modifications And Site-specific Histone Eviction Length = 292

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 51/93 (54%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           V  ++ +  D+WPF  PV++   P+YY+ I  PMDL  + + +   +Y++   F  D  L
Sbjct: 178 VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 237
Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
           I+ N  KYNG +++YT   + +  +    ++ Y
Sbjct: 238 ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEY 270

>pdb|1EQF|A Chain A, Crystal Structure Of The Double Bromodomain Module From Human Tafii250 Length = 280

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 51/93 (54%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           V  ++ +  D+WPF  PV++   P+YY+ I  PMDL  + + +   +Y++   F  D  L
Sbjct: 157 VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 216
Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
           I+ N  KYNG +++YT   + +  +    ++ Y
Sbjct: 217 ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEY 249

>pdb|3HME|A Chain A, Crystal Structure Of Human Bromodomain Containing 9 Isoform 1 (Brd9) Length = 123

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 41/69 (59%)
Query: 129 FCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDN 188
           F  PV +A AP Y   IK PMD   M++K+ A  YK+  +F+ADF+L+ DN   YN  D 
Sbjct: 34  FAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDT 93
Query: 189 EYTDMVRRL 197
            Y  + +++
Sbjct: 94  VYYKLAKKI 102

>pdb|3UV5|A Chain A, Crystal Structure Of The Tandem Bromodomains Of Human Transcription Initiation Factor Tfiid Subunit 1 (Taf1) Length = 265

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 51/93 (54%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           V  ++ +  D+WPF  PV++   P+YY+ I  PMDL  + + +   +Y++   F  D  L
Sbjct: 145 VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 204
Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
           I+ N  KYNG +++YT   + +  +    ++ Y
Sbjct: 205 ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEY 237

>pdb|3UV4|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Transcription Initiation Factor Tfiid Subunit 1 (Taf1) Length = 158

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 51/93 (54%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           V  ++ +  D+WPF  PV++   P+YY+ I  PMDL  + + +   +Y++   F  D  L
Sbjct: 38  VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 97
Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
           I+ N  KYNG +++YT   + +  +    ++ Y
Sbjct: 98  ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEY 130

>pdb|4A9E|A Chain A, N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-1,2,3,4- Tetrahydroquinazolin-2-One Length = 154

Iteration: 1
 Score = 60.8 bits (146), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 52/97 (53%), Gaps = 3/97 (3%)
Query: 113 MHKV-MNRLKSHEDAWPFCDPVDEATA--PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQF 169
           +HKV M  L  H+ AWPF  PVD      P+Y++ IK+PMD+  ++ +L+   Y    + 
Sbjct: 36  LHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASEC 95
Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
             DF  +  NC  YN   ++   M + L++IF   V+
Sbjct: 96  MQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVA 132

>pdb|2YDW|A Chain A, Crystal Structure Of The First Bromodomain Of Human Brd2 With The Inhibitor Gw841819x Length = 153

Iteration: 1
 Score = 60.8 bits (146), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 52/97 (53%), Gaps = 3/97 (3%)
Query: 113 MHKV-MNRLKSHEDAWPFCDPVDEATA--PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQF 169
           +HKV M  L  H+ AWPF  PVD      P+Y++ IK+PMD+  ++ +L+   Y    + 
Sbjct: 36  LHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASEC 95
Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
             DF  +  NC  YN   ++   M + L++IF   V+
Sbjct: 96  MQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVA 132

>pdb|2L5E|A Chain A, Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Length = 128

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 52/94 (55%), Gaps = 2/94 (2%)
Query: 116 VMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADF 173
           V+  L  H+ AWPF  PVD  +   P+Y++ IK PMD+  ++++L+   Y +  +   DF
Sbjct: 27  VVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDF 86
Query: 174 QLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
             +  NC  YN   ++   M + L++IF   V++
Sbjct: 87  NTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQ 120

>pdb|2NXB|A Chain A, Crystal Structure Of Human Bromodomain Containing Protein 3 (Brd3) Length = 123

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/101 (30%), Positives = 55/101 (54%), Gaps = 2/101 (1%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           L+   + V+  L  H+ AWPF  PVD  +   P+Y++ IK PMD+  ++++L+   Y + 
Sbjct: 18  LQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSA 77
Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
            +   DF  +  NC  YN   ++   M + L++IF   V++
Sbjct: 78  SECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQ 118

>pdb|2YW5|A Chain A, Solution Structure Of The Bromodomain From Human Bromodomain Containing Protein 3 Length = 138

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 52/94 (55%), Gaps = 2/94 (2%)
Query: 116 VMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADF 173
           V+  L  H+ AWPF  PVD  +   P+Y++ IK PMD+  ++++L+   Y +  +   DF
Sbjct: 29  VVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDF 88
Query: 174 QLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
             +  NC  YN   ++   M + L++IF   V++
Sbjct: 89  NTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQ 122

>pdb|2DWW|A Chain A, Crystal Structure Of Bromodomain-Containing Protein 4 Length = 114

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 126 AWPFCDPVD-EATA-PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
           AWPF  PVD EA    +Y + IK P D + ++ KL++  Y+   +F AD +L   NC KY
Sbjct: 28  AWPFYKPVDVEALGLHDYCDIIKHPXDXSTIKSKLESREYRDAQEFGADVRLXFSNCYKY 87
Query: 184 NGLDNEYTDMVRRLQQIF 201
           N  D+E     R+LQ +F
Sbjct: 88  NPPDHEVVAXARKLQDVF 105

>pdb|2WP2|A Chain A, Structure Of Brdt Bromodomain Bd1 Bound To A Diacetylated Histone H4 Peptide. Length = 120

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 49/94 (52%), Gaps = 2/94 (2%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATA--PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADF 173
           V+  L  H  +WPF  PVD      P+YY  IK PMDL  ++++L+   Y+   +   DF
Sbjct: 22  VLKALWKHGFSWPFQQPVDAVKLKLPDYYTIIKTPMDLNTIKKRLENKYYEKASECIEDF 81
Query: 174 QLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
             +  NC  YN   ++   M + L+++F   +S+
Sbjct: 82  NTMFSNCYLYNKTGDDIVVMAQALEKLFMQKLSQ 115

>pdb|2YYN|A Chain A, Crystal Sturcture Of Human Bromodomain Protein Length = 135

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 50/88 (56%), Gaps = 3/88 (3%)
Query: 120 LKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKL--DAGRYKTFGQFRADFQLIV 177
           L  HE +  F DPV   T P+YY+ IK PMDL+ ++++L  D   Y     F ADF+LI 
Sbjct: 32  LYCHEMSLAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIF 90
Query: 178 DNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
            NC ++N  D+E  +   +L+  F + +
Sbjct: 91  QNCAEFNEPDSEVANAGIKLENYFEELL 118

>pdb|3O33|A Chain A, Crystal Structure Of Trim24 Phd-Bromo In The Free State Length = 184

Iteration: 1
 Score = 57.4 bits (137), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 50/88 (56%), Gaps = 3/88 (3%)
Query: 120 LKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKL--DAGRYKTFGQFRADFQLIV 177
           L  HE +  F DPV   T P+YY+ IK PMDL+ ++++L  D   Y     F ADF+LI 
Sbjct: 93  LYCHEMSLAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIF 151
Query: 178 DNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
            NC ++N  D+E  +   +L+  F + +
Sbjct: 152 QNCAEFNEPDSEVANAGIKLENYFEELL 179

>pdb|3JVJ|A Chain A, Crystal Structure Of The Bromodomain 1 In Mouse Brd4 Length = 131

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 30/100 (30%), Positives = 51/100 (51%), Gaps = 2/100 (2%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           L+  +  V+  L  H+ AWPF  PVD      P+YY+ IK PMD+  ++++L+   Y   
Sbjct: 26  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNA 85
Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
            +   DF  +  NC  YN   ++   M   L+++F   ++
Sbjct: 86  QECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKIN 125

>pdb|4HBW|A Chain A, Crystal Structure Of The First Bromodomain Of Human Brd4 In Complex With A Quinazoline Ligand Length = 127

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 30/100 (30%), Positives = 51/100 (51%), Gaps = 2/100 (2%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           L+  +  V+  L  H+ AWPF  PVD      P+YY+ IK PMD+  ++++L+   Y   
Sbjct: 22  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNA 81
Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
            +   DF  +  NC  YN   ++   M   L+++F   ++
Sbjct: 82  QECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKIN 121

>pdb|4DON|A Chain A, Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihydro-3-methyl-2(1h)- Quinazolinon Length = 145

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 30/100 (30%), Positives = 51/100 (51%), Gaps = 2/100 (2%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           L+  +  V+  L  H+ AWPF  PVD      P+YY+ IK PMD+  ++++L+   Y   
Sbjct: 42  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNA 101
Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
            +   DF  +  NC  YN   ++   M   L+++F   ++
Sbjct: 102 QECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKIN 141

>pdb|2OSS|A Chain A, Crystal Structure Of The Bromo Domain 1 In Human Bromodomain Containing Protein 4 (Brd4) Length = 127

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/100 (30%), Positives = 51/100 (51%), Gaps = 2/100 (2%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           L+  +  V+  L  H+ AWPF  PVD      P+YY+ IK PMD+  ++++L+   Y   
Sbjct: 22  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNA 81
Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
            +   DF  +  NC  YN   ++   M   L+++F   ++
Sbjct: 82  QECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKIN 121

>pdb|2RFJ|A Chain A, Crystal Structure Of The Bromo Domain 1 In Human Bromodomain Containing Protein, Testis Specific (Brdt) Length = 119

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 48/94 (51%), Gaps = 2/94 (2%)
Query: 116 VMNRLKSHEDAWPFCDPVDEATA--PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADF 173
           V+  L  H  +WPF  PVD      P+YY  IK PMDL  ++++L+   Y    +   DF
Sbjct: 21  VLKDLWKHSFSWPFQRPVDAVKLQLPDYYTIIKNPMDLNTIKKRLENKYYAKASECIEDF 80
Query: 174 QLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
             +  NC  YN   ++   M + L+++F   +S+
Sbjct: 81  NTMFSNCYLYNKPGDDIVLMAQALEKLFMQKLSQ 114

>pdb|3AQA|A Chain A, Crystal Structure Of The Human Brd2 Bd1 Bromodomain In Complex With A Brd2-Interactive Compound, Bic1 Length = 128

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 49/97 (50%), Gaps = 3/97 (3%)
Query: 113 MHKVMNR-LKSHEDAWPFCDPVDEATA--PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQF 169
           +HKV+ + L  H+ AWPF  PVD      P+Y++ IK+P D   ++ +L+   Y    + 
Sbjct: 16  LHKVVXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRLENNYYWAASEC 75
Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
             DF     NC  YN   ++     + L++IF   V+
Sbjct: 76  XQDFNTXFTNCYIYNKPTDDIVLXAQTLEKIFLQKVA 112

>pdb|1X0J|A Chain A, Crystal Structure Analysis Of The N-Terminal Bromodomain Of Human Brd2 Length = 122

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 49/97 (50%), Gaps = 3/97 (3%)
Query: 113 MHKVMNR-LKSHEDAWPFCDPVDEATA--PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQF 169
           +HKV+ + L  H+ AWPF  PVD      P+Y++ IK+P D   ++ +L+   Y    + 
Sbjct: 10  LHKVVXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRLENNYYWAASEC 69
Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
             DF     NC  YN   ++     + L++IF   V+
Sbjct: 70  XQDFNTXFTNCYIYNKPTDDIVLXAQTLEKIFLQKVA 106

>pdb|3Q2E|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Bromodomain And Wd Repeat-Containing Protein 1 Isoform A (Wdr9) Length = 123

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/95 (33%), Positives = 49/95 (51%), Gaps = 3/95 (3%)
Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
           +++N +   ED+ PF  PVD    P+Y + I  PMD   + E LDAG Y +  +F  D +
Sbjct: 17  ELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIR 76
Query: 175 LIVDNCRKY--NGLDNEYTDMVRRLQQIFRDAVSR 207
           LI  N + Y  N     Y+ M  RL  +F + + +
Sbjct: 77  LIFSNAKAYTPNKRSKIYS-MTLRLSALFEEKMKK 110

>pdb|3DAI|A Chain A, Crystal Structure Of The Bromodomain Of The Human Atad2 Length = 130

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 41/80 (51%)
Query: 105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
           T  +LRI +  V +RL   +    F  PVD    P+Y   IK+PMDL+ +  K+D  +Y 
Sbjct: 7   TFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYL 66
Query: 165 TFGQFRADFQLIVDNCRKYN 184
           T   +  D  LI  N  +YN
Sbjct: 67  TVKDYLRDIDLICSNALEYN 86

>pdb|3I3J|A Chain A, Crystal Structure Of The Bromodomain Of Human Ep300 Length = 124

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 52/102 (50%), Gaps = 3/102 (2%)
Query: 107 EDLRIGMHKVMNRL-KSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLDAGRY 163
           E+LR  +   +  L +   ++ PF  PVD      P+Y++ +K PMDL+ ++ KLD G+Y
Sbjct: 15  EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQY 74
Query: 164 KTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           +   Q+  D  L+ +N   YN   +       +L ++F   +
Sbjct: 75  QEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEI 116

>pdb|3DWY|A Chain A, Crystal Structure Of The Bromodomain Of Human Crebbp Length = 119

Iteration: 1
 Score = 50.8 bits (120), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 52/102 (50%), Gaps = 3/102 (2%)
Query: 107 EDLRIGMHKVMNRL-KSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLDAGRY 163
           E+LR  +   +  L +   ++ PF  PVD      P+Y++ +K PMDL+ ++ KLD G+Y
Sbjct: 10  EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQY 69
Query: 164 KTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           +   Q+  D  L+ +N   YN   +       +L ++F   +
Sbjct: 70  QEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEI 111

>pdb|1JSP|B Chain B, Nmr Structure Of Cbp Bromodomain In Complex With P53 Peptide Length = 121

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 52/102 (50%), Gaps = 3/102 (2%)
Query: 107 EDLRIGMHKVMNRL-KSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLDAGRY 163
           E+LR  +   +  L +   ++ PF  PVD      P+Y++ +K PMDL+ ++ KLD G+Y
Sbjct: 12  EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQY 71
Query: 164 KTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           +   Q+  D  L+ +N   YN   +       +L ++F   +
Sbjct: 72  QEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEI 113

>pdb|3U5M|A Chain A, Crystal Structure Of Trim33 Phd-Bromo In The Free State Length = 207

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 4/75 (5%)
Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLD---AGRYKTFGQFRA 171
           +++  L  HE +  F +PV  A+ PNYY+ IK+PMDL+ +++KL    +  Y+    F A
Sbjct: 88  RLLLYLYCHELSIEFQEPV-PASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVA 146
Query: 172 DFQLIVDNCRKYNGL 186
           D +LI  NC ++N +
Sbjct: 147 DVRLIFKNCERFNEM 161

>pdb|2I7K|A Chain A, Solution Structure Of The Bromodomain Of Human Brd7 Protein Length = 117

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/89 (28%), Positives = 48/89 (53%)
Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
           L+  ++++M +L+  + +  F  PV +  AP Y   IK PMD + M+EK+    Y++  +
Sbjct: 9   LQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEE 68
Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRL 197
            + +F+L+  N   YN  +  Y    ++L
Sbjct: 69  LKDNFKLMCTNAMIYNKPETIYYKAAKKL 97

>pdb|3LXJ|A Chain A, Crystal Structure Of The Bromodomain Of Human Aaa Domain Containing 2b (Atad2b) Length = 136

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 40/81 (49%)
Query: 104 STEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRY 163
           +T  +LR+ +  V  RL + +    F  PVD     +Y E IK PMDL+ +  K+D   Y
Sbjct: 8   NTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNY 67
Query: 164 KTFGQFRADFQLIVDNCRKYN 184
            T   F  D  LI  N  +YN
Sbjct: 68  LTAKDFLKDIDLICSNALEYN 88

>pdb|3MB3|A Chain A, Crystal Structure Of The Second Bromodomain Of Pleckstrin Homology Domain Interacting Protein (Phip) Length = 135

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 1/96 (1%)
Query: 115 KVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ 174
           +++N +   ED+ PF  PVD    P+Y + I  PMD   + E L+AG Y++  +   D +
Sbjct: 28  ELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVR 87
Query: 175 LIVDNCRKYN-GLDNEYTDMVRRLQQIFRDAVSRYL 209
           LI  N + Y     +    M  RL   F + +S  L
Sbjct: 88  LIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVL 123

>pdb|3K2J|A Chain A, Crystal Structure Of The 3rd Bromodomain Of Human Poly-Bromodomain Containing Protein 1 (Pb1) Length = 130

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 40/77 (51%)
Query: 126 AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG 185
           A PF     +   P+YY+QIK P+ L ++  KL    Y+T      D  L+ +N ++YN 
Sbjct: 41  AEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNV 100
Query: 186 LDNEYTDMVRRLQQIFR 202
            ++     V +LQQ+ +
Sbjct: 101 PNSAIYKRVLKLQQVMQ 117

>pdb|2DKW|A Chain A, Solution Structure Of The Bromodomain Of Human Protein Kiaa1240 Length = 131

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 42/87 (48%), Gaps = 5/87 (5%)
Query: 98  STGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEK 157
           S+G   +T  +LR+ +  V  RL + +    F  PV +     Y E IK PMDL+ +  K
Sbjct: 2   SSGSSGNTLRELRLFLRDVTKRLATDKRFNIFSKPVSD-----YLEVIKEPMDLSTVITK 56
Query: 158 LDAGRYKTFGQFRADFQLIVDNCRKYN 184
           +D   Y T   F  D  LI  N  +YN
Sbjct: 57  IDKHNYLTAKDFLKDIDLICSNALEYN 83

>pdb|3FKM|X Chain X, Plasmodium Falciparum Bromodomain-Containing Protein Pf10_0328 Length = 166

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 114 HKVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
           ++++  L  +E    F   VD  +   P+YY+ IK P   + ++ KL  G+Y    +F  
Sbjct: 27  NQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPXSFSCIKTKLKKGQYAYPSEFVK 86
Query: 172 DFQLIVDNCRKYN 184
           D QLI DNC  YN
Sbjct: 87  DVQLIFDNCSLYN 99

>pdb|2DAT|A Chain A, Solution Structure Of The Bromodomain Of Human SwiSNF Related Matrix Associated Actin Dependent Regulator Of Cromatin Subfamily A Member 2 Length = 123

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 37/66 (56%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           P YYE I++P+D  +++E++   +Y++ G    D  L+  N + +N   ++  +    LQ
Sbjct: 50  PEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQ 109
Query: 199 QIFRDA 204
            +F+ A
Sbjct: 110 SVFKSA 115

>pdb|3MQM|A Chain A, Crystal Structure Of The Bromodomain Of Human Ash1l Length = 126

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 40/79 (50%)
Query: 126 AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG 185
           A P  +   +    +YYE+I  P+DL  +E+++  G YKT   F AD   +  N  KY G
Sbjct: 33  AAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYYG 92
Query: 186 LDNEYTDMVRRLQQIFRDA 204
             +     V RL++ + +A
Sbjct: 93  RKSPVGRDVCRLRKAYYNA 111

>pdb|3IU5|A Chain A, Crystal Structure Of The First Bromodomain Of Human Poly-Bromodomain Containing Protein 1 (Pb1) Length = 116

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 28/45 (62%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
           P+YYE + +P+DL ++++KL    Y       ADFQL+ +N + Y
Sbjct: 42  PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSY 86

>pdb|2KTB|B Chain B, Solution Structure Of The Second Bromodomain Of Human Polybr Complex With An Acetylated Peptide From Histone 3 Length = 121

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 10/68 (14%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           P+YY  IK P+DL  + +++  G YK+      D  L+  N + YN   +          
Sbjct: 46  PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGS---------- 95
Query: 199 QIFRDAVS 206
           Q+F+DA S
Sbjct: 96  QVFKDANS 103

>pdb|2R0V|A Chain A, Structure Of The Rsc4 Tandem Bromodomain Acetylated At K25 Length = 346

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 128 PFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN 184
           PF + VD+   P YYE +  PM L+ +++ L+ G+Y     F  D  L+  N   +N
Sbjct: 218 PFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFN 274

>pdb|2R10|A Chain A, Structure Of An Acetylated Rsc4 Tandem Bromodomain Histone Chimera Length = 361

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 128 PFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN 184
           PF + VD+   P YYE +  PM L+ +++ L+ G+Y     F  D  L+  N   +N
Sbjct: 233 PFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFN 289

>pdb|3LJW|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Polybromo Length = 120

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 10/68 (14%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           P+YY  IK P+DL  + +++  G YK+      D  L+  N + YN   +          
Sbjct: 45  PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGS---------- 94
Query: 199 QIFRDAVS 206
           Q+F+DA S
Sbjct: 95  QVFKDANS 102

>pdb|3HMF|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Poly-Bromodomain Containing Protein 1 (Pb1) Length = 116

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 10/68 (14%)
Query: 139 PNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQ 198
           P+YY  IK P+DL  + +++  G YK+      D  L+  N + YN   +          
Sbjct: 43  PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGS---------- 92
Query: 199 QIFRDAVS 206
           Q+F+DA S
Sbjct: 93  QVFKDANS 100

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	277
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	9e-39
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	4e-38
3d7c_A	112	General control of amino acid synthesis protein 5;	5e-38
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	7e-38
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	1e-37
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	4e-37
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	6e-37
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	1e-36
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	1e-36
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	5e-36
4alg_A	154	Bromodomain-containing protein 2; signaling protei	1e-34
3uv4_A	158	Second bromodomain of human transcription initiat	8e-34
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	2e-33
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	2e-33
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	8e-33
3p1f_A	119	CREB-binding protein; structural genomics consorti	2e-32
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	1e-31
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	2e-31
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	2e-27
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	3e-31
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	3e-28
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	5e-31
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	1e-30
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-30
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-30
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	4e-30
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	2e-29
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	2e-29
2grc_A	129	Probable global transcription activator SNF2L4; br	3e-29
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	2e-28
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	3e-18
2dat_A	123	Possible global transcription activator SNF2L2; br	2e-28
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	3e-28
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	5e-28
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	6e-28
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-26
2r10_A	361	Chromatin structure-remodeling complex protein RSC	8e-26
2r10_A	361	Chromatin structure-remodeling complex protein RSC	5e-17
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	4e-19
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	2e-18
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	2e-13
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	3e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-08
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-04

>3nxb_A CAT eye syndrome critical region protein 2; structural genomics consortium, SGC, CECR2, CAT eye syndrome chromosome region candidate 2, bromodomain; 1.83A {Homo sapiens} Length = 116

 Score =  130 bits (330), Expect = 9e-39
 Identities = 47/102 (46%), Positives = 71/102 (69%)

Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           +D    M+KV++ +K+H+D+WPF +PVDE+ APNYY+ IK PMD++ ME+KL+ G Y T 
Sbjct: 15  DDDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTK 74

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
            +F  D + +  NCRKYNG  +EYT M   L++ F  A+ ++
Sbjct: 75  EEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMKH 116

>2d9e_A Peregrin; four-helix bundle, transcription activator, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 121

 Score =  129 bits (326), Expect = 4e-38
 Identities = 36/115 (31%), Positives = 54/115 (46%)

Query: 104 STEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRY 163
           S      I + K + +L+  +    F +PV  +  P+Y + IK+PMD   M++ L+A RY
Sbjct: 3   SGSSGFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRY 62

Query: 164 KTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSE 218
             F  F  DF LIV NC KYN  D  +     RL++     + +        GS 
Sbjct: 63  LNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMGSG 117

>3d7c_A General control of amino acid synthesis protein 5; GCN5, bromodomain, structural genomics consortium, SGC, HOST-virus interaction, nucleus; 2.06A {Homo sapiens} SCOP: a.29.2.1 PDB: 1f68_A 1jm4_B* 1n72_A 1wug_A* 1wum_A* 1zs5_A* 2rnw_A* 2rnx_A* 3gg3_A Length = 112

 Score =  128 bits (325), Expect = 5e-38
 Identities = 38/100 (38%), Positives = 58/100 (58%)

Query: 104 STEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRY 163
              + L   +  ++ ++KSH  AWPF +PV ++ AP+YYE I+ P+DL  M E+L +  Y
Sbjct: 3   EDPDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYY 62

Query: 164 KTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
            T   F AD Q ++ NCR+YN  D+EY      L++ F  
Sbjct: 63  VTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYF 102

>1e6i_A Transcriptional activator GCN5; gene regulation, bromodomain, histone binding, N-acetyl lysine; HET: ALY; 1.87A {Saccharomyces cerevisiae} SCOP: a.29.2.1 Length = 121

 Score =  128 bits (325), Expect = 7e-38
 Identities = 37/110 (33%), Positives = 59/110 (53%)

Query: 103 RSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGR 162
           R         +  ++  L++H  AWPF  PV++   P+YY+ IK PMDL+ ME KL++ +
Sbjct: 8   RPKRGPHDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNK 67

Query: 163 YKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGE 212
           Y+    F  D +L+ +NCR YNG +  Y     RL++ F + V    +  
Sbjct: 68  YQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPEYS 117

>3g0l_A Hwalp4, bromodomain adjacent to zinc finger domain protei; BAZB2, KIAA1 WALP4, structural genomics consortium, SGC, transcription; 2.03A {Homo sapiens} PDB: 3q2f_A* 2e7o_A Length = 117

 Score =  128 bits (323), Expect = 1e-37
 Identities = 33/101 (32%), Positives = 55/101 (54%), Gaps = 1/101 (0%)

Query: 103 RSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGR 162
           R   +DL +    ++  +++HEDAWPF  PV+    P Y + IK+PMD + + EKL +G+
Sbjct: 9   RDDSKDLAL-CSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQ 67

Query: 163 YKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
           Y     F  D +L+ DNC  +N  D++       +++ F  
Sbjct: 68  YPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEK 108

>3hme_A Bromodomain-containing protein 9; BRD9, bromodomain containing 9 isoform 1, LAVS3040, rhabdomyosarcoma antigen MU-RMS-40.8; 2.23A {Homo sapiens} Length = 123

 Score =  127 bits (320), Expect = 4e-37
 Identities = 30/99 (30%), Positives = 52/99 (52%)

Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
           ++  +   + +L+  +    F  PV +A AP Y   IK PMD   M++K+ A  YK+  +
Sbjct: 14  IQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTE 73

Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
           F+ADF+L+ DN   YN  D  Y  + +++       +S+
Sbjct: 74  FKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSK 112

>3rcw_A Bromodomain-containing protein 1; transcription, structural genomics, structural consortium, SGC; 2.21A {Homo sapiens} Length = 135

 Score =  126 bits (319), Expect = 6e-37
 Identities = 40/127 (31%), Positives = 60/127 (47%), Gaps = 6/127 (4%)

Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
           L + +  V+++L+  + A  F  PV     P+Y + IK PMD   M ++L+A  YK   +
Sbjct: 14  LTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHE 73

Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEEEMAVEFQ 228
           F  DF LI+DNC KYN  D  +     RL+      + +      S G E+   M     
Sbjct: 74  FEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASGM----- 128

Query: 229 EELPPKP 235
             LP +P
Sbjct: 129 -HLPERP 134

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A* Length = 174

 Score =  127 bits (320), Expect = 1e-36
 Identities = 39/107 (36%), Positives = 56/107 (52%)

Query: 102 YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAG 161
                E    G+ +V+  L++H+ AWPF +PVD   AP+YY  IK PMDL  MEE++   
Sbjct: 66  LTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRR 125

Query: 162 RYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
            Y+   +F AD   I DNCR YN  D+ +      L+  F   +  +
Sbjct: 126 YYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGF 172

>2i7k_A Bromodomain-containing protein 7; helix, LEFT-handed four-helix bundle, transcription; NMR {Homo sapiens} Length = 117

 Score =  125 bits (315), Expect = 1e-36
 Identities = 26/100 (26%), Positives = 51/100 (51%)

Query: 109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQ 168
           L+  ++++M +L+  + +  F  PV +  AP Y   IK PMD + M+EK+    Y++  +
Sbjct: 9   LQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEE 68

Query: 169 FRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
            + +F+L+  N   YN  +  Y    ++L       +S+ 
Sbjct: 69  LKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQE 108

>3dai_A ATPase family AAA domain-containing protein 2; ancca, AAA+ nuclear coregulator cancer-associated Pro2000 protein, two AAA DOMA containing protein; 1.95A {Homo sapiens} PDB: 3lxj_A Length = 130

 Score =  124 bits (313), Expect = 5e-36
 Identities = 38/123 (30%), Positives = 56/123 (45%), Gaps = 3/123 (2%)

Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
            +LRI +  V +RL   +    F  PVD    P+Y   IK+PMDL+ +  K+D  +Y T 
Sbjct: 9   RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTV 68

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEEEMAVE 226
             +  D  LI  N  +YN   +    ++R      RD     +  E     ED E++  E
Sbjct: 69  KDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEEL---DEDFEQLCEE 125

Query: 227 FQE 229
            QE
Sbjct: 126 IQE 128

>4alg_A Bromodomain-containing protein 2; signaling protein, inhibitor, histone, epigenetic reader; HET: 1GH; 1.60A {Homo sapiens} PDB: 4a9e_A 4a9h_A* 4a9i_A* 4a9j_A* 4a9m_A* 4a9n_A* 4a9o_A* 4a9p_A* 4a9f_A* 4alh_A* 4akn_A* 2yek_A* 2ydw_A* 2yw5_A Length = 154

 Score =  121 bits (306), Expect = 1e-34
 Identities = 38/137 (27%), Positives = 59/137 (43%), Gaps = 17/137 (12%)

Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYK 164
             L+     VM  L  H+ AWPF  PVD  +   P+Y++ IK+PMD+  ++ +L+   Y 
Sbjct: 31  NQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYW 90

Query: 165 TFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEEEMA 224
              +   DF  +  NC  YN   ++   M + L++IF   V                 M 
Sbjct: 91  AASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKV---------------ASMP 135

Query: 225 VEFQEELPPKPKGKRGR 241
            E QE +   PK    +
Sbjct: 136 QEEQELVVTIPKNSHKK 152

>3uv4_A Second bromodomain of human transcription initiat TFIID subunit 1 (TAF1); structural genomics consortium, SGC; 1.89A {Homo sapiens} PDB: 3hmh_A Length = 158

 Score =  119 bits (300), Expect = 8e-34
 Identities = 33/128 (25%), Positives = 63/128 (49%), Gaps = 6/128 (4%)

Query: 88  DTSSLCSYQTSTGGYRSTEEDLRIGMHK-----VMNRLKSHEDAWPFCDPVDEATAPNYY 142
             SS     T    ++S ++D ++         V  ++ +  D+WPF  PV++   P+YY
Sbjct: 6   HHSSGVDLGTENLYFQSMDDD-QVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYY 64

Query: 143 EQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFR 202
           + I  PMDL  + + +   +Y++   F  D  LI+ N  KYNG +++YT   + +  +  
Sbjct: 65  KVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCY 124

Query: 203 DAVSRYLD 210
             ++ Y +
Sbjct: 125 QTLTEYDE 132

>2yyn_A Transcription intermediary factor 1-alpha; bromo domain, structural genomics, NPPSFA; 2.50A {Homo sapiens} Length = 135

 Score =  118 bits (297), Expect = 2e-33
 Identities = 39/132 (29%), Positives = 64/132 (48%), Gaps = 4/132 (3%)

Query: 89  TSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRP 148
           +S     + + G  + T  D R    +++  L  HE +  F DPV     P+YY+ IK P
Sbjct: 2   SSGSSGKKKTEGLVKLTPIDKRK-CERLLLFLYCHEMSLAFQDPVPLT-VPDYYKIIKNP 59

Query: 149 MDLTRMEEKL--DAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVS 206
           MDL+ ++++L  D   Y     F ADF+LI  NC ++N  D+E  +   +L+  F + + 
Sbjct: 60  MDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLK 119

Query: 207 RYLDGERSSGSE 218
                +R   S 
Sbjct: 120 NLYPEKRFPKSG 131

>2oss_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.35A {Homo sapiens} PDB: 2yel_A* 3mxf_A* 3p5o_A* 3svf_A* 3svg_A* 3u5j_A* 3u5k_A* 3u5l_A* 3uvw_A* 3uvx_A* 3uvy_A* 3uw9_A* 3zyu_A* 4a9l_A* 4e96_A* 3jvj_A 3jvk_A* 3muk_A* 3mul_A* 2nxb_A ... Length = 127

 Score =  117 bits (295), Expect = 2e-33
 Identities = 30/103 (29%), Positives = 51/103 (49%), Gaps = 2/103 (1%)

Query: 103 RSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDA 160
           +     L+  +  V+  L  H+ AWPF  PVD  +   P+YY+ IK PMD+  ++++L+ 
Sbjct: 16  KRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLEN 75

Query: 161 GRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
             Y    +   DF  +  NC  YN   ++   M   L+++F  
Sbjct: 76  NYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQ 118

>2dkw_A Hypothetical protein KIAA1240; bromodomain-like, five-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 131

 Score =  116 bits (291), Expect = 8e-33
 Identities = 35/129 (27%), Positives = 52/129 (40%), Gaps = 5/129 (3%)

Query: 98  STGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEK 157
           S+G   +T  +LR+ +  V  RL + +    F  PV      +Y E IK PMDL+ +  K
Sbjct: 2   SSGSSGNTLRELRLFLRDVTKRLATDKRFNIFSKPVS-----DYLEVIKEPMDLSTVITK 56

Query: 158 LDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGS 217
           +D   Y T   F  D  LI  N  +YN   +    ++R      +D     +  E     
Sbjct: 57  IDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEF 116

Query: 218 EDEEEMAVE 226
               E   E
Sbjct: 117 NKLCEEIKE 125

>3p1f_A CREB-binding protein; structural genomics consortium, SGC, CBP, crebbp, CREB bindi protein isoform A, KAT3A, RSTS, RST, bromodomain, transcrip; HET: 3PF; 1.63A {Homo sapiens} PDB: 3dwy_A 3p1d_A 3p1c_A 3p1e_A* 3svh_A* 4a9k_A* 1jsp_B* 2d82_A* 2l84_A* 2l85_A* 2rny_A* 3i3j_A Length = 119

 Score =  114 bits (288), Expect = 2e-32
 Identities = 29/111 (26%), Positives = 53/111 (47%), Gaps = 3/111 (2%)

Query: 103 RSTEEDLRIGMHKVMNRL-KSHEDAWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLD 159
               E+LR  +   +  L +   ++ PF  PVD      P+Y++ +K PMDL+ ++ KLD
Sbjct: 6   IFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLD 65

Query: 160 AGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLD 210
            G+Y+   Q+  D  L+ +N   YN   +       +L ++F   +   + 
Sbjct: 66  TGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQ 116

>3fkm_X Signaling protein; bromodomain, malaria, structural genomics, structural genomi consortium, SGC; 2.50A {Plasmodium falciparum 3D7} Length = 166

 Score =  114 bits (286), Expect = 1e-31
 Identities = 34/146 (23%), Positives = 62/146 (42%), Gaps = 2/146 (1%)

Query: 102 YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLD 159
           Y    +   +  ++++  L  +E    F   VD  +   P+YY+ IK PM  + ++ KL 
Sbjct: 15  YFQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLK 74

Query: 160 AGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSED 219
            G+Y    +F  D QLI DNC  YN  ++      + ++  F + +            + 
Sbjct: 75  KGQYAYPSEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFNNQLIVMGYNNFILKEKK 134

Query: 220 EEEMAVEFQEELPPKPKGKRGRKKKI 245
             +M    +EE     K K  + ++I
Sbjct: 135 INDMLKLVEEENIKWSKEKEDQIEEI 160

>3aad_A Transcription initiation factor TFIID subunit 1; protein-protein complex, bromodomain, transcription, transcr regulation, chromatin regulator, transcription-C complex; 3.30A {Homo sapiens} Length = 292

 Score =  117 bits (293), Expect = 2e-31
 Identities = 33/196 (16%), Positives = 74/196 (37%), Gaps = 17/196 (8%)

Query: 28  KEIERKLQKQKEEETRRHQEEEERLEEEWRK--------HKAARERQRRIENRERGSRSN 79
           + +   ++K+        +E  E + +             + ++      + + +     
Sbjct: 91  QTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDK 150

Query: 80  SEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAP 139
                   +       Q +            I  + V  ++ +  D+WPF  PV++   P
Sbjct: 151 LARLEKAINPLLDDDDQVAFS---------FILDNIVTQKMMAVPDSWPFHHPVNKKFVP 201

Query: 140 NYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQ 199
           +YY+ I  PMDL  + + +   +Y++   F  D  LI+ N  KYNG +++YT   + +  
Sbjct: 202 DYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVN 261

Query: 200 IFRDAVSRYLDGERSS 215
           +    ++ Y +     
Sbjct: 262 VCYQTLTEYDEHLTQL 277

>3aad_A Transcription initiation factor TFIID subunit 1; protein-protein complex, bromodomain, transcription, transcr regulation, chromatin regulator, transcription-C complex; 3.30A {Homo sapiens} Length = 292

 Score =  106 bits (266), Expect = 2e-27
 Identities = 27/145 (18%), Positives = 56/145 (38%)

Query: 64  ERQRRIENRERGSRSNSEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSH 123
               +   ++   +       T         +++           L   +  ++N ++  
Sbjct: 3   HMVLKFPKQQLPPKKKRRVGTTVHCDYLNRPHKSIHRRRTDPMVTLSSILESIINDMRDL 62

Query: 124 EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKY 183
            + +PF  PV+     +YY+ I RPMDL  + E +    Y +  +FR   +LIV N   Y
Sbjct: 63  PNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATY 122

Query: 184 NGLDNEYTDMVRRLQQIFRDAVSRY 208
           NG  +  T + + +  +  + +   
Sbjct: 123 NGPKHSLTQISQSMLDLCDEKLKEK 147

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A Length = 265

 Score =  115 bits (290), Expect = 3e-31
 Identities = 32/191 (16%), Positives = 73/191 (38%), Gaps = 17/191 (8%)

Query: 28  KEIERKLQKQKEEETRRHQEEEERLEEEWRK--------HKAARERQRRIENRERGSRSN 79
           + +   ++K+        +E  E + +             + ++      + + +     
Sbjct: 58  QTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDK 117

Query: 80  SEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAP 139
                   +       Q +               + V  ++ +  D+WPF  PV++   P
Sbjct: 118 LARLEKAINPLLDDDDQVAFSFIL---------DNIVTQKMMAVPDSWPFHHPVNKKFVP 168

Query: 140 NYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQ 199
           +YY+ I  PMDL  + + +   +Y++   F  D  LI+ N  KYNG +++YT   + +  
Sbjct: 169 DYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVN 228

Query: 200 IFRDAVSRYLD 210
           +    ++ Y +
Sbjct: 229 VCYQTLTEYDE 239

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A Length = 265

 Score =  108 bits (270), Expect = 3e-28
 Identities = 26/103 (25%), Positives = 48/103 (46%)

Query: 106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKT 165
              L   +  ++N ++   + +PF  PV+     +YY+ I RPMDL  + E +    Y +
Sbjct: 12  MVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPS 71

Query: 166 FGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRY 208
             +FR   +LIV N   YNG  +  T + + +  +  + +   
Sbjct: 72  REEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEK 114

>3q2e_A Bromodomain and WD repeat-containing protein 1; structural genomics consortium, SGC, cell cycle progression, signal transduction, apoptosis; 1.74A {Homo sapiens} Length = 123

 Score =  111 bits (279), Expect = 5e-31
 Identities = 31/103 (30%), Positives = 49/103 (47%), Gaps = 1/103 (0%)

Query: 102 YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAG 161
               E + +    +++N +   ED+ PF  PVD    P+Y + I  PMD   + E LDAG
Sbjct: 4   TNYVESNWKKQCKELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAG 63

Query: 162 RYKTFGQFRADFQLIVDNCRKYNGLD-NEYTDMVRRLQQIFRD 203
            Y +  +F  D +LI  N + Y     ++   M  RL  +F +
Sbjct: 64  NYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEE 106

>3jvl_A Bromodomain-containing protein 4; alpha helical, N-acetyl lysine binding domain, signaling protein; 1.20A {Mus musculus} PDB: 3jvm_A 2dww_A 2i8n_A 3oni_A* 2dvv_A* 2e3k_A* 2g4a_A 3s92_A* 2oo1_A* 2e7n_A 2wp1_A* Length = 120

 Score =  110 bits (276), Expect = 1e-30
 Identities = 35/93 (37%), Positives = 51/93 (54%), Gaps = 2/93 (2%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFR 170
           + K M   K    AWPF  PVD       +Y + IK PMD++ ++ KL++  Y+   +F 
Sbjct: 17  ILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFG 76

Query: 171 ADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
           AD +L+  NC KYN  D+E   M R+LQ +F  
Sbjct: 77  ADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEM 109

>3k2j_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo01D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.20A {Homo sapiens} Length = 130

 Score =  109 bits (275), Expect = 2e-30
 Identities = 28/118 (23%), Positives = 53/118 (44%), Gaps = 6/118 (5%)

Query: 94  SYQTSTGGYRSTEEDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKR 147
            +   + G     E+L     ++ + ++S  +      A PF     +   P+YY+QIK 
Sbjct: 3   HHHHHSSGVDLGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKM 62

Query: 148 PMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           P+ L ++  KL    Y+T      D  L+ +N ++YN  ++     V +LQQ+ +   
Sbjct: 63  PISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKK 120

>3iu5_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; 1.63A {Homo sapiens} Length = 116

 Score =  109 bits (274), Expect = 2e-30
 Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 6/113 (5%)

Query: 104 STEEDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEK 157
           S   D     H++ N ++ ++D         F         P+YYE + +P+DL ++++K
Sbjct: 1   SMTVDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQK 60

Query: 158 LDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLD 210
           L    Y       ADFQL+ +N + Y   D+       +L  ++    + ++ 
Sbjct: 61  LKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQ 113

>2ouo_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.89A {Homo sapiens} PDB: 2yem_A* Length = 130

 Score =  109 bits (274), Expect = 4e-30
 Identities = 36/91 (39%), Positives = 50/91 (54%), Gaps = 2/91 (2%)

Query: 115 KVMNRLKSHEDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           K M   K    AWPF  PVD       +Y + IK PMD++ ++ KL+A  Y+   +F AD
Sbjct: 32  KEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGAD 91

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
            +L+  NC KYN  D+E   M R+LQ +F  
Sbjct: 92  VRLMFSNCYKYNPPDHEVVAMARKLQDVFEM 122

>3mb3_A PH-interacting protein; PHIP, pleckstrin homology domain interacting protein, DCAF14 DDB1 and CUL4 associated factor 14, SGC; 2.25A {Homo sapiens} Length = 135

 Score =  107 bits (269), Expect = 2e-29
 Identities = 31/109 (28%), Positives = 50/109 (45%), Gaps = 1/109 (0%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
             +++N +   ED+ PF  PVD    P+Y + I  PMD   + E L+AG Y++  +   D
Sbjct: 26  CEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKD 85

Query: 173 FQLIVDNCRKYNGLDN-EYTDMVRRLQQIFRDAVSRYLDGERSSGSEDE 220
            +LI  N + Y          M  RL   F + +S  L   +S+    +
Sbjct: 86  VRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSDYKSALRFHK 134

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A Length = 184

 Score =  108 bits (272), Expect = 2e-29
 Identities = 33/99 (33%), Positives = 53/99 (53%), Gaps = 3/99 (3%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKL--DAGRYKTFGQFR 170
             +++  L  HE +  F DPV   T P+YY+ IK PMDL+ ++++L  D   Y     F 
Sbjct: 86  CERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFV 144

Query: 171 ADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL 209
           ADF+LI  NC ++N  D+E  +   +L+  F + +    
Sbjct: 145 ADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLY 183

>2grc_A Probable global transcription activator SNF2L4; bromodomain, BRG1, chromatin remodelling, acely-lysine binding, protein-protein interactions; 1.50A {Homo sapiens} PDB: 3uvd_A 2h60_A Length = 129

 Score =  106 bits (267), Expect = 3e-29
 Identities = 21/107 (19%), Positives = 44/107 (41%)

Query: 112 GMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRA 171
            + K  +     + +  F         P YYE I++P+D  +++E++   +Y++      
Sbjct: 22  AVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEK 81

Query: 172 DFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSE 218
           D  L+  N + +N   +   +    LQ +F     +    + S G E
Sbjct: 82  DVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSEGEE 128

>2r0y_A Chromatin structure-remodeling complex protein RSC4; bromodomain, chromatin, remodeler, RSC, acetylation, transcription, chromatin regulator, nucleus, phosphorylation; HET: ALY; 1.75A {Saccharomyces cerevisiae} PDB: 2r0s_A Length = 311

 Score =  109 bits (273), Expect = 2e-28
 Identities = 30/142 (21%), Positives = 50/142 (35%), Gaps = 1/142 (0%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
                N     + + PF + VD+   P YYE +  PM L+ +++ L+ G+Y     F  D
Sbjct: 168 ASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIID 227

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEE-EMAVEFQEEL 231
             L+  N   +N            L   F   + +    E    +E  E  +  +  E  
Sbjct: 228 MLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKFEFE 287

Query: 232 PPKPKGKRGRKKKIVLSPRSLT 253
                G  G      L+  +L 
Sbjct: 288 NYLAIGGGGPAAAGALAISALD 309

>2r0y_A Chromatin structure-remodeling complex protein RSC4; bromodomain, chromatin, remodeler, RSC, acetylation, transcription, chromatin regulator, nucleus, phosphorylation; HET: ALY; 1.75A {Saccharomyces cerevisiae} PDB: 2r0s_A Length = 311

 Score = 82.0 bits (202), Expect = 3e-18
 Identities = 16/99 (16%), Positives = 33/99 (33%), Gaps = 3/99 (3%)

Query: 105 TEEDLRIGMHKVMNRLKSHED--AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGR 162
                   +   ++ L          F         P YY +I++PM +  ++ +     
Sbjct: 25  HIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDY-EY 83

Query: 163 YKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
                 F  D +L+  NC+ YN  D+       ++  + 
Sbjct: 84  EDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLI 122

>2dat_A Possible global transcription activator SNF2L2; bromodomain, all alpha protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 123

 Score =  104 bits (261), Expect = 2e-28
 Identities = 22/109 (20%), Positives = 50/109 (45%), Gaps = 6/109 (5%)

Query: 103 RSTEEDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEE 156
                 L   M+ +++ + +++D      +  F         P YYE I++P+D  +++E
Sbjct: 8   SPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKE 67

Query: 157 KLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
           ++   +Y++ G    D  L+  N + +N   ++  +    LQ +F+ A 
Sbjct: 68  RIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSAR 116

>3ljw_A Protein polybromo-1; alpha helix, alternative splicing, bromodomain, chromatin RE DNA-binding, nucleus, phosphoprotein, transcription; 1.50A {Homo sapiens} PDB: 2ktb_B* 3hmf_A Length = 120

 Score =  103 bits (259), Expect = 3e-28
 Identities = 22/117 (18%), Positives = 48/117 (41%), Gaps = 6/117 (5%)

Query: 104 STEEDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEK 157
           S+   L+  + +++  +    +      +  F     +   P+YY  IK P+DL  + ++
Sbjct: 4   SSPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQR 63

Query: 158 LDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERS 214
           +  G YK+      D  L+  N + YN   ++       +++IF    +     E +
Sbjct: 64  IQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEHHEMA 120

>3mqm_A Probable histone-lysine N-methyltransferase ASH1L; KIAA1420, absent small and homeotic disks prote homolog, lysine N-methyltransferase 2H, KMT2H; 2.54A {Homo sapiens} Length = 126

 Score =  103 bits (258), Expect = 5e-28
 Identities = 27/101 (26%), Positives = 48/101 (47%), Gaps = 6/101 (5%)

Query: 113 MHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
             ++ + + S++D      A P  +   +    +YYE+I  P+DL  +E+++  G YKT 
Sbjct: 14  FKEICDGIISYKDSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTV 73

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
             F AD   +  N  KY G  +     V RL++ + +A   
Sbjct: 74  EAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHE 114

>3mb4_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo-1D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 1.66A {Homo sapiens} PDB: 3g0j_A 2yqd_A Length = 124

 Score =  103 bits (258), Expect = 6e-28
 Identities = 20/107 (18%), Positives = 46/107 (42%), Gaps = 6/107 (5%)

Query: 107 EDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDA 160
             ++  +++V   +K++ D      +  F      +  P+YY  IK+PMD+ ++   + A
Sbjct: 14  TPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMA 73

Query: 161 GRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSR 207
            +Y+       DF ++ +N   YN  ++        L ++  +    
Sbjct: 74  NKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRD 120

>3tlp_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo-1D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.13A {Homo sapiens} Length = 150

 Score = 99.1 bits (247), Expect = 5e-26
 Identities = 18/93 (19%), Positives = 36/93 (38%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           + +             F     +   P+YY+ I  PMDL  +E  +   +Y        D
Sbjct: 36  VLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIED 95

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAV 205
            +L+  N R YN   ++  +    L+++ ++  
Sbjct: 96  MKLMFRNARHYNEEGSQVYNDAHILEKLLKEKR 128

>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A* Length = 361

 Score =  103 bits (257), Expect = 8e-26
 Identities = 31/148 (20%), Positives = 52/148 (35%), Gaps = 1/148 (0%)

Query: 108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFG 167
              +G     N     + + PF + VD+   P YYE +  PM L+ +++ L+ G+Y    
Sbjct: 213 QALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIY 272

Query: 168 QFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEE-EMAVE 226
            F  D  L+  N   +N            L   F   + +    E    +E  E  +  +
Sbjct: 273 DFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFD 332

Query: 227 FQEELPPKPKGKRGRKKKIVLSPRSLTP 254
             E       G  G      L+  +L  
Sbjct: 333 KFEFENYLAIGGGGPAAAGALAISALDN 360

>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A* Length = 361

 Score = 79.1 bits (194), Expect = 5e-17
 Identities = 22/167 (13%), Positives = 52/167 (31%), Gaps = 3/167 (1%)

Query: 37  QKEEETRRHQEEEERLEEEWRKHKAARERQRRIENRERGSRSNSEDRWTTEDTSSLCSYQ 96
              + T      +  +  + RK                G    ++++    D ++  + +
Sbjct: 7   TARKSTGGKAPRKGGMVVKKRKLATEAGGSDERPKYLPGKHPKNQEKTPHVDYNAPLNPK 66

Query: 97  TSTGGYRSTEEDLRIGMHKVMNRLKSHED--AWPFCDPVDEATAPNYYEQIKRPMDLTRM 154
           +               +   ++ L          F         P YY +I++PM +  +
Sbjct: 67  SELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEI 126

Query: 155 EEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
           + + D         F  D +L+  NC+ YN  D+       ++  + 
Sbjct: 127 KSR-DYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLI 172

>3iu6_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; HET: OCS; 1.79A {Homo sapiens} Length = 147

 Score = 80.7 bits (199), Expect = 4e-19
 Identities = 23/132 (17%), Positives = 48/132 (36%), Gaps = 2/132 (1%)

Query: 109 LRIGMHKVMNRLKSHEDAW--PFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           ++  +H +   + SH+D     + D + E  A +     K P+    + + ++  RY+  
Sbjct: 8   IQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPNFPNKPPLTFDIIRKNVENNRYRRL 67

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDEEEMAVE 226
             F+     +++  R+ N  D+E  +    LQQ F               S         
Sbjct: 68  DLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCKNGEILLSPALSYTTKH 127

Query: 227 FQEELPPKPKGK 238
              ++  + K K
Sbjct: 128 LHNDVEKERKEK 139

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A* Length = 207

 Score = 80.3 bits (197), Expect = 2e-18
 Identities = 28/104 (26%), Positives = 49/104 (47%), Gaps = 4/104 (3%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKL---DAGRYKTFGQF 169
             +++  L  HE +  F +PV   + PNYY+ IK+PMDL+ +++KL    +  Y+    F
Sbjct: 86  CERLLLYLYCHELSIEFQEPVPA-SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDF 144

Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGER 213
            AD +LI  NC ++N +           +   +        G+ 
Sbjct: 145 VADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKA 188

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A Length = 183

 Score = 66.2 bits (160), Expect = 2e-13
 Identities = 20/117 (17%), Positives = 43/117 (36%), Gaps = 11/117 (9%)

Query: 93  CSYQTSTGGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLT 152
           C+ +       + E++L+I + +V+  L +                       ++P+DL 
Sbjct: 60  CTERHPAEWRLALEKELQISLKQVLTALLNSRTTSHLLRYRQ-----------QQPLDLE 108

Query: 153 RMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL 209
            ++ K+D G Y +  +F  D   I+      +G   E       ++  F   + R  
Sbjct: 109 GVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVF 165

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens} Length = 189

 Score = 66.0 bits (160), Expect = 3e-13
 Identities = 19/111 (17%), Positives = 37/111 (33%), Gaps = 6/111 (5%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKL---DAGRYKTFGQF 169
             +V+  L  HE   P      ++      +Q    +DLT +  +L    +  Y +  +F
Sbjct: 81  CERVLLALFCHEPCRPLHQLATDS--TFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEF 138

Query: 170 RADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERSSGSEDE 220
             D   +     K      +    +  LQ+ F   ++      + S    E
Sbjct: 139 AQDVGRMFKQFNKLTEDKADVQ-SIIGLQRFFETRMNEAFGDTKFSAVLVE 188

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.2 bits (124), Expect = 7e-08
 Identities = 41/255 (16%), Positives = 79/255 (30%), Gaps = 63/255 (24%)

Query: 20  RIEKLKH------SKEIERKLQKQKEEETRRHQEE-----------EERLEEEWRKHKAA 62
             +  KH      +  IE  L   +  E R+  +               L   W      
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI-- 400

Query: 63  RERQRRIENRERGSRSNSEDRWTTEDTSSLCSYQTSTGGYRSTEEDLRIGMHK-VMNRLK 121
           +     + N +    S   ++   E T S+ S        +   E+    +H+ +++   
Sbjct: 401 KSDVMVVVN-KLHKYS-LVEKQPKESTISIPSIYLE---LKVKLENEY-ALHRSIVDHYN 454

Query: 122 SHE--DAWPFCDPVDEATAPNYY-----------EQIKRP-------MDLTRMEEKL--- 158
             +  D+     P  +     Y+           E  +R        +D   +E+K+   
Sbjct: 455 IPKTFDSDDLIPPYLD----QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHD 510

Query: 159 ------DAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRL-QQIFRDAVSRYLDG 211
                       T  Q +     I DN  KY  L N   D + ++ + +     S+Y D 
Sbjct: 511 STAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLIC---SKYTDL 567

Query: 212 ERSSGSEDEEEMAVE 226
            R +   ++E +  E
Sbjct: 568 LRIALMAEDEAIFEE 582

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 5/67 (7%)

Query: 19  TRIEKLKHSKEIERKLQKQKEEETRRHQEEEERLEEEWRKHKAARERQ----RRIENRER 74
            + ++L    E  RK ++++ +  +      + +E+EWR+ KA ++ +    R+ E  E+
Sbjct: 75  AQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWRE-KAKKDLEEWNQRQSEQVEK 133

Query: 75  GSRSNSE 81
              +N  
Sbjct: 134 NKINNRI 140

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	277
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.97
3d7c_A	112	General control of amino acid synthesis protein 5;	99.97
2grc_A	129	Probable global transcription activator SNF2L4; br	99.97
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.96
2dat_A	123	Possible global transcription activator SNF2L2; br	99.96
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.96
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.96
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.96
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.96
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.96
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.96
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.96
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.96
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.96
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.96
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.96
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.96
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.96
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.96
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.96
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.96
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.95
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.95
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.95
3uv4_A	158	Second bromodomain of human transcription initiat	99.95
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.94
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.94
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.94
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.93
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.93
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.92
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.92
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.92
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.91
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.9
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.89
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.88
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.85
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.85
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.84
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.65

>3g0l_A Hwalp4, bromodomain adjacent to zinc finger domain protei; BAZB2, KIAA1 WALP4, structural genomics consortium, SGC, transcription; 2.03A {Homo sapiens} PDB: 3q2f_A* 2e7o_A

Probab=99.97  E-value=5.7e-30  Score=203.13  Aligned_cols=103  Identities=29%  Similarity=0.588  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      .....|..||..|..++.+++|..||+...+||||++|++||||+||++||.+|.|.++++|.+||+|||.||+.||+++
T Consensus        13 ~~~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~   92 (117)
T 3g0l_A           13 KDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDD   92 (117)
T ss_dssp             THHHHHHHHHHHHHTSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCSS
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCcCChhhcCChHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            55678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        188 NEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      |.+|.+|..|++.|+..|.+++.
T Consensus        93 s~~~~~A~~L~~~f~~~~~~~~~  115 (117)
T 3g0l_A           93 SDIGRAGHNMRKYFEKKWTDTFK  115 (117)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999875

>3d7c_A General control of amino acid synthesis protein 5; GCN5, bromodomain, structural genomics consortium, SGC, HOST-virus interaction, nucleus; 2.06A {Homo sapiens} SCOP: a.29.2.1 PDB: 1f68_A 1jm4_B* 1n72_A 1wug_A* 1wum_A* 1zs5_A* 2rnw_A* 2rnx_A* 3gg3_A

Probab=99.97  E-value=3.7e-30  Score=202.73  Aligned_cols=105  Identities=36%  Similarity=0.661  Sum_probs=101.6

Q ss_pred             ChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       105 ~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      ....|...|..||+.|..++.+++|..||++..+||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||
T Consensus         4 ~~~~l~~~~~~il~~l~~~~~~~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN   83 (112)
T 3d7c_A            4 DPDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYN   83 (112)
T ss_dssp             SHHHHHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHHHHcCCCchhhcCCCCcccccCHHHHccCCcCHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHC
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhh
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRYL  209 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~~  209 (277)
                      +++|.+|.+|..|+..|+..+.++.
T Consensus        84 ~~~s~~~~~A~~L~~~f~~~~~~~~  108 (112)
T 3d7c_A           84 PPDSEYCRCASALEKFFYFKLKEGG  108 (112)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            9999999999999999999998764

>2grc_A Probable global transcription activator SNF2L4; bromodomain, BRG1, chromatin remodelling, acely-lysine binding, protein-protein interactions; 1.50A {Homo sapiens} PDB: 3uvd_A 2h60_A

Probab=99.97  E-value=4.9e-30  Score=206.89  Aligned_cols=113  Identities=19%  Similarity=0.360  Sum_probs=105.1

Q ss_pred             CCCChHHHHHHHHHHHHHHHcCC-------CCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHH
Q psy16435        102 YRSTEEDLRIGMHKVMNRLKSHE-------DAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQ  174 (277)
Q Consensus       102 ~~~~~~~l~~~l~~il~~l~~~~-------~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~  174 (277)
                      +.+.+..|...|..||+.|..+.       .+++|..||+...+||||++|++||||+||++||.+|.|.++.+|.+||+
T Consensus         5 ~~~~~~~l~~~~~~il~~l~~~~d~~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~   84 (129)
T 2grc_A            5 LSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVM   84 (129)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHH
T ss_pred             cCCCcHHHHHHHHHHHHHHHhcccccccCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            44566799999999999999875       48899999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhcCCCCHHHHHHHHHHHHHHHHHHHhhcccCC
Q psy16435        175 LIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERS  214 (277)
Q Consensus       175 lm~~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~~  214 (277)
                      |||.||++||+++|.+|.+|..|+++|...+.++.....+
T Consensus        85 Li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~~~~  124 (129)
T 2grc_A           85 LLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDS  124 (129)
T ss_dssp             HHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHHTC-
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccCCCcc
Confidence            9999999999999999999999999999999999876543

>2oss_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.35A {Homo sapiens} PDB: 2yel_A* 3mxf_A* 3p5o_A* 3svf_A* 3svg_A* 3u5j_A* 3u5k_A* 3u5l_A* 3uvw_A* 3uvx_A* 3uvy_A* 3uw9_A* 3zyu_A* 4a9l_A* 4e96_A* 3jvj_A 3jvk_A* 3muk_A* 3mul_A* 2nxb_A ...

Probab=99.96  E-value=1.1e-29  Score=204.38  Aligned_cols=108  Identities=28%  Similarity=0.553  Sum_probs=102.0

Q ss_pred             CCChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhh
Q psy16435        103 RSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNC  180 (277)
Q Consensus       103 ~~~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na  180 (277)
                      .....+|+..|..||..|+.++.+++|..||+..  .+||||++|++||||+||++||.+|.|.++.+|.+||+|||.||
T Consensus        16 ~r~~~~l~~~~~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na   95 (127)
T 2oss_A           16 KRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNC   95 (127)
T ss_dssp             CCCCHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHhCccchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            3445789999999999999999999999999975  89999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        181 RKYNGLDNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       181 ~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      ++||+++|.+|.+|..|++.|+..+.+++.
T Consensus        96 ~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  125 (127)
T 2oss_A           96 YIYNKPGDDIVLMAEALEKLFLQKINELPT  125 (127)
T ss_dssp             HHHSCTTCHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            999999999999999999999999988754

>2dat_A Possible global transcription activator SNF2L2; bromodomain, all alpha protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.96  E-value=9e-30  Score=203.75  Aligned_cols=109  Identities=19%  Similarity=0.372  Sum_probs=102.6

Q ss_pred             CCCChHHHHHHHHHHHHHHHcCC------CCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHH
Q psy16435        102 YRSTEEDLRIGMHKVMNRLKSHE------DAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL  175 (277)
Q Consensus       102 ~~~~~~~l~~~l~~il~~l~~~~------~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~l  175 (277)
                      ...+...|...|..||+.|..+.      .+++|..||+...+||||++|++||||+||++||.++.|.++++|.+||+|
T Consensus         7 ~~~~~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~l   86 (123)
T 2dat_A            7 GSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVML   86 (123)
T ss_dssp             CSCCCHHHHHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCTTTSCHHHHHCSSCCCHHHHHHHHTTTCCCSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhhcccCCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence            34456799999999999999886      488999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhhcCCCCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        176 IVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       176 m~~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      ||.||++||+++|.+|.+|..|+++|+..+++++.
T Consensus        87 i~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~ps  121 (123)
T 2dat_A           87 LCHNAQTFNLEGSQIYEDSIVLQSVFKSARQSGPS  121 (123)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHcCC
Confidence            99999999999999999999999999999988764

>2i7k_A Bromodomain-containing protein 7; helix, LEFT-handed four-helix bundle, transcription; NMR {Homo sapiens}

Probab=99.96  E-value=1.4e-29  Score=200.96  Aligned_cols=106  Identities=25%  Similarity=0.420  Sum_probs=102.0

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ..+|+..|..||..|+.++.+++|..||++..+||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||+
T Consensus         6 ~~~l~~~l~~il~~L~~~~~~~~F~~PVd~~~~pdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Li~~Na~~yN~   85 (117)
T 2i7k_A            6 QTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNK   85 (117)
T ss_dssp             HHHHHHHHHHHHHHHHTSSGGGTSSSCCCTTTSSSHHHHCSCCCCHHHHHHHHTTTSCCSHHHHHHHHHHHHHHHHHTSC
T ss_pred             hHHHHHHHHHHHHHHHhCcccHHhcCCCCccccCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            56889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        186 LDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      ++|.+|.+|..|++.|...+..++-.
T Consensus        86 ~~s~i~~~A~~L~~~f~~~~~~~~~~  111 (117)
T 2i7k_A           86 PETIYYKAAKKLLHSGMKILSQERLE  111 (117)
T ss_dssp             SSSSHHHHHHHHHHHHHHHHHHHTCS
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999987643

>2d9e_A Peregrin; four-helix bundle, transcription activator, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.96  E-value=1.6e-29  Score=201.76  Aligned_cols=104  Identities=32%  Similarity=0.563  Sum_probs=100.3

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCC
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGL  186 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~  186 (277)
                      .+|...|..||+.|+.++.+++|..||++..+||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||++
T Consensus         6 ~pl~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~   85 (121)
T 2d9e_A            6 SGFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAK   85 (121)
T ss_dssp             CHHHHHHHHHHHHHHHHCSSCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCT
T ss_pred             cHHHHHHHHHHHHHHcCCccHhhCCcCCccccCCHHHHcCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        187 DNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       187 ~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      +|.+|.+|..|++.|...+.++..
T Consensus        86 ~s~~~~~A~~L~~~~~~~l~~~~~  109 (121)
T 2d9e_A           86 DTIFYRAAVRLREQGGAVLRQARR  109 (121)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999987754

>4alg_A Bromodomain-containing protein 2; signaling protein, inhibitor, histone, epigenetic reader; HET: 1GH; 1.60A {Homo sapiens} PDB: 4a9e_A 4a9h_A* 4a9i_A* 4a9j_A* 4a9m_A* 4a9n_A* 4a9o_A* 4a9p_A* 4a9f_A* 4alh_A* 4akn_A* 2yek_A* 2ydw_A* 2yw5_A

Probab=99.96  E-value=1e-29  Score=210.94  Aligned_cols=110  Identities=29%  Similarity=0.496  Sum_probs=104.1

Q ss_pred             CCCChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHh
Q psy16435        102 YRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDN  179 (277)
Q Consensus       102 ~~~~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~N  179 (277)
                      -.....+|+..|..||+.|+.++.+++|..||+..  .+||||++|++||||+||++||.++.|.++++|..||+|||.|
T Consensus        26 ~~r~t~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N  105 (154)
T 4alg_A           26 PGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTN  105 (154)
T ss_dssp             CCCCBHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             CCcchHHHHHHHHHHHHHHHhCcCchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            34456799999999999999999999999999988  6999999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        180 CRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       180 a~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      |++||+++|.||.+|..|+++|+..+.++...
T Consensus       106 a~~YN~~~s~i~~~A~~L~~~f~~~~~~l~~~  137 (154)
T 4alg_A          106 CYIYNKPTDDIVLMAQTLEKIFLQKVASMPQE  137 (154)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHTTSCSS
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHCCch
Confidence            99999999999999999999999999988654

>3q2e_A Bromodomain and WD repeat-containing protein 1; structural genomics consortium, SGC, cell cycle progression, signal transduction, apoptosis; 1.74A {Homo sapiens}

Probab=99.96  E-value=1.3e-29  Score=202.77  Aligned_cols=109  Identities=28%  Similarity=0.479  Sum_probs=102.7

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ...|+..|..||+.|..++.+++|..||++..+||||++|++||||+||++||.+|.|.++.+|..||+|||.||+.||+
T Consensus         8 ~~~~~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   87 (123)
T 3q2e_A            8 ESNWKKQCKELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTP   87 (123)
T ss_dssp             --CHHHHHHHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHhCCCcHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C-CCHHHHHHHHHHHHHHHHHHHhhcccCC
Q psy16435        186 L-DNEYTDMVRRLQQIFRDAVSRYLDGERS  214 (277)
Q Consensus       186 ~-~s~i~~~A~~L~~~f~~~~~~~~~~~~~  214 (277)
                      + +|.+|.+|..|+.+|+..+.++++....
T Consensus        88 ~~~s~i~~~A~~L~~~f~~~~~~~~~~~~~  117 (123)
T 3q2e_A           88 NKRSKIYSMTLRLSALFEEKMKKISSDFKI  117 (123)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6 9999999999999999999999876543

>1e6i_A Transcriptional activator GCN5; gene regulation, bromodomain, histone binding, N-acetyl lysine; HET: ALY; 1.87A {Saccharomyces cerevisiae} SCOP: a.29.2.1

Probab=99.96  E-value=1.9e-29  Score=201.29  Aligned_cols=102  Identities=35%  Similarity=0.771  Sum_probs=98.3

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCC
Q psy16435        109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDN  188 (277)
Q Consensus       109 l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s  188 (277)
                      ....|..||..|+.++.+++|..||+...+||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||+++|
T Consensus        14 ~~~~~~~il~~l~~~~~a~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s   93 (121)
T 1e6i_A           14 HDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENT   93 (121)
T ss_dssp             THHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTS
T ss_pred             HHHHHHHHHHHHHcCCCchhhCCCCChhhCcCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhc
Q psy16435        189 EYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       189 ~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      .+|.+|..|++.|+..+..++.
T Consensus        94 ~i~~~A~~L~~~f~~~~~~~p~  115 (121)
T 1e6i_A           94 SYYKYANRLEKFFNNKVKEIPE  115 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSGG
T ss_pred             HHHHHHHHHHHHHHHHHHHccc
Confidence            9999999999999999988754

>3p1f_A CREB-binding protein; structural genomics consortium, SGC, CBP, crebbp, CREB bindi protein isoform A, KAT3A, RSTS, RST, bromodomain, transcrip; HET: 3PF; 1.63A {Homo sapiens} SCOP: a.29.2.1 PDB: 3dwy_A 3p1d_A 3p1c_A 3p1e_A* 3svh_A* 4a9k_A* 1jsp_B* 2d82_A* 2l84_A* 2l85_A* 2rny_A* 3i3j_A

Probab=99.96  E-value=5e-29  Score=198.25  Aligned_cols=108  Identities=27%  Similarity=0.531  Sum_probs=102.5

Q ss_pred             CCChHHHHHHHHHHHHHHHc-CCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHh
Q psy16435        103 RSTEEDLRIGMHKVMNRLKS-HEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDN  179 (277)
Q Consensus       103 ~~~~~~l~~~l~~il~~l~~-~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~N  179 (277)
                      .....+|...|..+|..|.. ++.+++|..||++.  .+||||++|++||||+||++||.+|.|.++++|.+||+|||.|
T Consensus         6 ~~~~~el~~~l~~~l~~l~~~~~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~N   85 (119)
T 3p1f_A            6 IFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNN   85 (119)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHhCCCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            34578999999999999988 67999999999988  7999999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        180 CRKYNGLDNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       180 a~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      |++||+++|.+|.+|..|+..|++.+..++.
T Consensus        86 a~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  116 (119)
T 3p1f_A           86 AWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQ  116 (119)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999998865

>3nxb_A CAT eye syndrome critical region protein 2; structural genomics consortium, SGC, CECR2, CAT eye syndrome chromosome region candidate 2, bromodomain; 1.83A {Homo sapiens} SCOP: a.29.2.0

Probab=99.96  E-value=2.1e-29  Score=199.57  Aligned_cols=100  Identities=47%  Similarity=0.838  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      ++...|..+|..|+.++.+++|..||++..+||||++|++||||+||++||.+|.|.++++|..||+|||.||+.||+++
T Consensus        16 ~~~~~~~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~   95 (116)
T 3nxb_A           16 DDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGES   95 (116)
T ss_dssp             CHHHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHHhCCCcHhhcCcCChhhccChHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q psy16435        188 NEYTDMVRRLQQIFRDAVSR  207 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~~  207 (277)
                      |.++.+|..|+.+|+..|.+
T Consensus        96 s~~~~~A~~L~~~f~~~~~k  115 (116)
T 3nxb_A           96 SEYTKMSDNLERCFHRAMMK  115 (116)
T ss_dssp             CHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999998864

>3mb3_A PH-interacting protein; PHIP, pleckstrin homology domain interacting protein, DCAF14 DDB1 and CUL4 associated factor 14, SGC; 2.25A {Homo sapiens}

Probab=99.96  E-value=2.2e-29  Score=204.62  Aligned_cols=107  Identities=28%  Similarity=0.460  Sum_probs=102.8

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ...|...|..||+.|..++.+++|..||+...+||||++|++||||+||++||.+|.|.++++|..||.|||.||+.||+
T Consensus        19 ~~~l~~~~~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   98 (135)
T 3mb3_A           19 IQAWKKQCEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTP   98 (135)
T ss_dssp             SSTHHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHhCCCChhhcCCCChhhCCCHHHHhCCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C-CCHHHHHHHHHHHHHHHHHHHhhccc
Q psy16435        186 L-DNEYTDMVRRLQQIFRDAVSRYLDGE  212 (277)
Q Consensus       186 ~-~s~i~~~A~~L~~~f~~~~~~~~~~~  212 (277)
                      + +|.||.+|..|+++|+..+..+++..
T Consensus        99 ~~~s~i~~~A~~L~~~f~~~~~~~~~~~  126 (135)
T 3mb3_A           99 SKRSRIYSMSLRLSAFFEEHISSVLSDY  126 (135)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7 89999999999999999999987753

>3ljw_A Protein polybromo-1; alpha helix, alternative splicing, bromodomain, chromatin RE DNA-binding, nucleus, phosphoprotein, transcription; 1.50A {Homo sapiens} PDB: 2ktb_B* 3hmf_A

Probab=99.96  E-value=7.3e-29  Score=197.63  Aligned_cols=107  Identities=19%  Similarity=0.364  Sum_probs=101.8

Q ss_pred             ChHHHHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q psy16435        105 TEEDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVD  178 (277)
Q Consensus       105 ~~~~l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~  178 (277)
                      .+..|+..|..+++.|..+.+      +++|..||+...+||||++|++||||+||++||.+|.|.++.+|..||+|||.
T Consensus         5 ~p~~l~~~~~~ll~~l~~~~d~~g~~~s~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~   84 (120)
T 3ljw_A            5 SPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAK   84 (120)
T ss_dssp             CHHHHHHHHHHHHHHHHHCBCTTSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHhccCcCCCcccHHhcCCCCcccCCChHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHH
Confidence            356889999999999998877      99999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        179 NCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       179 Na~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      ||+.||+++|.+|.+|..|+++|+..+.++...
T Consensus        85 Na~~yN~~~s~~~~~A~~L~~~f~~~~~~i~~~  117 (120)
T 3ljw_A           85 NAKTYNEPGSQVFKDANSIKKIFYMKKAEIEHH  117 (120)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence            999999999999999999999999999988643

>3hme_A Bromodomain-containing protein 9; BRD9, bromodomain containing 9 isoform 1, LAVS3040, rhabdomyosarcoma antigen MU-RMS-40.8; 2.23A {Homo sapiens}

Probab=99.96  E-value=9e-29  Score=197.93  Aligned_cols=101  Identities=30%  Similarity=0.499  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      +++..|..||..|..++.+++|..||++..+||||++|++||||+||++||.+|.|.++++|..||+|||.||+.||+++
T Consensus        13 p~~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~   92 (123)
T 3hme_A           13 PIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPD   92 (123)
T ss_dssp             HHHHHHHHHHHHHHTTCTTCSSSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHHHhCCccHhhcCCCChhhccCHHHHCCCCCCHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHh
Q psy16435        188 NEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      |.+|.+|..|.+.|...+.+.
T Consensus        93 s~~~~~A~~L~~~~~~~~~~~  113 (123)
T 3hme_A           93 TVYYKLAKKILHAGFKMMSKE  113 (123)
T ss_dssp             SHHHHHHHHHHHHHHHHTCHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999987653

>3rcw_A Bromodomain-containing protein 1; transcription, structural genomics, structural consortium, SGC; 2.21A {Homo sapiens}

Probab=99.96  E-value=1.4e-28  Score=199.82  Aligned_cols=103  Identities=32%  Similarity=0.587  Sum_probs=100.3

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        108 DLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      +|...|..||+.|+.++.+++|..||+...+||||++|++||||+||++||.+|.|.++++|..||+|||.||+.||+++
T Consensus        13 ~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~   92 (135)
T 3rcw_A           13 PLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD   92 (135)
T ss_dssp             HHHHHHHHHHHHHHHTCTTCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHHHhCCcchhhcCCCChhhcCCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        188 NEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      |.+|.+|..|.+.|...+..+..
T Consensus        93 s~~~~~A~~L~~~~~~~~~~~~~  115 (135)
T 3rcw_A           93 TVFYRAAVRLRDQGGVVLRQARR  115 (135)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998744

>3mb4_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo-1D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 1.66A {Homo sapiens} PDB: 3g0j_A 2yqd_A

Probab=99.96  E-value=8.5e-29  Score=198.34  Aligned_cols=103  Identities=18%  Similarity=0.349  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHHHcC------CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhh
Q psy16435        107 EDLRIGMHKVMNRLKSH------EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNC  180 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~------~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na  180 (277)
                      .+|+..|..||+.|..+      ..+++|..||+...+||||++|++||||+||++||.+|.|.++++|..||+|||.||
T Consensus        14 ~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na   93 (124)
T 3mb4_A           14 TPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNA   93 (124)
T ss_dssp             CHHHHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhHhcccCCcccHHhhcCCCccccCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            38899999999999984      447999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q psy16435        181 RKYNGLDNEYTDMVRRLQQIFRDAVSRYL  209 (277)
Q Consensus       181 ~~YN~~~s~i~~~A~~L~~~f~~~~~~~~  209 (277)
                      ++||+++|.+|.+|..|+++|...+.++.
T Consensus        94 ~~yN~~~s~i~~~A~~L~~~f~~~~~~l~  122 (124)
T 3mb4_A           94 CTYNEPESLIYKDALVLHKVLLETRRDLE  122 (124)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999874

>3k2j_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo01D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.20A {Homo sapiens}

Probab=99.96  E-value=1.4e-28  Score=198.60  Aligned_cols=110  Identities=25%  Similarity=0.458  Sum_probs=103.3

Q ss_pred             CCChHHHHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHH
Q psy16435        103 RSTEEDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLI  176 (277)
Q Consensus       103 ~~~~~~l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm  176 (277)
                      ......|...|..+++.|....+      +++|..||+...+||||++|++||||+||++||.++.|.|+++|..||+||
T Consensus        12 ~~~~~kl~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~~~PdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~Li   91 (130)
T 3k2j_A           12 DLGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLM   91 (130)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHHHhcccCCCccHhhcCCCChhhCccHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            34567899999999999998755      899999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhcCCCCHHHHHHHHHHHHHHHHHHHhhccc
Q psy16435        177 VDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGE  212 (277)
Q Consensus       177 ~~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~~  212 (277)
                      |.||++||+++|.+|.+|..|++.|+..+.++....
T Consensus        92 f~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~~  127 (130)
T 3k2j_A           92 FENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARRD  127 (130)
T ss_dssp             HHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            999999999999999999999999999999987643

>2ouo_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.89A {Homo sapiens} PDB: 2yem_A*

Probab=99.96  E-value=7.6e-29  Score=200.18  Aligned_cols=105  Identities=32%  Similarity=0.611  Sum_probs=97.6

Q ss_pred             hHHHHHHHHHHHHHHHcCCC---CCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhh
Q psy16435        106 EEDLRIGMHKVMNRLKSHED---AWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNC  180 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~---s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na  180 (277)
                      .......|..||..|..++.   +++|..||++.  .+||||++|++||||+||++||.+|.|.++.+|.+||+|||.||
T Consensus        20 ~~~~l~~c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na   99 (130)
T 2ouo_A           20 VSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNC   99 (130)
T ss_dssp             HHHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            34556779999999998875   89999999987  49999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        181 RKYNGLDNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       181 ~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      ++||+++|.+|.+|..|+.+|+..|.+++.
T Consensus       100 ~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  129 (130)
T 2ouo_A          100 YKYNPPDHEVVAMARKLQDVFEMRFAKMPD  129 (130)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            999999999999999999999999998764

>3mqm_A Probable histone-lysine N-methyltransferase ASH1L; KIAA1420, absent small and homeotic disks prote homolog, lysine N-methyltransferase 2H, KMT2H; 2.54A {Homo sapiens}

Probab=99.96  E-value=9.4e-29  Score=198.59  Aligned_cols=106  Identities=26%  Similarity=0.393  Sum_probs=100.3

Q ss_pred             HHHHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhh
Q psy16435        107 EDLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNC  180 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na  180 (277)
                      ..|+..|..+++.|..+.+      +++|..||+...+||||++|++||||+||++||.+|.|.++++|.+||+|||.||
T Consensus         8 ~~l~~~~~~i~~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na   87 (126)
T 3mqm_A            8 ARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNA   87 (126)
T ss_dssp             HHHHHHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGGGCTTHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCcCCCChhHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            4788899999999998754      8999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHhhccc
Q psy16435        181 RKYNGLDNEYTDMVRRLQQIFRDAVSRYLDGE  212 (277)
Q Consensus       181 ~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~~  212 (277)
                      +.||+++|.+|.+|..|+++|+..+.++.+..
T Consensus        88 ~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~~l  119 (126)
T 3mqm_A           88 EKYYGRKSPVGRDVCRLRKAYYNARHEASAQI  119 (126)
T ss_dssp             HHHHCTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999887653

>3fkm_X Signaling protein; bromodomain, malaria, structural genomics, structural genomi consortium, SGC; 2.50A {Plasmodium falciparum 3D7}

Probab=99.96  E-value=1.1e-28  Score=207.04  Aligned_cols=110  Identities=25%  Similarity=0.410  Sum_probs=100.0

Q ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q psy16435        100 GGYRSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIV  177 (277)
Q Consensus       100 ~~~~~~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~  177 (277)
                      ....+...+|+..|..||..|+.++.+++|..||++.  .+||||++|++||||+||++||.+|.|.++.+|..||+|||
T Consensus        13 ~~~~p~~~~~~~~~~~il~~L~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~Dv~Lif   92 (166)
T 3fkm_X           13 NLYFQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIF   92 (166)
T ss_dssp             ----CTTHHHHHHHHHHHHHHTTSTTGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHH
T ss_pred             cCCCcccHHHHHHHHHHHHHHHhCCCChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence            3445567899999999999999999999999999976  69999999999999999999999999999999999999999


Q ss_pred             HhhhhhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q psy16435        178 DNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL  209 (277)
Q Consensus       178 ~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~~~  209 (277)
                      .||++||+++|.||.+|..|+++|...|.++.
T Consensus        93 ~Na~~yN~~~s~i~~~A~~L~~~f~~~l~~~~  124 (166)
T 3fkm_X           93 DNCSLYNTSNSVVAITGKNIETYFNNQLIVMG  124 (166)
T ss_dssp             HHHHHSSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            99999999999999999999999999998864

>3iu5_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; 1.63A {Homo sapiens}

Probab=99.95  E-value=1.6e-28  Score=194.59  Aligned_cols=103  Identities=22%  Similarity=0.443  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhh
Q psy16435        109 LRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRK  182 (277)
Q Consensus       109 l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~  182 (277)
                      ....|..|++.|..+.+      +++|..||+...+||||++|++||||+||++||.+|.|.++.+|..||+|||.||+.
T Consensus         6 ~~~~c~~il~~l~~~~d~~g~~~s~~F~~p~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~   85 (116)
T 3iu5_A            6 PIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKS   85 (116)
T ss_dssp             HHHHHHHHHHHHHHCBCTTCCBGGGGGSSCCCGGGCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhccCCCeeeHHhcCCCCcccCCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence            46779999999998744      899999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        183 YNGLDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       183 YN~~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      ||+++|.+|.+|..|+++|+..+.+++..
T Consensus        86 yN~~~s~~~~~A~~L~~~f~~~~~~l~~~  114 (116)
T 3iu5_A           86 YYKPDSPEYKAACKLWDLYLRTRNEFVQK  114 (116)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999764

>3jvl_A Bromodomain-containing protein 4; alpha helical, N-acetyl lysine binding domain, signaling protein; 1.20A {Mus musculus} PDB: 3jvm_A 2dww_A 2i8n_A 3oni_A* 2dvv_A* 2e3k_A* 2g4a_A 3s92_A* 2oo1_A* 2e7n_A 2wp1_A*

Probab=99.95  E-value=4.4e-29  Score=198.88  Aligned_cols=104  Identities=32%  Similarity=0.621  Sum_probs=98.5

Q ss_pred             HHHHHHHHHHHHHHcCCC---CCCCCCCCCCCC--CcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhh
Q psy16435        108 DLRIGMHKVMNRLKSHED---AWPFCDPVDEAT--APNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRK  182 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~---s~~F~~pv~~~~--~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~  182 (277)
                      +....|..||..|..++.   +++|..||++..  +||||++|++||||+||++||.+|.|.++++|..||+|||.||++
T Consensus         9 ~~l~~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~   88 (120)
T 3jvl_A            9 EQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYK   88 (120)
T ss_dssp             HHHHHHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHH
Confidence            567789999999999887   899999999987  999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        183 YNGLDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       183 YN~~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      ||+++|.+|.+|..|+..|+..+.+++..
T Consensus        89 yN~~~s~~~~~A~~L~~~f~~~~~~~p~~  117 (120)
T 3jvl_A           89 YNPPDHEVVAMARKLQDVFEMRFAKMPDE  117 (120)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHTTCCC-
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHCcCC
Confidence            99999999999999999999999988653

>2yyn_A Transcription intermediary factor 1-alpha; bromo domain, structural genomics, NPPSFA; 2.50A {Homo sapiens}

Probab=99.95  E-value=3.6e-28  Score=197.41  Aligned_cols=106  Identities=31%  Similarity=0.534  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhC--CCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDA--GRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~--~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      +..+..|..||..|+.++.+++|..||+. .+||||++|++||||+||++||.+  +.|.++.+|.+||+|||.||++||
T Consensus        19 p~~~~~c~~il~~L~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmDL~tI~~kL~~~~~~Y~s~~ef~~Dv~Lif~Na~~yN   97 (135)
T 2yyn_A           19 PIDKRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFN   97 (135)
T ss_dssp             HHHHHHHHHHHHHHHTSGGGGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHHSSSCCCSSHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHhCccchhhcCCCcc-cCCCHHHHcCCCCCHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHHC
Confidence            34567899999999999999999999997 799999999999999999999998  599999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhcccC
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRYLDGER  213 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~~~~~~  213 (277)
                      +++|.+|.+|..|+.+|+..+.++++...
T Consensus        98 ~~~s~i~~~A~~L~~~f~~~~~~~~~~~~  126 (135)
T 2yyn_A           98 EPDSEVANAGIKLENYFEELLKNLYPEKR  126 (135)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhccccC
Confidence            99999999999999999999999987653

>3uv4_A Second bromodomain of human transcription initiat TFIID subunit 1 (TAF1); structural genomics consortium, SGC; 1.89A {Homo sapiens} PDB: 3hmh_A

Probab=99.95  E-value=1.6e-27  Score=198.46  Aligned_cols=106  Identities=25%  Similarity=0.595  Sum_probs=96.2

Q ss_pred             hHHHHHHHHHHHHH-HHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        106 EEDLRIGMHKVMNR-LKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       106 ~~~l~~~l~~il~~-l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      ...|...|..|+.. |+.++.+++|..||++..+||||++|++||||+||++||.+|.|.++.+|..||+|||.||++||
T Consensus        27 ~~~l~~iL~~i~~~kl~~~~~s~~F~~PVd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~yN  106 (158)
T 3uv4_A           27 QVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYN  106 (158)
T ss_dssp             HHHHHHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCchhhcCcCChhhcccHHHHcCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            34555566666554 67789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      +++|.+|.+|..|...|...+.++...
T Consensus       107 ~~~s~i~~~A~~L~~~~~~~l~e~~~~  133 (158)
T 3uv4_A          107 GPESQYTKTAQEIVNVCYQTLTEYDEH  133 (158)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999988654

>3dai_A ATPase family AAA domain-containing protein 2; ancca, AAA+ nuclear coregulator cancer-associated Pro2000 protein, two AAA DOMA containing protein; 1.95A {Homo sapiens} PDB: 3lxj_A

Probab=99.94  E-value=6.2e-27  Score=188.95  Aligned_cols=103  Identities=28%  Similarity=0.402  Sum_probs=95.1

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ...|+..|..+++.|..++.+++|..||++..+||||++|++||||+||++||.+|.|.++.+|..||+|||.||++||+
T Consensus         8 l~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   87 (130)
T 3dai_A            8 FRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP   87 (130)
T ss_dssp             HHHHHHHHHHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHcCCccHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            34788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHH----HHHHHHHHHHHHHHHHHh
Q psy16435        186 LDNEY----TDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       186 ~~s~i----~~~A~~L~~~f~~~~~~~  208 (277)
                      ++|++    +.+|..|...+...+..-
T Consensus        88 ~~s~~~~~i~~~A~~L~~~~~~~i~~e  114 (130)
T 3dai_A           88 DRDPGDRLIRHRACALRDTAYAIIKEE  114 (130)
T ss_dssp             SSSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHH
Confidence            99976    677888888888777633

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=99.94  E-value=2.7e-27  Score=199.87  Aligned_cols=103  Identities=38%  Similarity=0.723  Sum_probs=98.4

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      .......|..||..|..++.+++|..||++..+|+||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||+
T Consensus        70 ~~~~~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~  149 (174)
T 2ri7_A           70 TEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNP  149 (174)
T ss_dssp             CHHHHHHHHHHHHHHHTSGGGTTTSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCBHHHHHHHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHHHHHHhhhhhhhhhcCCCcccCCchHHHhCCcCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHh
Q psy16435        186 LDNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      ++|.+|.+|..|+++|++.+..+
T Consensus       150 ~~s~~~~~A~~L~~~f~~~~~~~  172 (174)
T 2ri7_A          150 SDSPFYQCAEVLESFFVQKLKGF  172 (174)
T ss_dssp             TTSHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999988765

>3tlp_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo-1D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.13A {Homo sapiens}

Probab=99.94  E-value=9e-27  Score=192.39  Aligned_cols=103  Identities=19%  Similarity=0.308  Sum_probs=95.5

Q ss_pred             HHHHHHHHHHHHcCCC-------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhh
Q psy16435        110 RIGMHKVMNRLKSHED-------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRK  182 (277)
Q Consensus       110 ~~~l~~il~~l~~~~~-------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~  182 (277)
                      ...|..|++.|.....       +.+|..||+...+||||++|++||||+||++||.+|.|.++.+|..||+|||.||++
T Consensus        26 ~~~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~  105 (150)
T 3tlp_A           26 KQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARH  105 (150)
T ss_dssp             HHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccCCcccHHhcCCCchhhCcCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            5677888888876544       899999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHHhhccc
Q psy16435        183 YNGLDNEYTDMVRRLQQIFRDAVSRYLDGE  212 (277)
Q Consensus       183 YN~~~s~i~~~A~~L~~~f~~~~~~~~~~~  212 (277)
                      ||+++|.+|.+|..|+++|...+.++.+..
T Consensus       106 yN~~~s~i~~~A~~L~~~f~~~~~~l~~~p  135 (150)
T 3tlp_A          106 YNEEGSQVYNDAHILEKLLKEKRKELGPLP  135 (150)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHCCC-
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHccCCC
Confidence            999999999999999999999999997543

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=99.94  E-value=1.7e-26  Score=196.77  Aligned_cols=107  Identities=30%  Similarity=0.503  Sum_probs=100.8

Q ss_pred             CCChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhC--CCCCCHHHHHHHHHHHHHhh
Q psy16435        103 RSTEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDA--GRYKTFGQFRADFQLIVDNC  180 (277)
Q Consensus       103 ~~~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~--~~Y~s~~~f~~Dv~lm~~Na  180 (277)
                      ......++..|..||..|..++.+++|..||+. .+|+||++|++||||+||++||.+  |.|.++.+|.+||+|||.||
T Consensus        76 ~~l~~~~~~~c~~il~~l~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmdL~tI~~kl~~~~~~Y~s~~ef~~Dv~li~~Na  154 (184)
T 3o36_A           76 VKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNC  154 (184)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHSTTCHHHHSCCCT-TSTTHHHHCSSCCCHHHHHHHHHSTTCSCCSHHHHHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHHHHHhchhhhhhcccccc-CCCchhhhcCCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence            345567889999999999999999999999995 599999999999999999999998  79999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        181 RKYNGLDNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       181 ~~YN~~~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      ++||+++|.||.+|..|+++|++.+.++++
T Consensus       155 ~~yN~~~s~v~~~a~~L~~~f~~~~~~~~P  184 (184)
T 3o36_A          155 AEFNEPDSEVANAGIKLENYFEELLKNLYP  184 (184)
T ss_dssp             HHHSCTTCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHhCc
Confidence            999999999999999999999999998864

>2dkw_A Hypothetical protein KIAA1240; bromodomain-like, five-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.93  E-value=1.5e-25  Score=180.88  Aligned_cols=101  Identities=30%  Similarity=0.428  Sum_probs=93.8

Q ss_pred             ChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       105 ~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      +..+|+..|..||+.|..++.+++|..|     +||||++|++||||+||++||.+|.|.++.+|..||+|||.||++||
T Consensus         9 ~~~~L~~~~~~il~~l~~~~~~~~F~~P-----~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN   83 (131)
T 2dkw_A            9 TLRELRLFLRDVTKRLATDKRFNIFSKP-----VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN   83 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHSGGGCTTSSC-----CSSCTTSCSSCCCHHHHHHHHHTTCCCSSHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHhCccchhhcCc-----CccHHhHcCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            4568899999999999999999999998     89999999999999999999999999999999999999999999999


Q ss_pred             CCCCH----HHHHHHHHHHHHHHHHHHhhc
Q psy16435        185 GLDNE----YTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       185 ~~~s~----i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      +++|+    ++.+|..|...|...+..-+.
T Consensus        84 ~~~s~~~~~i~~~A~~L~~~~~~~l~~~l~  113 (131)
T 2dkw_A           84 PDKDPGDKIIRHRACTLKDTAHAIIAAELD  113 (131)
T ss_dssp             CCSSTTHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99995    578999999999988865443

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A

Probab=99.93  E-value=2e-25  Score=200.42  Aligned_cols=104  Identities=25%  Similarity=0.510  Sum_probs=100.7

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ...|...|..||..|..++.+++|..||++..+||||.+|++||||+||++||.+|.|.++.+|..||+|||.||++||+
T Consensus        12 ~~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   91 (265)
T 3uv5_A           12 MVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNG   91 (265)
T ss_dssp             HHHHHHHHHHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHcCCCchhhhCCCChhhcCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhhhcCC
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhh
Q psy16435        186 LDNEYTDMVRRLQQIFRDAVSRYL  209 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~~~~~  209 (277)
                      ++|.+|.+|..|...|...+.++.
T Consensus        92 ~~s~i~~~A~~l~~~~~~~~~~~~  115 (265)
T 3uv5_A           92 PKHSLTQISQSMLDLCDEKLKEKE  115 (265)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHTH
T ss_pred             CCChHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999998764

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=99.92  E-value=4e-25  Score=191.69  Aligned_cols=107  Identities=29%  Similarity=0.505  Sum_probs=101.3

Q ss_pred             ChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhC---CCCCCHHHHHHHHHHHHHhhh
Q psy16435        105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDA---GRYKTFGQFRADFQLIVDNCR  181 (277)
Q Consensus       105 ~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~---~~Y~s~~~f~~Dv~lm~~Na~  181 (277)
                      .....+..|..||..|..++.+++|..||+. .+|+||++|++||||+||++||.+   |.|.++.+|..||+|||.||+
T Consensus        78 ls~~~~~~c~~il~~l~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li~~Na~  156 (207)
T 3u5n_A           78 LSPVDQRKCERLLLYLYCHELSIEFQEPVPA-SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCE  156 (207)
T ss_dssp             SCHHHHHHHHHHHHHHHTSTTCGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccchhhhhccCCh-hhccHhHHhCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHHH
Confidence            3456788899999999999999999999996 799999999999999999999997   799999999999999999999


Q ss_pred             hhcC-----------------CCCHHHHHHHHHHHHHHHHHHHhhccc
Q psy16435        182 KYNG-----------------LDNEYTDMVRRLQQIFRDAVSRYLDGE  212 (277)
Q Consensus       182 ~YN~-----------------~~s~i~~~A~~L~~~f~~~~~~~~~~~  212 (277)
                      +||+                 ++|.++.+|..|+.+|+..+.+++++.
T Consensus       157 ~yN~~~s~v~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~~~~~~p~~  204 (207)
T 3u5n_A          157 RFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDR  204 (207)
T ss_dssp             HHHHHHHHHC----------CCCCHHHHHHHHHHHHHHHHHHHHSTTC
T ss_pred             HHCCCcchHHHHHHHHHhcccccCHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            9999                 999999999999999999999998764

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A

Probab=99.92  E-value=1.1e-24  Score=195.51  Aligned_cols=105  Identities=26%  Similarity=0.595  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHH-HHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        107 EDLRIGMHKVMNR-LKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       107 ~~l~~~l~~il~~-l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ..+...|..++.. |..++.+++|..||+...+||||++|++||||+||++||.+|.|.++.+|..||+|||.||++||+
T Consensus       135 ~~~~~il~~i~~~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~lif~Na~~yN~  214 (265)
T 3uv5_A          135 VAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG  214 (265)
T ss_dssp             HHHHHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTC
T ss_pred             hHHHHHHHHHHHHHHHhhhhhHHHhCCCChhHhCcHHHHhCCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            3456666666654 788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        186 LDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      ++|.+|.+|..|...|...+.++...
T Consensus       215 ~~s~~~~~A~~l~~~~~~~~~~~~~~  240 (265)
T 3uv5_A          215 PESQYTKTAQEIVNVCYQTLTEYDEH  240 (265)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999988644

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=99.92  E-value=4.1e-25  Score=189.03  Aligned_cols=103  Identities=17%  Similarity=0.237  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhcc--CCCcHHHHHHHHhCC---CCCCHHHHHHHHHHHHHhhh
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIK--RPMDLTRMEEKLDAG---RYKTFGQFRADFQLIVDNCR  181 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk--~PmdL~tI~~kl~~~---~Y~s~~~f~~Dv~lm~~Na~  181 (277)
                      ..-+..|..||..|..|+.++||++||+    |+||.+|+  +||||+||++||.++   .|.++++|++||+|||+||+
T Consensus        75 ~~~~~~c~~iL~~l~~~~~s~pF~~pV~----~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~Y~s~~eF~~Dv~Lif~N~~  150 (189)
T 2ro1_A           75 PANQRKCERVLLALFCHEPCRPLHQLAT----DSTFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFN  150 (189)
T ss_dssp             HHHHHHHHHHHHHHHHSTTHHHHHSCSC----CTTCSSSCSSCCCCHHHHHHHHHTSSSSCCSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccCccchhhcCCCC----hhhhccccCCCcccHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHH
Confidence            3445679999999999999999999999    78999998  899999999999999   99999999999999999999


Q ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHHHhhcccCC
Q psy16435        182 KYNGLDNEYTDMVRRLQQIFRDAVSRYLDGERS  214 (277)
Q Consensus       182 ~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~~  214 (277)
                      +|| +++.+|.+|..|+++|+..|.++++....
T Consensus       151 ~yN-~~s~~~~~a~~L~~~Fe~~~~~~~~~~~~  182 (189)
T 2ro1_A          151 KLT-EDKADVQSIIGLQRFFETRMNEAFGDTKF  182 (189)
T ss_dssp             HHC-CSSCSSHHHHHHHHHHHHHHHHHTTTSCS
T ss_pred             HHC-CCCHHHHHHHHHHHHHHHHHHHhcCcccC
Confidence            999 58889999999999999999999886543

>3aad_A Transcription initiation factor TFIID subunit 1; protein-protein complex, bromodomain, transcription, transcr regulation, chromatin regulator, transcription-C complex; 3.30A {Homo sapiens}

Probab=99.91  E-value=2.3e-24  Score=196.00  Aligned_cols=103  Identities=25%  Similarity=0.524  Sum_probs=97.9

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ...|...|..||+.|+.++.+++|+.||++..+||||++|++||||+||++||.+|.|.++.+|..||+|||.||++||+
T Consensus        45 ~~~l~~~~~~il~~l~~~~~a~~F~~pV~~~~~pdY~~iIk~PmDL~tIk~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~  124 (292)
T 3aad_A           45 MVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNG  124 (292)
T ss_dssp             HHHHHHHHHHHHHHHSSSTTCGGGSSSCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHhCCcchhhcCCCCchhcccHHHHcCCcCCHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHHHcC
Confidence            36678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHh
Q psy16435        186 LDNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      ++|.++.+|..|..+|...+..+
T Consensus       125 ~~s~i~~~A~~L~~~~~~~~~~~  147 (292)
T 3aad_A          125 PKHSLTQISQSMLDLCDEKLKEK  147 (292)
T ss_dssp             SSSHHHHHHTHHHHTTTTTGGGS
T ss_pred             CchHHHHHHHHHHHHHHhhhhcc
Confidence            99999999999999998777653

>3aad_A Transcription initiation factor TFIID subunit 1; protein-protein complex, bromodomain, transcription, transcr regulation, chromatin regulator, transcription-C complex; 3.30A {Homo sapiens}

Probab=99.90  E-value=5.3e-24  Score=193.58  Aligned_cols=103  Identities=26%  Similarity=0.621  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHH-HHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCC
Q psy16435        108 DLRIGMHKVMN-RLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGL  186 (277)
Q Consensus       108 ~l~~~l~~il~-~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~  186 (277)
                      .+...|..++. .|+.++.+++|..||+...+||||++|++||||+||++||.+|.|.++.+|..||+|||.||++||++
T Consensus       169 ~~~~~l~~i~~~~l~~~~~s~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~  248 (292)
T 3aad_A          169 AFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGP  248 (292)
T ss_dssp             HHHHHHHHHHHHTGGGSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHhhhhhhcCcchhHHHhcccccccccHHHHcCCcCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            34445555554 47889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        187 DNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       187 ~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      +|.+|.+|..|+..|...+..+..
T Consensus       249 ~s~i~~~A~~L~~~~~~~~~~~~~  272 (292)
T 3aad_A          249 ESQYTKTAQEIVNVCYQTLTEYDE  272 (292)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999988754

>2r0y_A Chromatin structure-remodeling complex protein RSC4; bromodomain, chromatin, remodeler, RSC, acetylation, transcription, chromatin regulator, nucleus, phosphorylation; HET: ALY; 1.75A {Saccharomyces cerevisiae} PDB: 2r0s_A

Probab=99.89  E-value=1.9e-23  Score=191.37  Aligned_cols=87  Identities=24%  Similarity=0.429  Sum_probs=84.0

Q ss_pred             cCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHH
Q psy16435        122 SHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF  201 (277)
Q Consensus       122 ~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f  201 (277)
                      .+..+++|+.||+...+||||+||++||||+||++||.+|.|.++.+|..||+|||.||++||+++|.+|.+|..|+.+|
T Consensus       177 ~~~~s~~F~~pvd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f  256 (311)
T 2r0y_A          177 KVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYF  256 (311)
T ss_dssp             SSCTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHH
T ss_pred             CCccHHHHhCCCChhhcccHHHHhCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHh
Q psy16435        202 RDAVSRY  208 (277)
Q Consensus       202 ~~~~~~~  208 (277)
                      +..+.+.
T Consensus       257 ~~~~~~~  263 (311)
T 2r0y_A          257 NYLIQKE  263 (311)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHh
Confidence            9999974

>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A*

Probab=99.88  E-value=3.7e-23  Score=193.18  Aligned_cols=86  Identities=24%  Similarity=0.434  Sum_probs=83.6

Q ss_pred             CCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHHHHHH
Q psy16435        123 HEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFR  202 (277)
Q Consensus       123 ~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s~i~~~A~~L~~~f~  202 (277)
                      +..+++|+.||+...+||||+||++||||+||++||.+|.|.++.+|..||+|||.||++||+++|.||.+|..|+.+|+
T Consensus       228 ~~~s~~F~~pvd~~~~PdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f~  307 (361)
T 2r10_A          228 VKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFN  307 (361)
T ss_dssp             SCTTGGGSSCCCTTTCTHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHH
T ss_pred             CcchhcccCCCChhhcccHHHHhcCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence            56799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHh
Q psy16435        203 DAVSRY  208 (277)
Q Consensus       203 ~~~~~~  208 (277)
                      ..+.+.
T Consensus       308 ~~~~~~  313 (361)
T 2r10_A          308 YLIQKE  313 (361)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            999973

>3iu6_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; HET: OCS; 1.79A {Homo sapiens}

Probab=99.85  E-value=4.4e-21  Score=156.17  Aligned_cols=101  Identities=19%  Similarity=0.344  Sum_probs=94.9

Q ss_pred             HHHHHHHHHHHHHHcCCC------CCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhh
Q psy16435        108 DLRIGMHKVMNRLKSHED------AWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCR  181 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~~~------s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~  181 (277)
                      .++..+..|++.|..+.+      +.+|+..|+..  |+||.  +.||+|.+|++||.+|.|.++++|..||.+||.||+
T Consensus         7 ~lq~~l~~l~~~v~~~~De~GR~lsd~F~~LPsk~--pdYY~--k~Pi~l~~Ikkri~~~~Y~sld~f~~D~~lmf~NAr   82 (147)
T 3iu6_A            7 LIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERAR   82 (147)
T ss_dssp             HHHHHHHHHHHHHHTCBCTTSCBGGGGGTTCCSSC--TTSTT--SCCCCHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhcCCCCCcchHHHhHCCCCC--ccccC--CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence            678889999999998765      67999999987  89998  999999999999999999999999999999999999


Q ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHHHhhccc
Q psy16435        182 KYNGLDNEYTDMVRRLQQIFRDAVSRYLDGE  212 (277)
Q Consensus       182 ~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~~  212 (277)
                      .||.++|+||.+|..|+++|.....++....
T Consensus        83 ~yN~e~S~IyeDAv~Lq~~f~~~r~eL~~~g  113 (147)
T 3iu6_A           83 RMNRTDSEIYEDAVELQQFFIKIRDELCKNG  113 (147)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HhCCCCCHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            9999999999999999999999999997764

>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A*

Probab=99.85  E-value=9.2e-22  Score=183.71  Aligned_cols=99  Identities=18%  Similarity=0.294  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHHHHHcC--CCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCC-CHHHHHHHHHHHHHhhhhhc
Q psy16435        108 DLRIGMHKVMNRLKSH--EDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK-TFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       108 ~l~~~l~~il~~l~~~--~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~-s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      .|...|..+|+.+...  ..+++|+.||+...+||||+||++||||+||++||  +.|. ++.+|..||+|||.||++||
T Consensus        78 ~~~~~~~~~l~~l~~~~~~~~~~F~~p~~~~~~PdY~~iIk~Pmdl~tI~~kl--~~y~~~~~~f~~D~~li~~Na~~yN  155 (361)
T 2r10_A           78 KFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAYN  155 (361)
T ss_dssp             THHHHHHHHHHHHHHHTHHHHGGGSSCCCTTTCTTHHHHCSSCCCHHHHHTSC--CCSTTHHHHHHHHHHHHHHHHHHHB
T ss_pred             HHHHHHHHHHHHHHHcCCcccHHhcCCCCcccCCChHhhcCCCcCHHHHHHHh--hccCCCHHHHHHHHHHHHHHHhhcC
Confidence            4567888899888654  34799999999999999999999999999999998  4454 89999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHh
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      +++|.||.+|..|+++|...|.+.
T Consensus       156 ~~~s~i~~~a~~l~~~~~~~~~k~  179 (361)
T 2r10_A          156 EYDSLIVKNSMQVVMLIEFEVLKA  179 (361)
T ss_dssp             CSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999988765

>2r0y_A Chromatin structure-remodeling complex protein RSC4; bromodomain, chromatin, remodeler, RSC, acetylation, transcription, chromatin regulator, nucleus, phosphorylation; HET: ALY; 1.75A {Saccharomyces cerevisiae} PDB: 2r0s_A

Probab=99.84  E-value=1.4e-21  Score=178.97  Aligned_cols=99  Identities=18%  Similarity=0.294  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHHHHHc--CCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCC-CHHHHHHHHHHHHHhhhhhc
Q psy16435        108 DLRIGMHKVMNRLKS--HEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYK-TFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       108 ~l~~~l~~il~~l~~--~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~-s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      .|...|..+|..+..  ...+++|+.||+...+||||+||++||||+||++||  +.|. ++.+|..||+|||.||++||
T Consensus        28 ~~~~~~~~~L~~~~~~~r~~~~~F~~p~~~~~~PdY~~iIk~PmDL~tI~~kl--~~y~~s~~~f~~D~~li~~Na~~yN  105 (311)
T 2r0y_A           28 KFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAYN  105 (311)
T ss_dssp             THHHHHHHHHHHHHHHSHHHHGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHSC--CCSTTHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHcCCchhHHhcCCCCcccCCChHHHcCCCCCHHHHHHHH--hcccCCHHHHHHHHHHHHHHHHHcc
Confidence            445555566666654  235899999999999999999999999999999998  4555 89999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHh
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      +++|.||.+|..|+++|...|.+.
T Consensus       106 ~~~s~i~~~A~~l~~~~~~~~~k~  129 (311)
T 2r0y_A          106 EYDSLIVKNSMQVVMLIEFEVLKA  129 (311)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999988765

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=99.65  E-value=2.3e-16  Score=133.67  Aligned_cols=98  Identities=19%  Similarity=0.326  Sum_probs=88.7

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcC
Q psy16435        106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNG  185 (277)
Q Consensus       106 ~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~  185 (277)
                      ...|+..|..||..|..++.++||+..           .++.||||+||++||++|.|.|+.+|+.||.|||.||..||.
T Consensus        73 ~~el~~~l~~vl~~L~~~~~s~~~~~y-----------~~k~PmDL~~i~kKl~~~~Y~s~~eF~~Dv~lIf~n~~~~~~  141 (183)
T 3lqh_A           73 EKELQISLKQVLTALLNSRTTSHLLRY-----------RQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDG  141 (183)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHTC-----------CC--CCSHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHhccccHhhhhh-----------hhcCCccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhccC
Confidence            457788899999999999999999873           259999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhcccCC
Q psy16435        186 LDNEYTDMVRRLQQIFRDAVSRYLDGERS  214 (277)
Q Consensus       186 ~~s~i~~~A~~L~~~f~~~~~~~~~~~~~  214 (277)
                      +++.+..++..|..+|.+.++++++....
T Consensus       142 ~~~e~~~ag~~l~~~f~~~l~~vfpwf~~  170 (183)
T 3lqh_A          142 GQPEIKKANSMVKSFFIRQMERVFPWFSV  170 (183)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHCTTSCG
T ss_pred             CChhhhhhhhHHHHHHHHHHHHHCCCCCc
Confidence            99999999999999999999999987643

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	277
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	7e-26
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	1e-24
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	2e-24
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	3e-24
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	1e-23
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	2e-23

>d1eqfa1 a.29.2.1 (A:1359-1497) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]} Length = 139

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 97.4 bits (242), Expect = 7e-26
 Identities = 27/105 (25%), Positives = 49/105 (46%)

Query: 106 EEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKT 165
              L   +  ++N ++   + +PF  PV+     +YY+ I RPMDL  + E +    Y +
Sbjct: 24  MVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPS 83

Query: 166 FGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLD 210
             +FR   +LIV N   YNG  +  T + + +  +  + +    D
Sbjct: 84  REEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKED 128

>d1e6ia_ a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 111

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 92.7 bits (230), Expect = 1e-24
 Identities = 35/91 (38%), Positives = 56/91 (61%)

Query: 113 MHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRAD 172
           +  ++  L++H  AWPF  PV++   P+YY+ IK PMDL+ ME KL++ +Y+    F  D
Sbjct: 8   IQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYD 67

Query: 173 FQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
            +L+ +NCR YNG +  Y     RL++ F +
Sbjct: 68  ARLVFNNCRMYNGENTSYYKYANRLEKFFNN 98

>d3d7ca1 a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.0 bits (228), Expect = 2e-24
 Identities = 38/95 (40%), Positives = 58/95 (61%)

Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           + L   +  ++ ++KSH  AWPF +PV ++ AP+YYE I+ P+DL  M E+L +  Y T 
Sbjct: 1   DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTR 60

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIF 201
             F AD Q ++ NCR+YN  D+EY      L++ F
Sbjct: 61  KLFVADLQRVIANCREYNPPDSEYCRCASALEKFF 95

>d1eqfa2 a.29.2.1 (A:1498-1625) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]} Length = 128

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.7 bits (230), Expect = 3e-24
 Identities = 28/95 (29%), Positives = 52/95 (54%)

Query: 116 VMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQL 175
           V  ++ +  D+WPF  PV++   P+YY+ I  PMDL  + + +   +Y++   F  D  L
Sbjct: 18  VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 77

Query: 176 IVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYLD 210
           I+ N  KYNG +++YT   + +  +    ++ Y +
Sbjct: 78  ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDE 112

>d3dwya1 a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: CREB-binding protein, CBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 90.4 bits (224), Expect = 1e-23
 Identities = 29/108 (26%), Positives = 52/108 (48%), Gaps = 3/108 (2%)

Query: 105 TEEDLRIGMHKVMNRLKSH-EDAWPFCDPVD--EATAPNYYEQIKRPMDLTRMEEKLDAG 161
             E+LR  +   +  L     ++ PF  PVD      P+Y++ +K PMDL+ ++ KLD G
Sbjct: 3   KPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTG 62

Query: 162 RYKTFGQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRDAVSRYL 209
           +Y+   Q+  D  L+ +N   YN   +       +L ++F   +   +
Sbjct: 63  QYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVM 110

>d1wuma1 a.29.2.1 (A:715-832) P300/CAF histone acetyltransferase bromodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 118

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: P300/CAF histone acetyltransferase bromodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 89.7 bits (222), Expect = 2e-23
 Identities = 36/97 (37%), Positives = 54/97 (55%)

Query: 107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTF 166
           + L   +  ++ ++KSH+ AWPF +PV    AP YYE I+ PMDL  M E+L    Y + 
Sbjct: 12  DQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSK 71

Query: 167 GQFRADFQLIVDNCRKYNGLDNEYTDMVRRLQQIFRD 203
             F AD Q +  NC++YN  ++EY      L++ F  
Sbjct: 72  KLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFS 108

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	277
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.97
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.96
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.96
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.96
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.95
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.95

>d3d7ca1 a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.1e-30  Score=199.08  Aligned_cols=101  Identities=38%  Similarity=0.717  Sum_probs=97.7

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCC
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGL  186 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~  186 (277)
                      ++|...|..||..|..|+.+++|..||++..+|+||++|++||||+||++||++|.|.|+.+|.+||.|||.||+.||++
T Consensus         1 d~L~~~l~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~   80 (102)
T d3d7ca1           1 DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPP   80 (102)
T ss_dssp             HHHHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCT
T ss_pred             ChHHHHHHHHHHHHHhCCCCCccCCCCChhhCcCHHHHcCCccCHHHHHHHhccCccCCHHHHHHHHHHHHHHHHHHCCC
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q psy16435        187 DNEYTDMVRRLQQIFRDAVSR  207 (277)
Q Consensus       187 ~s~i~~~A~~L~~~f~~~~~~  207 (277)
                      +|.+|.+|..|+++|.+.+++
T Consensus        81 ~s~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          81 DSEYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999988764

>d1e6ia_ a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.96  E-value=1.2e-29  Score=197.58  Aligned_cols=102  Identities=35%  Similarity=0.771  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCCC
Q psy16435        109 LRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLDN  188 (277)
Q Consensus       109 l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~s  188 (277)
                      +...|..||..|++|+.|+||..||++..+|+||++|++||||+||++||.+|.|.|+.+|..||.|||.||+.||+++|
T Consensus         4 ~~~~l~~il~~l~~~~~a~pF~~pvd~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s   83 (111)
T d1e6ia_           4 HDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENT   83 (111)
T ss_dssp             THHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTS
T ss_pred             HHHHHHHHHHHHHhCCCChhhcCCCCchhCcCHHHHcCCchhHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHCCCCC
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhc
Q psy16435        189 EYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       189 ~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      .++.+|..|++.|.+.+.+++.
T Consensus        84 ~i~~~A~~l~~~f~~~~~~ipe  105 (111)
T d1e6ia_          84 SYYKYANRLEKFFNNKVKEIPE  105 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSGG
T ss_pred             HHHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999988754

>d3dwya1 a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: CREB-binding protein, CBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=4.1e-29  Score=195.47  Aligned_cols=107  Identities=27%  Similarity=0.556  Sum_probs=100.9

Q ss_pred             ChHHHHHHHHHHHHHHHcC-CCCCCCCCCCCCC--CCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhh
Q psy16435        105 TEEDLRIGMHKVMNRLKSH-EDAWPFCDPVDEA--TAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCR  181 (277)
Q Consensus       105 ~~~~l~~~l~~il~~l~~~-~~s~~F~~pv~~~--~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~  181 (277)
                      ++++|+..|..+|+.|+.+ +.|++|..||++.  .+||||++|++||||+||++||.+|.|.|+++|.+||+|||.||+
T Consensus         3 ~p~el~~~l~~~l~~l~~~~p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~   82 (114)
T d3dwya1           3 KPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAW   82 (114)
T ss_dssp             CHHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCcCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCccccHHHHHHHHHHHHHHHH
Confidence            3678999999999999977 5899999999976  699999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q psy16435        182 KYNGLDNEYTDMVRRLQQIFRDAVSRYLDG  211 (277)
Q Consensus       182 ~YN~~~s~i~~~A~~L~~~f~~~~~~~~~~  211 (277)
                      .||+++|.++.+|..|++.|++.+..++..
T Consensus        83 ~yN~~~s~~~~~A~~L~~~f~~~~~~i~~~  112 (114)
T d3dwya1          83 LYNRKTSRVYKFCSKLAEVFEQEIDPVMQS  112 (114)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999988653

>d1wuma1 a.29.2.1 (A:715-832) P300/CAF histone acetyltransferase bromodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: P300/CAF histone acetyltransferase bromodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=2e-29  Score=198.38  Aligned_cols=104  Identities=35%  Similarity=0.673  Sum_probs=100.9

Q ss_pred             ChHHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhc
Q psy16435        105 TEEDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYN  184 (277)
Q Consensus       105 ~~~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN  184 (277)
                      .+.+|...|..||..|+.++.+++|..||++..+|+||++|++||||+||++||.+|.|.++++|.+||.|||.||++||
T Consensus        10 ~~~~l~~~l~~il~~l~~~~~a~~F~~pv~~~~~pdY~~iI~~PmdL~~I~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yn   89 (118)
T d1wuma1          10 DPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYN   89 (118)
T ss_dssp             SHHHHHHHHHHHHHHHHHSSSCHHHHSCCCSSSSSSCTTTCSSCCCHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHHHHhCCCcCcccCCCChhhCcCHHHHcCChhhHHHHHHHhcccccCchHHHHHHHHHHHHHHHHHC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHh
Q psy16435        185 GLDNEYTDMVRRLQQIFRDAVSRY  208 (277)
Q Consensus       185 ~~~s~i~~~A~~L~~~f~~~~~~~  208 (277)
                      +++|.++.+|..|+.+|.+.+.++
T Consensus        90 ~~~s~~~~~A~~l~~~f~~~~~e~  113 (118)
T d1wuma1          90 PPESEYYKCANILEKFFFSKIKEA  113 (118)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999875

>d1eqfa1 a.29.2.1 (A:1359-1497) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2e-28  Score=197.94  Aligned_cols=104  Identities=26%  Similarity=0.531  Sum_probs=100.1

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCC
Q psy16435        107 EDLRIGMHKVMNRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGL  186 (277)
Q Consensus       107 ~~l~~~l~~il~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~  186 (277)
                      ..|...|..||+.|..++.+++|..||++..+||||++|++||||+||++||.+|.|.|+++|..||.|||.||+.||++
T Consensus        25 ~~l~~~l~~il~~l~~~~~s~pF~~Pvd~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~  104 (139)
T d1eqfa1          25 VTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGP  104 (139)
T ss_dssp             HHHHHHHHHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCT
T ss_pred             HHHHHHHHHHHHHHHcCCCchhhhCCCChhhccCHHHHcCChhhHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHHCCC
Confidence            45788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        187 DNEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       187 ~s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      +|.++.+|..|...|...|.++..
T Consensus       105 ~s~i~~~A~~L~~~~~~~~~~~~~  128 (139)
T d1eqfa1         105 KHSLTQISQSMLDLCDEKLKEKED  128 (139)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999988754

>d1eqfa2 a.29.2.1 (A:1498-1625) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=3.5e-28  Score=193.81  Aligned_cols=102  Identities=26%  Similarity=0.629  Sum_probs=91.8

Q ss_pred             HHHHHHHHH-HHHHcCCCCCCCCCCCCCCCCcchhhhccCCCcHHHHHHHHhCCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q psy16435        109 LRIGMHKVM-NRLKSHEDAWPFCDPVDEATAPNYYEQIKRPMDLTRMEEKLDAGRYKTFGQFRADFQLIVDNCRKYNGLD  187 (277)
Q Consensus       109 l~~~l~~il-~~l~~~~~s~~F~~pv~~~~~PdYy~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~lm~~Na~~YN~~~  187 (277)
                      |...|..++ ..+..++.|+||+.||++..+|+||++|++||||+||++||.+|.|.|+.+|..||+|||.||+.||+++
T Consensus        10 ~~~il~~l~~~~~~~~p~a~pF~~pVd~~~~PdY~~vIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~   89 (128)
T d1eqfa2          10 FSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPE   89 (128)
T ss_dssp             HHHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHHcCCCCChhcCCCCcccCcCHHHHcCCcccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHCCCC
Confidence            334444443 4456778899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHhhc
Q psy16435        188 NEYTDMVRRLQQIFRDAVSRYLD  210 (277)
Q Consensus       188 s~i~~~A~~L~~~f~~~~~~~~~  210 (277)
                      |.++.+|..|...|...+.++..
T Consensus        90 s~i~~~A~~L~~~~~~~l~~~~~  112 (128)
T d1eqfa2          90 SQYTKTAQEIVNVCYQTLTEYDE  112 (128)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHhHH
Confidence            99999999999999999988743