Citrus Sinensis ID: 016116

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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-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-----
Protein Sequence
MEPMSGLNQDLGNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKKLPPNT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccccHHHHHHHHHHHHHHcccccccccEEEEEcccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccHHHcccccHHHHccccccHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHHcccHHccccccHHccccccccHHHccccccccHHHHHHHHHHHcccHHHHHccccccc
Coil and Loop (DISEMBL)
mepmsglnqdlgnvglgkaegdtveveGLNKTIDDILQKVTQLEQKLNDVEQFYltkdnnqpntskSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQhkwawpfmhpvdveglglhdyyeviekpmdfstiknkmdgkdgtgyrNVREIYADVRLVFKNAmkynderdDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVaennpsfhataqevdldmdaQSELTLWRLKVFVQESLKAAsrssgdmggnnnnnnddnnnekdnsnkknknnpkrKKEICDALAKpavkrtkklppnt
Flexible Loop (DISEMBL)
mepmsglnqdlgnvglgkAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFyltkdnnqpntskSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPmdfstiknkmdgkdgtgyrnVREIYADVRLVFKNAmkynderdDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQkcrkmsteekknlgtaltrlsPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAasrssgdmggnnnnnnddnnnekdnsnkknknnpkrkkeicdalakpavkrtkklppnt
Low Complexity Region (SEG)
MEPMSGLNQDLGNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMeeekrqeeeeakaqLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGnnnnnnddnnnekdnsnkknknnpkrkkEICDALAKPAVKRTKKLPPNT
Disordered region (IsUnstruct)
**********************TVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYL*************************************************KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP*****************************************************************************EDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQ****************************************************************
Disordered Region (DISOPRED)
*********************************************************************************************************RQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWL**********************************************************************************DLCKALEIVAE*N*******QEVDLDMDAQSELTLWRLKVFVQ****************************************************************
Disordered Region (DISEMBL)
********QDLGNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVM***************DMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESL********DMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVK*********
Disordered Region (DISPRO)
*******N**L*N*****AEGDTVEVEGLNKTIDDILQKVTQLEQKLND*************************************************RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP*********************************************************RKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAAS****************************************ALAK*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEPMSGLNQDLGNVGLGKAEGDTVExxxxxxxxxxxxxxxxxxxxxxxxxxxxYLTKDNNQPNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPxxxxxxxxxxxxxxxxxxxxxLTQEAVQTNKxxxxxxxxxxxxxxxxxxxxxVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKKLPPNT
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	395	2.2.26 [Sep-21-2011]
Q84XV2	386	Transcription factor GTE1	yes	no	0.908	0.930	0.531	1e-114
Q9FT54	369	Transcription factor GTE6	no	no	0.812	0.869	0.552	7e-91
Q9LNC4	766	Transcription factor GTE4	no	no	0.539	0.278	0.318	3e-26
Q6MGA9	798	Bromodomain-containing pr	yes	no	0.298	0.147	0.406	7e-21
Q7JJ13	798	Bromodomain-containing pr	yes	no	0.298	0.147	0.406	7e-21
Q5TJG6	803	Bromodomain-containing pr	yes	no	0.298	0.146	0.406	7e-21
Q32S26	803	Bromodomain-containing pr	yes	no	0.298	0.146	0.406	7e-21
P25440	801	Bromodomain-containing pr	yes	no	0.298	0.147	0.406	7e-21
Q9S7T1	461	Transcription factor GTE3	no	no	0.648	0.555	0.264	1e-20
Q9LXA7	581	Transcription factor GTE2	no	no	0.225	0.153	0.478	2e-20

>sp|Q84XV2|GTE1_ARATH Transcription factor GTE1 OS=Arabidopsis thaliana GN=GTE1 PE=2 SV=1

 Score =  413 bits (1061), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 217/408 (53%), Positives = 279/408 (68%), Gaps = 49/408 (12%)

Query: 2   EPMSGLNQDLGNVGLGKAEGDT-VEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDN- 59
           EP+   N D+ N  L    G+   E+E     +D+I  +V QLEQK+ +VE FY TKD  
Sbjct: 8   EPVLVPNCDVENTELAVFNGNGESELENFGTCVDEITDRVNQLEQKVVEVEHFYSTKDGA 67

Query: 60  -----------------NQPNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQ 102
                            +QPN SK  S  KEK K +HV+S                    
Sbjct: 68  AQTNTSKSNSGGKKIAISQPNNSKGNSAGKEKSKGKHVSS-------------------P 108

Query: 103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 162
           +L RQFA +FRQI QHKWAWPF+ PVDV+GLGLHDYY+VIEKPMD  TIK KM+  +   
Sbjct: 109 DLMRQFATMFRQIAQHKWAWPFLEPVDVKGLGLHDYYKVIEKPMDLGTIKKKMESSE--- 165

Query: 163 YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEE 222
           Y NVREIYADVRLVFKNAM+YN+E++DV+VMA+SLLEKFEEKWL ++PK++EEEK+Q +E
Sbjct: 166 YSNVREIYADVRLVFKNAMRYNEEKEDVYVMAESLLEKFEEKWLLIMPKLVEEEKKQVDE 225

Query: 223 EAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTAL 282
           EA+   + QLT EA Q   A++L +EL E+D+QLE LRE+V+Q+CRK+ST+EKK L  AL
Sbjct: 226 EAEKHANKQLTMEAAQAEMARDLSNELYEIDLQLEKLRESVVQRCRKLSTQEKKGLSAAL 285

Query: 283 TRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSG 342
            RLSPEDL KAL++V+E+NPSF A A EV+LD+D Q+++TLWRLKVFVQE+LKAA++SSG
Sbjct: 286 GRLSPEDLSKALKMVSESNPSFPAGAPEVELDIDVQTDVTLWRLKVFVQEALKAANKSSG 345

Query: 343 DMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 390
                NNNN          + + NKNN KR++EI DA+ K ++KR KK
Sbjct: 346 GTNAQNNNNT--------GTGEINKNNAKRRREISDAINKASIKRAKK 385

Transcription activator that plays a role in the promotion of seed germination by both negatively and positively regulating the abscisic acid (ABA) and phytochrome A (phyA) transduction pathways, respectively.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FT54|GTE6_ARATH Transcription factor GTE6 OS=Arabidopsis thaliana GN=GTE6 PE=2 SV=1

 Score =  334 bits (856), Expect = 7e-91,   Method: Compositional matrix adjust.
 Identities = 180/326 (55%), Positives = 233/326 (71%), Gaps = 5/326 (1%)

Query: 12  GNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSISIA 71
           G+V  G  +G +V+ E + + +D++LQ V  LE KL +VE+FY     +    S S SI 
Sbjct: 7   GHVAGGGLQGFSVDAECIKQRVDEVLQWVDSLEHKLKEVEEFY-----SSIGVSNSGSIG 61

Query: 72  KEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVE 131
           K+  K RHV  I K QQ+A  RE  A +RMQ+L RQF  IFRQITQHK AWPFMHPV+VE
Sbjct: 62  KDTEKGRHVVGIRKIQQEAARREAVAAKRMQDLMRQFGTIFRQITQHKCAWPFMHPVNVE 121

Query: 132 GLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVH 191
           GLGLHDY+EVI+KPMDFSTIKN+M+ KDGTGY++V +IYAD+RLVF+NAM YN+E  DV+
Sbjct: 122 GLGLHDYFEVIDKPMDFSTIKNQMEAKDGTGYKHVMQIYADMRLVFENAMNYNEETSDVY 181

Query: 192 VMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNE 251
            MAK LLEKFEEKW   LPKV EEEK +EEEE +A  +  L +EA      +EL +E+  
Sbjct: 182 SMAKKLLEKFEEKWAHFLPKVQEEEKIREEEEKQAAKEALLAKEASHIKTTRELGNEICH 241

Query: 252 VDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEV 311
            + +LE L   V+++CRK++ EEK+N+G AL +LSP+DL K L IVA+ NPSF   A+EV
Sbjct: 242 ANDELEKLMRKVVERCRKITIEEKRNIGLALLKLSPDDLQKVLGIVAQANPSFQPRAEEV 301

Query: 312 DLDMDAQSELTLWRLKVFVQESLKAA 337
            ++MD   E TLWRLK FV+++L  A
Sbjct: 302 SIEMDILDEPTLWRLKFFVKDALDNA 327

Regulates differences in leaf patterning between juvenile and mature leaves by controlling differences in the development of primordia produced during juvenile and mature phases. Acts by activating transcription of the myb-domain protein AS1, a gene involved in leaf-axis specification. Associates with the promoter and the start of the transcribed region of AS1 and up-regulates expression of AS1 through acetylation of histones H3 and H4.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LNC4|GTE4_ARATH Transcription factor GTE4 OS=Arabidopsis thaliana GN=GTE4 PE=2 SV=1

 Score =  119 bits (299), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 122/251 (48%), Gaps = 38/251 (15%)

Query: 109 AAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVRE 168
           +A+  ++ +HK  W F  PVDV+GLGL DYY +IE PMD  TIK+ +       Y++ RE
Sbjct: 426 SALLERLMKHKHGWVFNAPVDVKGLGLLDYYTIIEHPMDLGTIKSAL---MKNLYKSPRE 482

Query: 169 IYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQL 228
              DVRL F NAM YN E  DVH+MA +LL+ FEE+W      V+E +  +E        
Sbjct: 483 FAEDVRLTFHNAMTYNPEGQDVHLMAVTLLQIFEERW-----AVIEADYNREMRFVTG-Y 536

Query: 229 DMQLTQEAVQTNKAKEL-------RSELNEVDMQ---------------LENLRETVIQK 266
           +M L    +++     +       R+ ++  D                   + R   ++K
Sbjct: 537 EMNLPTPTMRSRLGPTMPPPPINVRNTIDRADWSNRQPTTTPGRTPTSATPSGRTPALKK 596

Query: 267 C-------RKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQS 319
                   R M+ EEK+ L   L  L P+ L   ++IV + N +     +E+++D+D+  
Sbjct: 597 PKANEPNKRDMTYEEKQKLSGHLQNLPPDKLDAIVQIVNKRNTAVKLRDEEIEVDIDSVD 656

Query: 320 ELTLWRLKVFV 330
             TLW L  FV
Sbjct: 657 PETLWELDRFV 667

Involved in the activation and maintenance of cell division in the meristems and by this controls cell numbers in differentiated organs. Its action in cell cycle regulation may be directed through the RB-E2F pathway.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6MGA9|BRD2_RAT Bromodomain-containing protein 2 OS=Rattus norvegicus GN=Brd2 PE=2 SV=1

 Score =  102 bits (253), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 52/128 (40%), Positives = 77/128 (60%), Gaps = 10/128 (7%)

Query: 84  EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
           + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct: 332 DSQQQ---HQSSKKGKLSEQLK-HCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 387

Query: 141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
           +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct: 388 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 444

Query: 201 FEEKWLQL 208
           FE ++ ++
Sbjct: 445 FEFRYAKM 452

May play a role in spermatogenesis or folliculogenesis.

Rattus norvegicus (taxid: 10116)

>sp|Q7JJ13|BRD2_MOUSE Bromodomain-containing protein 2 OS=Mus musculus GN=Brd2 PE=1 SV=1

 Score =  102 bits (253), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 52/128 (40%), Positives = 77/128 (60%), Gaps = 10/128 (7%)

Query: 84  EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
           + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct: 332 DSQQQ---HQSSKKGKLSEQLK-HCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 387

Query: 141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
           +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct: 388 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 444

Query: 201 FEEKWLQL 208
           FE ++ ++
Sbjct: 445 FEFRYAKM 452

May play a role in spermatogenesis or folliculogenesis.

Mus musculus (taxid: 10090)

>sp|Q5TJG6|BRD2_CANFA Bromodomain-containing protein 2 OS=Canis familiaris GN=BRD2 PE=3 SV=1

 Score =  102 bits (253), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 52/128 (40%), Positives = 77/128 (60%), Gaps = 10/128 (7%)

Query: 84  EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
           + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct: 333 DSQQQ---HQSSKKGKLSEQLK-HCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 388

Query: 141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
           +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct: 389 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 445

Query: 201 FEEKWLQL 208
           FE ++ ++
Sbjct: 446 FEFRYAKM 453

Canis familiaris (taxid: 9615)

>sp|Q32S26|BRD2_BOVIN Bromodomain-containing protein 2 OS=Bos taurus GN=BRD2 PE=3 SV=1

 Score =  102 bits (253), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 52/128 (40%), Positives = 77/128 (60%), Gaps = 10/128 (7%)

Query: 84  EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
           + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct: 333 DSQQQ---HQSSKKGKLSEQLK-HCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 388

Query: 141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
           +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct: 389 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 445

Query: 201 FEEKWLQL 208
           FE ++ ++
Sbjct: 446 FEFRYAKM 453

Bos taurus (taxid: 9913)

>sp|P25440|BRD2_HUMAN Bromodomain-containing protein 2 OS=Homo sapiens GN=BRD2 PE=1 SV=2

 Score =  102 bits (253), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 52/128 (40%), Positives = 77/128 (60%), Gaps = 10/128 (7%)

Query: 84  EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
           + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct: 333 DSQQQ---HQSSKKGKLSEQLK-HCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 388

Query: 141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
           +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct: 389 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 445

Query: 201 FEEKWLQL 208
           FE ++ ++
Sbjct: 446 FEFRYAKM 453

May play a role in spermatogenesis or folliculogenesis.

Homo sapiens (taxid: 9606)

>sp|Q9S7T1|GTE3_ARATH Transcription factor GTE3, chloroplastic OS=Arabidopsis thaliana GN=GTE3 PE=1 SV=1

 Score =  100 bits (250), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 130/303 (42%), Gaps = 47/303 (15%)

Query: 96  AAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKM 155
           AA +   ++ +    +  ++ +HK  W F  PVDV  LGLHDY+ +I++PMD  T+K ++
Sbjct: 111 AADKGTVQILKSCNNLLTKLMKHKSGWIFNTPVDVVTLGLHDYHNIIKEPMDLGTVKTRL 170

Query: 156 DGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL------- 208
                + Y++  E   DVRL F NAM YN    DV+ MA+ LL  FEEKW+ L       
Sbjct: 171 ---SKSLYKSPLEFAEDVRLTFNNAMLYNPVGHDVYHMAEILLNLFEEKWVPLETQYELL 227

Query: 209 -------------------------LPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAK 243
                                    LP              K   +  L +    TN  K
Sbjct: 228 IRKQQPVRDIDFHAPVSTNTHNVEALPLPAPTPSLSPPPPPKVVENRTLERAESMTNPVK 287

Query: 244 ELRSELNEVDMQLENLRETVIQKC---RKMSTEEKKNLGTALTRLSPEDLCKALEIVAEN 300
                       L  + E ++++    R ++ +EK+ L   L  L  + L   ++I+ + 
Sbjct: 288 P---------AVLPVVPEKLVEEASANRDLTFDEKRQLSEDLQDLPYDKLEAVVQIIKKR 338

Query: 301 NPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKD 360
            P       E++LD+D+    TLW L  FV E  ++ S+   + G ++  + +  +N   
Sbjct: 339 TPELSQQDDEIELDIDSLDLETLWELFRFVTEYKESLSKKKEEQGLDSERDAESFHNSVH 398

Query: 361 NSN 363
            SN
Sbjct: 399 ESN 401

Probable transcription factor that binds to acetylated histone H3.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LXA7|GTE2_ARATH Transcription factor GTE2 OS=Arabidopsis thaliana GN=GTE2 PE=2 SV=2

 Score =  100 bits (249), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 44/92 (47%), Positives = 66/92 (71%), Gaps = 3/92 (3%)

Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           I  ++ +HKW+W F++PVDV GLGLHDY+ +++KPMD  T+  KM+ + G  YR+  +  
Sbjct: 181 ILVKLMKHKWSWVFLNPVDVVGLGLHDYHRIVDKPMDLGTV--KMNLEKGL-YRSPIDFA 237

Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFE 202
           +DVRL F NAM YN +  DV++MA+ LL +F+
Sbjct: 238 SDVRLTFTNAMSYNPKGQDVYLMAEKLLSQFD 269

Arabidopsis thaliana (taxid: 3702)

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	395
359486529	440	PREDICTED: transcription factor GTE1-lik	0.941	0.845	0.655	1e-130
356565711	738	PREDICTED: uncharacterized protein LOC10	0.858	0.459	0.663	1e-127
297742702	421	unnamed protein product [Vitis vinifera]	0.954	0.895	0.647	1e-126
147779795	377	hypothetical protein VITISV_019973 [Viti	0.926	0.970	0.657	1e-125
359484096	377	PREDICTED: transcription factor GTE1-lik	0.926	0.970	0.657	1e-125
449452116	378	PREDICTED: transcription factor GTE1-lik	0.896	0.936	0.673	1e-124
255577689	391	bromodomain-containing protein, putative	0.962	0.971	0.610	1e-120
224098028	370	global transcription factor group [Popul	0.921	0.983	0.613	1e-119
296086052	362	unnamed protein product [Vitis vinifera]	0.863	0.941	0.623	1e-117
224109720	318	global transcription factor group [Popul	0.794	0.987	0.690	1e-117

>gi|359486529|ref|XP_002276963.2| PREDICTED: transcription factor GTE1-like [Vitis vinifera]

 Score =  471 bits (1211), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 249/380 (65%), Positives = 292/380 (76%), Gaps = 8/380 (2%)

Query: 1   MEPMSGLNQDLGNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNN 60
           MEPM     D  N+  GK +G+  +VE L   +DDI  KV +LEQ++N+VEQFYLT    
Sbjct: 52  MEPMDASISDTRNMETGKNQGNAAQVESLKSRVDDIFTKVDKLEQRVNEVEQFYLTASKK 111

Query: 61  QPNTSKSISIAKEKLKD--RHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQH 118
           Q N SK  SI K+K KD  RHVAS++KQQQDA  RE AA +RMQEL RQF  I RQITQH
Sbjct: 112 QLNVSKGSSIVKDKDKDKERHVASVKKQQQDASRREAAAAKRMQELMRQFGTILRQITQH 171

Query: 119 KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK 178
           KWAWPFM PVDVEGLGLHDYYEVIEKPMDFSTIKNKM+ KDG GY+NVREI ADVRLVFK
Sbjct: 172 KWAWPFMQPVDVEGLGLHDYYEVIEKPMDFSTIKNKMEAKDGAGYKNVREICADVRLVFK 231

Query: 179 NAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQ 238
           NAMKYNDER DVHVMAK+LL KFEEKWLQLLPKV EE+KR+EEEEA+AQLDM L QEA  
Sbjct: 232 NAMKYNDERRDVHVMAKTLLGKFEEKWLQLLPKVAEEDKRREEEEAEAQLDMHLAQEAAH 291

Query: 239 TNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVA 298
              A+++ +EL E+DM L+++RE ++QKCRK STEEK+ LG AL+RLS EDL KALEIVA
Sbjct: 292 AKMARDISNELFEIDMHLDDIREIIVQKCRKTSTEEKRKLGAALSRLSAEDLSKALEIVA 351

Query: 299 ENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNE 358
           ++NPSF ATA+EV LD+DAQ E TLWRLK FV+++L+   +SS  MGGNN          
Sbjct: 352 QSNPSFQATAEEVHLDIDAQRESTLWRLKFFVKDALEIQGKSSASMGGNNTATT------ 405

Query: 359 KDNSNKKNKNNPKRKKEICD 378
            +N++    NN KRKKEICD
Sbjct: 406 TNNNHPTTNNNSKRKKEICD 425

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565711|ref|XP_003551081.1| PREDICTED: uncharacterized protein LOC100797746 [Glycine max]

 Score =  462 bits (1188), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 237/357 (66%), Positives = 284/357 (79%), Gaps = 18/357 (5%)

Query: 25  EVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSISIAKEKLKDRHVASIE 84
           E+EG  + +D+I+ KV +LEQK++D+E FY + + NQ +T K  S AK+K K++HV SI+
Sbjct: 390 EIEGFKQRVDEIISKVDKLEQKVHDIENFYSSMNKNQTSTPKGNSAAKDKDKEKHVPSIK 449

Query: 85  KQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEK 144
           KQQQDA  RE AA +RMQ+L RQF  I RQITQHKWAWPFM PVD+EGLGLHDYYEVI+K
Sbjct: 450 KQQQDASRREAAASKRMQDLMRQFGTILRQITQHKWAWPFMQPVDIEGLGLHDYYEVIDK 509

Query: 145 PMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           PMDFSTIKN+M+ KDGTGY++VREI ADVRLVFKNAMKYNDER DVHVMAK+LL KFEEK
Sbjct: 510 PMDFSTIKNQMEAKDGTGYKHVREICADVRLVFKNAMKYNDERSDVHVMAKTLLSKFEEK 569

Query: 205 WLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVI 264
           WLQLLPKV EEE R+EEEEA+AQL +Q+ QEA Q   A++L +EL EVD+ LE LRE V+
Sbjct: 570 WLQLLPKVTEEETRREEEEAEAQLALQVAQEAAQAKMARDLSNELYEVDVILEELREMVV 629

Query: 265 QKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLW 324
           ++ RKMSTEEK+ LG ALTRLSPEDL KALEIVA+NNPSF ATA+EVDLDMDAQSE TLW
Sbjct: 630 KRFRKMSTEEKRKLGDALTRLSPEDLSKALEIVAQNNPSFQATAEEVDLDMDAQSESTLW 689

Query: 325 RLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALA 381
           RLK FV+E+L+   ++SG MGGN N NN                  KRK+E+CDA+A
Sbjct: 690 RLKFFVKEALEVQGKNSGSMGGNENQNN------------------KRKRELCDAIA 728

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742702|emb|CBI35336.3| unnamed protein product [Vitis vinifera]

 Score =  457 bits (1175), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 253/391 (64%), Positives = 300/391 (76%), Gaps = 14/391 (3%)

Query: 2   EPMSGLNQDLGNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQ 61
           EPM     ++ NV +GK +G+T +VEG    +DDI  KV +LEQ++N+VE FYLT    Q
Sbjct: 43  EPMDASITNVRNVEIGKHKGNTDQVEGFKSCVDDIFTKVDKLEQRVNEVELFYLTASKRQ 102

Query: 62  PNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWA 121
            N  K  S+ K+K  +RHVAS +KQQQDA  RE AA +RMQEL RQF  I RQI QHKWA
Sbjct: 103 LNGYKGSSVLKDK--ERHVASAKKQQQDASRREAAAVKRMQELMRQFGTILRQIMQHKWA 160

Query: 122 WPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM 181
            PF+HPVDVEGLGLHDYYEVI+KPMDFSTIKN+M+ KDGTGY+NVREI ADVRLVFKNAM
Sbjct: 161 GPFLHPVDVEGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKNVREICADVRLVFKNAM 220

Query: 182 KYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNK 241
           KYNDER DVHVMAK+LL KFEEKWLQLLPKV EEEKR+EEEEA+AQLDMQL QEA     
Sbjct: 221 KYNDERHDVHVMAKTLLGKFEEKWLQLLPKVAEEEKRREEEEAEAQLDMQLAQEAAHAKM 280

Query: 242 AKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENN 301
           A+E+ +EL ++DM LE +RE VI+KCRKMSTEEK+ LG AL+RLS EDL KALEIVA+NN
Sbjct: 281 AREISNELYDIDMHLEEVREMVIRKCRKMSTEEKRKLGAALSRLSAEDLSKALEIVAQNN 340

Query: 302 PSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDN 361
           PSF ATA+EVDLD+DAQ+E TLWRLK FV+++L+   +SS   G            +  N
Sbjct: 341 PSFQATAEEVDLDIDAQTESTLWRLKFFVKDALEVQGKSSASKG------------DNTN 388

Query: 362 SNKKNKNNPKRKKEICDALAKPAVKRTKKLP 392
           +     NN KRKKEICDA+AK A K++KKLP
Sbjct: 389 TTTTATNNNKRKKEICDAIAKTAKKKSKKLP 419

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147779795|emb|CAN62295.1| hypothetical protein VITISV_019973 [Vitis vinifera]

 Score =  454 bits (1169), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 250/380 (65%), Positives = 294/380 (77%), Gaps = 14/380 (3%)

Query: 13  NVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSISIAK 72
           NV +GK +G+T +VEG    +DDI  KV +LEQ++N+VE FYLT    Q N  K  S+ K
Sbjct: 10  NVEIGKHKGNTDQVEGFKSCVDDIFTKVDKLEQRVNEVELFYLTASKRQLNGYKGSSVLK 69

Query: 73  EKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEG 132
           +K  +RHVAS +KQQQDA  RE AA +RMQEL RQF  I RQI QHKWA PF+HPVDVEG
Sbjct: 70  DK--ERHVASAKKQQQDASRREAAAAKRMQELMRQFGTILRQIMQHKWAGPFLHPVDVEG 127

Query: 133 LGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHV 192
           LGLHDYYEVI+KPMDFSTIKN+M+ KDGTGY+NVREI ADVRLVFKNAMKYNDER DVHV
Sbjct: 128 LGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKNVREICADVRLVFKNAMKYNDERHDVHV 187

Query: 193 MAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEV 252
           MAK+LL KFEEKWLQLLPKV EEEKR+EEEEA+AQLDMQL QEA     A+E+ +EL  +
Sbjct: 188 MAKTLLGKFEEKWLQLLPKVAEEEKRREEEEAEAQLDMQLAQEAAHAKMAREISNELYXI 247

Query: 253 DMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVD 312
           DM LE +RE VI+KCRKMSTEEK+ LG AL+RLS EDL KALEIVA+NNPSF ATA+EVD
Sbjct: 248 DMHLEEVREMVIRKCRKMSTEEKRKLGAALSRLSAEDLSKALEIVAQNNPSFQATAEEVD 307

Query: 313 LDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKR 372
           LD+DAQ+E TLWRLK FV+++L+   +SS   G            +  N+     NN KR
Sbjct: 308 LDIDAQTESTLWRLKFFVKDALEVQGKSSASKG------------DNTNTTTTATNNNKR 355

Query: 373 KKEICDALAKPAVKRTKKLP 392
           KKEICDA+AK A K++KKLP
Sbjct: 356 KKEICDAIAKTAKKKSKKLP 375

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359484096|ref|XP_003633062.1| PREDICTED: transcription factor GTE1-like [Vitis vinifera]

 Score =  454 bits (1167), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 250/380 (65%), Positives = 295/380 (77%), Gaps = 14/380 (3%)

Query: 13  NVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSISIAK 72
           NV +GK +G+T +VEG    +DDI  KV +LEQ++N+VE FYLT    Q N  K  S+ K
Sbjct: 10  NVEIGKHKGNTDQVEGFKSCVDDIFTKVDKLEQRVNEVELFYLTASKRQLNGYKGSSVLK 69

Query: 73  EKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEG 132
           +K  +RHVAS +KQQQDA  RE AA +RMQEL RQF  I RQI QHKWA PF+HPVDVEG
Sbjct: 70  DK--ERHVASAKKQQQDASRREAAAVKRMQELMRQFGTILRQIMQHKWAGPFLHPVDVEG 127

Query: 133 LGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHV 192
           LGLHDYYEVI+KPMDFSTIKN+M+ KDGTGY+NVREI ADVRLVFKNAMKYNDER DVHV
Sbjct: 128 LGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKNVREICADVRLVFKNAMKYNDERHDVHV 187

Query: 193 MAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEV 252
           MAK+LL KFEEKWLQLLPKV EEEKR+EEEEA+AQLDMQL QEA     A+E+ +EL ++
Sbjct: 188 MAKTLLGKFEEKWLQLLPKVAEEEKRREEEEAEAQLDMQLAQEAAHAKMAREISNELYDI 247

Query: 253 DMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVD 312
           DM LE +RE VI+KCRKMSTEEK+ LG AL+RLS EDL KALEIVA+NNPSF ATA+EVD
Sbjct: 248 DMHLEEVREMVIRKCRKMSTEEKRKLGAALSRLSAEDLSKALEIVAQNNPSFQATAEEVD 307

Query: 313 LDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKR 372
           LD+DAQ+E TLWRLK FV+++L+   +SS   G            +  N+     NN KR
Sbjct: 308 LDIDAQTESTLWRLKFFVKDALEVQGKSSASKG------------DNTNTTTTATNNNKR 355

Query: 373 KKEICDALAKPAVKRTKKLP 392
           KKEICDA+AK A K++KKLP
Sbjct: 356 KKEICDAIAKTAKKKSKKLP 375

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452116|ref|XP_004143806.1| PREDICTED: transcription factor GTE1-like [Cucumis sativus] gi|449485919|ref|XP_004157310.1| PREDICTED: transcription factor GTE1-like [Cucumis sativus]

 Score =  451 bits (1161), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 245/364 (67%), Positives = 292/364 (80%), Gaps = 10/364 (2%)

Query: 21  GDTV--EVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSISIAKEKLKDR 78
           GDTV  EV+G    +D+I  KV +LEQ +N++EQFYLT    QPN +K  SI K+K K+R
Sbjct: 12  GDTVHTEVDGFRHQVDEIFLKVDRLEQNVNEIEQFYLTLKKKQPNGNKGSSIVKDKDKER 71

Query: 79  HVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDY 138
           HV SI+KQQQ+A  RE AA +RMQEL RQF  I RQI+QHKWAWPFM PVDVEGLGLHDY
Sbjct: 72  HVPSIKKQQQEAARREAAATKRMQELMRQFGTILRQISQHKWAWPFMQPVDVEGLGLHDY 131

Query: 139 YEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLL 198
           YEVI+KPMDFSTIKN+M+ KDGTGY+NVREI +DVRLVFKNAMKYNDER DVHVMAK+LL
Sbjct: 132 YEVIDKPMDFSTIKNQMEAKDGTGYKNVREICSDVRLVFKNAMKYNDERSDVHVMAKTLL 191

Query: 199 EKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLEN 258
            KFEEKWLQLLPKV EEEKR+E+EEA+A LDMQL QEA Q   A+++ +E+ EVDMQLE 
Sbjct: 192 AKFEEKWLQLLPKVTEEEKRREDEEAEALLDMQLAQEAAQAKMARDISNEIYEVDMQLEE 251

Query: 259 LRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQ 318
           LRE V+Q CRK+STEEK+ LG ALT+LSPED+ KALEIVAENNPSF ATA+EVDLD+DAQ
Sbjct: 252 LRELVVQNCRKISTEEKRKLGAALTKLSPEDISKALEIVAENNPSFQATAEEVDLDIDAQ 311

Query: 319 SELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICD 378
           SE TLWRLK FV+++L+  ++SS   GG NN N+         ++    +N KRKKEICD
Sbjct: 312 SESTLWRLKFFVKDALEVHAKSSASTGGGNNQNH--------TNSNNINSNNKRKKEICD 363

Query: 379 ALAK 382
           A+A+
Sbjct: 364 AIAR 367

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255577689|ref|XP_002529721.1| bromodomain-containing protein, putative [Ricinus communis] gi|223530823|gb|EEF32687.1| bromodomain-containing protein, putative [Ricinus communis]

 Score =  437 bits (1123), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 243/398 (61%), Positives = 295/398 (74%), Gaps = 18/398 (4%)

Query: 1   MEPMSGLNQDLGNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNN 60
           ME ++    D G+   G    ++VE++G    +D++  KV +LEQ++N+VE FYL  +  
Sbjct: 1   MEAITSSIPDFGSYDFG----NSVEIDGYKHRVDELFHKVDKLEQRVNEVELFYLNVNKK 56

Query: 61  QPNTSKSISIAKEKL-------KDRH-VASIEKQQQDAFHREEAAGRRMQELKRQFAAIF 112
           Q   S     +K          K+RH V SI KQQQDA  RE AA +RMQEL RQF  I 
Sbjct: 57  QQQQSGGGGNSKGSSIVKDNNNKERHSVPSIRKQQQDASKREAAASKRMQELMRQFGTIL 116

Query: 113 RQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 172
           RQITQHKWAWPFM PVDV+GLGLHDYYEVI+KPMDFSTIKN+M+ KDGTGY+NVREI AD
Sbjct: 117 RQITQHKWAWPFMQPVDVKGLGLHDYYEVIDKPMDFSTIKNQMETKDGTGYKNVREICAD 176

Query: 173 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQL 232
           VRLVFKNAMKYNDER DVHVMAK+LL KFEEKWLQLLPKV EEEKR+E EEA+AQLDMQL
Sbjct: 177 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREMEEAEAQLDMQL 236

Query: 233 TQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCK 292
            QEAV    A+EL +EL E+D  L+ LR+ V+QKCRK+STEEK+ LG ALTRLSPEDL K
Sbjct: 237 AQEAVHAKMARELSNELYEIDTHLDELRDMVVQKCRKISTEEKRKLGAALTRLSPEDLTK 296

Query: 293 ALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNN 352
           ALEIVA+NNP F ATA+EVDLD+DAQ+E TLWRLK FV+++L+   +++       +   
Sbjct: 297 ALEIVAQNNPGFQATAEEVDLDIDAQTESTLWRLKFFVKDALEVQGKNA------ASAGG 350

Query: 353 DDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 390
           ++NNN  + +   N +N KRKKEICDA+AK A KR KK
Sbjct: 351 NNNNNNSNTTTNNNNSNNKRKKEICDAIAKTAKKRNKK 388

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224098028|ref|XP_002311109.1| global transcription factor group [Populus trichocarpa] gi|222850929|gb|EEE88476.1| global transcription factor group [Populus trichocarpa]

 Score =  433 bits (1113), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 241/393 (61%), Positives = 288/393 (73%), Gaps = 29/393 (7%)

Query: 1   MEPMSGLNQDLGNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFY---LTK 57
           ME +S    D GN+ +  ++    E EG   ++D+ILQKV +LEQ++N+VEQFY    +K
Sbjct: 1   MEAISPSIVDSGNLPIRNSDA---EAEGFKHSVDEILQKVDKLEQRVNEVEQFYSKNTSK 57

Query: 58  DNNQPNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQ 117
                ++    S  K+K K+RH+ +              A +RMQEL RQF  I RQITQ
Sbjct: 58  KQQSGSSKGGSSTVKDKDKERHIPT--------------AAKRMQELMRQFGTILRQITQ 103

Query: 118 HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 177
           HKWAWPFM PVDV+GLGLHDYYEVI+KPMDFSTIKN+M+ KDGTGY++VREI ADVRLVF
Sbjct: 104 HKWAWPFMQPVDVKGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKSVREICADVRLVF 163

Query: 178 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAV 237
           KNAMKYNDER DVHVMAK+LL KFEEKWLQ LPKV EEEKR+EEEEA+AQLDMQL QEA 
Sbjct: 164 KNAMKYNDERSDVHVMAKTLLGKFEEKWLQFLPKVTEEEKRREEEEAEAQLDMQLAQEAA 223

Query: 238 QTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIV 297
               A++L +EL EVDM LE LRE V+QKCRKMSTEEK+ LG ALTRLSPEDL KALEIV
Sbjct: 224 HAKMARDLGNELYEVDMHLEELREMVVQKCRKMSTEEKRKLGAALTRLSPEDLTKALEIV 283

Query: 298 AENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNN 357
           A+NNP F ATA+EVDLD+DAQSE TLWRLK FV+++L+   +S+   GG NN        
Sbjct: 284 AQNNPGFQATAEEVDLDIDAQSETTLWRLKFFVKDALEVQGKSAASAGGRNNTT------ 337

Query: 358 EKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 390
                +  N NN KRK+EICDA+AK A KR+KK
Sbjct: 338 ---TPSNNNNNNNKRKREICDAIAKTAKKRSKK 367

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086052|emb|CBI31493.3| unnamed protein product [Vitis vinifera]

 Score =  429 bits (1102), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 230/369 (62%), Positives = 270/369 (73%), Gaps = 28/369 (7%)

Query: 10  DLGNVGLGKAEGDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNNQPNTSKSIS 69
           D  N+  GK +G+  +VE L   +DDI  KV +LEQ++N+VEQFYLT    Q N SK   
Sbjct: 7   DTRNMETGKNQGNAAQVESLKSRVDDIFTKVDKLEQRVNEVEQFYLTASKKQLNVSK--- 63

Query: 70  IAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVD 129
                              DA  RE AA +RMQEL RQF  I RQITQHKWAWPFM PVD
Sbjct: 64  -------------------DASRREAAAAKRMQELMRQFGTILRQITQHKWAWPFMQPVD 104

Query: 130 VEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDD 189
           VEGLGLHDYYEVIEKPMDFSTIKNKM+ KDG GY+NVREI ADVRLVFKNAMKYNDER D
Sbjct: 105 VEGLGLHDYYEVIEKPMDFSTIKNKMEAKDGAGYKNVREICADVRLVFKNAMKYNDERRD 164

Query: 190 VHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSEL 249
           VHVMAK+LL KFEEKWLQLLPKV EE+KR+EEEEA+AQLDM L QEA     A+++ +EL
Sbjct: 165 VHVMAKTLLGKFEEKWLQLLPKVAEEDKRREEEEAEAQLDMHLAQEAAHAKMARDISNEL 224

Query: 250 NEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQ 309
            E+DM L+++RE ++QKCRK STEEK+ LG AL+RLS EDL KALEIVA++NPSF ATA+
Sbjct: 225 FEIDMHLDDIREIIVQKCRKTSTEEKRKLGAALSRLSAEDLSKALEIVAQSNPSFQATAE 284

Query: 310 EVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNN 369
           EV LD+DAQ E TLWRLK FV+++L+   +SS  MGGNN           +N++    NN
Sbjct: 285 EVHLDIDAQRESTLWRLKFFVKDALEIQGKSSASMGGNNTATT------TNNNHPTTNNN 338

Query: 370 PKRKKEICD 378
            KRKKEICD
Sbjct: 339 SKRKKEICD 347

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224109720|ref|XP_002315289.1| global transcription factor group [Populus trichocarpa] gi|222864329|gb|EEF01460.1| global transcription factor group [Populus trichocarpa]

 Score =  426 bits (1096), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 219/317 (69%), Positives = 254/317 (80%), Gaps = 3/317 (0%)

Query: 21  GDTVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYL---TKDNNQPNTSKSISIAKEKLKD 77
           G+  + EG   ++D+I QKV +LEQ++N VEQFYL    K  +  +     SI K+K K+
Sbjct: 1   GNDADTEGFKHSVDEIFQKVDKLEQRMNGVEQFYLDISKKQQSGSSKGGGSSIVKDKDKE 60

Query: 78  RHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHD 137
           RHV SI KQQQDA  RE AA +RMQEL RQF  I RQITQHKWAWPFM PVDV+GL LHD
Sbjct: 61  RHVTSIRKQQQDASKREAAAAKRMQELMRQFGTILRQITQHKWAWPFMQPVDVKGLRLHD 120

Query: 138 YYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSL 197
           YYEVI+KPMDFSTIKN+M+ KDGTGY+NVREI ADVRLVFKNAMKYNDER DVHVMAK+L
Sbjct: 121 YYEVIDKPMDFSTIKNQMEAKDGTGYKNVREISADVRLVFKNAMKYNDERSDVHVMAKTL 180

Query: 198 LEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLE 257
           L KFEEKWLQLLPKV EEEKR+E+EE +A+LDMQL QEA     A++L +EL EVDM LE
Sbjct: 181 LGKFEEKWLQLLPKVTEEEKRREDEEVEAKLDMQLAQEAAHAKMARDLSNELYEVDMHLE 240

Query: 258 NLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDA 317
            LR+ V+QKCRKMSTEEK+ LG ALTRLSPEDL KALEIVA +NP F ATA+EVDLD+DA
Sbjct: 241 ELRDIVVQKCRKMSTEEKRKLGVALTRLSPEDLTKALEIVARSNPGFQATAEEVDLDIDA 300

Query: 318 QSELTLWRLKVFVQESL 334
           Q+E TLWRLK  V++ L
Sbjct: 301 QTESTLWRLKFLVKDVL 317

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

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	395
TAIR|locus:2044722	386	IMB1 "AT2G34900" [Arabidopsis	0.946	0.968	0.501	3e-92
TAIR|locus:2038565	766	GTE4 "AT1G06230" [Arabidopsis	0.488	0.251	0.360	1.1e-27
TAIR|locus:2155715	590	GTE7 "AT5G65630" [Arabidopsis	0.351	0.235	0.368	2.1e-25
UNIPROTKB|H9L2H3	859	LOC100859056 "Uncharacterized	0.374	0.172	0.358	2.6e-25
MGI|MGI:99495	798	Brd2 "bromodomain containing 2	0.298	0.147	0.406	6.6e-24
RGD|1303324	798	Brd2 "bromodomain containing 2	0.298	0.147	0.406	6.6e-24
UNIPROTKB|P25440	801	BRD2 "Bromodomain-containing p	0.298	0.147	0.406	6.7e-24
UNIPROTKB|Q5TJG6	803	BRD2 "Bromodomain-containing p	0.298	0.146	0.406	6.8e-24
UNIPROTKB|Q32S26	803	BRD2 "Bromodomain-containing p	0.298	0.146	0.406	6.8e-24
UNIPROTKB|A5D9K6	803	BRD2 "Uncharacterized protein"	0.298	0.146	0.406	6.8e-24

TAIR|locus:2044722 IMB1 "AT2G34900" [Arabidopsis thaliana (taxid:3702)]

 Score = 919 (328.6 bits), Expect = 3.0e-92, P = 3.0e-92
 Identities = 197/393 (50%), Positives = 260/393 (66%)

Query:     2 EPMSGLNQDLGNVGLGKAEGD-TVEVEGLNKTIDDILQKVTQLEQKLNDVEQFYLTKDNN 60
             EP+   N D+ N  L    G+   E+E     +D+I  +V QLEQK+ +VE FY TKD  
Sbjct:     8 EPVLVPNCDVENTELAVFNGNGESELENFGTCVDEITDRVNQLEQKVVEVEHFYSTKDGA 67

Query:    61 -QPNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQ--ELKRQFAAIFRQITQ 117
              Q NTSKS S  K K+    ++     + ++  +E++ G+ +   +L RQFA +FRQI Q
Sbjct:    68 AQTNTSKSNSGGK-KIA---ISQPNNSKGNSAGKEKSKGKHVSSPDLMRQFATMFRQIAQ 123

Query:   118 HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 177
             HKWAWPF+ PVDV+GLGLHDYY+VIEKPMD  TIK KM+  +   Y NVREIYADVRLVF
Sbjct:   124 HKWAWPFLEPVDVKGLGLHDYYKVIEKPMDLGTIKKKMESSE---YSNVREIYADVRLVF 180

Query:   178 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMXXXXXXXXXXXXXXLDMQLTQEAV 237
             KNAM+YN+E++DV+VMA+SLLEKFEEKWL ++PK++               + QLT EA 
Sbjct:   181 KNAMRYNEEKEDVYVMAESLLEKFEEKWLLIMPKLVEEEKKQVDEEAEKHANKQLTMEAA 240

Query:   238 QTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIV 297
             Q   A++L +EL E+D+QLE LRE+V+Q+CRK+ST+EKK L  AL RLSPEDL KAL++V
Sbjct:   241 QAEMARDLSNELYEIDLQLEKLRESVVQRCRKLSTQEKKGLSAALGRLSPEDLSKALKMV 300

Query:   298 AENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGXXXXXXXXXXX 357
             +E+NPSF A A EV+LD+D Q+++TLWRLKVFVQE+LKAA++SSG               
Sbjct:   301 SESNPSFPAGAPEVELDIDVQTDVTLWRLKVFVQEALKAANKSSGGTNAQNNNNTGTGEI 360

Query:   358 XXXXXXXXXXXXXXXXXEICDALAKPAVKRTKK 390
                              EI DA+ K ++KR KK
Sbjct:   361 NKNNAKRRR--------EISDAINKASIKRAKK 385

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0010030 "positive regulation of seed germination" evidence=IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IMP

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

TAIR|locus:2038565 GTE4 "AT1G06230" [Arabidopsis thaliana (taxid:3702)]

 Score = 256 (95.2 bits), Expect = 1.1e-27, Sum P(2) = 1.1e-27
 Identities = 75/208 (36%), Positives = 111/208 (53%)

Query:     5 SGLNQDLGNVGLGKAE-GDTVEVEGLNKTIDDILQKVTQLEQKLND-VEQFYLTKDNNQP 62
             +G+N   G +  G A  G   EV    + ++ +   V +  Q +N+ VE+   T   NQ 
Sbjct:   320 TGINNGGGRILSGFASAGLPREVIRAPRPVNQLSISVLENTQGVNEHVEKEKRTPKANQF 379

Query:    63 NTSKSISIAKEKL-----KDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQ 117
               +    +  +KL       +  +S +KQ  D  H    AG ++    +  +A+  ++ +
Sbjct:   380 YRNSEFLLG-DKLPPAESNKKSKSSSKKQGGDVGHGF-GAGTKVF---KNCSALLERLMK 434

Query:   118 HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 177
             HK  W F  PVDV+GLGL DYY +IE PMD  TIK+ +  K+   Y++ RE   DVRL F
Sbjct:   435 HKHGWVFNAPVDVKGLGLLDYYTIIEHPMDLGTIKSALM-KNL--YKSPREFAEDVRLTF 491

Query:   178 KNAMKYNDERDDVHVMAKSLLEKFEEKW 205
              NAM YN E  DVH+MA +LL+ FEE+W
Sbjct:   492 HNAMTYNPEGQDVHLMAVTLLQIFEERW 519

GO:0003677 "DNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0009294 "DNA mediated transformation" evidence=RCA;IMP

GO:0045931 "positive regulation of mitotic cell cycle" evidence=IMP

GO:0048364 "root development" evidence=IMP

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

TAIR|locus:2155715 GTE7 "AT5G65630" [Arabidopsis thaliana (taxid:3702)]

 Score = 233 (87.1 bits), Expect = 2.1e-25, Sum P(2) = 2.1e-25
 Identities = 53/144 (36%), Positives = 81/144 (56%)

Query:    59 NNQPNTSKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQH 118
             NN       +   K+K K ++V+ +++  Q      E+  + +  +    + I  ++ +H
Sbjct:   126 NNFTGEKNDLGPKKKKQK-KNVSGLKRSNQFGPSDPESE-KLLAGMLNTCSQILVKLMKH 183

Query:   119 KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK 178
             KWAW F  PVDV GLGLHDY++V++KPMD  T+K  +D   G  Y +  +   DVRL F 
Sbjct:   184 KWAWVFNTPVDVVGLGLHDYHQVVKKPMDLGTVKLNLD--KGF-YVSPIDFATDVRLTFD 240

Query:   179 NAMKYNDERDDVHVMAKSLLEKFE 202
             NAM YN +  DV+ MA  LL+ F+
Sbjct:   241 NAMTYNPKGQDVYFMADKLLDHFD 264

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0009294 "DNA mediated transformation" evidence=RCA;IMP

UNIPROTKB|H9L2H3 LOC100859056 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 249 (92.7 bits), Expect = 2.6e-25, Sum P(2) = 2.6e-25
 Identities = 56/156 (35%), Positives = 90/156 (57%)

Query:    57 KDNNQPNTSKSISIAKEKLKDRHVASIEKQQQDAF-HREEAAGRRMQELKRQFAAIFRQI 115
             + ++ P   KS  +   +   R V   +K   D+  H  E + +  ++LK   + I +++
Sbjct:   303 ESSSLPTEPKSTKLGPRRESSRPVKPPKKDVPDSQQHMVEKSSKVSEQLK-YCSGIIKEM 361

Query:   116 TQHK---WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 172
                K   +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct:   362 FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDLSTIKSKLENRE---YRDAQEFAAD 418

Query:   173 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct:   419 VRLMFSNCYKYNPADHEVVAMARKLQDVFEMRFAKM 454

GO:0000114 "regulation of transcription involved in G1 phase of mitotic cell cycle" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0001833 "inner cell mass cell proliferation" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0010971 "positive regulation of G2/M transition of mitotic cell cycle" evidence=IEA

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0043983 "histone H4-K12 acetylation" evidence=IEA

GO:0044154 "histone H3-K14 acetylation" evidence=IEA

MGI|MGI:99495 Brd2 "bromodomain containing 2" [Mus musculus (taxid:10090)]

 Score = 248 (92.4 bits), Expect = 6.6e-24, Sum P(2) = 6.6e-24
 Identities = 52/128 (40%), Positives = 77/128 (60%)

Query:    84 EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
             + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct:   332 DSQQQ---HQSSKKGKLSEQLKH-CNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 387

Query:   141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
             +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct:   388 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 444

Query:   201 FEEKWLQL 208
             FE ++ ++
Sbjct:   445 FEFRYAKM 452

GO:0003682 "chromatin binding" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006334 "nucleosome assembly" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0016568 "chromatin modification" evidence=IEA

GO:0070577 "histone acetyl-lysine binding" evidence=ISO

RGD|1303324 Brd2 "bromodomain containing 2" [Rattus norvegicus (taxid:10116)]

 Score = 248 (92.4 bits), Expect = 6.6e-24, Sum P(2) = 6.6e-24
 Identities = 52/128 (40%), Positives = 77/128 (60%)

Query:    84 EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
             + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct:   332 DSQQQ---HQSSKKGKLSEQLKH-CNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 387

Query:   141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
             +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct:   388 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 444

Query:   201 FEEKWLQL 208
             FE ++ ++
Sbjct:   445 FEFRYAKM 452

GO:0003682 "chromatin binding" evidence=ISO;ISS

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006334 "nucleosome assembly" evidence=ISO;ISS

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO;ISS

GO:0016568 "chromatin modification" evidence=IEA

GO:0070577 "histone acetyl-lysine binding" evidence=ISO;ISS

UNIPROTKB|P25440 BRD2 "Bromodomain-containing protein 2" [Homo sapiens (taxid:9606)]

 Score = 248 (92.4 bits), Expect = 6.7e-24, Sum P(2) = 6.7e-24
 Identities = 52/128 (40%), Positives = 77/128 (60%)

Query:    84 EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
             + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct:   333 DSQQQ---HQSSKKGKLSEQLKH-CNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 388

Query:   141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
             +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct:   389 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 445

Query:   201 FEEKWLQL 208
             FE ++ ++
Sbjct:   446 FEFRYAKM 453

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0070577 "histone acetyl-lysine binding" evidence=IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0003682 "chromatin binding" evidence=IDA

GO:0006334 "nucleosome assembly" evidence=IMP

GO:0007283 "spermatogenesis" evidence=TAS

UNIPROTKB|Q5TJG6 BRD2 "Bromodomain-containing protein 2" [Canis lupus familiaris (taxid:9615)]

 Score = 248 (92.4 bits), Expect = 6.8e-24, Sum P(2) = 6.8e-24
 Identities = 52/128 (40%), Positives = 77/128 (60%)

Query:    84 EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
             + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct:   333 DSQQQ---HQSSKKGKLSEQLKH-CNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 388

Query:   141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
             +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct:   389 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 445

Query:   201 FEEKWLQL 208
             FE ++ ++
Sbjct:   446 FEFRYAKM 453

GO:0070577 "histone acetyl-lysine binding" evidence=ISS

GO:0003682 "chromatin binding" evidence=ISS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0006334 "nucleosome assembly" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|Q32S26 BRD2 "Bromodomain-containing protein 2" [Bos taurus (taxid:9913)]

 Score = 248 (92.4 bits), Expect = 6.8e-24, Sum P(2) = 6.8e-24
 Identities = 52/128 (40%), Positives = 77/128 (60%)

Query:    84 EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
             + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct:   333 DSQQQ---HQSSKKGKLSEQLKH-CNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 388

Query:   141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
             +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct:   389 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 445

Query:   201 FEEKWLQL 208
             FE ++ ++
Sbjct:   446 FEFRYAKM 453

GO:0070577 "histone acetyl-lysine binding" evidence=ISS

GO:0003682 "chromatin binding" evidence=ISS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0006334 "nucleosome assembly" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|A5D9K6 BRD2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 248 (92.4 bits), Expect = 6.8e-24, Sum P(2) = 6.8e-24
 Identities = 52/128 (40%), Positives = 77/128 (60%)

Query:    84 EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYE 140
             + QQQ   H+    G+  ++LK     I +++   K   +AWPF  PVD   LGLHDY++
Sbjct:   333 DSQQQ---HQSSKKGKLSEQLKH-CNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHD 388

Query:   141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
             +I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + 
Sbjct:   389 IIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDV 445

Query:   201 FEEKWLQL 208
             FE ++ ++
Sbjct:   446 FEFRYAKM 453

GO:0070577 "histone acetyl-lysine binding" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q84XV2	GTE1_ARATH	No assigned EC number	0.5318	0.9088	0.9300	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00002627001 SubName- Full=Chromosome undetermined scaffold_133, whole genome shotgun sequence; (438 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	395
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	1e-45
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	4e-31
smart00297	107	smart00297, BROMO, bromo domain	4e-27
cd04369	99	cd04369, Bromodomain, Bromodomain	5e-25
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	5e-22
pfam00439	84	pfam00439, Bromodomain, Bromodomain	3e-21
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	1e-20
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	2e-19
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	4e-17
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	9e-17
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	2e-15
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	4e-15
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	5e-14
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	7e-14
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	6e-13
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	7e-13
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	2e-11
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	5e-10
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	4e-09
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	1e-08
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	1e-08
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	5e-08
COG5076	371	COG5076, COG5076, Transcription factor involved in	1e-07
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	2e-07
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	3e-07
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	1e-06
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	2e-06
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	2e-06
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	5e-06
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	3e-05
cd05501	102	cd05501, Bromo_SP100C_like, Bromodomain, SP100C_li	4e-04
cd05494	114	cd05494, Bromodomain_1, Bromodomain; uncharacteriz	5e-04
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	0.001
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	0.001

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

 Score =  152 bits (385), Expect = 1e-45
 Identities = 48/100 (48%), Positives = 65/100 (65%), Gaps = 3/100 (3%)

Query: 106 RQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRN 165
           +Q   + R++ +HKW W F  PVDV  LGL DY+++I+KPMD  T+K K++      Y +
Sbjct: 3   KQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKG---EYSS 59

Query: 166 VREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
             E  ADVRL F NAM+YN   +DVH MAK LL+ FE +W
Sbjct: 60  PEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETRW 99

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|99930 cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_like subfamily, repeat II

 Score =  113 bits (286), Expect = 4e-31
 Identities = 46/90 (51%), Positives = 62/90 (68%), Gaps = 4/90 (4%)

Query: 117 QHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRL 175
           +HK +AWPF  PVD E LGLHDY+++I+ PMD STIK K+D ++   Y + +E  ADVRL
Sbjct: 16  KHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNRE---YADAQEFAADVRL 72

Query: 176 VFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
           +F N  KYN     VH MA+ L + FE++W
Sbjct: 73  MFSNCYKYNPPDHPVHAMARKLQDVFEDRW 102

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|197636 smart00297, BROMO, bromo domain

 Score =  103 bits (259), Expect = 4e-27
 Identities = 39/110 (35%), Positives = 61/110 (55%), Gaps = 5/110 (4%)

Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
           +  ++L+    A+  ++  H  +WPF+ PV  +     DYY++I+KPMD  TIK K++  
Sbjct: 3   KLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEA--PDYYDIIKKPMDLKTIKKKLENG 60

Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
               Y +V E  AD  L+F NA  YN    +V+  AK L + FE+K  +L
Sbjct: 61  ---KYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

Length = 107

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score = 97.4 bits (243), Expect = 5e-25
 Identities = 39/104 (37%), Positives = 59/104 (56%), Gaps = 7/104 (6%)

Query: 104 LKRQFAAIFRQITQHKW--AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGT 161
           LK++  ++   + + K   + PF+ PVD +     DYYEVI+ PMD STIK K+   +  
Sbjct: 1   LKKKLRSLLDALKKLKRDLSEPFLEPVDPKEA--PDYYEVIKNPMDLSTIKKKLKNGE-- 56

Query: 162 GYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
            Y+++ E  ADVRL+F NA  YN     ++  AK L + FE+  
Sbjct: 57  -YKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 99

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

>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score = 89.3 bits (222), Expect = 5e-22
 Identities = 36/89 (40%), Positives = 53/89 (59%), Gaps = 5/89 (5%)

Query: 118 HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNK-MDGKDGTGYRNVREIYADVRLV 176
             + WPF+ PVD   L + +Y+ +I+KPMD  TI  K  +G+    Y++ +E   DVRL+
Sbjct: 18  SAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQ----YQSAKEFERDVRLI 73

Query: 177 FKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
           FKN   +N E  DV++M   L E F +KW
Sbjct: 74  FKNCYTFNPEGTDVYMMGHQLEEVFNDKW 102

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|215921 pfam00439, Bromodomain, Bromodomain

 Score = 86.7 bits (215), Expect = 3e-21
 Identities = 36/88 (40%), Positives = 50/88 (56%), Gaps = 5/88 (5%)

Query: 108 FAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVR 167
              I   + +H  A PF+ PVD E     DYYEVI++PMD STI+ K+       Y+++ 
Sbjct: 1   CLEILEDLMEHPLAEPFLEPVDPEEY--PDYYEVIKEPMDLSTIRQKLKSGK---YKSLA 55

Query: 168 EIYADVRLVFKNAMKYNDERDDVHVMAK 195
           E   DV L+F NA+ YN E  D++  AK
Sbjct: 56  EFLKDVELIFSNAITYNGEDSDIYKDAK 83

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|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score = 85.3 bits (212), Expect = 1e-20
 Identities = 37/102 (36%), Positives = 54/102 (52%), Gaps = 5/102 (4%)

Query: 103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 162
            L  Q   +   +  HK AWPF+ PVD E     DYY+VI+KPMD ST++ K++      
Sbjct: 1   PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEA--PDYYDVIKKPMDLSTMEEKLENGY--- 55

Query: 163 YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           Y  + E  AD++L+F N   YN    + +  A  L + F +K
Sbjct: 56  YVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKK 97

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|99929 cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like subfamily, repeat I

 Score = 82.5 bits (204), Expect = 2e-19
 Identities = 36/92 (39%), Positives = 53/92 (57%), Gaps = 3/92 (3%)

Query: 117 QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV 176
           +HK+AWPF  PVD   L L DY+++I+ PMD  TIK +++      Y +  E   D   +
Sbjct: 19  KHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNY---YWSASECIQDFNTM 75

Query: 177 FKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           F N   YN   DDV +MA++L + F +K  Q+
Sbjct: 76  FTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQM 107

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|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 75.8 bits (187), Expect = 4e-17
 Identities = 32/95 (33%), Positives = 45/95 (47%), Gaps = 3/95 (3%)

Query: 108 FAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVR 167
             +  R + + K A PF+ PVD   L +  Y  +I+KPMD  TI+ K+       Y +V 
Sbjct: 9   LLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKL---KSNVYTSVE 65

Query: 168 EIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFE 202
           E  AD  L+  N + +N     V  M K L   FE
Sbjct: 66  EFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAFE 100

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|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 75.0 bits (185), Expect = 9e-17
 Identities = 35/89 (39%), Positives = 50/89 (56%), Gaps = 3/89 (3%)

Query: 123 PFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK 182
           PF  PV      + +YY++I+ PMD S I+ K+  K    Y +  E  ADVRL+FKN  K
Sbjct: 24  PFHEPV---SPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

Query: 183 YNDERDDVHVMAKSLLEKFEEKWLQLLPK 211
           +N+E  +V    K L   FEE+  ++LP 
Sbjct: 81  FNEEDSEVAQAGKELELFFEEQLKEILPD 109

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|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily

 Score = 71.7 bits (176), Expect = 2e-15
 Identities = 33/91 (36%), Positives = 51/91 (56%), Gaps = 5/91 (5%)

Query: 114 QITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADV 173
           +I +HK +WPF+ PV    +   DYY++I+KPMD  TIK K++  +   Y+   E  +D+
Sbjct: 23  EIVKHKDSWPFLRPVSKIEVP--DYYDIIKKPMDLGTIKEKLNMGE---YKLAEEFLSDI 77

Query: 174 RLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           +LVF N   YN E   V+     L   F ++
Sbjct: 78  QLVFSNCFLYNPEHTSVYKAGTRLQRFFIKR 108

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|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily

 Score = 70.6 bits (173), Expect = 4e-15
 Identities = 35/103 (33%), Positives = 57/103 (55%), Gaps = 4/103 (3%)

Query: 102 QELKRQFAAIFRQI-TQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 160
           +EL++       ++  Q   + PF  PVD + LG+ DY+++++ PMD STI+ K+D   G
Sbjct: 2   EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLD--TG 59

Query: 161 TGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEE 203
             Y++  +   DV L+F NA  YN +   V+     L E FE+
Sbjct: 60  Q-YQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101

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|99935 cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BAZ2B_like subfamily

 Score = 67.0 bits (164), Expect = 5e-14
 Identities = 35/98 (35%), Positives = 57/98 (58%), Gaps = 11/98 (11%)

Query: 111 IFRQITQHKWAWPFMHPVD---VEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVR 167
           I  ++  H+ AWPF+ PV+   V G     Y ++I+KPMDFSTI+ K++      Y+ + 
Sbjct: 8   ILDEMEAHEDAWPFLEPVNTKLVPG-----YRKIIKKPMDFSTIREKLESG---QYKTLE 59

Query: 168 EIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
           E   DVRLVF N   +N++  +V     ++ + FE++W
Sbjct: 60  EFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFFEKRW 97

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|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup

 Score = 67.0 bits (164), Expect = 7e-14
 Identities = 32/95 (33%), Positives = 53/95 (55%), Gaps = 5/95 (5%)

Query: 105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 164
           K+    ++R +  H++A  F+ PV  +      Y+ V+ +PMD STIK  ++  +GT  R
Sbjct: 5   KKAILLVYRTLASHRYASVFLKPVTEDIA--PGYHSVVYRPMDLSTIKKNIE--NGT-IR 59

Query: 165 NVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLE 199
           +  E   DV L+F+NA+ YN    DV++MA  +  
Sbjct: 60  STAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEMQR 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 = 64.8 bits (158), Expect = 6e-13
 Identities = 35/117 (29%), Positives = 57/117 (48%), Gaps = 6/117 (5%)

Query: 105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 164
           K+Q   +   +   + + PF  PVD+  L   DY ++I+ PMD  T+K  + G +   Y 
Sbjct: 7   KKQCKELVNLMWDCEDSEPFRQPVDL--LKYPDYRDIIDTPMDLGTVKETLFGGN---YD 61

Query: 165 NVREIYADVRLVFKNAMKYN-DERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQE 220
           +  E   DVRL+F N+  Y  ++R  ++ M   L   FEE   +++       KR E
Sbjct: 62  DPMEFAKDVRLIFSNSKSYTPNKRSRIYSMTLRLSALFEEHIKKIISDWKSALKRNE 118

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|99943 cd05511, Bromo_TFIID, Bromodomain, TFIID-like subfamily

 Score = 64.2 bits (157), Expect = 7e-13
 Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 18/121 (14%)

Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           I  ++     +WPF  PV+     + DYY++I++PMD  TI+ K+       Y++  E  
Sbjct: 8   IVNELKNLPDSWPFHTPVN--KKKVPDYYKIIKRPMDLQTIRKKISKH---KYQSREEFL 62

Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDM 230
            D+ L+  N++ YN         AK +LE             + EE   E EE   QL+ 
Sbjct: 63  EDIELIVDNSVLYNGPDSVYTKKAKEMLE-------------LAEELLAEREEKLTQLEK 109

Query: 231 Q 231
            
Sbjct: 110 N 110

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

 Score = 59.9 bits (145), Expect = 2e-11
 Identities = 33/99 (33%), Positives = 54/99 (54%), Gaps = 9/99 (9%)

Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           I  +I +++++WPF  PV  +     DY +VI  PMD  T++ K        Y +V+E  
Sbjct: 8   ILSKILKYRFSWPFREPVTADEA--EDYKKVITNPMDLQTMQTKCSCGS---YSSVQEFL 62

Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL 209
            D++LVF NA KY +  +  +V+  S + K E+  + LL
Sbjct: 63  DDMKLVFSNAEKYYE--NGSYVL--SCMRKTEQCCVNLL 97

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|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V

 Score = 56.2 bits (136), Expect = 5e-10
 Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 7/71 (9%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVH----V 192
           DYY+VI+KP+D   I++K++G     Y+++ ++ +D  L+F NA KYN+    ++     
Sbjct: 38  DYYDVIKKPIDMEKIRSKIEGN---QYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALT 94

Query: 193 MAKSLLEKFEE 203
           + K LLE   E
Sbjct: 95  LQKVLLETKRE 105

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

 Score = 53.5 bits (129), Expect = 4e-09
 Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 5/66 (7%)

Query: 123 PFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK 182
            F  PVD E +   DYYE+I++PMD  TI  K+D      Y   ++   D+ L+  NA++
Sbjct: 23  AFTKPVDEEEV--PDYYEIIKQPMDLQTILQKLDTHQ---YLTAKDFLKDIDLIVTNALE 77

Query: 183 YNDERD 188
           YN +RD
Sbjct: 78  YNPDRD 83

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|99944 cd05512, Bromo_brd1_like, Bromodomain; brd1_like subfamily

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 5/61 (8%)

Query: 124 FMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY 183
           F  PVD+  +   DY + I++PMDFST++ K++ +    YR + +  AD  L+  N + Y
Sbjct: 22  FSEPVDLSEV--PDYLDHIKQPMDFSTMRKKLESQ---RYRTLEDFEADFNLIINNCLAY 76

Query: 184 N 184
           N
Sbjct: 77  N 77

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|99945 cd05513, Bromo_brd7_like, Bromodomain, brd7_like subgroup

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 25/61 (40%), Positives = 36/61 (59%), Gaps = 3/61 (4%)

Query: 138 YYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSL 197
           Y  +I+ PMDFST+K K+   D   Y+++ E   D +L+ +NAMKYN      +  AK L
Sbjct: 34  YSSIIKHPMDFSTMKEKIKNND---YQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90

Query: 198 L 198
           L
Sbjct: 91  L 91

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|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 50.5 bits (121), Expect = 5e-08
 Identities = 36/128 (28%), Positives = 62/128 (48%), Gaps = 19/128 (14%)

Query: 84  EKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVD-VEGLGLHDYYEVI 142
           E+  Q+ F+  E+  + + ELK          T+H  + PF+  V   E     DYY++I
Sbjct: 1   ERIGQEEFY--ESLDKVLNELK--------TYTEH--STPFLTKVSKREA---PDYYDII 45

Query: 143 EKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFE 202
           +KPMD  T+  K+       Y++  E   D+ L++KN + YN +         + ++K  
Sbjct: 46  KKPMDLGTMLKKLKNLQ---YKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHANFMKKKA 102

Query: 203 EKWLQLLP 210
           E  L+L+P
Sbjct: 103 EHLLKLIP 110

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

 Score = 52.5 bits (126), Expect = 1e-07
 Identities = 30/121 (24%), Positives = 53/121 (43%), Gaps = 7/121 (5%)

Query: 113 RQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 172
           R        +              DYYE+I+ PMD  TI+ K+       Y++  E  +D
Sbjct: 160 RDGRFLSSIFL----GLPSKREYPDYYEIIKSPMDLLTIQKKLKN---GRYKSFEEFVSD 212

Query: 173 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQL 232
           + L+F N   YN     V+V AK L + F +   ++  +++E   +   EE + +  + +
Sbjct: 213 LNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLELSIKPGREEREERESVLI 272

Query: 233 T 233
           T
Sbjct: 273 T 273

Length = 371

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

 Score = 49.3 bits (118), Expect = 2e-07
 Identities = 30/121 (24%), Positives = 55/121 (45%), Gaps = 6/121 (4%)

Query: 82  SIEKQQQDAFHREEAAGRRMQE-LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYE 140
           S E +  D    +       +E L      +   + Q + A  F +PVD+      DY+ 
Sbjct: 6   SSEWELFDPGWEQPHIRDEERERLISGLDKLLLSL-QLEIAEYFEYPVDL-RAWYPDYWN 63

Query: 141 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEK 200
            +  PMD  TI+++++ +    YR++  +  DVRL+  NA  +N+   ++   AK L + 
Sbjct: 64  RVPVPMDLETIRSRLENR---YYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDW 120

Query: 201 F 201
            
Sbjct: 121 L 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|99949 cd05518, Bromo_polybromo_IV, Bromodomain, polybromo repeat IV

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 7/69 (10%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE----RDDVHV 192
           DYY++I +P+D  TI++ +       Y    E+  D +L+F+NA  YN+E     +D ++
Sbjct: 38  DYYKIILEPIDLKTIEHNIRNDK---YATEEELMDDFKLMFRNARHYNEEGSQVYEDANI 94

Query: 193 MAKSLLEKF 201
           + K L EK 
Sbjct: 95  LEKVLKEKR 103

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|99951 cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 196
           DYY+ I+ P+    I+ K+  K+G  Y  + E+ AD+ L+F+NA +YN     ++  A+ 
Sbjct: 38  DYYQEIKNPISLQQIRTKL--KNG-EYETLEELEADLNLMFENAKRYNVPNSRIYKDAEK 94

Query: 197 LLEKFEEK 204
           L +  + K
Sbjct: 95  LQKLMQAK 102

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 = 45.4 bits (108), Expect = 2e-06
 Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 3/68 (4%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 196
           DYY +I++P+    IK +++G     Y+++ E   D  L+F NA  YN E   V+  A  
Sbjct: 38  DYYVIIKRPIALDQIKRRIEG---RAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVE 94

Query: 197 LLEKFEEK 204
           + + F++K
Sbjct: 95  MEKAFKKK 102

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

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 31/109 (28%), Positives = 54/109 (49%), Gaps = 15/109 (13%)

Query: 103 ELKRQFAAIFRQITQHK------WAWPFMH-PVDVEGLGLHDYYEVIEKPMDFSTIKNKM 155
           EL ++   I   + ++K       A  F+  P   E   L +YYE+I KP+DF  IK ++
Sbjct: 1   ELTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKE---LPEYYELIRKPVDFKKIKERI 57

Query: 156 -DGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEE 203
            + K    YR++ ++  DV L+ +NA  +N E   ++  +  L   F+ 
Sbjct: 58  RNHK----YRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKS 102

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|99952 cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 196
           DYY++I+ P+  +T+K ++       Y N +E   D+  +  NA  YN +   ++  A  
Sbjct: 39  DYYKIIKNPLSLNTVKKRL-----PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYAL- 92

Query: 197 LLEKF 201
           +LEK+
Sbjct: 93  ILEKY 97

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 = 106

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

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 196
           +YYEV+  P+D   I+ K+  ++   Y +V ++ AD  L+  NA  Y       H  A  
Sbjct: 40  EYYEVVSNPIDLLKIQQKLKTEE---YDDVDDLTADFELLINNAKAYYKPDSPEHKDACK 96

Query: 197 LLEKFEE 203
           L E F  
Sbjct: 97  LWELFLS 103

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|99933 cd05501, Bromo_SP100C_like, Bromodomain, SP100C_like subfamily

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 196
           DY + I++PM  + +K +++ +    Y  V     D+RL+F N   +  + D   V    
Sbjct: 32  DYCQGIKEPMWLNKVKERLNER---VYHTVEGFVRDMRLIFHNHKLFYKDDDFGQVGIT- 87

Query: 197 LLEKFEE 203
           L +KFE+
Sbjct: 88  LEKKFEK 94

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 = 39.0 bits (91), Expect = 5e-04
 Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 8/59 (13%)

Query: 95  EAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKN 153
           EA  R ++ELKR          +++ AWPF+ PV+    G  DY +VI++PM F T  N
Sbjct: 3   EALERVLRELKR--------HRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVN 53

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

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE 186
           +YY+ I  P+    IK K+  +    Y++  +   D+ L+F+NA  YN+ 
Sbjct: 39  EYYQEISNPISLDDIKKKVKRRK---YKSFDQFLNDLNLMFENAKLYNEN 85

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 = 38.1 bits (89), Expect = 0.001
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 5/67 (7%)

Query: 137 DYYEVIEKPMDFSTIKNKMDGKDGTG-YRNVREIYADVRLVFKNAMKYNDERDDVHVMAK 195
           DYYE I  P+D STI+ ++     TG Y+      +D+  VF+NA KY   +  +     
Sbjct: 40  DYYERITDPVDLSTIEKQIL----TGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVC 95

Query: 196 SLLEKFE 202
            L + + 
Sbjct: 96  RLRKAYY 102

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	395
KOG1474	640	consensus Transcription initiation factor TFIID, s	100.0
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.96
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.95
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.95
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.95
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.94
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.94
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.94
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.94
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.94
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.94
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.94
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.94
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.93
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.93
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.93
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.93
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.93
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.93
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.92
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.92
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.92
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.91
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.91
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.91
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.9
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.9
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.9
smart00297	107	BROMO bromo domain.	99.9
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.9
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.9
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.87
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.87
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.86
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.86
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.84
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.77
KOG1245	1404	consensus Chromatin remodeling complex WSTF-ISWI,	99.74
COG5076	371	Transcription factor involved in chromatin remodel	99.71
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	99.64
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.39
KOG0008	1563	consensus Transcription initiation factor TFIID, s	98.98
KOG0955	1051	consensus PHD finger protein BR140/LIN-49 [General	98.98
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	98.97
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	98.97
KOG1827	629	consensus Chromatin remodeling complex RSC, subuni	98.81
KOG0008	1563	consensus Transcription initiation factor TFIID, s	98.71
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	98.71
KOG1474	640	consensus Transcription initiation factor TFIID, s	98.6
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	98.09
COG5076	371	Transcription factor involved in chromatin remodel	98.03
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	97.88
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	96.01
KOG0644	1113	consensus Uncharacterized conserved protein, conta	86.36
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	85.75

>KOG1474 consensus Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription]

Probab=100.00  E-value=9.8e-34  Score=302.64  Aligned_cols=237  Identities=34%  Similarity=0.529  Sum_probs=174.1

Q ss_pred             hhccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhch
Q 016116           97 AGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV  176 (395)
Q Consensus        97 ~~~~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LI  176 (395)
                      ..+.+..++++|..||..|+.|+++|||..|||+..||+||||+||++||||+||+.||.++.   |.++.+|++|||||
T Consensus       216 ~~~~~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~---Y~~~~eF~~DVRL~  292 (640)
T KOG1474|consen  216 KSKLTVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGE---YKSAEEFAADVRLT  292 (640)
T ss_pred             cccccHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccc---cCCHHHHHHHHHHH
Confidence            456788999999999999999999999999999999999999999999999999999999999   99999999999999


Q ss_pred             hhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCcCchHHHhhhHHHH----------------------HH---Hh-hhH
Q 016116          177 FKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEE----------------------AK---AQ-LDM  230 (395)
Q Consensus       177 f~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~~~~e~~~~~ee----------------------~~---~~-~~~  230 (395)
                      |.||++||++|++||.||..|+++|+.+|..+.............+.                      ..   .. ...
T Consensus       293 F~Ncm~YNp~g~dV~~Ma~~L~~~Fe~rw~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  372 (640)
T KOG1474|consen  293 FDNCMTYNPEGSDVYAMAKKLQEVFEERWASMPLEIEESESAVKEEAGMASSDQIPSNSVEGPRSSSFESRESASEPSSE  372 (640)
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccccccCcccccchhcccccCcccc
Confidence            99999999999999999999999999999997665432211110000                      00   00 000


Q ss_pred             hHhHHHhhhhhHHHHhHhHHHhhHhHH-----------------------HH------------HHHHHhhhcCCCHHHH
Q 016116          231 QLTQEAVQTNKAKELRSELNEVDMQLE-----------------------NL------------RETVIQKCRKMSTEEK  275 (395)
Q Consensus       231 ~l~~~~~~~~~~~~l~~el~~~~~~le-----------------------~l------------~~~~~~~~r~mt~eEK  275 (395)
                      ....+ ........+...+..+..++.                       .+            ........+.||..++
T Consensus       373 ~~~~~-e~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~t~~~~  451 (640)
T KOG1474|consen  373 LMSEE-ERKKLLAELKLLLKDVPPQLIALLQRPVSKPPRKIEEELESDKRPLVTGKLIKEKNKKEKAANENKRDMTAPEK  451 (640)
T ss_pred             cccHH-hhhhhHhhhhcchhhhhHHHHhhhhccccCccccccccccccccccchhhhhhhhhcccccccccccccccccc
Confidence            00000 000000000000000000000                       00            0011123478999999


Q ss_pred             HHHHHHhccC-ChHhHHHHHHHH--HhcCCCCCCCCCeEEEeCCCCC-------------HHHHHHHHHHHHHHHHhc
Q 016116          276 KNLGTALTRL-SPEDLCKALEIV--AENNPSFHATAQEVDLDMDAQS-------------ELTLWRLKVFVQESLKAA  337 (395)
Q Consensus       276 ~~L~~~I~~L-~~e~L~~vi~II--~~~~P~~~~~~~evElDid~L~-------------~~TL~~L~~yV~~~L~~~  337 (395)
                      ..|...+..| ++..+..+++|+  ....+.+....+++++|++.++             ..|+|++..++...-...
T Consensus       452 ~~l~~~~~~~~~p~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vd~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~  529 (640)
T KOG1474|consen  452 AKLKELLQNLLPPNKLESIVEILKPEKRQLDLSQNDDEIELDLDSVDGSQSREPSSNPLEIETIRETLKLSTERELEL  529 (640)
T ss_pred             ccchhhccCCCCCccccCcccccchhhhcccccccccchhhcccccccccccCCCcccchhhhhhccccchhhHHHHH
Confidence            9999999994 999999999999  5567778788999999999999             999999998887653333

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.96  E-value=6.4e-29  Score=212.50  Aligned_cols=107  Identities=29%  Similarity=0.489  Sum_probs=101.4

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      .+|.++|..||..|++|+.++||+.||++..  +||||++|++||||+||++||.++.   |.++.+|.+||+|||.||+
T Consensus         4 ~~w~~~c~~il~~l~~~~~s~~F~~PVd~~~--~pdY~~iIk~PmDL~tIk~kL~~~~---Y~~~~ef~~D~~lif~Na~   78 (119)
T cd05496           4 SDWKKQCKELVNLMWDCEDSEPFRQPVDLLK--YPDYRDIIDTPMDLGTVKETLFGGN---YDDPMEFAKDVRLIFSNSK   78 (119)
T ss_pred             HHHHHHHHHHHHHHHhCCccccccCCCChhh--cCcHHHHhCCcccHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHHH
Confidence            3688999999999999999999999999987  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCC-CCHHHHHHHHHHHHHHHHHHhhCcCch
Q 016116          182 KYNDE-RDDVHVMAKSLLEKFEEKWLQLLPKVM  213 (395)
Q Consensus       182 ~YN~~-~S~v~~~A~~L~~~Fe~~~~~~~~~~~  213 (395)
                      +||++ +|.||.+|..|+..|+++|..+.+.+.
T Consensus        79 ~yN~~~~s~i~~~a~~L~~~F~~~~~~l~~~~~  111 (119)
T cd05496          79 SYTPNKRSRIYSMTLRLSALFEEHIKKIISDWK  111 (119)
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99985 999999999999999999999876543

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.

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.95  E-value=2.5e-28  Score=205.39  Aligned_cols=101  Identities=37%  Similarity=0.656  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          104 LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      +.-.+..||..|++|+.|+||..||++..+++||||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.|
T Consensus         6 ~~~~~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~---Y~s~~ef~~D~~li~~Na~~y   82 (107)
T cd05497           6 LQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNY---YWSASECIQDFNTMFTNCYIY   82 (107)
T ss_pred             HHHHHHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            33355788999999999999999999987779999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHh
Q 016116          184 NDERDDVHVMAKSLLEKFEEKWLQ  207 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~~~  207 (395)
                      |+++|+++.+|..|++.|++++.+
T Consensus        83 N~~~s~i~~~A~~l~~~f~~~l~~  106 (107)
T cd05497          83 NKPGDDVVLMAQTLEKLFLQKLAQ  106 (107)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999875

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.

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.95  E-value=2.7e-28  Score=205.52  Aligned_cols=105  Identities=31%  Similarity=0.579  Sum_probs=100.1

Q ss_pred             HHHHHHHHHHHHHHHcC-CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhh
Q 016116          102 QELKRQFAAIFRQITQH-KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  180 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~-~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na  180 (395)
                      .+|.+.|..+++.|+++ +.||||..||++..+++||||++|++||||+||++||.++.   |.++.+|.+||+|||.||
T Consensus         2 ~~l~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~---Y~s~~ef~~D~~li~~Na   78 (108)
T cd05495           2 EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQ---YQDPWQYVDDVWLMFDNA   78 (108)
T ss_pred             HHHHHHHHHHHHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHH
Confidence            36888999999999999 99999999999987779999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          181 MKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       181 ~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      +.||+++|.+|.+|..|++.|++.+..++
T Consensus        79 ~~yN~~~s~i~~~a~~l~~~F~~~~~~~~  107 (108)
T cd05495          79 WLYNRKTSRVYKYCTKLAEVFEQEIDPVM  107 (108)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999987653

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.

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

Probab=99.95  E-value=5.7e-28  Score=199.74  Aligned_cols=94  Identities=30%  Similarity=0.540  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCC
Q 016116          106 RQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYND  185 (395)
Q Consensus       106 ~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~  185 (395)
                      +.|..||+.|++++.++||..||++..  +||||++|++||||+||++||+.+.   |.|+.+|.+||+|||.||+.||+
T Consensus         3 ~~c~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~D~~li~~Na~~yN~   77 (97)
T cd05505           3 QKCEEILSKILKYRFSWPFREPVTADE--AEDYKKVITNPMDLQTMQTKCSCGS---YSSVQEFLDDMKLVFSNAEKYYE   77 (97)
T ss_pred             HHHHHHHHHHHhCCCcccccCCCChhh--cccHHHHcCCcCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHHHHHCC
Confidence            679999999999999999999999887  9999999999999999999999999   99999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHH
Q 016116          186 ERDDVHVMAKSLLEKFEEK  204 (395)
Q Consensus       186 ~~S~v~~~A~~L~~~Fe~~  204 (395)
                      +||.|+.+|..|++.|.+.
T Consensus        78 ~~s~i~~~a~~le~~f~~~   96 (97)
T cd05505          78 NGSYVLSCMRKTEQCCVNL   96 (97)
T ss_pred             CCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999875

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.94  E-value=2.1e-27  Score=196.88  Aligned_cols=99  Identities=48%  Similarity=0.944  Sum_probs=95.6

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          104 LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      ++++|..||+.|++++.+++|..||++...++|+||++|++||||+||++||+++.   |.++.+|..||++||.||+.|
T Consensus         1 ~~~~c~~il~~l~~~~~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI~~kL~~~~---Y~s~~ef~~D~~li~~Na~~y   77 (99)
T cd05506           1 VMKQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGE---YSSPEEFAADVRLTFANAMRY   77 (99)
T ss_pred             CHHHHHHHHHHHHhCCCCccccCCCCccccCCCCHHHHHcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999886669999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Q 016116          184 NDERDDVHVMAKSLLEKFEEKW  205 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~  205 (395)
                      |+++|.++.+|..|++.|+++|
T Consensus        78 n~~~s~i~~~a~~l~~~fe~~w   99 (99)
T cd05506          78 NPPGNDVHTMAKELLKIFETRW   99 (99)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999987

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.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.94  E-value=2.1e-27  Score=196.40  Aligned_cols=96  Identities=34%  Similarity=0.720  Sum_probs=93.4

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccC
Q 016116          105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN  184 (395)
Q Consensus       105 ~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN  184 (395)
                      +..|..||..|++|+.+++|+.||++..  +|+||++|++||||+||++||+++.   |.|+.+|.+||+|||.||+.||
T Consensus         2 ~~~c~~il~~l~~~~~~~~F~~pv~~~~--~p~Y~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~li~~Na~~yN   76 (97)
T cd05503           2 LALCETILDEMEAHEDAWPFLEPVNTKL--VPGYRKIIKKPMDFSTIREKLESGQ---YKTLEEFAEDVRLVFDNCETFN   76 (97)
T ss_pred             HHHHHHHHHHHHcCCCchhhcCCCCccc--cCCHHHHhCCCCCHHHHHHHHccCC---CCCHHHHHHHHHHHHHHHHHHC
Confidence            4689999999999999999999999987  9999999999999999999999999   9999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q 016116          185 DERDDVHVMAKSLLEKFEEKW  205 (395)
Q Consensus       185 ~~~S~v~~~A~~L~~~Fe~~~  205 (395)
                      +++|.++.+|..|++.|+.+|
T Consensus        77 ~~~s~i~~~a~~l~~~f~~~~   97 (97)
T cd05503          77 EDDSEVGRAGHNMRKFFEKRW   97 (97)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999987

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.94  E-value=2.8e-27  Score=201.46  Aligned_cols=105  Identities=32%  Similarity=0.562  Sum_probs=99.6

Q ss_pred             cHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          100 RMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       100 ~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      .+......|..||..|+.++.+++|..||+...  +||||++|++||||+||++||..+.   |.|+.+|.+||+|||.|
T Consensus         9 ~~~~~~~~c~~il~~l~~~~~s~~F~~pvd~~~--~pdY~~vI~~PmDL~tI~~kL~~~~---Y~s~~~f~~Dv~LI~~N   83 (115)
T cd05504           9 HGPLNLSALEQLLVEIVKHKDSWPFLRPVSKIE--VPDYYDIIKKPMDLGTIKEKLNMGE---YKLAEEFLSDIQLVFSN   83 (115)
T ss_pred             CCHHHHHHHHHHHHHHHhCCCchhhcCCCCccc--cccHHHHhcCcccHHHHHHHHccCC---CCCHHHHHHHHHHHHHH
Confidence            345677899999999999999999999999877  9999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      |+.||+++|.+|.+|..|+++|+++++++.
T Consensus        84 a~~yN~~~s~i~~~A~~l~~~f~~~~~~~~  113 (115)
T cd05504          84 CFLYNPEHTSVYKAGTRLQRFFIKRCRKLG  113 (115)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999999998763

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.94  E-value=7.8e-27  Score=196.95  Aligned_cols=103  Identities=36%  Similarity=0.625  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCC---CCCCCCCHHHHHHHHhchhhh
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK---DGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~---~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      ...+.|..||..|++|+.++||..||++ .  +|+||++|++||||+||++||+.+   .   |.++++|.+||+|||.|
T Consensus         4 ~~~~~c~~il~~l~~~~~s~~F~~pv~~-~--~p~Y~~iI~~PmdL~tI~~kL~~~~~~~---Y~s~~~f~~D~~li~~N   77 (109)
T cd05502           4 IDQRKCERLLLELYCHELSLPFHEPVSP-S--VPNYYKIIKTPMDLSLIRKKLQPKSPQH---YSSPEEFVADVRLMFKN   77 (109)
T ss_pred             HHHHHHHHHHHHHHhCCCChhhcCCCCC-C--CCCHHHHCCCCccHHHHHHHHhcCCCCC---CCCHHHHHHHHHHHHHH
Confidence            4567899999999999999999999998 4  999999999999999999999984   6   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHHhhCcC
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK  211 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~  211 (395)
                      |+.||+++|.++.+|..|+..|+++|.+++|.
T Consensus        78 a~~yN~~~s~i~~~a~~l~~~f~~~~~~~~p~  109 (109)
T cd05502          78 CYKFNEEDSEVAQAGKELELFFEEQLKEILPD  109 (109)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHCcC
Confidence            99999999999999999999999999999873

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.

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.94  E-value=7e-27  Score=195.70  Aligned_cols=101  Identities=32%  Similarity=0.528  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      .|.+.|..|+..|+.|+.++||..||+...  +||||++|++||||+||++||+++.   |.++++|.+||+|||.||..
T Consensus         3 ~~~~~~~~il~~l~~~~~a~~F~~pV~~~~--~p~Y~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~D~~li~~Na~~   77 (104)
T cd05507           3 AWKKAILLVYRTLASHRYASVFLKPVTEDI--APGYHSVVYRPMDLSTIKKNIENGT---IRSTAEFQRDVLLMFQNAIM   77 (104)
T ss_pred             HHHHHHHHHHHHHHcCCCCHhhcCCCCccc--cCCHHHHhCCCcCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            477899999999999999999999999876  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      ||+++|.+|.+|..|++.|...+..+
T Consensus        78 yN~~~s~v~~~A~~l~~~~~~~~~~~  103 (104)
T cd05507          78 YNSSDHDVYLMAVEMQREVMSQIQQL  103 (104)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHhhcc
Confidence            99999999999999999999887653

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.94  E-value=1.2e-26  Score=193.36  Aligned_cols=98  Identities=46%  Similarity=0.901  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHHHcC---CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          105 KRQFAAIFRQITQH---KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       105 ~~~~~~il~~l~~~---~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      ++.|..||..|+++   +.++||+.||++...++||||++|++||||+||++||.++.   |.++.+|..||+|||.||+
T Consensus         2 ~~~c~~il~~l~~~~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I~~kl~~~~---Y~s~~ef~~D~~li~~Na~   78 (102)
T cd05498           2 LKFCSGILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNRE---YADAQEFAADVRLMFSNCY   78 (102)
T ss_pred             hhHHHHHHHHHHhCCCccccCcccCcCCccccCCCcHHHHccCCCcHHHHHHHHccCC---CCCHHHHHHHHHHHHHHHH
Confidence            46899999999999   89999999999986679999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHH
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKW  205 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~  205 (395)
                      .||+++|.++.+|..|++.|+++|
T Consensus        79 ~yn~~~s~i~~~a~~l~~~fe~~~  102 (102)
T cd05498          79 KYNPPDHPVHAMARKLQDVFEDRW  102 (102)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999987

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.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.94  E-value=1.5e-26  Score=192.97  Aligned_cols=98  Identities=36%  Similarity=0.773  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHcC---CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          105 KRQFAAIFRQITQH---KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       105 ~~~~~~il~~l~~~---~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      ++.|..||..|+++   +.++||+.||++...++||||++|++||||+||++||+++.   |.++.+|.+||+|||.||+
T Consensus         2 ~~~c~~Il~~l~~~~~~~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I~~kl~~~~---Y~s~~ef~~D~~li~~N~~   78 (102)
T cd05499           2 LKFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQ---YQSAKEFERDVRLIFKNCY   78 (102)
T ss_pred             hHHHHHHHHHHHcccCCcccchhcCCCCccccCCCCHHHHhcCCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHHH
Confidence            36799999999994   57999999999985559999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHH
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKW  205 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~  205 (395)
                      .||+++|.++.+|..|++.|+++|
T Consensus        79 ~yn~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          79 TFNPEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999987

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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.94  E-value=1.5e-26  Score=191.84  Aligned_cols=96  Identities=28%  Similarity=0.514  Sum_probs=90.6

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      ++...|..++..|. |+.+|||..||++..  +||||++|++||||+||++||+++.   |.++++|.+||+|||.||+.
T Consensus         3 ~l~~~L~~~~~~~~-~~~s~~F~~PV~~~~--~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~Dv~LI~~Na~~   76 (99)
T cd05508           3 QLSKLLKFALERMK-QPGAEPFLKPVDLEQ--FPDYAQYVFKPMDLSTLEKNVRKKA---YGSTDAFLADAKWILHNAII   76 (99)
T ss_pred             HHHHHHHHHHHHHh-CcCcchhcCCCChhh--CCCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            56667888899998 999999999999987  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHH
Q 016116          183 YNDERDDVHVMAKSLLEKFEEK  204 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~  204 (395)
                      ||+++|.++.+|..|.+.|+..
T Consensus        77 YN~~~s~i~~~A~~l~~~~~~e   98 (99)
T cd05508          77 YNGGDHKLTQAAKAIVKICEQE   98 (99)
T ss_pred             HCCCCCHHHHHHHHHHHHHHhh
Confidence            9999999999999999998764

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.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.93  E-value=2.8e-26  Score=194.37  Aligned_cols=102  Identities=25%  Similarity=0.478  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHHHHcC-CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhh
Q 016116          102 QELKRQFAAIFRQITQH-KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  180 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~-~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na  180 (395)
                      .++...|..|+..|++| +.++||+.||++..  +||||++|++||||+||++||.++.   |+++.+|.+||+|||.||
T Consensus         6 ~~~~~~~~~il~~l~~~~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~Li~~N~   80 (112)
T cd05510           6 EEFYESLDKVLNELKTYTEHSTPFLTKVSKRE--APDYYDIIKKPMDLGTMLKKLKNLQ---YKSKAEFVDDLNLIWKNC   80 (112)
T ss_pred             HHHHHHHHHHHHHHHhcCccccchhcCCChhh--cCCHHHHhcCccCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHH
Confidence            36888999999999999 89999999999987  9999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCC-HHHHHHHHHHHHHHHHHHhh
Q 016116          181 MKYNDERD-DVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       181 ~~YN~~~S-~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      +.||+++| .++.+|..|++.|+..+..+
T Consensus        81 ~~yN~~~s~~~~~~A~~l~~~~~~~~~~~  109 (112)
T cd05510          81 LLYNSDPSHPLRRHANFMKKKAEHLLKLI  109 (112)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence            99999876 67899999999999998776

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.

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.93  E-value=2.5e-26  Score=191.11  Aligned_cols=100  Identities=38%  Similarity=0.653  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          104 LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      ++.+|..|++.|++|+.+++|..||++..  +|+||++|++||||+||++||.++.   |.++.+|..||+|||.||+.|
T Consensus         2 ~~~~~~~il~~l~~~~~a~~F~~pv~~~~--~p~Y~~~I~~PmdL~tI~~kl~~~~---Y~s~~~f~~Dv~li~~Na~~y   76 (101)
T cd05509           2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEE--APDYYDVIKKPMDLSTMEEKLENGY---YVTLEEFVADLKLIFDNCRLY   76 (101)
T ss_pred             hHHHHHHHHHHHHhCCCchhhcCCCChhh--cCCHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            56789999999999999999999999988  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          184 NDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      |+++|.++.+|..|+..|+++++++
T Consensus        77 N~~~s~~~~~a~~l~~~f~~~~~~~  101 (101)
T cd05509          77 NGPDTEYYKCANKLEKFFWKKLKEL  101 (101)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999998653

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.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.93  E-value=2.6e-26  Score=191.84  Aligned_cols=99  Identities=32%  Similarity=0.526  Sum_probs=95.1

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      .+.+.|..|++.|++++.++||..||++...++||||++|++||||+||+.||.++.   |.++.+|..||+|||.||+.
T Consensus         4 ~~~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~~   80 (103)
T cd05500           4 HQHKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNV---YTSVEEFTADFNLMVDNCLT   80 (103)
T ss_pred             HHHHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            466799999999999999999999999887779999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHH
Q 016116          183 YNDERDDVHVMAKSLLEKFEEK  204 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~  204 (395)
                      ||+++|.++.+|..|++.|++.
T Consensus        81 yN~~~s~~~~~A~~l~~~fe~~  102 (103)
T cd05500          81 FNGPEHPVSQMGKRLQAAFEKH  102 (103)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999875

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.

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.93  E-value=4.7e-26  Score=189.27  Aligned_cols=97  Identities=20%  Similarity=0.349  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccC
Q 016116          105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN  184 (395)
Q Consensus       105 ~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN  184 (395)
                      ++.|..|+..|.+++.+++|..++  ..  +||||++|++||||+||++||.++.   |.++++|.+||+|||.||+.||
T Consensus         4 l~~ce~il~~l~~~~~s~~f~~~p--~~--~pdY~~iIk~PMDL~tI~~kL~~~~---Y~s~~ef~~D~~Lif~N~~~yN   76 (102)
T cd05501           4 LLKCEFLLLKVYCMSKSGFFISKP--YY--IRDYCQGIKEPMWLNKVKERLNERV---YHTVEGFVRDMRLIFHNHKLFY   76 (102)
T ss_pred             HHHHHHHHHHHHhCcccccccCCC--CC--CCchHHHcCCCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHHHHHc
Confidence            456999999999999999997743  33  9999999999999999999999999   9999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          185 DERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       185 ~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      +++ .++.+|..|++.|+++|.+++
T Consensus        77 ~~~-~~~~~a~~L~~~Fek~~~~~f  100 (102)
T cd05501          77 KDD-DFGQVGITLEKKFEKNFKEVF  100 (102)
T ss_pred             CCC-HHHHHHHHHHHHHHHHHHHHh
Confidence            999 999999999999999998875

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.

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

Probab=99.93  E-value=7.3e-26  Score=191.87  Aligned_cols=104  Identities=29%  Similarity=0.503  Sum_probs=98.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      ++...|..|+..|+.|+.+++|..||++..  +||||++|++||||+||++||+++.   |.|+.+|.+||+|||.||+.
T Consensus         3 ~lr~~L~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~vI~~PmdL~tI~~kl~~~~---Y~s~~ef~~Dv~li~~Na~~   77 (112)
T cd05528           3 ELRLFLRDVLKRLASDKRFNAFTKPVDEEE--VPDYYEIIKQPMDLQTILQKLDTHQ---YLTAKDFLKDIDLIVTNALE   77 (112)
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCCCCccc--cCcHHHHHcCCCCHHHHHHHHcCCC---cCCHHHHHHHHHHHHHHHHH
Confidence            566688999999999999999999999988  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCC----CCHHHHHHHHHHHHHHHHHHhhCcC
Q 016116          183 YNDE----RDDVHVMAKSLLEKFEEKWLQLLPK  211 (395)
Q Consensus       183 YN~~----~S~v~~~A~~L~~~Fe~~~~~~~~~  211 (395)
                      ||++    ||.++.+|..|++.|.+++.+.+|.
T Consensus        78 yN~~~s~~~s~i~~~A~~L~~~~~~~~~~~~~~  110 (112)
T cd05528          78 YNPDRDPADKLIRSRACELRDEVHAMIEAELDP  110 (112)
T ss_pred             HCCCCCccccHHHHHHHHHHHHHHHHHHhcCCC
Confidence            9999    4799999999999999999988774

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

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

Probab=99.93  E-value=4.6e-26  Score=191.69  Aligned_cols=100  Identities=28%  Similarity=0.427  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHHHHHcCCC------CCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhch
Q 016116          103 ELKRQFAAIFRQITQHKW------AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV  176 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~------a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LI  176 (395)
                      +|.++|..|++.|..+..      ++||..||+...  +||||++|++||||+||++||.++.   |.++.+|..||.||
T Consensus         1 ~l~~~~~~il~~v~~~~d~~g~~~s~~F~~~p~~~~--~pdYy~iI~~Pmdl~tI~~kl~~~~---Y~s~~ef~~D~~li   75 (107)
T cd05516           1 ELTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKE--LPEYYELIRKPVDFKKIKERIRNHK---YRSLEDLEKDVMLL   75 (107)
T ss_pred             CHHHHHHHHHHHHHhhhCcCCCEeeHHhhcCCCccc--CCCHHHHcCCCCCHHHHHHHHccCC---CCCHHHHHHHHHHH
Confidence            366789999999998876      899999999887  9999999999999999999999999   99999999999999


Q ss_pred             hhhhcccCCCCCHHHHHHHHHHHHHHHHHHh
Q 016116          177 FKNAMKYNDERDDVHVMAKSLLEKFEEKWLQ  207 (395)
Q Consensus       177 f~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~  207 (395)
                      |.||+.||++||.+|.+|..|++.|++.++.
T Consensus        76 ~~Na~~yN~~~s~i~~~a~~l~~~f~~~~~~  106 (107)
T cd05516          76 CQNAQTFNLEGSLIYEDSIVLQSVFKSARQK  106 (107)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999998865

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=99.92  E-value=2e-25  Score=184.78  Aligned_cols=92  Identities=34%  Similarity=0.499  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          104 LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      |...|..|++.|+.++.+++|..||+...  +||||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.|
T Consensus         2 l~~~l~~il~~l~~~~~~~~F~~PV~~~~--~pdY~~vIk~PmDL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~~y   76 (98)
T cd05513           2 LQKALEQLIRQLQRKDPHGFFAFPVTDFI--APGYSSIIKHPMDFSTMKEKIKNND---YQSIEEFKDDFKLMCENAMKY   76 (98)
T ss_pred             HHHHHHHHHHHHHcCCccccccCcCCccc--cccHHHHHcCccCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            45678999999999999999999999877  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHH
Q 016116          184 NDERDDVHVMAKSLLEK  200 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~  200 (395)
                      |+++|.+|.+|..|...
T Consensus        77 N~~~s~~~~~A~~L~~~   93 (98)
T cd05513          77 NKPDTIYYKAAKKLLHS   93 (98)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            99999999999998664

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=99.92  E-value=4.8e-25  Score=182.64  Aligned_cols=91  Identities=29%  Similarity=0.505  Sum_probs=86.9

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccC
Q 016116          105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN  184 (395)
Q Consensus       105 ~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN  184 (395)
                      ...|..++++|+.|+.+++|..||+...  +||||++|++||||+||++||.++.   |.++++|..||+|||.||+.||
T Consensus         3 ~~~l~~il~~l~~~~~~~~F~~pVd~~~--~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~D~~li~~Na~~yN   77 (98)
T cd05512           3 EVLLRKTLDQLQEKDTAEIFSEPVDLSE--VPDYLDHIKQPMDFSTMRKKLESQR---YRTLEDFEADFNLIINNCLAYN   77 (98)
T ss_pred             HHHHHHHHHHHHhCCCchhhcCCCCccc--cCCHHHHhcCCcCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHHHHHC
Confidence            3468899999999999999999999987  9999999999999999999999999   9999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 016116          185 DERDDVHVMAKSLLEK  200 (395)
Q Consensus       185 ~~~S~v~~~A~~L~~~  200 (395)
                      +++|.+|.+|..|++.
T Consensus        78 ~~~s~~~~~A~~l~~~   93 (98)
T cd05512          78 AKDTIFYRAAVRLRDQ   93 (98)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            9999999999999764

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.

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.92  E-value=4.9e-25  Score=186.91  Aligned_cols=99  Identities=29%  Similarity=0.535  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCC
Q 016116          107 QFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE  186 (395)
Q Consensus       107 ~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~  186 (395)
                      .+..|+.+|++|+.++||..||++..  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.||+.||++
T Consensus         4 ~l~~ii~~l~~~~~s~~F~~pv~~~~--~p~Y~~~I~~PmdL~tI~~kl~~~~---Y~s~~ef~~Dv~li~~Na~~yN~~   78 (112)
T cd05511           4 ILDEIVNELKNLPDSWPFHTPVNKKK--VPDYYKIIKRPMDLQTIRKKISKHK---YQSREEFLEDIELIVDNSVLYNGP   78 (112)
T ss_pred             HHHHHHHHHHhCCCchhhcCCCChhh--cccHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHHCCC
Confidence            46789999999999999999999987  9999999999999999999999999   999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          187 RDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       187 ~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      +|.++.+|..|...|+..+..+..
T Consensus        79 ~s~i~~~A~~l~~~~~~~~~~~~~  102 (112)
T cd05511          79 DSVYTKKAKEMLELAEELLAEREE  102 (112)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhHH
Confidence            999999999999999999987743

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.

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

Probab=99.91  E-value=6.7e-25  Score=183.35  Aligned_cols=96  Identities=27%  Similarity=0.505  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHH------cCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhh
Q 016116          105 KRQFAAIFRQIT------QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  178 (395)
Q Consensus       105 ~~~~~~il~~l~------~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~  178 (395)
                      .+.|..|++.|+      .++.+++|..||+...  +||||++|++||||+||++||+.+.   |.++.+|..||+|||.
T Consensus         2 ~~~~~~i~~~v~~~~~~~~~~~~~~F~~~p~~~~--~pdYy~iIk~Pmdl~~I~~kl~~~~---Y~s~~~f~~D~~li~~   76 (103)
T cd05519           2 KAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKL--YPDYYVIIKRPIALDQIKRRIEGRA---YKSLEEFLEDFHLMFA   76 (103)
T ss_pred             HHHHHHHHHHHHHhcCcCCCchhHHhcCCCCCCC--CcCHHHHcCCCcCHHHHHHHHccCC---CCCHHHHHHHHHHHHH
Confidence            467888888888      4456999999999888  9999999999999999999999999   9999999999999999


Q ss_pred             hhcccCCCCCHHHHHHHHHHHHHHHHH
Q 016116          179 NAMKYNDERDDVHVMAKSLLEKFEEKW  205 (395)
Q Consensus       179 Na~~YN~~~S~v~~~A~~L~~~Fe~~~  205 (395)
                      ||+.||+++|.+|.+|..|++.|++++
T Consensus        77 Na~~yn~~~s~i~~~A~~l~~~f~~~~  103 (103)
T cd05519          77 NARTYNQEGSIVYEDAVEMEKAFKKKY  103 (103)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999998864

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.

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.91  E-value=1.5e-24  Score=184.14  Aligned_cols=102  Identities=24%  Similarity=0.364  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHHHHcC------CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchh
Q 016116          104 LKRQFAAIFRQITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  177 (395)
Q Consensus       104 l~~~~~~il~~l~~~------~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      ..+.|..|++.|+++      +.+.+|..+|+...  +||||++|++||||+||++||.++.   |.++.+|.+||+|||
T Consensus         3 ~~~~c~~il~~l~~~~~~~g~~l~~~F~~~p~~~~--~PdYy~iI~~Pmdl~tI~~kl~~~~---Y~s~~~f~~D~~lm~   77 (113)
T cd05524           3 PIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRN--EPEYYEVVSNPIDLLKIQQKLKTEE---YDDVDDLTADFELLI   77 (113)
T ss_pred             HHHHHHHHHHHHHhhcccCCCchhHHHhcCCCccc--CCCHHHHhCCccCHHHHHHHhCcCC---CCCHHHHHHHHHHHH
Confidence            457899999999965      45678999999877  9999999999999999999999999   999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      .||+.||+++|.+|.+|..|++.|++.+.++.+
T Consensus        78 ~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~  110 (113)
T cd05524          78 NNAKAYYKPDSPEHKDACKLWELFLSARNEVLS  110 (113)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999999999887754

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.

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.91  E-value=2.5e-24  Score=180.56  Aligned_cols=96  Identities=26%  Similarity=0.504  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHHcC------CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          106 RQFAAIFRQITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       106 ~~~~~il~~l~~~------~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      .+|..|++.|..+      +.+++|+.||+...  +||||++|++||||+||++||.++.   |.++++|..||.|||.|
T Consensus         3 ~~~~~~~~~i~~~~d~~~~~~a~~F~~~p~~~~--~pdYy~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~l~~~N   77 (105)
T cd05515           3 QKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSE--YPDYYDVIKKPIDMEKIRSKIEGNQ---YQSLDDMVSDFVLMFDN   77 (105)
T ss_pred             HHHHHHHHHHHHhhCcCCCcccHHhccCCCccc--CCcHHHHcCCCcCHHHHHHHHccCC---CCCHHHHHHHHHHHHHH
Confidence            4566666666654      56899999999988  9999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHH
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWL  206 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~  206 (395)
                      |+.||+++|.+|.+|..|++.|.+...
T Consensus        78 a~~yN~~~s~i~~~A~~L~~~~~~~~~  104 (105)
T cd05515          78 ACKYNEPDSQIYKDALTLQKVLLETKR  104 (105)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999988753

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.

>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III

Probab=99.90  E-value=4.1e-24  Score=178.65  Aligned_cols=82  Identities=28%  Similarity=0.504  Sum_probs=78.8

Q ss_pred             CCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHHH
Q 016116          118 HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSL  197 (395)
Q Consensus       118 ~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~L  197 (395)
                      ++.++||+.||+...  +||||++|++||||+||+.||.++.   |.++.+|..||+|||.||+.||+++|.+|.+|..|
T Consensus        21 ~~~s~pF~~~p~~~~--~PdYy~iI~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~L   95 (103)
T cd05520          21 QLLAEPFLKLPSKRK--YPDYYQEIKNPISLQQIRTKLKNGE---YETLEELEADLNLMFENAKRYNVPNSRIYKDAEKL   95 (103)
T ss_pred             CCccHhhhcCCCccc--CCCHHHHcCCCcCHHHHHHHHccCC---CCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence            357999999999887  9999999999999999999999999   99999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 016116          198 LEKFEEK  204 (395)
Q Consensus       198 ~~~Fe~~  204 (395)
                      +++|+++
T Consensus        96 ~~~f~~~  102 (103)
T cd05520          96 QKLMQAK  102 (103)
T ss_pred             HHHHHHh
Confidence            9999875

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=99.90  E-value=3.9e-24  Score=178.76  Aligned_cols=100  Identities=28%  Similarity=0.421  Sum_probs=87.1

Q ss_pred             ccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhh
Q 016116           99 RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  178 (395)
Q Consensus        99 ~~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~  178 (395)
                      ++|..++..+....+ ...+..+.+|+.+|+...  +||||++|++||||+||+.||.++.   |.++.+|.+||+|||.
T Consensus         3 ~~~~~l~~~v~~~~d-~~gr~~~~~F~~~p~~~~--~pdYy~iIk~Pmdl~tI~~kl~~~~---Y~s~~ef~~D~~li~~   76 (103)
T cd05518           3 KRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKD--YPDYYKIILEPIDLKTIEHNIRNDK---YATEEELMDDFKLMFR   76 (103)
T ss_pred             HHHHHHHHHHHHhhc-cCCCcccHHHhcCCCccc--CccHHHHcCCCcCHHHHHHHHCCCC---CCCHHHHHHHHHHHHH
Confidence            344455544444422 345678999999999988  9999999999999999999999999   9999999999999999


Q ss_pred             hhcccCCCCCHHHHHHHHHHHHHHHH
Q 016116          179 NAMKYNDERDDVHVMAKSLLEKFEEK  204 (395)
Q Consensus       179 Na~~YN~~~S~v~~~A~~L~~~Fe~~  204 (395)
                      ||+.||++||.||.+|..|+++|+++
T Consensus        77 Na~~yN~~~s~i~~~A~~le~~~~~~  102 (103)
T cd05518          77 NARHYNEEGSQVYEDANILEKVLKEK  102 (103)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999864

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=99.90  E-value=7.5e-24  Score=177.90  Aligned_cols=96  Identities=27%  Similarity=0.383  Sum_probs=87.9

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchh
Q 016116          104 LKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  177 (395)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      |...|..|++.|..++      .++||+.+|++..  +||||++|++||||+||+.||.++.   |.++++|..||.|||
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   77 (106)
T cd05525           3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKK--NPDYYERITDPVDLSTIEKQILTGY---YKTPEAFDSDMLKVF   77 (106)
T ss_pred             HHHHHHHHHHHHHHhhccCCCcccHhhccCCCccc--CCchhhhCCCCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHH
Confidence            4456777777777654      5799999999988  9999999999999999999999999   999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHH
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEK  204 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~  204 (395)
                      .||+.||+++|.+|.+|..|++.|++.
T Consensus        78 ~Na~~yn~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          78 RNAEKYYGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999864

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.

>smart00297 BROMO bromo domain

Probab=99.90  E-value=1.7e-23  Score=174.84  Aligned_cols=101  Identities=41%  Similarity=0.732  Sum_probs=96.5

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      ..+...|..|+..+.+|+.+++|..||++..  +|+||++|++||||++|++||+++.   |.++.+|.+||++||.||+
T Consensus         6 ~~~~~~~~~i~~~~~~~~~~~~F~~~~~~~~--~p~Y~~~i~~P~dl~~I~~kl~~~~---Y~s~~ef~~D~~li~~Na~   80 (107)
T smart00297        6 KKLQSLLKAVLDKLDSHRLSWPFLKPVDRKE--APDYYDIIKKPMDLSTIKKKLENGK---YSSVEEFVADVQLMFSNAK   80 (107)
T ss_pred             HHHHHHHHHHHHHHHhCccchhhccCCChhh--ccCHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHH
Confidence            3466789999999999999999999999988  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHh
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKWLQ  207 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~~~  207 (395)
                      .||+++|.++.+|..|...|++.|++
T Consensus        81 ~~n~~~s~~~~~a~~l~~~f~~~~~~  106 (107)
T smart00297       81 TYNGPDSEVYKDAKKLEKFFEKKLRE  106 (107)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999999875

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.90  E-value=1.7e-23  Score=181.44  Aligned_cols=99  Identities=26%  Similarity=0.437  Sum_probs=93.5

Q ss_pred             HHHHHHHHHHHHHH---cCCCCCCCCCCCCcc-ccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhh
Q 016116          103 ELKRQFAAIFRQIT---QHKWAWPFMHPVDVE-GLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  178 (395)
Q Consensus       103 ~l~~~~~~il~~l~---~~~~a~~F~~PVd~~-~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~  178 (395)
                      ++...|..++..|+   +++.+++|..||+.. .  +|+||++|++||||+||++||.++.   |.++++|..||+|||.
T Consensus        24 ~~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~~--~p~Y~~iI~~PmdL~tI~~kl~~~~---Y~s~~~f~~Dv~Li~~   98 (128)
T cd05529          24 EERERLISGLDKLLLSLQLEIAEYFEYPVDLRAW--YPDYWNRVPVPMDLETIRSRLENRY---YRSLEALRHDVRLILS   98 (128)
T ss_pred             HHHHHHHHHHHHHHhcccCcccccccCCCCcccc--CCcHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHH
Confidence            45567888888898   899999999999998 6  9999999999999999999999999   9999999999999999


Q ss_pred             hhcccCCCCCHHHHHHHHHHHHHHHHHH
Q 016116          179 NAMKYNDERDDVHVMAKSLLEKFEEKWL  206 (395)
Q Consensus       179 Na~~YN~~~S~v~~~A~~L~~~Fe~~~~  206 (395)
                      ||+.||+++|.++.+|..|+..|...+.
T Consensus        99 Na~~yN~~~s~i~~~A~~l~~~~~~~l~  126 (128)
T cd05529          99 NAETFNEPNSEIAKKAKRLSDWLLRILS  126 (128)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999998874

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.

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.90  E-value=7e-24  Score=177.23  Aligned_cols=93  Identities=22%  Similarity=0.385  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          106 RQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       106 ~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      +.|..|++.|+.+.      .+++|..+|+...  +||||++|++||||+||++||.++.   |.++.+|..||+|||.|
T Consensus         3 ~~~~~l~~~i~~~~d~~gr~~~~~F~~lp~~~~--~pdYy~vI~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~lm~~N   77 (103)
T cd05517           3 QILEQLLEAVMTATDPSGRLISELFQKLPSKVL--YPDYYAVIKEPIDLKTIAQRIQSGY---YKSIEDMEKDLDLMVKN   77 (103)
T ss_pred             HHHHHHHHHHHHhhCcCCCChhHHHhcCCCCCC--CCCHHHHcCCCcCHHHHHHHHCcCC---CCCHHHHHHHHHHHHHH
Confidence            46777777777754      5799999999988  9999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHH
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEE  203 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~  203 (395)
                      |+.||++||.+|.+|..|++.|+.
T Consensus        78 a~~yN~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          78 AKTFNEPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHh
Confidence            999999999999999999999975

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.

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

Probab=99.87  E-value=2.7e-22  Score=167.98  Aligned_cols=82  Identities=23%  Similarity=0.358  Sum_probs=78.9

Q ss_pred             CCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHHH
Q 016116          118 HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSL  197 (395)
Q Consensus       118 ~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~L  197 (395)
                      ++.+++|+.+|+...  +||||++|++||||+||++||..+.   |.++.+|..||+|||.||+.||+++|.+|.+|..|
T Consensus        22 ~~l~~~F~~~p~~~~--~pdYy~~I~~Pmdl~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l   96 (104)
T cd05522          22 RLLTLHFEKLPDKAR--EPEYYQEISNPISLDDIKKKVKRRK---YKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL   96 (104)
T ss_pred             CcccHHHhcCCCccc--cCcHHHHhCCCcCHHHHHHHHccCC---CCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence            578999999999887  9999999999999999999999999   99999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 016116          198 LEKFEEK  204 (395)
Q Consensus       198 ~~~Fe~~  204 (395)
                      ++.|+..
T Consensus        97 ~~~f~~l  103 (104)
T cd05522          97 EKEARLL  103 (104)
T ss_pred             HHHHHHh
Confidence            9999873

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.

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

Probab=99.87  E-value=5.4e-22  Score=166.59  Aligned_cols=96  Identities=22%  Similarity=0.314  Sum_probs=86.7

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchh
Q 016116          104 LKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  177 (395)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      |.++|..|++.|+..+      .+.+|..+|+...  +||||++|++||||+||++||.+     |.++.+|.+||.|||
T Consensus         2 l~~~~~~l~~~i~~~~~~~g~~~~~~F~~lp~~~~--~pdYy~iI~~PmdL~tI~~kl~~-----Y~s~~ef~~D~~li~   74 (106)
T cd05521           2 LSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKD--YPDYYKIIKNPLSLNTVKKRLPH-----YTNAQEFVNDLAQIP   74 (106)
T ss_pred             HHHHHHHHHHHHHhhcCcCCCCchHhhhcCCcccc--CccHHHHhcCCCCHHHHHHHHHc-----CCCHHHHHHHHHHHH
Confidence            4466777888777654      4679999998877  99999999999999999999996     999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHHHH
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEKWL  206 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~  206 (395)
                      .||+.||++||.+|.+|..|+++|..++.
T Consensus        75 ~Na~~yN~~~s~i~~~A~~le~~~~~~~~  103 (106)
T cd05521          75 WNARLYNTKGSVIYKYALILEKYINDVII  103 (106)
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999999998763

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=99.86  E-value=4.7e-22  Score=158.99  Aligned_cols=84  Identities=38%  Similarity=0.706  Sum_probs=79.5

Q ss_pred             HHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCC
Q 016116          108 FAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDER  187 (395)
Q Consensus       108 ~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~  187 (395)
                      |..|++.|++|+.+++|..||+...  +|+|+++|++||||++|+.||+++.   |.++.+|..||++||.||+.||+++
T Consensus         1 C~~il~~l~~~~~~~~F~~~~~~~~--~p~y~~~i~~P~dL~~I~~kl~~~~---Y~s~~~f~~Dv~~i~~Na~~yn~~~   75 (84)
T PF00439_consen    1 CREILEELMKHPISSPFSKPVDPKE--YPDYYEIIKNPMDLSTIRKKLENGK---YKSIEEFEADVRLIFQNARRYNPPD   75 (84)
T ss_dssp             HHHHHHHHHTSTTGGGGSSSTHTTT--STTHHHHSSSS--HHHHHHHHHTTS---SSSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CHHHHHHHHcCCCchhhcCCCChhh--CCCHHHHHhhccchhhhhHHhhccc---hhhHHHHHHHHHHHHHHHHHHCCCc
Confidence            8899999999999999999998887  9999999999999999999999999   9999999999999999999999999


Q ss_pred             CHHHHHHHH
Q 016116          188 DDVHVMAKS  196 (395)
Q Consensus       188 S~v~~~A~~  196 (395)
                      |.+|.+|.+
T Consensus        76 s~~~~~A~~   84 (84)
T PF00439_consen   76 SPIYKAAEK   84 (84)
T ss_dssp             SHHHHHHHH
T ss_pred             CHHHHHhcC
Confidence            999999974

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=99.86  E-value=6.3e-22  Score=160.88  Aligned_cols=95  Identities=38%  Similarity=0.646  Sum_probs=91.0

Q ss_pred             HHHHHHHHHHHcC--CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          106 RQFAAIFRQITQH--KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       106 ~~~~~il~~l~~~--~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      ..|..|++.+..+  +.+++|..||++..  +|+||++|++||||++|+.||..+.   |.++.+|.+||++||.||+.|
T Consensus         3 ~~~~~i~~~l~~~~~~~~~~F~~~~~~~~--~~~Y~~~i~~P~~l~~I~~kl~~~~---Y~s~~~f~~D~~li~~Na~~~   77 (99)
T cd04369           3 KKLRSLLDALKKLKRDLSEPFLEPVDPKE--APDYYEVIKNPMDLSTIKKKLKNGE---YKSLEEFEADVRLIFSNAKTY   77 (99)
T ss_pred             HHHHHHHHHHHhhcccccHHHhcCCChhc--CCCHHHHHhCcccHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            4688999999999  99999999999977  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Q 016116          184 NDERDDVHVMAKSLLEKFEEKW  205 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~  205 (395)
                      |+++|.++.+|..|...|++.|
T Consensus        78 n~~~~~~~~~a~~l~~~~~~~~   99 (99)
T cd04369          78 NGPGSPIYKDAKKLEKLFEKLL   99 (99)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999998764

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=99.84  E-value=7.7e-21  Score=160.03  Aligned_cols=98  Identities=16%  Similarity=0.174  Sum_probs=85.4

Q ss_pred             HHHHHHHHHc-CCCCCCCCCCCCcc---ccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          108 FAAIFRQITQ-HKWAWPFMHPVDVE---GLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       108 ~~~il~~l~~-~~~a~~F~~PVd~~---~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      +..++..+.+ -+.++||..||...   ..++|+||++|++||||+||++||.++.   |+++++|.+||.|||+||..|
T Consensus         5 L~f~~~~~k~~lp~~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~Dv~LI~~N~~~y   81 (109)
T cd05492           5 LKFIVSRMKSWLPPDTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEK---YTSLEEFKADALLLLHNTAIF   81 (109)
T ss_pred             HHHHHHHHHhcCcccccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            4456677766 56789999999733   3349999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          184 NDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      |+++|.++.+|..|.......+.++
T Consensus        82 Ng~~s~~~~~A~~l~~d~~~el~Ei  106 (109)
T cd05492          82 HGADSEQYDAARWLYRDTCHDLREL  106 (109)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999988877666544

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=99.77  E-value=1.3e-18  Score=146.28  Aligned_cols=98  Identities=17%  Similarity=0.231  Sum_probs=88.1

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchh
Q 016116          104 LKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  177 (395)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      +...+..|+..+++|.      .+.+|++.|+  .  .|+||.+|+.||||.+|++||..+.   |.++++|..||.+||
T Consensus         4 vq~~l~~l~~~V~~~~D~~Gr~~s~~f~~LP~--~--~~~~~~~ik~Pi~l~~Ik~ki~~~~---Y~~ld~~~~D~~lmf   76 (110)
T cd05526           4 VQELLATLFVSVMNHQDEEGRCYSDSLAELPE--L--AVDGVGPKKIPLTLDIIKRNVDKGR---YRRLDKFQEDMFEVL   76 (110)
T ss_pred             HHHHHHHHHHHHHhccCCCCCCchHHHHHCCC--c--ccCchhhhcCCccHHHHHHHHHcCC---cCcHHHHHHHHHHHH
Confidence            3446677888888875      6899999888  2  6788999999999999999999999   999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      .||++||.+||.+|.+|..|+.+|.....++
T Consensus        77 ~NAr~yN~~~S~iy~dA~eLq~~f~~~rd~~  107 (110)
T cd05526          77 ERARRLSRTDSEIYEDAVELQQFFIKIRDEL  107 (110)
T ss_pred             HHHHHhCcccCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999887654

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.

>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]

Probab=99.74  E-value=1.3e-18  Score=197.73  Aligned_cols=97  Identities=35%  Similarity=0.732  Sum_probs=94.8

Q ss_pred             HHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCC
Q 016116          108 FAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDER  187 (395)
Q Consensus       108 ~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~  187 (395)
                      |..|+.+|+.|..||||++||++..  +||||+||++||||+||+.++..+.   |.++.+|..||.|||.||.+||.+ 
T Consensus      1306 ~e~il~e~~~~~~awPFlepVn~~~--vp~Y~~IIk~Pmdl~tir~k~~~~~---Y~~~eef~~Di~lvf~Nc~~yN~~- 1379 (1404)
T KOG1245|consen 1306 CEDILHELVVHKAAWPFLEPVNPKE--VPDYYDIIKKPMDLSTIREKLSKGI---YPSPEEFATDIELVFDNCETYNED- 1379 (1404)
T ss_pred             HHHHHHHHHHhhhcchhhccCChhh--cccHHHHhcChhHHHHHHHHHhccc---CCCHHHHHHHHHHHHHHHHHhccc-
Confidence            8999999999999999999999999  9999999999999999999999999   999999999999999999999999 


Q ss_pred             CHHHHHHHHHHHHHHHHHHhhCc
Q 016116          188 DDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       188 S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      |.++.++..|..+|+..|...+|
T Consensus      1380 s~i~~ag~~l~~ff~~~~~~~~~ 1402 (1404)
T KOG1245|consen 1380 SEIGRAGTCLRRFFHKRWRKKFP 1402 (1404)
T ss_pred             hhhhhhcchHHHHHHHHHHhhcC
Confidence            99999999999999999987765

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

Probab=99.71  E-value=1.3e-17  Score=168.69  Aligned_cols=90  Identities=29%  Similarity=0.441  Sum_probs=85.6

Q ss_pred             CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHHHH
Q 016116          119 KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLL  198 (395)
Q Consensus       119 ~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~L~  198 (395)
                      ..+++|+.+|+...  +|+||.||+.||||++|+++|..+.   |.++++|..|+.|||.||.+||+++|.||.+|..|+
T Consensus       164 ~~s~~F~~~p~k~~--~PdYy~iIk~Pm~L~~i~kkl~~~~---Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~  238 (371)
T COG5076         164 FLSSIFLGLPSKRE--YPDYYEIIKSPMDLLTIQKKLKNGR---YKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELE  238 (371)
T ss_pred             ccccccccCCcccc--CCChheeecchhhHHHHHHHHHhhh---hhhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHH
Confidence            57999999999998  9999999999999999999999999   999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhCcCch
Q 016116          199 EKFEEKWLQLLPKVM  213 (395)
Q Consensus       199 ~~Fe~~~~~~~~~~~  213 (395)
                      ..|...+..+.+...
T Consensus       239 ~~~~~~i~~~~~~~~  253 (371)
T COG5076         239 KYFLKLIEEIPEEML  253 (371)
T ss_pred             HHHHHHHHhccccch
Confidence            999999998866543

>KOG1472 consensus Histone acetyltransferase SAGA/ADA, catalytic subunit PCAF/GCN5 and related proteins [Chromatin structure and dynamics; Transcription]

Probab=99.64  E-value=1.7e-16  Score=168.56  Aligned_cols=143  Identities=25%  Similarity=0.401  Sum_probs=118.4

Q ss_pred             CCCCCchhhhccccCCC---CCchhhhhhhhhhhhHh-hhccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCch
Q 016116           63 NTSKSISIAKEKLKDRH---VASIEKQQQDAFHREEA-AGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDY  138 (395)
Q Consensus        63 ~~~~g~s~~k~~~r~r~---~~~~kk~~~~~~~~e~~-~~~~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdY  138 (395)
                      .+++|.++++++....+   +|+.+...+.....+-. .......+...+..|+.+|..|..+|||..||...+  +|||
T Consensus       562 kv~~gl~~~~~~~~~~~~~~iPg~~E~~~~~~~~~~r~~~~~~~~~~s~~~~il~~l~~h~~awPf~~Pv~~~e--~pdy  639 (720)
T KOG1472|consen  562 KVYPGLECFKDGVPQIPPRKIPGFRESGWKPEKESYRQEYKKPGKLFSAIQNILDQLQNHGDAWPFLKPVNKKE--VPDY  639 (720)
T ss_pred             ccccccccccccccccCcccCCCchhhccCcchHHHHhhhcccchhhHHHHhHHhhhhcCCccCCccCcccccc--CCcH
Confidence            37899999998866554   44444433322211111 113344566788999999999999999999999998  9999


Q ss_pred             hhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          139 YEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       139 y~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      |.+|++||||.||+.+|..+.   |..+..|++|+..||.||+.||+..+..|..|..|...|..++...+.
T Consensus       640 y~~I~~pmDl~tM~~~l~~~~---y~~~~~f~ad~~~vf~ncr~yn~~~~~y~k~~~~le~~~~~k~~~~i~  708 (720)
T KOG1472|consen  640 YDVIKHPMDLRTMQNRLKDNQ---YTEVELFMADVVRVFANCRMYNGSDTQYYKCAQALEKFFLFKLNELIL  708 (720)
T ss_pred             HHHhcccccHHHHhhhccccc---hhhHHHHHHHHHHHHhhhhccCCccchheecccchhhhhcchhhhhhh
Confidence            999999999999999999999   999999999999999999999999999999999999999988876643

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=99.39  E-value=2.9e-13  Score=115.22  Aligned_cols=83  Identities=22%  Similarity=0.239  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCC----CCCCCCHHHHHHHHhchhh
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKD----GTGYRNVREIYADVRLVFK  178 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~----~~~Y~s~~ef~~Dv~LIf~  178 (395)
                      +.+..|..++..++.++.+|||..||++...++||||++|++||||+||+.+|....    ...|..-..+.+++..++.
T Consensus         3 e~~~~~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (114)
T cd05494           3 EALERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEG   82 (114)
T ss_pred             HHHHHHHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHcccccccccccccccccccccccccc
Confidence            345678888888888999999999999966669999999999999999999999863    1125555566777777777


Q ss_pred             hhcccCC
Q 016116          179 NAMKYND  185 (395)
Q Consensus       179 Na~~YN~  185 (395)
                      ||..+|.
T Consensus        83 ~~~~~~~   89 (114)
T cd05494          83 RRSPSNI   89 (114)
T ss_pred             ccCcccc
Confidence            7777765

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

>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]

Probab=98.98  E-value=4.2e-10  Score=124.71  Aligned_cols=94  Identities=28%  Similarity=0.494  Sum_probs=84.9

Q ss_pred             HHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCC
Q 016116          107 QFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE  186 (395)
Q Consensus       107 ~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~  186 (395)
                      .+-.|+.+++.-+.+|+|.+||+++.  +|+||.+|++||||.+|.+++..+.   |.+.++|.+||++|+.||..||+.
T Consensus      1386 ~~d~~vs~~~~ipes~~f~~~v~~k~--~~~yy~kik~pmdl~~i~~n~~~~~---y~s~~e~l~dv~~i~~n~~~~ng~ 1460 (1563)
T KOG0008|consen 1386 ILDNIVSQMKEIPESWPFHEPVNKKR--VPDYYKKIKNPMDLETILKNIPPHK---YDSRSEFLDDVNLIYVNSVEYNGA 1460 (1563)
T ss_pred             hhhhHHHHHHhcchhcccccccchhh--chHHHHHhcChhhHHHHhhcCCccc---cccHHHHhhhhHhhcccceeecCc
Confidence            34567888888899999999999999  9999999999999999999999999   999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHH
Q 016116          187 RDDVHVMAKSLLEKFEEKW  205 (395)
Q Consensus       187 ~S~v~~~A~~L~~~Fe~~~  205 (395)
                      .+.+..-|+.+-++-...+
T Consensus      1461 e~~y~~k~~k~~ev~~~~~ 1479 (1563)
T KOG0008|consen 1461 ESAYTKKARKIGEVGLANL 1479 (1563)
T ss_pred             cccccHHHHHHHHHHHHHH
Confidence            9998888887666655444

>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]

Probab=98.98  E-value=6.1e-10  Score=123.55  Aligned_cols=102  Identities=27%  Similarity=0.427  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          104 LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      ..+.+..+++.+...+-...|..||+..+  +|||.++|++||||.|++.++.++.   |.++++|.+|+.||..||+.|
T Consensus       566 ~~kLl~~~l~~lq~kD~~gif~~pvd~~e--~pdy~~iik~pmd~~t~~~kl~s~~---y~tle~ieed~~l~~~nc~~y  640 (1051)
T KOG0955|consen  566 FKKLLQKSLDKLQKKDSYGIFAEPVDPSE--LPDYIDIIKKPMDFFTMRLKLESGA---YSTLEPIEEDVNLIVSNCMEY  640 (1051)
T ss_pred             HHHHHHHHHHHhhcccccCceeeccChhh--cccHHHHhcCccchhhhhhhccccc---hhhhhHHHHhHhHhHhHHHHh
Confidence            44556788889999999999999999998  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          184 NDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      |.-+..+|..|..+++.....+.....
T Consensus       641 n~~dtv~~r~av~~~e~~~~~~~~ark  667 (1051)
T KOG0955|consen  641 NAKDTVYYRAAVRLRELIKKDFRNARK  667 (1051)
T ss_pred             hccCeehHhhhHHHHhhhhhHHHhccc
Confidence            999999999999999998887766543

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=98.97  E-value=3.2e-10  Score=96.21  Aligned_cols=41  Identities=20%  Similarity=0.396  Sum_probs=39.2

Q ss_pred             CCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCC
Q 016116          144 KPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDER  187 (395)
Q Consensus       144 ~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~  187 (395)
                      .||||+||++||.++.   |.++.+|++||+|||.||+.||.++
T Consensus        63 y~MDL~tIe~RL~ng~---Y~tp~~F~~DiklI~~Nc~~ynd~d  103 (119)
T cd05491          63 YNMDLDTIEERLWNGY---YATPKDFLKDIKRIVRDAKTIGDRE  103 (119)
T ss_pred             eccCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHhCCHH
Confidence            6899999999999999   9999999999999999999999863

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.

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=98.97  E-value=7.9e-10  Score=120.18  Aligned_cols=100  Identities=26%  Similarity=0.405  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHcC------CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          106 RQFAAIFRQITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       106 ~~~~~il~~l~~~------~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      +.|..|+.....+      ..+..|...++.+.  +||||.||+.||++..|.++|..+.   |.+..+...||.++|.|
T Consensus      1027 ~~~~~i~~~~~~~~~~~~r~~~~~~~~~~s~k~--~~d~~~~i~~~~~~~~~~~~i~~~~---~~~~~~~~~~~~~~~~n 1101 (1157)
T KOG0386|consen 1027 KQALKIASTSIKYKDSAGRELSEVFLKLPSRKE--YPDYYEIIKKPVAIDKIKKRIENHK---YNSLKELEKDFMLLFNN 1101 (1157)
T ss_pred             HHHHHHHHHHHhcccccccccchhcccCccccc--ccchHHHhcchhhHHHHhhhccccc---cchHHHHHHHHHhhcch
Confidence            4577788777754      45889999999998  9999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      |+.||.+||.||.+|..|+.+|......+..
T Consensus      1102 a~~~~~egs~~y~d~~~l~~~~~~~~~~~~~ 1132 (1157)
T KOG0386|consen 1102 ARTYNEEGSRVYEDAIVLQSVFKSARQEISK 1132 (1157)
T ss_pred             hhhhccCCceechhHHHHHHHHhhhHHHHhc
Confidence            9999999999999999999999998877754

>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]

Probab=98.81  E-value=5.6e-09  Score=110.21  Aligned_cols=98  Identities=22%  Similarity=0.257  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchh
Q 016116          104 LKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  177 (395)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      +..++..||..+..+.      ....|.+.++...  .|+||.+|..||.|..|+.|+..+.   |.+.+.|..|+.|||
T Consensus        53 ~~~~f~~il~~~~~~~d~~gk~~~d~feklp~~~~--~p~yy~~i~~pisl~~ik~kv~k~~---y~~~~~f~~D~~lm~  127 (629)
T KOG1827|consen   53 LIPKFKTILASLLDLKDDEGKQLFDKFEKLPSRKE--FPEYYYVIQQPISLDQIKRKVKKGR---YKRLSFFQLDFLLMT  127 (629)
T ss_pred             HHHHHHHHHHHHHhhccccCcccchhHhhcccccc--CCCcceeecCcccHHHHHHHHHhcc---cccHHHHHHHHHHHH
Confidence            4446777777776663      5788999999998  9999999999999999999999999   999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHHHH
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEKWL  206 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~  206 (395)
                      .||+.||.++|.+|.+|..|+..|.....
T Consensus       128 ena~~~n~~ds~~~~~s~~l~~~~~~~~~  156 (629)
T KOG1827|consen  128 ENARLYNRPDSLIYKDSGELEKYFISLED  156 (629)
T ss_pred             HHHHHhcCcchhhhhhhhhhhcchhhhhc
Confidence            99999999999999999999999987653

>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]

Probab=98.71  E-value=1.6e-08  Score=112.45  Aligned_cols=99  Identities=27%  Similarity=0.446  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          104 LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      +...+..|+.++...+...+|..||+.+.  ++|||.||+.||||.|+++.+....   |.+-++|..|+.||++|..+|
T Consensus      1262 ~ss~l~~i~n~~~~~~~t~~f~~Pv~~k~--v~dyy~vi~~P~~lq~~kk~v~kr~---y~~r~~fle~~~~~~~ns~~y 1336 (1563)
T KOG0008|consen 1262 LSSILETIINQARSSPNTYPFPTPVNAKE--VKDYYRVITPPMDLQTQKKLVRKRL---YESREHFLEELPLIVSNSTKY 1336 (1563)
T ss_pred             cccchHHHHHHHhcCCCCcCCCCccchhh--ccchhhccCCCcchHHHHHHHHHHH---HHHHHHHHHHhHHHhhchhhh
Confidence            44457889999999999999999999998  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHh
Q 016116          184 NDERDDVHVMAKSLLEKFEEKWLQ  207 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~~~  207 (395)
                      |++-+.+...+..+....-+.|..
T Consensus      1337 ng~~~~~t~~~q~mls~~~~~~~e 1360 (1563)
T KOG0008|consen 1337 NGPLASLTRQQQSMLSLCFEKLKE 1360 (1563)
T ss_pred             cCchHHHHHHHHHHHHHHHHhhch
Confidence            999999998888877766655543

>KOG1472 consensus Histone acetyltransferase SAGA/ADA, catalytic subunit PCAF/GCN5 and related proteins [Chromatin structure and dynamics; Transcription]

Probab=98.71  E-value=8.2e-09  Score=110.55  Aligned_cols=81  Identities=27%  Similarity=0.481  Sum_probs=70.5

Q ss_pred             cCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHH
Q 016116          117 QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS  196 (395)
Q Consensus       117 ~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~  196 (395)
                      .+..+++|..+|+...  .|+||.||+.||||+|+..++....   |.+.++|+.|+.+||.||..||.+.+.....-..
T Consensus       300 ~~~~s~~~~~kvs~~~--a~~y~~i~k~pmdl~t~~~k~~~~~---y~~~~~fv~d~~~~~~n~~~~n~ee~~~~~~~~v  374 (720)
T KOG1472|consen  300 RTEHSTPFLEKVSKED--APNYYQIIKAPMDLSTELKKLKSGP---YCSKEEFVNDLMLIWRNCEKYNSEESHGLIEFAV  374 (720)
T ss_pred             ccccccccccCCChhh--CcchHHhhhcchHHHHHHHHhcccc---ccchhHHHHHHHHHHhcchhhccccchhhhhhhh
Confidence            4889999999999998  9999999999999999999999999   9999999999999999999999976655444444


Q ss_pred             HHHHHH
Q 016116          197 LLEKFE  202 (395)
Q Consensus       197 L~~~Fe  202 (395)
                      +..-+.
T Consensus       375 v~~~~s  380 (720)
T KOG1472|consen  375 IMNSKS  380 (720)
T ss_pred             hhccCc
Confidence            443333

>KOG1474 consensus Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription]

Probab=98.60  E-value=1.3e-08  Score=110.00  Aligned_cols=91  Identities=40%  Similarity=0.698  Sum_probs=84.6

Q ss_pred             HHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHH
Q 016116          115 ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMA  194 (395)
Q Consensus       115 l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A  194 (395)
                      ...|.++|+|..||+...+++|+||.+|++|||++||..++.++.   |.+..+..+|+.-+|.||..||..+.+|+.++
T Consensus         4 ~~~~~~~~~f~~~v~~v~l~~~~~~~~~~~~~d~~~~~~~~e~n~---~~~~~~~~~~f~~~~sn~~~~~~~~~~v~~~~   80 (640)
T KOG1474|consen    4 ARKHKLAWPFLEPVDAVALNLPAYYEIIKRPMDIGTIEKRVENNY---YFSASECIADFKTKFSNCYLFNDSGDDVVRMK   80 (640)
T ss_pred             cccccccccccCccchhhccchhhhcccCCCCCchhhhhhhccCc---cccHhhhhhhccccccchhcccCCccchhhcc
Confidence            456889999999999999999999999999999999999999966   99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 016116          195 KSLLEKFEEKWLQL  208 (395)
Q Consensus       195 ~~L~~~Fe~~~~~~  208 (395)
                      ..++..|.......
T Consensus        81 ~~~~~~~~~~~~~~   94 (640)
T KOG1474|consen   81 QSLEKLFPKKLRSM   94 (640)
T ss_pred             ccchhhcccccccc
Confidence            99999997665554

>KOG1828 consensus IRF-2-binding protein CELTIX-1, contains BROMO domain [Transcription]

Probab=98.09  E-value=7.4e-07  Score=88.78  Aligned_cols=88  Identities=26%  Similarity=0.263  Sum_probs=76.9

Q ss_pred             HHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCH
Q 016116          110 AIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDD  189 (395)
Q Consensus       110 ~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~  189 (395)
                      .++..+-+...-..|..||....  .|+|.+||+.|||+.|++.+++-+.   |.+..+|..|.+++..||..||...+.
T Consensus        26 hhlrkl~sKdp~q~fafplt~~m--ap~y~~iis~Pmd~~t~r~kidd~~---yl~L~~m~~d~kl~~~na~~yn~~~Tv  100 (418)
T KOG1828|consen   26 HHLRKLPSKDPKQKFAFPLTDKM--APNYLEIISEPMDRITKRSKIDDTR---YLVLSQMEFDRKLPDGNATLYNLHPTV  100 (418)
T ss_pred             HHHHhccccChhhhhccccchhh--ccchHhhhhcccccccccccCCCcc---ceechhhhhhhcccccchhhhhcCCcc
Confidence            44555555555667777888887  9999999999999999999999999   999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 016116          190 VHVMAKSLLEKFE  202 (395)
Q Consensus       190 v~~~A~~L~~~Fe  202 (395)
                      ++..|++|..+-.
T Consensus       101 ~~~aaKrL~~v~~  113 (418)
T KOG1828|consen  101 PIVAAKRLCPVRL  113 (418)
T ss_pred             ccccccccchhhc
Confidence            9999999876644

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

Probab=98.03  E-value=1.6e-06  Score=88.09  Aligned_cols=159  Identities=23%  Similarity=0.317  Sum_probs=117.8

Q ss_pred             HHHHHHHHH-----HHHHHHhhhhhhhhccCCCCCCCCCCCchhhhccccCCC--------CCchhhhhhhhhhhhHhhh
Q 016116           32 TIDDILQKV-----TQLEQKLNDVEQFYLTKDNNQPNTSKSISIAKEKLKDRH--------VASIEKQQQDAFHREEAAG   98 (395)
Q Consensus        32 ~l~~i~~k~-----~~le~~~~~~~~~~~~~~~~~~~~~~g~s~~k~~~r~r~--------~~~~kk~~~~~~~~e~~~~   98 (395)
                      .|..|+.++     ..+|+-+.+...|++++..+   +.+++++...+.....        ++....   ........ .
T Consensus       190 ~L~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~y---N~~~s~v~~~a~~l~~~~~~~i~~~~~~~~---~~~~~~~~-~  262 (371)
T COG5076         190 DLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLY---NGPDSSVYVDAKELEKYFLKLIEEIPEEML---ELSIKPGR-E  262 (371)
T ss_pred             hHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhc---cCCCcchhhhhHHHHHHHHHHHHhccccch---hhccCccc-c
Confidence            356677766     68999999999999999988   6677666654322110        000000   00000000 0


Q ss_pred             ccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhh
Q 016116           99 RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  178 (395)
Q Consensus        99 ~~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~  178 (395)
                      .+.    .+-..++.....+..+|+|..++....  .|+|+++|..+|+++|.+.++..+.   |....+|..|..++|.
T Consensus       263 ~~~----~~~~~~i~~~~~~~~~~~~~~~~~~~~--~p~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~  333 (371)
T COG5076         263 ERE----ERESVLITNSQAHVGAWPFLRPVSDEE--VPDYYKDIRDPMDLSTKELKLRNNY---YRPEETFVRDAKLFFD  333 (371)
T ss_pred             ccc----cchhhcccccccccccccccccCCccc--ccchhhhhhcccccccchhhhhccc---CCCccccccccchhhh
Confidence            000    023334555577788999999999988  9999999999999999999999999   9999999999999999


Q ss_pred             hhcccCCCCCHHHHHHHHHHHHHHHHHH
Q 016116          179 NAMKYNDERDDVHVMAKSLLEKFEEKWL  206 (395)
Q Consensus       179 Na~~YN~~~S~v~~~A~~L~~~Fe~~~~  206 (395)
                      ||..||+.-..++..+..+..+|.....
T Consensus       334 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  361 (371)
T COG5076         334 NCVMYNGEVTDYYKNANVLEDFVIKKTR  361 (371)
T ss_pred             cccccchhhhhhhhhccchhhhHhhhhh
Confidence            9999999999999999998888877654

>KOG1828 consensus IRF-2-binding protein CELTIX-1, contains BROMO domain [Transcription]

Probab=97.88  E-value=7.1e-06  Score=81.90  Aligned_cols=82  Identities=13%  Similarity=0.059  Sum_probs=73.4

Q ss_pred             HHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHH
Q 016116          112 FRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVH  191 (395)
Q Consensus       112 l~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~  191 (395)
                      .+++........|..+|-...  +|.|.-+|++|+|++|++.+..++.   |.| -+|..|+.||+.||++||.+...+|
T Consensus       217 ~~kl~~~~p~~~lnyg~tas~--aP~YSm~Ik~~~~~~Tygdk~~and---y~S-~~f~~D~kl~~l~amT~gehsk~yy  290 (418)
T KOG1828|consen  217 EDKLNRVDPVAYLNYGPTASF--APGYSMTITEVEPPGTYGDKSSAND---YES-LSFTQDRKLIALKAVTNGEHSKSYY  290 (418)
T ss_pred             HHHhcccCchhhhcccchhhh--cccccccccccCCCcchhhhhhhhh---hhh-hhhhcccchhhHHHHhcCCcchHHH
Confidence            345555566778888888777  9999999999999999999999999   999 9999999999999999999999999


Q ss_pred             HHHHHHHH
Q 016116          192 VMAKSLLE  199 (395)
Q Consensus       192 ~~A~~L~~  199 (395)
                      .+|..+..
T Consensus       291 elank~lh  298 (418)
T KOG1828|consen  291 ELANKQLH  298 (418)
T ss_pred             HHHHhhhh
Confidence            99998766

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

Probab=96.01  E-value=0.0069  Score=52.74  Aligned_cols=68  Identities=15%  Similarity=0.271  Sum_probs=57.3

Q ss_pred             CCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCcCchHH
Q 016116          145 PMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEE  215 (395)
Q Consensus       145 PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~~~~  215 (395)
                      |.||..|++||+.|.   |+++.+|.+||-.|+.-++.-.+....+-.....+..+|...+.++++++..+
T Consensus        59 p~dL~~V~kkl~~G~---Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~vf~Wf~~~  126 (131)
T cd05493          59 PLDLEAVGKKLEAGF---YTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFNSE  126 (131)
T ss_pred             cccHHHHHHHHhccc---eehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHhccccccc
Confidence            899999999999999   99999999999999998886666555555556677788999999998877543

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 Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]

Probab=86.36  E-value=0.59  Score=51.70  Aligned_cols=60  Identities=18%  Similarity=0.394  Sum_probs=52.4

Q ss_pred             ccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHHHHHHHHHH
Q 016116          142 IEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK  204 (395)
Q Consensus       142 Ik~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~L~~~Fe~~  204 (395)
                      -.-|..|..|..+|++..   |++.+.|..||..|.+||.+|.+-+--+...+..|...|..-
T Consensus      1050 fpvpls~evi~~rlEn~y---Yrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~T 1109 (1113)
T KOG0644|consen 1050 FPVPLSLEVIRSRLENNY---YRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRT 1109 (1113)
T ss_pred             CCCcccHHHHHHHHHhhh---hhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhhh
Confidence            345789999999999999   999999999999999999999998887777777777777654

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=85.75  E-value=0.52  Score=53.73  Aligned_cols=64  Identities=22%  Similarity=0.260  Sum_probs=55.6

Q ss_pred             CCCCCCCCCcc---ccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHH--HHhchhhhhcccCCCC
Q 016116          121 AWPFMHPVDVE---GLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYA--DVRLVFKNAMKYNDER  187 (395)
Q Consensus       121 a~~F~~PVd~~---~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~--Dv~LIf~Na~~YN~~~  187 (395)
                      +..|-.|++..   .+.+++|..+|+.|||+...-.++..+.   |.++.+|..  ++.|||.|++.||+..
T Consensus       533 ~~~~s~Pl~~~~~~ll~~~~~~~~iq~~~~va~~~~k~~e~~---~~~v~~~e~~~~i~lic~~~lli~~~~  601 (1080)
T KOG0732|consen  533 SVIFSRPLSTYLKPLLPFQDALEDIQGLMDVASSMAKIEEHL---KLLVRSFESNFAIRLICRPRLLINGGK  601 (1080)
T ss_pred             ccCCCCCCCcceecccchHHHHHHhhcchhHHhhhhhHHHHh---HHHHHhhhcccchhhhcCcHHhcCCCc
Confidence            56677777632   2225699999999999999999999999   999999999  9999999999999965

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	395
2dvv_A	112	Crystal Structure Of The Second Bromodomain Of The		6e-20
3oni_A	114	Crystal Structure Of The Second Bromodomain Of Huma		6e-20
2i8n_A	114	Solution Structure Of The Second Bromodomain Of Brd		7e-20
2g4a_A	116	Solution Structure Of A Bromodomain From Ring3 Prot		9e-20
2ouo_A	130	Crystal Structure Of The Bromo Domain 2 In Human Br		1e-19
2lsp_B	128	Solution Structures Of Brd4 Second Bromodomain With		1e-19
3jvl_A	120	Crystal Structure Of Bromodomain 2 Of Mouse Brd4 Le		3e-19
2wp1_A	126	Structure Of Brdt Bromodomain 2 Bound To An Acetyla		2e-18
2oo1_A	113	Crystal Structure Of The Bromo Domain 2 Of Human Br		3e-18
2e7n_A	117	Solution Structure Of The Second Bromodomain From H		4e-18
2dww_A	114	Crystal Structure Of Bromodomain-Containing Protein		1e-16
3jvj_A	131	Crystal Structure Of The Bromodomain 1 In Mouse Brd		8e-15
2oss_A	127	Crystal Structure Of The Bromo Domain 1 In Human Br		9e-15
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		1e-14
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		1e-14
2wp2_A	120	Structure Of Brdt Bromodomain Bd1 Bound To A Diacet		3e-14
2ydw_A	153	Crystal Structure Of The First Bromodomain Of Human		5e-14
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		5e-14
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		5e-14
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		6e-14
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		6e-14
2nxb_A	123	Crystal Structure Of Human Bromodomain Containing P		7e-14
3aqa_A	128	Crystal Structure Of The Human Brd2 Bd1 Bromodomain		1e-11
3g0l_A	117	Crystal Structure Of Human Bromodomain Adjacent To		2e-11
1x0j_A	122	Crystal Structure Analysis Of The N-Terminal Bromod		3e-11
2e7o_A	112	Solution Structure Of The Bromodomain From Human Br		3e-11
3dwy_A	119	Crystal Structure Of The Bromodomain Of Human Crebb		6e-11
1jsp_B	121	Nmr Structure Of Cbp Bromodomain In Complex With P5		7e-11
3i3j_A	124	Crystal Structure Of The Bromodomain Of Human Ep300		9e-11
3nxb_A	116	Crystal Structure Of The Bromodomain Of Human Cecr2		1e-09
1e6i_A	121	Bromodomain From Gcn5 Complexed With Acetylated H4		2e-09
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		1e-08
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		1e-08
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		2e-08
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		2e-08
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		2e-08
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		3e-08
3u5m_A	207	Crystal Structure Of Trim33 Phd-Bromo In The Free S		3e-08
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		3e-08
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		5e-08
2yyn_A	135	Crystal Sturcture Of Human Bromodomain Protein Leng		5e-08
3o33_A	184	Crystal Structure Of Trim24 Phd-Bromo In The Free S		5e-08
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		6e-08
3lxj_A	136	Crystal Structure Of The Bromodomain Of Human Aaa D		4e-07
2f6j_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		6e-07
1f68_A	103	Nmr Solution Structure Of The Bromodomain From Huma		2e-06
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		2e-06
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		2e-06
3d7c_A	112	Crystal Structure Of The Bromodomain Of Human Gcn5,		2e-06
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		2e-06
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		6e-06
3uv4_A	158	Crystal Structure Of The Second Bromodomain Of Huma		6e-06
3hmh_A	155	Crystal Structure Of The Second Bromodomain Of Huma		2e-05
2dkw_A	131	Solution Structure Of The Bromodomain Of Human Prot		4e-05
2i7k_A	117	Solution Structure Of The Bromodomain Of Human Brd7		1e-04
3hme_A	123	Crystal Structure Of Human Bromodomain Containing 9		2e-04
3fkm_X	166	Plasmodium Falciparum Bromodomain-Containing Protei		3e-04
3tlp_A	150	Crystal Structure Of The Fourth Bromodomain Of Huma		7e-04
3dai_A	130	Crystal Structure Of The Bromodomain Of The Human A		9e-04

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

Iteration: 1
 Score = 95.1 bits (235), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 49/114 (42%), Positives = 71/114 (62%), Gaps = 7/114 (6%)
Query: 98  GRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNK 154
           G  M++LK     I +++   K   +AWPF  PVD   LGLHDY+++I+ PMD ST+K K
Sbjct: 1   GSHMEQLK-HCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRK 59
Query: 155 MDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           M+ +D   YR+ +E  ADVRL+F N  KYN    DV  MA+ L + FE ++ ++
Sbjct: 60  MENRD---YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKM 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 = 95.1 bits (235), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)
Query: 120 WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 179
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 27  YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 83
Query: 180 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             KYN    DV  MA+ L + FE ++ ++
Sbjct: 84  CYKYNPPDHDVVAMARKLQDVFEFRYAKM 112

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

Iteration: 1
 Score = 94.7 bits (234), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 63/90 (70%), Gaps = 3/90 (3%)
Query: 120 WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 179
           +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  ADVRL+F N
Sbjct: 21  YAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGADVRLMFSN 77
Query: 180 AMKYNDERDDVHVMAKSLLEKFEEKWLQLL 209
             KYN    +V  MA+ L + FE ++ ++L
Sbjct: 78  CYKYNPPDHEVVAMARKLQDVFEMRFAKML 107

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)
Query: 120 WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 179
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 21  YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 77
Query: 180 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             KYN    DV  MA+ L + FE ++ ++
Sbjct: 78  CYKYNPPDHDVVAMARKLQDVFEFRYAKM 106

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 62/89 (69%), Gaps = 3/89 (3%)
Query: 120 WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 179
           +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  ADVRL+F N
Sbjct: 42  YAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGADVRLMFSN 98
Query: 180 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             KYN    +V  MA+ L + FE ++ ++
Sbjct: 99  CYKYNPPDHEVVAMARKLQDVFEMRFAKM 127

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

Iteration: 1
 Score = 94.0 bits (232), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 62/89 (69%), Gaps = 3/89 (3%)
Query: 120 WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 179
           +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  ADVRL+F N
Sbjct: 40  YAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGADVRLMFSN 96
Query: 180 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             KYN    +V  MA+ L + FE ++ ++
Sbjct: 97  CYKYNPPDHEVVAMARKLQDVFEMRFAKM 125

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

Iteration: 1
 Score = 92.4 bits (228), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 48/116 (41%), Positives = 74/116 (63%), Gaps = 6/116 (5%)
Query: 96  AAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIK 152
           A G ++ E  +  + I +++   K   +AWPF  PVDVE LGLHDY ++I+ PMD STIK
Sbjct: 2   AMGSKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIK 61
Query: 153 NKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           +K++ ++   YR+ +E  ADVRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 62  SKLESRE---YRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 114

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/83 (49%), Positives = 57/83 (68%), Gaps = 3/83 (3%)
Query: 120 WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 179
           +AWPF +PVD + LGLH+YY+V++ PMD  TIK KMD ++   Y++  E  ADVRL+F N
Sbjct: 34  YAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQE---YKDAYEFAADVRLMFMN 90
Query: 180 AMKYNDERDDVHVMAKSLLEKFE 202
             KYN    +V  MA++L + FE
Sbjct: 91  CYKYNPPDHEVVAMARTLQDVFE 113

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

Iteration: 1
 Score = 89.7 bits (221), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 46/112 (41%), Positives = 69/112 (61%), Gaps = 6/112 (5%)
Query: 100 RMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 156
           ++ E  R   +I R++   K   +AWPF  PVD E L LHDY+++I+ PMD ST+K KMD
Sbjct: 4   KLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMD 63
Query: 157 GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           G++   Y + +   ADVRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 64  GRE---YPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 112

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

Iteration: 1
 Score = 89.0 bits (219), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 46/112 (41%), Positives = 69/112 (61%), Gaps = 6/112 (5%)
Query: 100 RMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 156
           ++ E  R   +I R++   K   +AWPF  PVD E L LHDY+++I+ PMD ST+K KMD
Sbjct: 9   KLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMD 68
Query: 157 GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           G++   Y + +   ADVRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 69  GRE---YPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 117

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

Iteration: 1
 Score = 84.3 bits (207), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 41/86 (47%), Positives = 57/86 (66%), Gaps = 3/86 (3%)
Query: 120 WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 179
           +AWPF  PVDVE LGLHDY ++I+ P D STIK+K++ ++   YR+ +E  ADVRL F N
Sbjct: 27  YAWPFYKPVDVEALGLHDYCDIIKHPXDXSTIKSKLESRE---YRDAQEFGADVRLXFSN 83
Query: 180 AMKYNDERDDVHVMAKSLLEKFEEKW 205
             KYN    +V   A+ L + FE ++
Sbjct: 84  CYKYNPPDHEVVAXARKLQDVFEXRF 109

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

Iteration: 1
 Score = 78.2 bits (191), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 60/106 (56%), Gaps = 3/106 (2%)
Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
           R+  +L+     + + + +H++AWPF  PVD   L L DYY++I+ PMD  TIK ++   
Sbjct: 21  RQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRL--- 77
Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           +   Y N +E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 78  ENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 123

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

Iteration: 1
 Score = 77.8 bits (190), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 60/106 (56%), Gaps = 3/106 (2%)
Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
           R+  +L+     + + + +H++AWPF  PVD   L L DYY++I+ PMD  TIK ++   
Sbjct: 17  RQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRL--- 73
Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           +   Y N +E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 74  ENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 119

>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 = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 60/106 (56%), Gaps = 3/106 (2%)
Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
           R+  +L+     + + + +H++AWPF  PVD   L L DYY++I+ PMD  TIK ++   
Sbjct: 37  RQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRL--- 93
Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           +   Y N +E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 94  ENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 139

>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 = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 59/106 (55%), Gaps = 3/106 (2%)
Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
           R   +L+     + + + +H++AWPF  PVD   L L DYY++I+ PMD  TIK ++   
Sbjct: 17  RETNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRL--- 73
Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           +   Y N +E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 74  ENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 119

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

Iteration: 1
 Score = 76.3 bits (186), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 39/112 (34%), Positives = 61/112 (54%), Gaps = 3/112 (2%)
Query: 97  AGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 156
           +GR   +L+     + + + +H ++WPF  PVD   L L DYY +I+ PMD +TIK +++
Sbjct: 8   SGRLTNQLQFLQRVVLKALWKHGFSWPFQQPVDAVKLKLPDYYTIIKTPMDLNTIKKRLE 67
Query: 157 GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
            K    Y    E   D   +F N   YN   DD+ VMA++L + F +K  Q+
Sbjct: 68  NK---YYEKASECIEDFNTMFSNCYLYNKTGDDIVVMAQALEKLFMQKLSQM 116

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

Iteration: 1
 Score = 75.5 bits (184), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 37/107 (34%), Positives = 60/107 (56%), Gaps = 3/107 (2%)
Query: 98  GRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG 157
           GR   +L+     + + + +H++AWPF  PVD   LGL DY+++I++PMD  TIK ++  
Sbjct: 27  GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRL-- 84
Query: 158 KDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
            +   Y    E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 85  -ENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQK 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 = 75.5 bits (184), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 37/107 (34%), Positives = 60/107 (56%), Gaps = 3/107 (2%)
Query: 98  GRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG 157
           GR   +L+     + + + +H++AWPF  PVD   LGL DY+++I++PMD  TIK ++  
Sbjct: 27  GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRL-- 84
Query: 158 KDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
            +   Y    E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 85  -ENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQK 130

>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 = 75.5 bits (184), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 38/111 (34%), Positives = 60/111 (54%), Gaps = 3/111 (2%)
Query: 98  GRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG 157
           GR   +L+     + + + +H ++WPF  PVD   L L DYY +I+ PMD +TIK +++ 
Sbjct: 8   GRLTNQLQYLQKVVLKDLWKHSFSWPFQRPVDAVKLQLPDYYTIIKNPMDLNTIKKRLEN 67
Query: 158 KDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           K    Y    E   D   +F N   YN   DD+ +MA++L + F +K  Q+
Sbjct: 68  K---YYAKASECIEDFNTMFSNCYLYNKPGDDIVLMAQALEKLFMQKLSQM 115

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 62/112 (55%), Gaps = 3/112 (2%)
Query: 97  AGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 156
            GR+  +L+     + + + +H++AWPF  PVD   L L DY+++I+ PMD  TIK ++ 
Sbjct: 15  PGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRL- 73
Query: 157 GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             +   Y +  E   D   +F N   YN   DD+ +MA++L + F +K  Q+
Sbjct: 74  --ENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 123

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 62/112 (55%), Gaps = 3/112 (2%)
Query: 97  AGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 156
            GR+  +L+     + + + +H++AWPF  PVD   L L DY+++I+ PMD  TIK ++ 
Sbjct: 13  PGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRL- 71
Query: 157 GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             +   Y +  E   D   +F N   YN   DD+ +MA++L + F +K  Q+
Sbjct: 72  --ENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 121

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 62/112 (55%), Gaps = 3/112 (2%)
Query: 97  AGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 156
            GR+  +L+     + + + +H++AWPF  PVD   L L DY+++I+ PMD  TIK ++ 
Sbjct: 11  PGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRL- 69
Query: 157 GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             +   Y +  E   D   +F N   YN   DD+ +MA++L + F +K  Q+
Sbjct: 70  --ENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 119

>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 = 67.4 bits (163), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 35/109 (32%), Positives = 59/109 (54%), Gaps = 3/109 (2%)
Query: 96  AAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKM 155
           ++GR   +L+     + + + +H++AWPF  PVD   LGL DY+++I++P D  TIK ++
Sbjct: 5   SSGRVTNQLQYLHKVVXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRL 64
Query: 156 DGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
              +   Y    E   D    F N   YN   DD+ + A++L + F +K
Sbjct: 65  ---ENNYYWAASECXQDFNTXFTNCYIYNKPTDDIVLXAQTLEKIFLQK 110

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 57/97 (58%), Gaps = 5/97 (5%)
Query: 109 AAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVRE 168
           + I  ++  H+ AWPF+ PV+++ +    Y +VI+KPMDFSTI+ K+       Y N+  
Sbjct: 19  SMILTEMETHEDAWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREKLSSGQ---YPNLET 73
Query: 169 IYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
              DVRLVF N   +N++  D+     ++ + FE+KW
Sbjct: 74  FALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKW 110

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/107 (32%), Positives = 57/107 (53%), Gaps = 3/107 (2%)
Query: 98  GRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG 157
           GR   +L+     + + + +H++AWPF  PVD   LGL DY+++I++P D  TIK ++  
Sbjct: 1   GRVTNQLQYLHKVVXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRL-- 58
Query: 158 KDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
            +   Y    E   D    F N   YN   DD+ + A++L + F +K
Sbjct: 59  -ENNYYWAASECXQDFNTXFTNCYIYNKPTDDIVLXAQTLEKIFLQK 104

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 57/97 (58%), Gaps = 5/97 (5%)
Query: 109 AAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVRE 168
           + I  ++  H+ AWPF+ PV+++ +    Y +VI+KPMDFSTI+ K+       Y N+  
Sbjct: 16  SMILTEMETHEDAWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREKLSSGQ---YPNLET 70
Query: 169 IYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
              DVRLVF N   +N++  D+     ++ + FE+KW
Sbjct: 71  FALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKW 107

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 39/103 (37%), Positives = 57/103 (55%), Gaps = 8/103 (7%)
Query: 102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGT 161
           Q L     A++RQ  +   + PF  PVD + LG+ DY+++++ PMD STIK K+D    T
Sbjct: 14  QALMPTLEALYRQDPE---SLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLD----T 66
Query: 162 G-YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEE 203
           G Y+   +   DV L+F NA  YN +   V+     L E FE+
Sbjct: 67  GQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQ 109

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 39/103 (37%), Positives = 57/103 (55%), Gaps = 8/103 (7%)
Query: 102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGT 161
           Q L     A++RQ  +   + PF  PVD + LG+ DY+++++ PMD STIK K+D    T
Sbjct: 16  QALMPTLEALYRQDPE---SLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLD----T 68
Query: 162 G-YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEE 203
           G Y+   +   DV L+F NA  YN +   V+     L E FE+
Sbjct: 69  GQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQ 111

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 38/103 (36%), Positives = 57/103 (55%), Gaps = 8/103 (7%)
Query: 102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGT 161
           Q L     A++RQ  +   + PF  PVD + LG+ DY+++++ PMD STIK K+D    T
Sbjct: 19  QALMPTLEALYRQDPE---SLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLD----T 71
Query: 162 G-YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEE 203
           G Y+   +   D+ L+F NA  YN +   V+     L E FE+
Sbjct: 72  GQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQ 114

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 61/112 (54%), Gaps = 8/112 (7%)
Query: 93  REEAAGRRMQELKRQFAAIFRQ---ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFS 149
           REE   + + EL   F A+++    +  HK +WPF+ PVD E     +YY++I+ PMD S
Sbjct: 3   REEKKTKDLFELDDDFTAMYKVLDVVKAHKDSWPFLEPVD-ESYA-PNYYQIIKAPMDIS 60
Query: 150 TIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 201
           +++ K+   +G  Y    E   D++ +F+N  KYN E  +   M+ +L   F
Sbjct: 61  SMEKKL---NGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCF 109

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/101 (34%), Positives = 55/101 (54%), Gaps = 6/101 (5%)
Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           I  ++  H  AWPF+ PV+ E +   DYY+ I++PMD ST++ K++      Y+ + +  
Sbjct: 21  ILTELQNHAAAWPFLQPVNKEEVP--DYYDFIKEPMDLSTMEIKLES---NKYQKMEDFI 75
Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 211
            D RLVF N   YN E    +  A   LEKF    ++ +P+
Sbjct: 76  YDARLVFNNCRMYNGENTSYYKYANR-LEKFFNNKVKEIPE 115

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/100 (35%), Positives = 53/100 (53%), Gaps = 8/100 (8%)
Query: 103 ELKRQFAAIFRQITQHKWAWPFMHPVD-VEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGT 161
           +L     +I +Q+  H+ AWPFM PV   E  G   YYEVI  PMD  T+  ++  +   
Sbjct: 15  QLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPG---YYEVIRFPMDLKTMSERLKNR--- 68
Query: 162 GYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 201
            Y + +   AD++ VF N  +YN    + +  A ++LEKF
Sbjct: 69  YYVSKKLFMADLQRVFTNCKEYNPPESEYYKCA-NILEKF 107

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/100 (35%), Positives = 53/100 (53%), Gaps = 8/100 (8%)
Query: 103 ELKRQFAAIFRQITQHKWAWPFMHPVD-VEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGT 161
           +L     +I +Q+  H+ AWPFM PV   E  G   YYEVI  PMD  T+  ++  +   
Sbjct: 13  QLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPG---YYEVIRFPMDLKTMSERLKNR--- 66
Query: 162 GYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 201
            Y + +   AD++ VF N  +YN    + +  A ++LEKF
Sbjct: 67  YYVSKKLFMADLQRVFTNCKEYNPPESEYYKCA-NILEKF 105

>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 = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/160 (28%), Positives = 74/160 (46%), Gaps = 13/160 (8%)
Query: 49  DVEQFYLTKDNNQP-NTSKSISI--AKEKLKDRHVASIEKQQQDAFHREEAAGRRMQE-L 104
           D  +FY+  D  Q     + + I  ++ +L D +V    +  +DA         +  E L
Sbjct: 18  DESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGL 77
Query: 105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 164
           KR    + R +  HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y 
Sbjct: 78  KR----VLRSLQAHKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYE 128
Query: 165 NVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
            + E  AD+  +F N   YN      +  A+ L   F +K
Sbjct: 129 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 168

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/160 (28%), Positives = 74/160 (46%), Gaps = 13/160 (8%)
Query: 49  DVEQFYLTKDNNQP-NTSKSISI--AKEKLKDRHVASIEKQQQDAFHREEAAGRRMQE-L 104
           D  +FY+  D  Q     + + I  ++ +L D +V    +  +DA         +  E L
Sbjct: 18  DESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGL 77
Query: 105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 164
           KR    + R +  HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y 
Sbjct: 78  KR----VLRSLQAHKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYE 128
Query: 165 NVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
            + E  AD+  +F N   YN      +  A+ L   F +K
Sbjct: 129 KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 168

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 5/94 (5%)
Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           + R +  HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  
Sbjct: 28  VLRSLQAHKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYEKLTEFV 82
Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           AD+  +F N   YN      +  A+ L   F +K
Sbjct: 83  ADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 116

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 5/94 (5%)
Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           + R +  HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  
Sbjct: 21  VLRSLQAHKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYEKLTEFV 75
Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           AD+  +F N   YN      +  A+ L   F +K
Sbjct: 76  ADMTAIFDNCRYYNPSDSPFYQCAEVLESFFVQK 109

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 50/92 (54%), Gaps = 3/92 (3%)
Query: 105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 164
           +R+   +   +  H+ +  F  PV      + +YY++I+KPMD ST+K K+  K    Y+
Sbjct: 83  QRKCERLLLYLYCHELSIEFQEPVPA---SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQ 139
Query: 165 NVREIYADVRLVFKNAMKYNDERDDVHVMAKS 196
              +  ADVRL+FKN  ++N+    V V A +
Sbjct: 140 IPDDFVADVRLIFKNCERFNEMMKVVQVYADT 171

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 58/112 (51%), Gaps = 6/112 (5%)
Query: 93  REEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIK 152
           R  A    +Q  K+Q   +   I Q + + PF  PVD+  L   DY ++I+ PMDF+T++
Sbjct: 11  RNRAQSYDIQAWKKQCEELLNLIFQCEDSEPFRQPVDL--LEYPDYRDIIDTPMDFATVR 68
Query: 153 NKMDGKDGTGYRNVREIYADVRLVFKNAMKYN-DERDDVHVMAKSLLEKFEE 203
             +   +   Y +  E+  DVRL+F N+  Y   +R  ++ M+  L   FEE
Sbjct: 69  ETL---EAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEE 117

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 5/94 (5%)
Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           + R +  HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  
Sbjct: 21  VLRSLQAHKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYEKLTEFV 75
Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           AD+  +F N   YN      +  A+ L   F +K
Sbjct: 76  ADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 109

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 54/106 (50%), Gaps = 4/106 (3%)
Query: 105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 164
           KR+   +   +  H+ +  F  PV    L + DYY++I+ PMD STIK ++  +D + Y 
Sbjct: 22  KRKCERLLLFLYCHEMSLAFQDPV---PLTVPDYYKIIKNPMDLSTIKKRLQ-EDYSMYS 77
Query: 165 NVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP 210
              +  AD RL+F+N  ++N+   +V      L   FEE    L P
Sbjct: 78  KPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 123

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 54/106 (50%), Gaps = 4/106 (3%)
Query: 105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 164
           KR+   +   +  H+ +  F  PV    L + DYY++I+ PMD STIK ++  +D + Y 
Sbjct: 83  KRKCERLLLFLYCHEMSLAFQDPV---PLTVPDYYKIIKNPMDLSTIKKRLQ-EDYSMYS 138
Query: 165 NVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP 210
              +  AD RL+F+N  ++N+   +V      L   FEE    L P
Sbjct: 139 KPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 184

>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 = 55.5 bits (132), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 54/101 (53%), Gaps = 6/101 (5%)
Query: 105 KRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 164
           K+Q   +   I Q + + PF  PVD+  +   DY ++I+ PMDF T++  +D  +   Y 
Sbjct: 12  KKQCKELVNLIFQCEDSEPFRQPVDL--VEYPDYRDIIDTPMDFGTVRETLDAGN---YD 66
Query: 165 NVREIYADVRLVFKNAMKYN-DERDDVHVMAKSLLEKFEEK 204
           +  E   D+RL+F NA  Y  ++R  ++ M   L   FEEK
Sbjct: 67  SPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEK 107

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 49/88 (55%), Gaps = 5/88 (5%)
Query: 101 MQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 160
           ++EL+     + +++   K    F  PVD+E +   DY EVI++PMD ST+  K+D    
Sbjct: 10  LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVS--DYLEVIKEPMDLSTVITKIDKH-- 65
Query: 161 TGYRNVREIYADVRLVFKNAMKYNDERD 188
             Y   ++   D+ L+  NA++YN ++D
Sbjct: 66  -NYLTAKDFLKDIDLICSNALEYNPDKD 92

>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 = 52.0 bits (123), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           + R +  HK AWPF+ PVD       DYY VI++P D +T + ++  +    Y  + E  
Sbjct: 80  VLRSLQAHKXAWPFLEPVDPNDAP--DYYGVIKEPXDLATXEERVQRR---YYEKLTEFV 134
Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           AD   +F N   YN      +  A+ L   F +K
Sbjct: 135 ADXTKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 168

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/100 (34%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 162
           +L      +  QI  H  AWPFM PV        DYYEVI  P+D  T+  ++  +    
Sbjct: 3   QLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAP--DYYEVIRFPIDLKTMTERLRSR---- 56
Query: 163 YRNVREIY-ADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 201
           Y   R+++ AD++ V  N  +YN   D  +    S LEKF
Sbjct: 57  YYVTRKLFVADLQRVIANCREYNPP-DSEYCRCASALEKF 95

>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 = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 52/107 (48%), Gaps = 12/107 (11%)
Query: 85  KQQQDAFHREEAAGRRMQELKRQ--FAAIFRQITQHKW-----AWPFMHPVDVEGLGLHD 137
           K+++D   R E A   + +   Q  F+ I   I   K      +WPF HPV+ + +   D
Sbjct: 112 KEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--D 169
Query: 138 YYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN 184
           YY+VI  PMD  TI+  +       Y++      DV L+  N++KYN
Sbjct: 170 YYKVIVNPMDLETIRKNISKH---KYQSRESFLDDVNLILANSVKYN 213

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 52/107 (48%), Gaps = 12/107 (11%)
Query: 85  KQQQDAFHREEAAGRRMQELKRQ--FAAIFRQITQHKW-----AWPFMHPVDVEGLGLHD 137
           K+++D   R E A   + +   Q  F+ I   I   K      +WPF HPV+ + +   D
Sbjct: 124 KEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--D 181
Query: 138 YYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN 184
           YY+VI  PMD  TI+  +       Y++      DV L+  N++KYN
Sbjct: 182 YYKVIVNPMDLETIRKNISKH---KYQSRESFLDDVNLILANSVKYN 225

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/100 (34%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 162
           +L      +  QI  H  AWPFM PV        DYYEVI  P+D  T+  ++  +    
Sbjct: 7   QLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAP--DYYEVIRFPIDLKTMTERLRSR---- 60
Query: 163 YRNVREIY-ADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 201
           Y   R+++ AD++ V  N  +YN   D  +    S LEKF
Sbjct: 61  YYVTRKLFVADLQRVIANCREYNPP-DSEYCRCASALEKF 99

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 52/107 (48%), Gaps = 12/107 (11%)
Query: 85  KQQQDAFHREEAAGRRMQELKRQ--FAAIFRQITQHKW-----AWPFMHPVDVEGLGLHD 137
           K+++D   R E A   + +   Q  F+ I   I   K      +WPF HPV+ + +   D
Sbjct: 145 KEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--D 202
Query: 138 YYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN 184
           YY+VI  PMD  TI+  +       Y++      DV L+  N++KYN
Sbjct: 203 YYKVIVNPMDLETIRKNISKH---KYQSRESFLDDVNLILANSVKYN 246

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 49/95 (51%), Gaps = 6/95 (6%)
Query: 100 RMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKD 159
           R+  L     ++  Q+     A  F  PV ++ +   DY + I+ PMDF+T++ +++ + 
Sbjct: 10  RLTPLTVLLRSVLDQLQDKDPARIFAQPVSLKEVP--DYLDHIKHPMDFATMRKRLEAQ- 66
Query: 160 GTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMA 194
             GY+N+ E   D  L+  N MKYN  RD V   A
Sbjct: 67  --GYKNLHEFEEDFDLIIDNCMKYN-ARDTVFYRA 98

>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 = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 46/96 (47%), Gaps = 10/96 (10%)
Query: 94  EEAAGRRMQELKRQFAAIFRQITQHKW-----AWPFMHPVDVEGLGLHDYYEVIEKPMDF 148
           E    + M + +  F+ I   I   K      +WPF HPV+ + +   DYY+VI  PMD 
Sbjct: 16  ENLYFQSMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKVIVNPMDL 73
Query: 149 STIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN 184
            TI+  +       Y++      DV L+  N++KYN
Sbjct: 74  ETIRKNISKH---KYQSRESFLDDVNLILANSVKYN 106

>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 = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 10/89 (11%)
Query: 101 MQELKRQFAAIFRQITQHKW-----AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKM 155
            Q ++  F+ I   I   K      +WPF HPV+ + +   DYY++I  P+D  TI+  +
Sbjct: 20  FQSMQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKMIVNPVDLETIRKNI 77
Query: 156 DGKDGTGYRNVREIYADVRLVFKNAMKYN 184
                  Y++      DV L+  N++KYN
Sbjct: 78  SKH---KYQSRESFLDDVNLILANSVKYN 103

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/93 (29%), Positives = 49/93 (52%), Gaps = 10/93 (10%)
Query: 96  AAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKM 155
           ++G  ++EL+     + +++   K    F  PV        DY EVI++PMD ST+  K+
Sbjct: 5   SSGNTLRELRLFLRDVTKRLATDKRFNIFSKPVS-------DYLEVIKEPMDLSTVITKI 57
Query: 156 DGKDGTGYRNVREIYADVRLVFKNAMKYNDERD 188
           D  +   Y   ++   D+ L+  NA++YN ++D
Sbjct: 58  DKHN---YLTAKDFLKDIDLICSNALEYNPDKD 87

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 54/105 (51%), Gaps = 16/105 (15%)
Query: 94  EEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKN 153
           +EA  + M++L+R+  + F       +++P     D    G   Y  +I+ PMDFST+K 
Sbjct: 10  QEALNQLMRQLQRKDPSAF-------FSFPV---TDFIAPG---YSMIIKHPMDFSTMKE 56
Query: 154 KMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLL 198
           K+   D   Y+++ E+  + +L+  NAM YN      +  AK LL
Sbjct: 57  KIKNND---YQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLL 98

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 138 YYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSL 197
           Y  +I+ PMDF T+K+K+   +   Y++V E  AD +L+  NAM YN      + +AK +
Sbjct: 46  YSMIIKHPMDFGTMKDKIVANE---YKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKI 102
Query: 198 LE 199
           L 
Sbjct: 103 LH 104

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 124 FMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY 183
           F   VD +     DYY+VI+ P  FS IK K+  K G  Y    E   DV+L+F N   Y
Sbjct: 42  FEKLVDAKKQNCPDYYDVIKNPXSFSCIKTKL--KKGQ-YAYPSEFVKDVQLIFDNCSLY 98
Query: 184 NDERDDVHVMAKSLLEKF 201
           N     V +  K++   F
Sbjct: 99  NTSNSVVAITGKNIETYF 116

>pdb|3TLP|A Chain A, Crystal Structure Of The Fourth Bromodomain Of Human Poly-Bromodomain Containing Protein 1 (Pb1) Length = 150

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 33/115 (28%), Positives = 54/115 (46%), Gaps = 28/115 (24%)
Query: 93  REEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIK 152
           RE  +GRR+ +L          +   K  +P             DYY++I +PMD   I+
Sbjct: 40  REPGSGRRLCDL--------FMVKPSKKDYP-------------DYYKIILEPMDLKIIE 78
Query: 153 NKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE----RDDVHVMAKSLLEKFEE 203
           + +      G   + E   D++L+F+NA  YN+E     +D H++ K L EK +E
Sbjct: 79  HNIRNDKYAGEEGMIE---DMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKE 130

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 5/65 (7%)
Query: 124 FMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY 183
           F  PVD + +   DY  VI++PMD S++ +K+D      Y  V++   D+ L+  NA++Y
Sbjct: 31  FTKPVDPDEVP--DYVTVIKQPMDLSSVISKIDLHK---YLTVKDYLRDIDLICSNALEY 85
Query: 184 NDERD 188
           N +RD
Sbjct: 86  NPDRD 90

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	395
4alg_A	154	Bromodomain-containing protein 2; signaling protei	1e-46
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	5e-43
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	7e-43
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	1e-42
3p1f_A	119	CREB-binding protein; structural genomics consorti	2e-42
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	1e-41
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	6e-41
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	3e-40
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	1e-39
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	3e-39
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	2e-37
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	3e-37
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	3e-34
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	2e-33
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	1e-32
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	3e-32
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	3e-32
3d7c_A	112	General control of amino acid synthesis protein 5;	9e-32
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	2e-30
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	2e-30
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	5e-30
3uv4_A	158	Second bromodomain of human transcription initiat	2e-29
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	1e-28
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	2e-24
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-28
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	2e-28
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	4e-24
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	2e-27
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	4e-27
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	2e-17
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	4e-27
2grc_A	129	Probable global transcription activator SNF2L4; br	3e-26
2r10_A	361	Chromatin structure-remodeling complex protein RSC	8e-26
2r10_A	361	Chromatin structure-remodeling complex protein RSC	1e-16
2dat_A	123	Possible global transcription activator SNF2L2; br	1e-25
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	1e-25
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-25
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-24
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-24
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	3e-20
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-16
2jns_A	90	Bromodomain-containing protein 4; ET-domain, struc	2e-13
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	2e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

>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 =  156 bits (395), Expect = 1e-46
 Identities = 41/151 (27%), Positives = 70/151 (46%), Gaps = 3/151 (1%)

Query: 76  KDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGL 135
              H +S    +       +  GR   +L+     + + + +H++AWPF  PVD   LGL
Sbjct: 5   HHHHHSSGLVPRGSHMSNPKKPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGL 64

Query: 136 HDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAK 195
            DY+++I++PMD  TIK +++      Y    E   D   +F N   YN   DD+ +MA+
Sbjct: 65  PDYHKIIKQPMDMGTIKRRLENNY---YWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQ 121

Query: 196 SLLEKFEEKWLQLLPKVMEEEKRQEEEEAKA 226
           +L + F +K   +  +  E      +   K 
Sbjct: 122 TLEKIFLQKVASMPQEEQELVVTIPKNSHKK 152

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

 Score =  146 bits (371), Expect = 5e-43
 Identities = 32/169 (18%), Positives = 67/169 (39%), Gaps = 3/169 (1%)

Query: 83  IEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVI 142
           +      +  RE    +  ++       +   +++++    F   VD +     DYY+VI
Sbjct: 1   MHHHHHHSSGRENLYFQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVI 60

Query: 143 EKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFE 202
           + PM FS IK K+       Y    E   DV+L+F N   YN     V +  K++   F 
Sbjct: 61  KNPMSFSCIKTKLKKGQ---YAYPSEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFN 117

Query: 203 EKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNE 251
            + + +       ++++  +  K   +  +     + ++ +E+    N 
Sbjct: 118 NQLIVMGYNNFILKEKKINDMLKLVEEENIKWSKEKEDQIEEIDELENN 166

>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 =  144 bits (366), Expect = 7e-43
 Identities = 49/122 (40%), Positives = 76/122 (62%), Gaps = 6/122 (4%)

Query: 96  AAGRRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIK 152
           A G ++ E  +  + I +++   K   +AWPF  PVDVE LGLHDY ++I+ PMD STIK
Sbjct: 2   AMGSKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIK 61

Query: 153 NKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV 212
           +K++ ++   YR+ +E  ADVRL+F N  KYN    +V  MA+ L + FE ++ ++  + 
Sbjct: 62  SKLESRE---YRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEP 118

Query: 213 ME 214
            E
Sbjct: 119 EE 120

>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 =  144 bits (365), Expect = 1e-42
 Identities = 38/111 (34%), Positives = 62/111 (55%), Gaps = 3/111 (2%)

Query: 98  GRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG 157
            R+  +L+     + + + +H++AWPF  PVD   L L DYY++I+ PMD  TIK +++ 
Sbjct: 16  KRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLEN 75

Query: 158 KDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
                Y N +E   D   +F N   YN   DD+ +MA++L + F +K  +L
Sbjct: 76  NY---YWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINEL 123

>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 =  143 bits (364), Expect = 2e-42
 Identities = 35/115 (30%), Positives = 59/115 (51%), Gaps = 4/115 (3%)

Query: 99  RRMQELKRQFAAIFRQI-TQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG 157
            + +EL++        +  Q   + PF  PVD + LG+ DY+++++ PMD STIK K+D 
Sbjct: 7   FKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDT 66

Query: 158 KDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV 212
                Y+   +   DV L+F NA  YN +   V+     L E FE++   ++  +
Sbjct: 67  GQ---YQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 118

>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 =  142 bits (359), Expect = 1e-41
 Identities = 46/113 (40%), Positives = 72/113 (63%), Gaps = 6/113 (5%)

Query: 99  RRMQELKRQFAAIFRQITQHK---WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKM 155
            ++ E  +  + I +++   K   +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K+
Sbjct: 18  SKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKL 77

Query: 156 DGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           + ++   YR+ +E  ADVRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 78  EARE---YRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 127

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

 Score =  140 bits (355), Expect = 6e-41
 Identities = 35/120 (29%), Positives = 58/120 (48%), Gaps = 4/120 (3%)

Query: 92  HREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTI 151
            + E   +     KR+   +   +  H+ +  F  PV    L + DYY++I+ PMD STI
Sbjct: 9   KKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVP---LTVPDYYKIIKNPMDLSTI 65

Query: 152 KNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 211
           K ++  +D + Y    +  AD RL+F+N  ++N+   +V      L   FEE    L P+
Sbjct: 66  KKRLQ-EDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPE 124

>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 =  138 bits (349), Expect = 3e-40
 Identities = 36/120 (30%), Positives = 59/120 (49%), Gaps = 6/120 (5%)

Query: 102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGT 161
              K+Q   +   I Q + + PF  PVD+  +   DY ++I+ PMDF T++  +D  +  
Sbjct: 9   SNWKKQCKELVNLIFQCEDSEPFRQPVDL--VEYPDYRDIIDTPMDFGTVRETLDAGN-- 64

Query: 162 GYRNVREIYADVRLVFKNAMKYN-DERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQE 220
            Y +  E   D+RL+F NA  Y  ++R  ++ M   L   FEEK  ++       +K  E
Sbjct: 65  -YDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKISSDFKIGQKFNE 123

>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 =  136 bits (345), Expect = 1e-39
 Identities = 37/129 (28%), Positives = 63/129 (48%), Gaps = 6/129 (4%)

Query: 93  REEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIK 152
           R  A    +Q  K+Q   +   I Q + + PF  PVD+  L   DY ++I+ PMDF+T++
Sbjct: 11  RNRAQSYDIQAWKKQCEELLNLIFQCEDSEPFRQPVDL--LEYPDYRDIIDTPMDFATVR 68

Query: 153 NKMDGKDGTGYRNVREIYADVRLVFKNAMKYN-DERDDVHVMAKSLLEKFEEKWLQLLPK 211
             ++  +   Y +  E+  DVRL+F N+  Y   +R  ++ M+  L   FEE    +L  
Sbjct: 69  ETLEAGN---YESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSD 125

Query: 212 VMEEEKRQE 220
                +  +
Sbjct: 126 YKSALRFHK 134

>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 =  135 bits (342), Expect = 3e-39
 Identities = 36/112 (32%), Positives = 59/112 (52%), Gaps = 5/112 (4%)

Query: 98  GRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG 157
            R   +     + I  ++  H+ AWPF+ PV+++ +    Y +VI+KPMDFSTI+ K+  
Sbjct: 8   KRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREKLSS 65

Query: 158 KDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL 209
                Y N+     DVRLVF N   +N++  D+     ++ + FE+KW    
Sbjct: 66  GQ---YPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTF 114

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

 Score =  131 bits (330), Expect = 2e-37
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 10/130 (7%)

Query: 98  GRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG 157
           G  ++EL+     + +++   K    F  PV        DY EVI++PMD ST+  K+D 
Sbjct: 7   GNTLRELRLFLRDVTKRLATDKRFNIFSKPVS-------DYLEVIKEPMDLSTVITKIDK 59

Query: 158 KDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEK 217
            +   Y   ++   D+ L+  NA++YN ++D    + +      ++    ++   ++ E 
Sbjct: 60  HN---YLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEF 116

Query: 218 RQEEEEAKAQ 227
            +  EE K  
Sbjct: 117 NKLCEEIKES 126

>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 =  132 bits (334), Expect = 3e-37
 Identities = 35/135 (25%), Positives = 58/135 (42%), Gaps = 4/135 (2%)

Query: 76  KDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGL 135
            +               + E   +     KR+   +   +  H+ +  F  PV    L +
Sbjct: 54  PEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVP---LTV 110

Query: 136 HDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAK 195
            DYY++I+ PMD STIK ++  +D + Y    +  AD RL+F+N  ++N+   +V     
Sbjct: 111 PDYYKIIKNPMDLSTIKKRLQ-EDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGI 169

Query: 196 SLLEKFEEKWLQLLP 210
            L   FEE    L P
Sbjct: 170 KLENYFEELLKNLYP 184

>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 =  122 bits (308), Expect = 3e-34
 Identities = 34/115 (29%), Positives = 54/115 (46%), Gaps = 5/115 (4%)

Query: 94  EEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKN 153
             A   +          I  ++  H  AWPF+ PV+ E +   DYY+ I++PMD ST++ 
Sbjct: 4   NIAQRPKRGPHDAAIQNILTELQNHAAAWPFLQPVNKEEV--PDYYDFIKEPMDLSTMEI 61

Query: 154 KMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           K++      Y+ + +   D RLVF N   YN E    +  A  L + F  K  ++
Sbjct: 62  KLESNK---YQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 113

>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 =  121 bits (306), Expect = 2e-33
 Identities = 33/124 (26%), Positives = 52/124 (41%), Gaps = 5/124 (4%)

Query: 85  KQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEK 144
            Q Q             ++       + R +  HK AWPF+ PVD       DYY VI++
Sbjct: 54  PQCQSTEDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDA--PDYYGVIKE 111

Query: 145 PMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 204
           PMD +T++ ++  +    Y  + E  AD+  +F N   YN      +  A+ L   F +K
Sbjct: 112 PMDLATMEERVQRRY---YEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 168

Query: 205 WLQL 208
               
Sbjct: 169 LKGF 172

>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 =  117 bits (296), Expect = 1e-32
 Identities = 36/118 (30%), Positives = 60/118 (50%), Gaps = 8/118 (6%)

Query: 93  REEAAGRRMQELKRQFAA---IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFS 149
           REE   + + EL   F A   +   +  HK +WPF+ PVD       +YY++I+ PMD S
Sbjct: 3   REEKKTKDLFELDDDFTAMYKVLDVVKAHKDSWPFLEPVDESYA--PNYYQIIKAPMDIS 60

Query: 150 TIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQ 207
           +++ K++G     Y    E   D++ +F+N  KYN E  +   M+ +L   F    ++
Sbjct: 61  SMEKKLNGGL---YCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 115

>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 =  117 bits (294), Expect = 3e-32
 Identities = 29/123 (23%), Positives = 53/123 (43%), Gaps = 5/123 (4%)

Query: 94  EEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKN 153
           + +A      +++      RQ+ +      F  PV         Y  +I+ PMDF T+K+
Sbjct: 4   KLSAENESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIA--PGYSMIIKHPMDFGTMKD 61

Query: 154 KMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVM 213
           K+   +   Y++V E  AD +L+  NAM YN      + +AK +L    +   +     +
Sbjct: 62  KIVANE---YKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLAL 118

Query: 214 EEE 216
           +  
Sbjct: 119 KRS 121

>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 =  117 bits (294), Expect = 3e-32
 Identities = 31/125 (24%), Positives = 61/125 (48%), Gaps = 5/125 (4%)

Query: 101 MQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 160
            +EL+     +  ++   K    F  PVD + +   DY  VI++PMD S++ +K+D    
Sbjct: 8   FRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEV--PDYVTVIKQPMDLSSVISKIDLHK- 64

Query: 161 TGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQE 220
             Y  V++   D+ L+  NA++YN +RD    + +       +    ++ + ++E+  Q 
Sbjct: 65  --YLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQL 122

Query: 221 EEEAK 225
            EE +
Sbjct: 123 CEEIQ 127

>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 =  115 bits (290), Expect = 9e-32
 Identities = 31/110 (28%), Positives = 46/110 (41%), Gaps = 5/110 (4%)

Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
               +L      +  QI  H  AWPFM PV        DYYEVI  P+D  T+  ++  +
Sbjct: 3   EDPDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEA--PDYYEVIRFPIDLKTMTERLRSR 60

Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
               Y   +   AD++ V  N  +YN    +    A +L + F  K  + 
Sbjct: 61  Y---YVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEG 107

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

 Score =  112 bits (281), Expect = 2e-30
 Identities = 31/124 (25%), Positives = 51/124 (41%), Gaps = 14/124 (11%)

Query: 100 RMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKD 159
               L+     + RQ+ +   +  F  PV         Y  +I+ PMDFST+K K+   D
Sbjct: 5   EQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIA--PGYSMIIKHPMDFSTMKEKIKNND 62

Query: 160 GTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQ 219
              Y+++ E+  + +L+  NAM YN      +  AK LL    +            ++R 
Sbjct: 63  ---YQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKIL---------SQERL 110

Query: 220 EEEE 223
           E   
Sbjct: 111 EHHH 114

>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 =  112 bits (281), Expect = 2e-30
 Identities = 26/115 (22%), Positives = 43/115 (37%), Gaps = 5/115 (4%)

Query: 102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGT 161
                       Q+ +      F  PV +  +   DY + I+KPMDF T+K  ++     
Sbjct: 6   SGFLILLRKTLEQLQEKDTGNIFSEPVPLSEV--PDYLDHIKKPMDFFTMKQNLEAYR-- 61

Query: 162 GYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE 216
            Y N  +   D  L+  N +KYN +    +  A  L E+      Q   +  +  
Sbjct: 62  -YLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMG 115

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

 Score =  111 bits (279), Expect = 5e-30
 Identities = 33/136 (24%), Positives = 58/136 (42%), Gaps = 8/136 (5%)

Query: 94  EEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKN 153
           + A   R+  L     ++  Q+     A  F  PV ++ +   DY + I+ PMDF+T++ 
Sbjct: 4   QVAMELRLTPLTVLLRSVLDQLQDKDPARIFAQPVSLKEV--PDYLDHIKHPMDFATMRK 61

Query: 154 KMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVM 213
           +++ +    Y+N+ E   D  L+  N MKYN      +  A  L ++      Q      
Sbjct: 62  RLEAQG---YKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARR--- 115

Query: 214 EEEKRQEEEEAKAQLD 229
           E +    EE +   L 
Sbjct: 116 EVDSIGLEEASGMHLP 131

>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 =  110 bits (277), Expect = 2e-29
 Identities = 29/123 (23%), Positives = 56/123 (45%), Gaps = 9/123 (7%)

Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           + +++     +WPF HPV+ + +   DYY+VI  PMD  TI+  +       Y++     
Sbjct: 38  VTQKMMAVPDSWPFHHPVNKKFV--PDYYKVIVNPMDLETIRKNISKHK---YQSRESFL 92

Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE----KRQEEEEAKA 226
            DV L+  N++KYN         A+ ++    +   +    + + E      +E    +A
Sbjct: 93  DDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEA 152

Query: 227 QLD 229
           +L+
Sbjct: 153 ELE 155

>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 =  111 bits (280), Expect = 1e-28
 Identities = 30/121 (24%), Positives = 56/121 (46%), Gaps = 9/121 (7%)

Query: 113 RQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 172
           +++     +WPF HPV+ + +   DYY+VI  PMD  TI+  +       Y++      D
Sbjct: 147 QKMMAVPDSWPFHHPVNKKFV--PDYYKVIVNPMDLETIRKNISKH---KYQSRESFLDD 201

Query: 173 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEK----RQEEEEAKAQL 228
           V L+  N++KYN         A+ ++    +   +    + + EK     +E    +A+L
Sbjct: 202 VNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAEL 261

Query: 229 D 229
           +
Sbjct: 262 E 262

>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 =  100 bits (249), Expect = 2e-24
 Identities = 29/123 (23%), Positives = 56/123 (45%), Gaps = 5/123 (4%)

Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
             M  L     +I   +      +PF  PV+ + +   DYY++I +PMD  T++  +  +
Sbjct: 10  DPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVV--KDYYKIITRPMDLQTLRENVRKR 67

Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKR 218
               Y +  E    + L+ KN+  YN  +  +  +++S+L+  +EK  +   K+   EK 
Sbjct: 68  L---YPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKA 124

Query: 219 QEE 221
              
Sbjct: 125 INP 127

>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 =  107 bits (270), Expect = 2e-28
 Identities = 31/135 (22%), Positives = 56/135 (41%), Gaps = 5/135 (3%)

Query: 93  REEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIK 152
           ++    +RM+ L           +  +    FM           DYY++I +PMD   I+
Sbjct: 21  KKNIRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSK--KDYPDYYKIILEPMDLKIIE 78

Query: 153 NKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV 212
           + +       Y     +  D++L+F+NA  YN+E   V+  A  L +  +EK  +L P  
Sbjct: 79  HNIRNDK---YAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKELGPLP 135

Query: 213 MEEEKRQEEEEAKAQ 227
            +++     E    Q
Sbjct: 136 DDDDMASPAENLYFQ 150

>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 =  112 bits (280), Expect = 2e-28
 Identities = 30/151 (19%), Positives = 60/151 (39%), Gaps = 5/151 (3%)

Query: 76  KDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGL 135
           K +       + + A +       ++         + +++     +WPF HPV+ + +  
Sbjct: 143 KLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFV-- 200

Query: 136 HDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAK 195
            DYY+VI  PMD  TI+  +       Y++      DV L+  N++KYN         A+
Sbjct: 201 PDYYKVIVNPMDLETIRKNISKH---KYQSRESFLDDVNLILANSVKYNGPESQYTKTAQ 257

Query: 196 SLLEKFEEKWLQLLPKVMEEEKRQEEEEAKA 226
            ++    +   +    + + EK     +  A
Sbjct: 258 EIVNVCYQTLTEYDEHLTQLEKDICTAKEAA 288

>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 =  100 bits (249), Expect = 4e-24
 Identities = 30/149 (20%), Positives = 61/149 (40%), Gaps = 5/149 (3%)

Query: 65  SKSISIAKEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPF 124
            K     K+K +       +   +            M  L     +I   +      +PF
Sbjct: 9   PKQQLPPKKKRRVGTTVHCDYLNRPHKSIHRRRTDPMVTLSSILESIINDMRDLPNTYPF 68

Query: 125 MHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN 184
             PV+ + +   DYY++I +PMD  T++  +  +    Y +  E    + L+ KN+  YN
Sbjct: 69  HTPVNAKVV--KDYYKIITRPMDLQTLRENVRKRL---YPSREEFREHLELIVKNSATYN 123

Query: 185 DERDDVHVMAKSLLEKFEEKWLQLLPKVM 213
             +  +  +++S+L+  +EK  +   K+ 
Sbjct: 124 GPKHSLTQISQSMLDLCDEKLKEKEDKLA 152

>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 (260), Expect = 2e-27
 Identities = 26/117 (22%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 98  GRRMQELKRQFAAIFRQITQHKW------AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTI 151
           G     LK     +   I           +  F            DYY +I++P+D  TI
Sbjct: 3   GSSPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQY--PDYYAIIKEPIDLKTI 60

Query: 152 KNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
             ++       Y+++  +  D+ L+ KNA  YN+    V   A S+ + F  K  ++
Sbjct: 61  AQRIQNGS---YKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEI 114

>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 =  108 bits (271), Expect = 4e-27
 Identities = 33/158 (20%), Positives = 62/158 (39%), Gaps = 8/158 (5%)

Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
           +++ +     ++      + K + PFM  VD + L   +YYE++  PM  S +K  ++  
Sbjct: 159 KKINQALLGASSPKNLDDKVKLSEPFMELVDKDEL--PEYYEIVHSPMALSIVKQNLEIG 216

Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVME---E 215
               Y  + +   D+ LVF+NA  +ND    ++  A +L   F     +     ++   E
Sbjct: 217 Q---YSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNE 273

Query: 216 EKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVD 253
                 E  K + +  L         A  L     + D
Sbjct: 274 RGEINLEFDKFEFENYLAIGGGGPAAAGALAISALDND 311

>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 = 80.9 bits (199), Expect = 2e-17
 Identities = 24/159 (15%), Positives = 45/159 (28%), Gaps = 10/159 (6%)

Query: 99  RRMQELKRQFAAIFRQITQH--KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 156
             + +  R  +     +          F+     +      YY  I++PM  + IK++  
Sbjct: 24  WHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFH--PQYYYKIQQPMSINEIKSRDY 81

Query: 157 GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE 216
                          DV L+ KN   YN+    +   +  ++   E + L+         
Sbjct: 82  EY----EDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYL 137

Query: 217 KRQEEEEAKAQLDMQLT--QEAVQTNKAKELRSELNEVD 253
              E +        +L    E           S  N  D
Sbjct: 138 INSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDD 176

>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 =  106 bits (264), Expect = 4e-27
 Identities = 35/156 (22%), Positives = 64/156 (41%), Gaps = 20/156 (12%)

Query: 72  KEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVE 131
             +   +     +        + + A       +R+   +   +  H+ +  F  PV   
Sbjct: 50  FCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVP-- 107

Query: 132 GLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVH 191
              + +YY++I+KPMD ST+K K+  K    Y+   +  ADVRL+FKN  ++N+    V 
Sbjct: 108 -ASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQ 166

Query: 192 VMA-----------------KSLLEKFEEKWLQLLP 210
           V A                 K++   FE+K  ++  
Sbjct: 167 VYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYS 202

>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 =  101 bits (253), Expect = 3e-26
 Identities = 29/133 (21%), Positives = 58/133 (43%), Gaps = 10/133 (7%)

Query: 92  HREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTI 151
                  ++M+++           +  + +  F+     + L   +YYE+I KP+DF  I
Sbjct: 7   PNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKEL--PEYYELIRKPVDFKKI 64

Query: 152 KNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 211
           K ++       YR++ ++  DV L+ +NA  +N E   ++  +  L   F         +
Sbjct: 65  KERIRNHK---YRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVR-----Q 116

Query: 212 VMEEEKRQEEEEA 224
            +E+E   E EE+
Sbjct: 117 KIEKEDDSEGEES 129

>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 =  106 bits (264), Expect = 8e-26
 Identities = 27/129 (20%), Positives = 56/129 (43%), Gaps = 5/129 (3%)

Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
           +++ +     ++      + K + PFM  VD + L   +YYE++  PM  S +K  ++  
Sbjct: 209 KKINQALLGASSPKNLDDKVKLSEPFMELVDKDEL--PEYYEIVHSPMALSIVKQNLEIG 266

Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKR 218
               Y  + +   D+ LVF+NA  +ND    ++  A +L   F     +     +++   
Sbjct: 267 Q---YSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNE 323

Query: 219 QEEEEAKAQ 227
           + E   +  
Sbjct: 324 RGEINLEFD 332

>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 = 79.5 bits (195), Expect = 1e-16
 Identities = 26/186 (13%), Positives = 51/186 (27%), Gaps = 10/186 (5%)

Query: 72  KEKLKDRHVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHK--WAWPFMHPVD 129
             K +++          +           + +  R  +     +          F+    
Sbjct: 47  HPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPS 106

Query: 130 VEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDD 189
            +      YY  I++PM  + IK++    D            DV L+ KN   YN+    
Sbjct: 107 RKFH--PQYYYKIQQPMSINEIKSR----DYEYEDGPSNFLLDVELLTKNCQAYNEYDSL 160

Query: 190 VHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLT--QEAVQTNKAKELRS 247
           +   +  ++   E + L+            E +        +L    E           S
Sbjct: 161 IVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASS 220

Query: 248 ELNEVD 253
             N  D
Sbjct: 221 PKNLDD 226

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

 Score = 99.7 bits (249), Expect = 1e-25
 Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 11/122 (9%)

Query: 93  REEAAGRRMQELKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPM 146
              +      +L +Q  AI   +  +K       +  F+     + L   +YYE+I KP+
Sbjct: 3   SGSSGSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKEL--PEYYELIRKPV 60

Query: 147 DFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWL 206
           DF  IK ++       YR++ ++  DV L+  NA  +N E   ++  +  L   F+    
Sbjct: 61  DFKKIKERIRNH---KYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQ 117

Query: 207 QL 208
             
Sbjct: 118 SG 119

>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 = 99.7 bits (249), Expect = 1e-25
 Identities = 30/123 (24%), Positives = 48/123 (39%), Gaps = 11/123 (8%)

Query: 100 RMQELKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKN 153
           R   L + F  I   I  +K       A P ++    +     DYYE I  P+D  TI+ 
Sbjct: 6   RAARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKKN--ADYYEKISDPLDLITIEK 63

Query: 154 KMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVM 213
           ++       Y+ V    AD+  VF+NA KY   +  V      L + +     +   ++ 
Sbjct: 64  QILTGY---YKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQID 120

Query: 214 EEE 216
           E  
Sbjct: 121 EIV 123

>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 = 98.6 bits (246), Expect = 3e-25
 Identities = 25/126 (19%), Positives = 49/126 (38%), Gaps = 11/126 (8%)

Query: 92  HREEAAGRRMQELKRQFAAIFRQITQ------HKWAWPFMHPVDVEGLGLHDYYEVIEKP 145
           H         + L  Q   ++  +           A PF H    +     DYY+ I+ P
Sbjct: 6   HHSSGVDLGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKY--PDYYQQIKMP 63

Query: 146 MDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
           +    I+ K+  ++   Y  +  +  D+ L+F+NA +YN     ++     L +  + K 
Sbjct: 64  ISLQQIRTKLKNQE---YETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKK 120

Query: 206 LQLLPK 211
            +L  +
Sbjct: 121 KELARR 126

>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 = 96.2 bits (240), Expect = 1e-24
 Identities = 24/115 (20%), Positives = 45/115 (39%), Gaps = 11/115 (9%)

Query: 103 ELKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 156
           +       ++  I  +K          F+           DYYEV+ +P+D   I+ K+ 
Sbjct: 5   DPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQ--PDYYEVVSQPIDLMKIQQKLK 62

Query: 157 GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 211
            ++   Y +V  + AD +L+F NA  Y       +  A  L + +     + + K
Sbjct: 63  MEE---YDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQK 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 = 95.5 bits (238), Expect = 3e-24
 Identities = 24/117 (20%), Positives = 48/117 (41%), Gaps = 11/117 (9%)

Query: 98  GRRMQELKRQFAAIFRQI------TQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTI 151
            + M  ++++   ++  +         + +  F+       L   DYY  I+KPMD   I
Sbjct: 10  SKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSEL--PDYYLTIKKPMDMEKI 67

Query: 152 KNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
           ++ M       Y+++  +  D  ++F NA  YN+    ++  A  L +   E    L
Sbjct: 68  RSHMMANK---YQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 121

>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 = 86.8 bits (214), Expect = 3e-20
 Identities = 20/135 (14%), Positives = 40/135 (29%), Gaps = 5/135 (3%)

Query: 86  QQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKP 145
              D         +     +R+   +   +  H+   P                +     
Sbjct: 59  LSLDGADSTGVVAKLSPANQRKCERVLLALFCHEPCRPLHQLATDS----TFSLDQPGGT 114

Query: 146 MDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
           +D + I+ ++  K    Y + +E   DV  +FK   K  +++ DV      L   FE + 
Sbjct: 115 LDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLTEDKADVQ-SIIGLQRFFETRM 173

Query: 206 LQLLPKVMEEEKRQE 220
            +            E
Sbjct: 174 NEAFGDTKFSAVLVE 188

>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 = 73.8 bits (181), Expect = 5e-16
 Identities = 18/149 (12%), Positives = 44/149 (29%), Gaps = 18/149 (12%)

Query: 102 QELKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKM 155
             ++     +F  +  H+      ++               D     + P+ F  I+  +
Sbjct: 6   LLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPA------VDPNFPNKPPLTFDIIRKNV 59

Query: 156 DGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEE 215
           +      YR +      +  V + A + N    +++  A  L + F +   +L       
Sbjct: 60  ENNR---YRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCK---NG 113

Query: 216 EKRQEEEEAKAQLDMQLTQEAVQTNKAKE 244
           E       +     +    E  +  K  +
Sbjct: 114 EILLSPALSYTTKHLHNDVEKERKEKLPK 142

>2jns_A Bromodomain-containing protein 4; ET-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 90

 Score = 65.0 bits (158), Expect = 2e-13
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 266 KCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQ-EVDLDMDAQSELTLW 324
           KC+ MS EEK+ L   + +L  E L + + I+    PS   +   E+++D +     TL 
Sbjct: 14  KCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLR 73

Query: 325 RLKVFVQESLKAASR 339
            L+ +V   L+   +
Sbjct: 74  ELERYVTSCLRKKRK 88

>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 = 55.8 bits (133), Expect = 2e-09
 Identities = 15/112 (13%), Positives = 39/112 (34%), Gaps = 16/112 (14%)

Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
              +EL+     +   +   +     +                 ++P+D   +K KMD  
Sbjct: 71  ALEKELQISLKQVLTALLNSRTTSHLLRYRQ-------------QQPLDLEGVKRKMDQG 117

Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP 210
           +   Y +V E   D+  + + A+  +  + ++      +   F  +  ++ P
Sbjct: 118 N---YTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFP 166

>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 = 45.6 bits (107), Expect = 2e-05
 Identities = 31/161 (19%), Positives = 57/161 (35%), Gaps = 33/161 (20%)

Query: 146 MDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
           MDF T   +   +           Y D+  VF++A   N +  DV  M KS+L K E   
Sbjct: 7   MDFET--GEHQYQ-----------YKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDH 53

Query: 206 LQLLPKVMEEEKR-------QEEEEAKA------QLDMQLTQEAVQT-NKAKELRSELNE 251
           + +    +    R       ++EE  +       +++ +     ++T  +   + + +  
Sbjct: 54  IIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI 113

Query: 252 VDMQLENLRETVIQKCRKMS---TEEKKNLGTALTRLSPED 289
              Q + L     Q   K +    +    L  AL  L P  
Sbjct: 114 --EQRDRLYNDN-QVFAKYNVSRLQPYLKLRQALLELRPAK 151

>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 = 44.8 bits (105), Expect = 4e-05
 Identities = 53/395 (13%), Positives = 110/395 (27%), Gaps = 135/395 (34%)

Query: 18  KAEGDTVEVEGLNKTI------DDILQKVTQLEQKL-----------NDVEQF------- 53
               D  +V+ + K+I      D I+     +   L             V++F       
Sbjct: 30  VDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRI 89

Query: 54  -Y------LTKDNNQPNTSKSISIAK--------EKLKDRHVASIEKQQQDAFHREEAAG 98
            Y      +  +  QP+    + I +        +     +V+ ++              
Sbjct: 90  NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP------------- 136

Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLG------LHDYYEVIEKPMDFSTIK 152
               +L++       ++   K        V ++G+       +      ++  + +  ++
Sbjct: 137 --YLKLRQA----LLELRPAKN-------VLIDGVLGSGKTWV-----ALDVCLSYK-VQ 177

Query: 153 NKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV 212
            KMD K                 +F   +K  +  + V  M + LL + +  W       
Sbjct: 178 CKMDFK-----------------IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS-RSDH 219

Query: 213 MEEEKRQEEEEAKAQLDMQLTQEA----------VQTNKA--------KEL---RSELNE 251
                +      +A+L   L  +           VQ  KA        K L   R +   
Sbjct: 220 SSNI-KLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVT 278

Query: 252 VDMQLENLRETVIQKCRKMSTEEK------KNLGTALTRLSPEDLCK----ALEIVAENN 301
             +         +       T ++      K L      L P ++       L I+AE+ 
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL-PREVLTTNPRRLSIIAESI 337

Query: 302 PSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKA 336
               AT             +   +L   ++ SL  
Sbjct: 338 RDGLATWDNWK-------HVNCDKLTTIIESSLNV 365

>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 = 43.7 bits (102), Expect = 1e-04
 Identities = 53/412 (12%), Positives = 114/412 (27%), Gaps = 117/412 (28%)

Query: 14  VGLGKAEGDTVEVEGLNKTIDDILQKVTQL-------EQKLNDVEQF--YLTKDNNQPN- 63
           + L         +E L K +  I    T         + +++ ++     L K     N 
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246

Query: 64  ------------------------TSKSISIAK--EKLKDRHVASIEKQQQDAFHREEA- 96
                                   T++   +          H++            +E  
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH--HSMTLTPDEVK 304

Query: 97  ------AGRRMQELKRQ-----------FAAIFRQITQHKWAWPFMHPVDVEGLGLHDYY 139
                    R Q+L R+            A   R        W              D +
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT---W--------------DNW 347

Query: 140 EVIEKPMDFSTIKNKMDGKDGTGYR-----------NVREIYADVRLVFKNAMKYNDERD 188
           + +      + I++ ++  +   YR           +   I   +  +    +  +D   
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH-IPTILLSLIWFDVIKSDVMV 406

Query: 189 DVHVMA-KSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRS 247
            V+ +   SL+EK  ++    +P +  E K + E E    L   +  +     K  +   
Sbjct: 407 VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE--YALHRSIV-DHYNIPKTFDSDD 463

Query: 248 EL-NEVDM--------QLENLRETVIQKCRKMST--------EEK-KNLGTALTRLSP-- 287
            +   +D          L+N+     ++              E+K ++  TA        
Sbjct: 464 LIPPYLDQYFYSHIGHHLKNIEHP--ERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSIL 521

Query: 288 ---EDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKV--FVQESL 334
              + L      + +N+P +      + LD   + E  L   K    ++ +L
Sbjct: 522 NTLQQLKFYKPYICDNDPKYERLVNAI-LDFLPKIEENLICSKYTDLLRIAL 572

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	395
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.96
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.96
3d7c_A	112	General control of amino acid synthesis protein 5;	99.95
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.95
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.95
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.95
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.95
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.95
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.95
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.95
2dat_A	123	Possible global transcription activator SNF2L2; br	99.95
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.95
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.95
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.95
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.95
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.95
2grc_A	129	Probable global transcription activator SNF2L4; br	99.94
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.94
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.94
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.94
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.94
3uv4_A	158	Second bromodomain of human transcription initiat	99.93
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.93
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.92
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.92
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.92
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.91
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.9
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.9
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.9
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.9
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.89
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.89
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.89
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.86
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.81
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.81
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.75
2jns_A	90	Bromodomain-containing protein 4; ET-domain, struc	99.7
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.56
2lm0_A	125	AF4/FMR2 family member 1/protein AF-9 chimera; int	96.03

>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=2.7e-29  Score=217.13  Aligned_cols=111  Identities=41%  Similarity=0.775  Sum_probs=102.6

Q ss_pred             hhccHHHHHHHHHHHHHHHHcCCC---CCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHH
Q 016116           97 AGRRMQELKRQFAAIFRQITQHKW---AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADV  173 (395)
Q Consensus        97 ~~~~~~~l~~~~~~il~~l~~~~~---a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv  173 (395)
                      ...++.+.++.|..||..|++++.   +|||+.||++..+++||||++|++||||+||++||.++.   |.++.+|.+||
T Consensus        16 k~~~~~~~l~~c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~Dv   92 (130)
T 2ouo_A           16 KSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGADV   92 (130)
T ss_dssp             ---CHHHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHH
T ss_pred             CCcccHHHHHHHHHHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCC---CCCHHHHHHHH
Confidence            345677788999999999999874   899999999987789999999999999999999999999   99999999999


Q ss_pred             hchhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          174 RLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       174 ~LIf~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      +|||.||++||+++|.||.+|..|+..|+++|.++..
T Consensus        93 ~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  129 (130)
T 2ouo_A           93 RLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD  129 (130)
T ss_dssp             HHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            9999999999999999999999999999999998753

>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=99.96  E-value=4e-29  Score=212.13  Aligned_cols=102  Identities=34%  Similarity=0.655  Sum_probs=98.7

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      ..++.|..||..|++|+.+|||..||++..  +||||++|++||||+||++||.++.   |.++++|.+||+|||.||+.
T Consensus        13 ~~~~~c~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na~~   87 (117)
T 3g0l_A           13 KDLALCSMILTEMETHEDAWPFLLPVNLKL--VPGYKKVIKKPMDFSTIREKLSSGQ---YPNLETFALDVRLVFDNCET   87 (117)
T ss_dssp             THHHHHHHHHHHHHTSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCcCChhh--cCChHHHcCCCCCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHHHH
Confidence            466889999999999999999999999988  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      ||+++|.+|.+|..|++.|++.|.+++
T Consensus        88 yN~~~s~~~~~A~~L~~~f~~~~~~~~  114 (117)
T 3g0l_A           88 FNEDDSDIGRAGHNMRKYFEKKWTDTF  114 (117)
T ss_dssp             HSCSSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999998875

>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=99.95  E-value=1.3e-28  Score=207.39  Aligned_cols=104  Identities=30%  Similarity=0.452  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhh
Q 016116          101 MQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  180 (395)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na  180 (395)
                      ...|...|..|+..|++|+.++||..||++..  +||||++|++||||+||++||+++.   |.++.+|.+||+|||.||
T Consensus         5 ~~~l~~~~~~il~~l~~~~~~~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~Dv~li~~Na   79 (112)
T 3d7c_A            5 PDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSE--APDYYEVIRFPIDLKTMTERLRSRY---YVTRKLFVADLQRVIANC   79 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCchhhcCCCCccc--ccCHHHHccCCcCHHHHHHHHcCCC---CcCHHHHHHHHHHHHHHH
Confidence            45688999999999999999999999999987  9999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          181 MKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       181 ~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      ++||+++|.+|.+|..|+..|++.|+++.
T Consensus        80 ~~yN~~~s~~~~~A~~L~~~f~~~~~~~~  108 (112)
T 3d7c_A           80 REYNPPDSEYCRCASALEKFFYFKLKEGG  108 (112)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            99999999999999999999999998864

>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=3.1e-29  Score=213.65  Aligned_cols=109  Identities=42%  Similarity=0.792  Sum_probs=103.5

Q ss_pred             ccHHHHHHHHHHHHHHHHcCCC---CCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhc
Q 016116           99 RRMQELKRQFAAIFRQITQHKW---AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRL  175 (395)
Q Consensus        99 ~~~~~l~~~~~~il~~l~~~~~---a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~L  175 (395)
                      ..+.+.++.|..||..|.+++.   +|||..||++..+++||||++|++||||+||++||.++.   |.++++|.+||+|
T Consensus         5 ~~~~~~l~~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~l   81 (120)
T 3jvl_A            5 SKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESRE---YRDAQEFGADVRL   81 (120)
T ss_dssp             CSSCHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCC---CCCHHHHHHHHHH
Confidence            4556788999999999999886   999999999998889999999999999999999999999   9999999999999


Q ss_pred             hhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          176 VFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       176 If~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      ||.||++||+++|.+|.+|..|+..|++.|.++..
T Consensus        82 i~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~p~  116 (120)
T 3jvl_A           82 MFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD  116 (120)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCcC
Confidence            99999999999999999999999999999988864

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

Probab=99.95  E-value=8.8e-29  Score=215.08  Aligned_cols=108  Identities=31%  Similarity=0.541  Sum_probs=102.3

Q ss_pred             cHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          100 RMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       100 ~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      .+..|.+.|..||..|.+|+.+++|..||++..  +||||++|++||||+||+.||.++.   |.++++|.+||+|||.|
T Consensus        18 ~~~~l~~~~~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~iI~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~li~~N   92 (135)
T 3mb3_A           18 DIQAWKKQCEELLNLIFQCEDSEPFRQPVDLLE--YPDYRDIIDTPMDFATVRETLEAGN---YESPMELCKDVRLIFSN   92 (135)
T ss_dssp             CSSTHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhCCCChhhcCCCChhh--CCCHHHHhCCCcCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHH
Confidence            445688999999999999999999999999977  9999999999999999999999999   99999999999999999


Q ss_pred             hcccCCC-CCHHHHHHHHHHHHHHHHHHhhCcCc
Q 016116          180 AMKYNDE-RDDVHVMAKSLLEKFEEKWLQLLPKV  212 (395)
Q Consensus       180 a~~YN~~-~S~v~~~A~~L~~~Fe~~~~~~~~~~  212 (395)
                      |+.||++ +|.||.+|..|++.|++.|..+++.+
T Consensus        93 a~~yN~~~~s~i~~~A~~L~~~f~~~~~~~~~~~  126 (135)
T 3mb3_A           93 SKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSDY  126 (135)
T ss_dssp             HHHHSCCTTCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999998 99999999999999999999886643

>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=99.95  E-value=2.3e-28  Score=210.45  Aligned_cols=105  Identities=35%  Similarity=0.666  Sum_probs=98.8

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      ++...|..||..|++|+.+|+|..||++..+++||||++|++||||+||++||+++.   |.++++|.+||+|||.||++
T Consensus        21 ~l~~~~~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~li~~Na~~   97 (127)
T 2oss_A           21 QLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNY---YWNAQECIQDFNTMFTNCYI   97 (127)
T ss_dssp             HHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCccchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            455677889999999999999999999875669999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      ||+++|.+|.+|..|++.|+++|+++..
T Consensus        98 yN~~~s~i~~~A~~L~~~f~~~~~~lp~  125 (127)
T 2oss_A           98 YNKPGDDIVLMAEALEKLFLQKINELPT  125 (127)
T ss_dssp             HSCTTCHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            9999999999999999999999988754

>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=99.95  E-value=2.5e-28  Score=206.90  Aligned_cols=101  Identities=29%  Similarity=0.572  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      .++.+.|..||..|++|+.++||..||++..  +||||++|++||||+||++||+++.   |.++++|.+||+|||.||+
T Consensus        15 ~~~~~~~~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na~   89 (116)
T 3nxb_A           15 DDDFTAMYKVLDVVKAHKDSWPFLEPVDESY--APNYYQIIKAPMDISSMEKKLNGGL---YCTKEEFVNDMKTMFRNCR   89 (116)
T ss_dssp             CCHHHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCcHhhcCcCChhh--ccChHHHcCCCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHHH
Confidence            3478899999999999999999999999987  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHh
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKWLQ  207 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~~~  207 (395)
                      .||+++|.+|.+|..|+..|++.|.+
T Consensus        90 ~yN~~~s~~~~~A~~L~~~f~~~~~k  115 (116)
T 3nxb_A           90 KYNGESSEYTKMSDNLERCFHRAMMK  115 (116)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999999864

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

Probab=99.95  E-value=2.7e-28  Score=208.83  Aligned_cols=105  Identities=32%  Similarity=0.546  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      .|.++|..||..|++|+.+++|..||++..  +||||++|++||||+||++||.++.   |.++.+|..||+|||.||+.
T Consensus        10 ~~~~~c~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na~~   84 (123)
T 3q2e_A           10 NWKKQCKELVNLIFQCEDSEPFRQPVDLVE--YPDYRDIIDTPMDFGTVRETLDAGN---YDSPLEFCKDIRLIFSNAKA   84 (123)
T ss_dssp             CHHHHHHHHHHHHHTSGGGGGGSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCcHhhcCCCChhh--cCCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            588899999999999999999999999987  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCC-CCHHHHHHHHHHHHHHHHHHhhCcCc
Q 016116          183 YNDE-RDDVHVMAKSLLEKFEEKWLQLLPKV  212 (395)
Q Consensus       183 YN~~-~S~v~~~A~~L~~~Fe~~~~~~~~~~  212 (395)
                      ||++ +|.||.+|..|+..|+++|..+++.+
T Consensus        85 yN~~~~s~i~~~A~~L~~~f~~~~~~~~~~~  115 (123)
T 3q2e_A           85 YTPNKRSKIYSMTLRLSALFEEKMKKISSDF  115 (123)
T ss_dssp             HSCCTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9996 99999999999999999999987654

>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=99.95  E-value=2.4e-28  Score=208.69  Aligned_cols=101  Identities=33%  Similarity=0.617  Sum_probs=97.3

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          104 LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      .+..|..||..|++|+.++||..||++..  +||||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.|
T Consensus        14 ~~~~~~~il~~l~~~~~a~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~~y   88 (121)
T 1e6i_A           14 HDAAIQNILTELQNHAAAWPFLQPVNKEE--VPDYYDFIKEPMDLSTMEIKLESNK---YQKMEDFIYDARLVFNNCRMY   88 (121)
T ss_dssp             THHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCchhhCCCCChhh--CcCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            45789999999999999999999999987  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          184 NDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      |+++|.+|.+|..|++.|+++|..+.
T Consensus        89 N~~~s~i~~~A~~L~~~f~~~~~~~p  114 (121)
T 1e6i_A           89 NGENTSYYKYANRLEKFFNNKVKEIP  114 (121)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHTSG
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            99999999999999999999998873

>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=99.95  E-value=5.8e-28  Score=205.51  Aligned_cols=106  Identities=32%  Similarity=0.564  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHHHHHHc-CCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          101 MQELKRQFAAIFRQITQ-HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       101 ~~~l~~~~~~il~~l~~-~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      ..++.+.|..+|..|.+ ++.+|||..||++..+++||||++|++||||+||++||+++.   |.++.+|.+||+|||.|
T Consensus         9 ~~el~~~l~~~l~~l~~~~~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~li~~N   85 (119)
T 3p1f_A            9 PEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQ---YQEPWQYVDDVWLMFNN   85 (119)
T ss_dssp             HHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHH
Confidence            45788899999999988 789999999999986669999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      |+.||+++|.+|.+|..|++.|++.|..++
T Consensus        86 a~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  115 (119)
T 3p1f_A           86 AWLYNRKTSRVYKFCSKLAEVFEQEIDPVM  115 (119)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999998764

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

Probab=99.95  E-value=5.8e-28  Score=206.82  Aligned_cols=104  Identities=27%  Similarity=0.415  Sum_probs=98.7

Q ss_pred             HHHHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhc
Q 016116          102 QELKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRL  175 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~L  175 (395)
                      ..+.+.|..||+.|++++      .+++|+.||+...  +||||++|++||||+||++||+++.   |.++++|.+||+|
T Consensus        12 ~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~l   86 (123)
T 2dat_A           12 PKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKE--LPEYYELIRKPVDFKKIKERIRNHK---YRSLGDLEKDVML   86 (123)
T ss_dssp             HHHHHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCTTT--SCHHHHHCSSCCCHHHHHHHHTTTC---CCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhcccCCeeeHHhcCCCCccc--CCCHHHHcCCCCCHHHHHHHHhCCC---CCCHHHHHHHHHH
Confidence            357889999999999986      6999999999887  9999999999999999999999999   9999999999999


Q ss_pred             hhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          176 VFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       176 If~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      ||.||++||+++|.+|.+|..|++.|++.|+++++
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            99999999999999999999999999999998764

>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=99.95  E-value=4.8e-28  Score=215.06  Aligned_cols=108  Identities=32%  Similarity=0.611  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      ..+...|..||..|++++.+|||+.||++..+++||||++|++||||+||++||+++.   |.++++|.+||+|||.||+
T Consensus        31 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~---Y~s~~ef~~Dv~Lif~Na~  107 (154)
T 4alg_A           31 NQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNY---YWAASECMQDFNTMFTNCY  107 (154)
T ss_dssp             HHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCcCchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHH
Confidence            3455677889999999999999999999987779999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKWLQLLPKV  212 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~  212 (395)
                      +||+++|.||.+|..|+++|++.|.++.+..
T Consensus       108 ~YN~~~s~i~~~A~~L~~~f~~~~~~l~~~~  138 (154)
T 4alg_A          108 IYNKPTDDIVLMAQTLEKIFLQKVASMPQEE  138 (154)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHTTSCSSC
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHCCchh
Confidence            9999999999999999999999999886543

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

Probab=99.95  E-value=9.1e-28  Score=203.91  Aligned_cols=106  Identities=28%  Similarity=0.354  Sum_probs=100.3

Q ss_pred             cHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          100 RMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       100 ~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      ....+...|..||+.|++++.+++|..||++..  +||||++|++||||+||++||.++.   |.++++|.+||+|||.|
T Consensus         5 ~~~~l~~~l~~il~~L~~~~~~~~F~~PVd~~~--~pdY~~iIk~PMDL~tI~~kl~~~~---Y~s~~ef~~Dv~Li~~N   79 (117)
T 2i7k_A            5 EQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFI--APGYSMIIKHPMDFSTMKEKIKNND---YQSIEELKDNFKLMCTN   79 (117)
T ss_dssp             THHHHHHHHHHHHHHHHTSSGGGTSSSCCCTTT--SSSHHHHCSCCCCHHHHHHHHTTTS---CCSHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHhCcccHHhcCCCCccc--cCCHHHHhCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHHHHHH
Confidence            345678899999999999999999999999876  9999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      |+.||+++|.+|.+|..|++.|++.|..+.-
T Consensus        80 a~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  110 (117)
T 2i7k_A           80 AMIYNKPETIYYKAAKKLLHSGMKILSQERL  110 (117)
T ss_dssp             HHHTSCSSSSHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999987653

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

Probab=99.95  E-value=6.3e-28  Score=216.79  Aligned_cols=108  Identities=25%  Similarity=0.385  Sum_probs=98.7

Q ss_pred             ccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhh
Q 016116           99 RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  178 (395)
Q Consensus        99 ~~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~  178 (395)
                      ....+|...|..||..|++++.++||..||++..+++||||++|++||||+||++||.++.   |.++.+|.+||+|||.
T Consensus        17 p~~~~~~~~~~~il~~L~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~---Y~s~~ef~~Dv~Lif~   93 (166)
T 3fkm_X           17 QGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQ---YAYPSEFVKDVQLIFD   93 (166)
T ss_dssp             CTTHHHHHHHHHHHHHHTTSTTGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTC---CCSHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhCCCChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHH
Confidence            3445788999999999999999999999999886679999999999999999999999999   9999999999999999


Q ss_pred             hhcccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          179 NAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       179 Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      ||++||+++|.||.+|..|+++|++.|.++.
T Consensus        94 Na~~yN~~~s~i~~~A~~L~~~f~~~l~~~~  124 (166)
T 3fkm_X           94 NCSLYNTSNSVVAITGKNIETYFNNQLIVMG  124 (166)
T ss_dssp             HHHHSSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            9999999999999999999999999998874

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

Probab=99.95  E-value=1.1e-27  Score=204.65  Aligned_cols=101  Identities=26%  Similarity=0.350  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      .+...|..||..|++|+.+++|..||++..  +||||++|++||||+||++||.++.   |.++.+|.+||+|||.||+.
T Consensus         7 pl~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~li~~Na~~   81 (121)
T 2d9e_A            7 GFLILLRKTLEQLQEKDTGNIFSEPVPLSE--VPDYLDHIKKPMDFFTMKQNLEAYR---YLNFDDFEEDFNLIVSNCLK   81 (121)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCSSSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCccHhhCCcCCccc--cCCHHHHcCCCcCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            466789999999999999999999999987  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      ||+++|.+|.+|..|++.|+..|.++
T Consensus        82 yN~~~s~~~~~A~~L~~~~~~~l~~~  107 (121)
T 2d9e_A           82 YNAKDTIFYRAAVRLREQGGAVLRQA  107 (121)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999765

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

Probab=99.95  E-value=1.1e-27  Score=208.19  Aligned_cols=105  Identities=30%  Similarity=0.518  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhC--CCCCCCCCHHHHHHHHhchhhhh
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG--KDGTGYRNVREIYADVRLVFKNA  180 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~--~~~~~Y~s~~ef~~Dv~LIf~Na  180 (395)
                      ..++.|..||..|++|+.+++|..||+. .  +||||++|++||||+||++||++  +.   |.++++|.+||+|||.||
T Consensus        20 ~~~~~c~~il~~L~~~~~s~~F~~Pv~~-~--~pdY~~iIk~PmDL~tI~~kL~~~~~~---Y~s~~ef~~Dv~Lif~Na   93 (135)
T 2yyn_A           20 IDKRKCERLLLFLYCHEMSLAFQDPVPL-T--VPDYYKIIKNPMDLSTIKKRLQEDYSM---YSKPEDFVADFRLIFQNC   93 (135)
T ss_dssp             HHHHHHHHHHHHHHTSGGGGGGSSCCCT-T--STTHHHHCSSCCCHHHHHHHHHSSSCC---CSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCccchhhcCCCcc-c--CCCHHHHcCCCCCHHHHHHHHhccccC---CCCHHHHHHHHHHHHHHH
Confidence            3557899999999999999999999997 3  99999999999999999999998  47   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhhCcCch
Q 016116          181 MKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVM  213 (395)
Q Consensus       181 ~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~~  213 (395)
                      ++||+++|.||.+|..|+..|++.|.++++...
T Consensus        94 ~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~  126 (135)
T 2yyn_A           94 AEFNEPDSEVANAGIKLENYFEELLKNLYPEKR  126 (135)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHhccccC
Confidence            999999999999999999999999999988654

>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=99.94  E-value=1.5e-27  Score=205.85  Aligned_cols=105  Identities=25%  Similarity=0.394  Sum_probs=98.8

Q ss_pred             HHHHHHHHHHHHHHHHcCC-------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHH
Q 016116          101 MQELKRQFAAIFRQITQHK-------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADV  173 (395)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~-------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv  173 (395)
                      ...+.+.|..||+.|++++       .+++|+.||+...  +||||++|++||||+||++||.++.   |.++.+|.+||
T Consensus         9 ~~~l~~~~~~il~~l~~~~d~~~~~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~Dv   83 (129)
T 2grc_A            9 PPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKE--LPEYYELIRKPVDFKKIKERIRNHK---YRSLNDLEKDV   83 (129)
T ss_dssp             CHHHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHhcccccccCeeeHHhcCCCCccc--CCCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHH
Confidence            3468889999999999875       5899999999877  9999999999999999999999999   99999999999


Q ss_pred             hchhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          174 RLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       174 ~LIf~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      +|||.||++||+++|.+|.+|..|+..|++.|..+..
T Consensus        84 ~Li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~  120 (129)
T 2grc_A           84 MLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEK  120 (129)
T ss_dssp             HHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccC
Confidence            9999999999999999999999999999999988743

>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=99.94  E-value=1.5e-27  Score=204.51  Aligned_cols=103  Identities=22%  Similarity=0.410  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHHHHc------CCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhc
Q 016116          102 QELKRQFAAIFRQITQ------HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRL  175 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~------~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~L  175 (395)
                      ..+.+.|..|++.|..      |+.+++|..||+...  +||||++|++||||+||++||.++.   |.++.+|.+||+|
T Consensus        14 ~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~l   88 (124)
T 3mb4_A           14 TPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSE--LPDYYLTIKKPMDMEKIRSHMMANK---YQDIDSMVEDFVM   88 (124)
T ss_dssp             CHHHHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhHhcccCCcccHHhhcCCCccc--cCCHHHHcCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHH
Confidence            3577889999999998      567899999999887  9999999999999999999999999   9999999999999


Q ss_pred             hhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          176 VFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       176 If~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      ||.||+.||+++|.+|.+|..|++.|++.|+++.
T Consensus        89 i~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~  122 (124)
T 3mb4_A           89 MFNNACTYNEPESLIYKDALVLHKVLLETRRDLE  122 (124)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999998874

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

Probab=99.94  E-value=3e-27  Score=205.40  Aligned_cols=106  Identities=26%  Similarity=0.440  Sum_probs=100.2

Q ss_pred             hccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchh
Q 016116           98 GRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  177 (395)
Q Consensus        98 ~~~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      ..++..+...|..||+.|++|+.+++|..||++..  +||||++|++||||+||++||.++.   |.++++|.+||+|||
T Consensus         8 ~~~~~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li~   82 (135)
T 3rcw_A            8 ELRLTPLTVLLRSVLDQLQDKDPARIFAQPVSLKE--VPDYLDHIKHPMDFATMRKRLEAQG---YKNLHEFEEDFDLII   82 (135)
T ss_dssp             -CCCCHHHHHHHHHHHHHHHTCTTCSSSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHH
T ss_pred             HhcchHHHHHHHHHHHHHHhCCcchhhcCCCChhh--cCCHHHHhCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHH
Confidence            34455688899999999999999999999999987  9999999999999999999999999   999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      .||+.||+++|.+|.+|..|++.|++.|.+.
T Consensus        83 ~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~  113 (135)
T 3rcw_A           83 DNCMKYNARDTVFYRAAVRLRDQGGVVLRQA  113 (135)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999766

>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=99.94  E-value=1.9e-27  Score=204.27  Aligned_cols=106  Identities=26%  Similarity=0.349  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhc
Q 016116          102 QELKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRL  175 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~L  175 (395)
                      ..+...|..|++.|..+.      .+|||..||+...  +||||++|++||||+||++||.++.   |.++++|.+||+|
T Consensus         8 ~~l~~~~~~i~~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~l   82 (126)
T 3mqm_A            8 ARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKK--NADYYEKISDPLDLITIEKQILTGY---YKTVEAFDADMLK   82 (126)
T ss_dssp             HHHHHHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGGG--CTTHHHHCSSCCCHHHHHHHHHHTC---CCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCcCCCChhHHhcCCCCccc--CCCHHHHcCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHH
Confidence            456778888888888865      5999999999987  9999999999999999999999999   9999999999999


Q ss_pred             hhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 016116          176 VFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV  212 (395)
Q Consensus       176 If~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~  212 (395)
                      ||.||+.||+++|.+|.+|..|++.|++.|.++.+.+
T Consensus        83 i~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~~l  119 (126)
T 3mqm_A           83 VFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQI  119 (126)
T ss_dssp             HHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999998876543

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

Probab=99.94  E-value=3.3e-27  Score=202.14  Aligned_cols=100  Identities=28%  Similarity=0.396  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      .+...|..|+..|.+++.+++|..||++..  +||||++|++||||+||++||.++.   |.++++|.+||+|||.||+.
T Consensus        13 p~~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na~~   87 (123)
T 3hme_A           13 PIQQLLEHFLRQLQRKDPHGFFAFPVTDAI--APGYSMIIKHPMDFGTMKDKIVANE---YKSVTEFKADFKLMCDNAMT   87 (123)
T ss_dssp             HHHHHHHHHHHHHHTTCTTCSSSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCccHhhcCCCChhh--ccCHHHHCCCCCCHHHHHHHhccCC---CCCHHHHHHHHHHHHHHHHH
Confidence            467789999999999999999999999987  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHh
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQ  207 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~  207 (395)
                      ||+++|.+|.+|..|++.|++.|.+
T Consensus        88 yN~~~s~~~~~A~~L~~~~~~~~~~  112 (123)
T 3hme_A           88 YNRPDTVYYKLAKKILHAGFKMMSK  112 (123)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHTCH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999998843

>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=99.94  E-value=3.8e-27  Score=199.66  Aligned_cols=102  Identities=23%  Similarity=0.361  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchh
Q 016116          104 LKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  177 (395)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      .++.|..|+..|+++.      .+++|..||+...  +||||++|++||||+||++||+++.   |.++++|.+||+|||
T Consensus         6 ~~~~c~~il~~l~~~~d~~g~~~s~~F~~p~~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~li~   80 (116)
T 3iu5_A            6 PIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRN--QPDYYEVVSQPIDLMKIQQKLKMEE---YDDVNLLTADFQLLF   80 (116)
T ss_dssp             HHHHHHHHHHHHHHCBCTTCCBGGGGGSSCCCGGG--CHHHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhccCCCeeeHHhcCCCCccc--CCCHHHHhCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHHHH
Confidence            5678999999999884      5999999999887  9999999999999999999999999   999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      .||+.||+++|.+|.+|..|++.|++.|+++..
T Consensus        81 ~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~l~~  113 (116)
T 3iu5_A           81 NNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQ  113 (116)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999988754

>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=99.94  E-value=5.5e-27  Score=202.61  Aligned_cols=106  Identities=23%  Similarity=0.397  Sum_probs=98.5

Q ss_pred             ccHHHHHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHH
Q 016116           99 RRMQELKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD  172 (395)
Q Consensus        99 ~~~~~l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~D  172 (395)
                      .+...+..+|..+++.|..+.      .++||..||+...  +||||++|++||||+||++||+++.   |.++++|.+|
T Consensus        13 ~~~~kl~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~~--~PdY~~iIk~PMdL~tI~~kL~~~~---Y~s~~ef~~D   87 (130)
T 3k2j_A           13 LGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKK--YPDYYQQIKMPISLQQIRTKLKNQE---YETLDHLECD   87 (130)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHhcccCCCccHhhcCCCChhh--CccHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHH
Confidence            345568889999999998865      4999999999887  9999999999999999999999999   9999999999


Q ss_pred             HhchhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          173 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       173 v~LIf~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      |+|||.||+.||+++|.||.+|..|++.|++.|+++.
T Consensus        88 v~Lif~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~  124 (130)
T 3k2j_A           88 LNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELA  124 (130)
T ss_dssp             HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999998773

>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=99.94  E-value=7.5e-27  Score=199.04  Aligned_cols=103  Identities=24%  Similarity=0.370  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHHHHHHHcCCC------CCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHh
Q 016116          101 MQELKRQFAAIFRQITQHKW------AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR  174 (395)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~~------a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~  174 (395)
                      ...|...|..+++.|..+..      +++|..||+...  +||||++|++||||+||++||.++.   |.++.+|.+||+
T Consensus         6 p~~l~~~~~~ll~~l~~~~d~~g~~~s~~F~~~~~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~   80 (120)
T 3ljw_A            6 PAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQ--YPDYYAIIKEPIDLKTIAQRIQNGS---YKSIHAMAKDID   80 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHCBCTTSCBTTGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHHTC---CCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccCcCCCcccHHhcCCCCccc--CCChHHHcCCCCCHHHHHHHHccCC---CCCHHHHHHHHH
Confidence            34577789999999988766      999999999987  9999999999999999999999999   999999999999


Q ss_pred             chhhhhcccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          175 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       175 LIf~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      |||.||+.||+++|.+|.+|..|++.|++.|+++
T Consensus        81 li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~i  114 (120)
T 3ljw_A           81 LLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEI  114 (120)
T ss_dssp             HHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999876

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

Probab=99.93  E-value=3.4e-26  Score=203.86  Aligned_cols=104  Identities=26%  Similarity=0.486  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHH-HHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          104 LKRQFAAIFRQ-ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       104 l~~~~~~il~~-l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      +...|..|+.. |+.++.+|||..||++..  +||||++|++||||+||++||.++.   |.++.+|.+||+|||.||++
T Consensus        30 l~~iL~~i~~~kl~~~~~s~~F~~PVd~~~--~PdY~~iIk~PMDL~tI~~kl~~~~---Y~s~~ef~~Dv~Lif~Na~~  104 (158)
T 3uv4_A           30 FSFILDNIVTQKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHK---YQSRESFLDDVNLILANSVK  104 (158)
T ss_dssp             HHHHHHHHHHHTTTTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCchhhcCcCChhh--cccHHHHcCCccCHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            33344444443 566889999999999987  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQLLPKV  212 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~  212 (395)
                      ||+++|.||.+|..|...|+..|.++...+
T Consensus       105 yN~~~s~i~~~A~~L~~~~~~~l~e~~~~l  134 (158)
T 3uv4_A          105 YNGPESQYTKTAQEIVNVCYQTLTEYDEHL  134 (158)
T ss_dssp             HHCTTCHHHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999998875443

>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=99.93  E-value=6.4e-26  Score=200.42  Aligned_cols=105  Identities=26%  Similarity=0.438  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHcC-------CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhh
Q 016116          106 RQFAAIFRQITQH-------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  178 (395)
Q Consensus       106 ~~~~~il~~l~~~-------~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~  178 (395)
                      .+|..|+..|.++       +.+++|+.||+...  +||||++|++||||+||++||+++.   |.++++|.+||+|||.
T Consensus        27 ~~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~li~~  101 (150)
T 3tlp_A           27 QRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKD--YPDYYKIILEPMDLKIIEHNIRNDK---YAGEEGMIEDMKLMFR  101 (150)
T ss_dssp             HHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcccCCcccHHhcCCCchhh--CcCHHHHhCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHH
Confidence            3566666666554       45999999999987  9999999999999999999999999   9999999999999999


Q ss_pred             hhcccCCCCCHHHHHHHHHHHHHHHHHHhhCcCchHH
Q 016116          179 NAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEE  215 (395)
Q Consensus       179 Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~~~~  215 (395)
                      ||+.||+++|.||.+|..|++.|++.|.++.+...++
T Consensus       102 Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~pd~d  138 (150)
T 3tlp_A          102 NARHYNEEGSQVYNDAHILEKLLKEKRKELGPLPDDD  138 (150)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHHHCCC----
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHccCCCChh
Confidence            9999999999999999999999999999998765443

>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=99.92  E-value=1e-25  Score=203.32  Aligned_cols=101  Identities=31%  Similarity=0.562  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      .....|..||..|..|+.++||+.||++..  +||||++|++||||+||++||+++.   |.++++|.+||+|||.||++
T Consensus        72 ~~~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~~I~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~~  146 (174)
T 2ri7_A           72 KDYEGLKRVLRSLQAHKMAWPFLEPVDPND--APDYYGVIKEPMDLATMEERVQRRY---YEKLTEFVADMTKIFDNCRY  146 (174)
T ss_dssp             HHHHHHHHHHHHHHTSGGGTTTSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTC---CCBHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhhhhhhcCCCccc--CCchHHHhCCcCCHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999987  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      ||+++|.+|.+|..|+++|+++|+.+
T Consensus       147 yN~~~s~~~~~A~~L~~~f~~~~~~~  172 (174)
T 2ri7_A          147 YNPSDSPFYQCAEVLESFFVQKLKGF  172 (174)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHTTTC
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999765

>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=99.92  E-value=3.8e-25  Score=191.01  Aligned_cols=103  Identities=28%  Similarity=0.441  Sum_probs=95.4

Q ss_pred             cHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          100 RMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       100 ~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      .+..+...|..++..|..|+.++||..||++..  +||||++|++||||+||++||.++.   |.++.+|.+||+|||.|
T Consensus         7 ~l~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li~~N   81 (130)
T 3dai_A            7 TFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDE--VPDYVTVIKQPMDLSSVISKIDLHK---YLTVKDYLRDIDLICSN   81 (130)
T ss_dssp             HHHHHHHHHHHHHHHHHTSGGGGGGSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCccHhhcCCCChhh--cCCHHHHcCCCCCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHH
Confidence            355677789999999999999999999999987  9999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCHH----HHHHHHHHHHHHHHHHh
Q 016116          180 AMKYNDERDDV----HVMAKSLLEKFEEKWLQ  207 (395)
Q Consensus       180 a~~YN~~~S~v----~~~A~~L~~~Fe~~~~~  207 (395)
                      |+.||+++|++    +.+|..|++.+...+..
T Consensus        82 a~~yN~~~s~~~~~i~~~A~~L~~~~~~~i~~  113 (130)
T 3dai_A           82 ALEYNPDRDPGDRLIRHRACALRDTAYAIIKE  113 (130)
T ss_dssp             HHHHCCSSSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCChhHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999977    68888888888888853

>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=99.92  E-value=1.9e-25  Score=203.55  Aligned_cols=103  Identities=31%  Similarity=0.538  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhC--CCCCCCCCHHHHHHHHhchhhh
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG--KDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~--~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      ..+.+.|..||..|+.|+.+++|..||+..   +||||++|++||||+||++||++  +.   |.++.+|.+||+|||.|
T Consensus        80 ~~~~~~c~~il~~l~~~~~s~~F~~Pv~~~---~pdY~~iIk~PmdL~tI~~kl~~~~~~---Y~s~~ef~~Dv~li~~N  153 (184)
T 3o36_A           80 PIDKRKCERLLLFLYCHEMSLAFQDPVPLT---VPDYYKIIKNPMDLSTIKKRLQEDYSM---YSKPEDFVADFRLIFQN  153 (184)
T ss_dssp             HHHHHHHHHHHHHHHHSTTCHHHHSCCCTT---STTHHHHCSSCCCHHHHHHHHHSTTCS---CCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhchhhhhhccccccC---CCchhhhcCCCCCHHHHHHHHHhcCCC---CCCHHHHHHHHHHHHHH
Confidence            456779999999999999999999999864   89999999999999999999998  57   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      |++||+++|.||.+|..|+.+|++.|++++|
T Consensus       154 a~~yN~~~s~v~~~a~~L~~~f~~~~~~~~P  184 (184)
T 3o36_A          154 CAEFNEPDSEVANAGIKLENYFEELLKNLYP  184 (184)
T ss_dssp             HHHHSCTTCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHhCc
Confidence            9999999999999999999999999999876

>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=99.91  E-value=2.2e-24  Score=207.33  Aligned_cols=105  Identities=25%  Similarity=0.501  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      ..|...|..||..|.+|+.++||..||++..  +||||++|++||||+||++||.++.   |.++.+|.+||+|||.||+
T Consensus        13 ~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na~   87 (265)
T 3uv5_A           13 VTLSSILESIINDMRDLPNTYPFHTPVNAKV--VKDYYKIITRPMDLQTLRENVRKRL---YPSREEFREHLELIVKNSA   87 (265)
T ss_dssp             HHHHHHHHHHHHHHHTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCchhhhCCCChhh--cCCHHHHhCCCCcHHHHHHHHHcCC---CCCHHHHHHHHHHHHhhhh
Confidence            3688899999999999999999999999998  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHhhCcC
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKWLQLLPK  211 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~  211 (395)
                      +||+++|.||.+|..|...|++.|.++...
T Consensus        88 ~yN~~~s~i~~~A~~l~~~~~~~~~~~~~~  117 (265)
T 3uv5_A           88 TYNGPKHSLTQISQSMLDLCDEKLKEKEDK  117 (265)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             hcCCCCChHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999999999999999999999887443

>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=99.90  E-value=1.7e-24  Score=208.10  Aligned_cols=172  Identities=19%  Similarity=0.326  Sum_probs=121.8

Q ss_pred             HHHHHHHHH-----HHHHHHhhhhhhhhccCCCCCCCCCCCchhhhccccCCCCC--chhhhhhhhhhhhHh-----hhc
Q 016116           32 TIDDILQKV-----TQLEQKLNDVEQFYLTKDNNQPNTSKSISIAKEKLKDRHVA--SIEKQQQDAFHREEA-----AGR   99 (395)
Q Consensus        32 ~l~~i~~k~-----~~le~~~~~~~~~~~~~~~~~~~~~~g~s~~k~~~r~r~~~--~~kk~~~~~~~~e~~-----~~~   99 (395)
                      .|..|+.++     ..+++-+.++..++.++..+   +.+++.++..+..-...-  ..+.........+..     ...
T Consensus        56 dL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~y---N~~~s~i~~~A~~l~~~~~~~~~~~~~~~~~~ek~i~p~~dd~  132 (265)
T 3uv5_A           56 DLQTLRENVRKRLYPSREEFREHLELIVKNSATY---NGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDD  132 (265)
T ss_dssp             CHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHSTTTTCH
T ss_pred             cHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhhhc---CCCCChHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhccccc
Confidence            345555555     34666777788888888777   556665555332211100  000000000000000     001


Q ss_pred             cHHHHHHHHHHHHHH-HHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhh
Q 016116          100 RMQELKRQFAAIFRQ-ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  178 (395)
Q Consensus       100 ~~~~l~~~~~~il~~-l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~  178 (395)
                      ....+...|..++.+ ++.|+.+|||+.||++..  +||||++|++||||+||++||.++.   |.++.+|..||+|||.
T Consensus       133 ~~~~~~~il~~i~~~~l~~~~~~~~F~~pv~~~~--~pdY~~iIk~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~lif~  207 (265)
T 3uv5_A          133 DQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHK---YQSRESFLDDVNLILA  207 (265)
T ss_dssp             HHHHHHHHHHHHHHHTTTTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHhhhhhHHHhCCCChhH--hCcHHHHhCCcccHHHHHHHHhcCC---CCCHHHHHHHHHHHHH
Confidence            112233345555543 778899999999999988  9999999999999999999999999   9999999999999999


Q ss_pred             hhcccCCCCCHHHHHHHHHHHHHHHHHHhhCcC
Q 016116          179 NAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK  211 (395)
Q Consensus       179 Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~  211 (395)
                      ||+.||+++|.||.+|..|+..|+..|.++...
T Consensus       208 Na~~yN~~~s~~~~~A~~l~~~~~~~~~~~~~~  240 (265)
T 3uv5_A          208 NSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEH  240 (265)
T ss_dssp             HHHHHTCTTCHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999887543

>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=99.90  E-value=3.6e-24  Score=198.67  Aligned_cols=108  Identities=30%  Similarity=0.528  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      ....+.|..||..|++|+.+++|+.||+. .  +||||++|++||||+||++||+++.++.|.++.+|.+||+|||.||+
T Consensus        80 ~~~~~~c~~il~~l~~~~~s~~F~~Pv~~-~--~pdY~~iIk~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li~~Na~  156 (207)
T 3u5n_A           80 PVDQRKCERLLLYLYCHELSIEFQEPVPA-S--IPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCE  156 (207)
T ss_dssp             HHHHHHHHHHHHHHHTSTTCGGGSSCCCT-T--STTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccchhhhhccCCh-h--hccHhHHhCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHHH
Confidence            45667899999999999999999999987 3  99999999999999999999997311229999999999999999999


Q ss_pred             ccCC-----------------CCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 016116          182 KYND-----------------ERDDVHVMAKSLLEKFEEKWLQLLPKV  212 (395)
Q Consensus       182 ~YN~-----------------~~S~v~~~A~~L~~~Fe~~~~~~~~~~  212 (395)
                      +||+                 ++|.++.+|..|+.+|+++|.+++|..
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                 999999999999999999999999853

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

Probab=99.90  E-value=7.9e-24  Score=183.04  Aligned_cols=100  Identities=28%  Similarity=0.492  Sum_probs=92.5

Q ss_pred             cHHHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          100 RMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       100 ~~~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      .+.+|...|..|+..|+.|+.++||..|       +||||++|++||||+||+.||.++.   |.++.+|.+||+|||.|
T Consensus         9 ~~~~L~~~~~~il~~l~~~~~~~~F~~P-------~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~~f~~D~~Li~~N   78 (131)
T 2dkw_A            9 TLRELRLFLRDVTKRLATDKRFNIFSKP-------VSDYLEVIKEPMDLSTVITKIDKHN---YLTAKDFLKDIDLICSN   78 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHSGGGCTTSSC-------CSSCTTSCSSCCCHHHHHHHHHTTC---CCSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCccchhhcCc-------CccHHhHcCCCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHH
Confidence            4557778999999999999999999998       7999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCH----HHHHHHHHHHHHHHHHHhhC
Q 016116          180 AMKYNDERDD----VHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       180 a~~YN~~~S~----v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      |+.||+++|+    ++.+|..|++.|...++.-+
T Consensus        79 a~~yN~~~s~~~~~i~~~A~~L~~~~~~~l~~~l  112 (131)
T 2dkw_A           79 ALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAEL  112 (131)
T ss_dssp             HHHSCCCSSTTHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHCCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999995    57899999999999885443

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

Probab=99.90  E-value=1.7e-24  Score=198.24  Aligned_cols=100  Identities=17%  Similarity=0.235  Sum_probs=93.3

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhcc--CCCChHHHHHHHhCC---CCCCCCCHHHHHHHHhchh
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIE--KPMDFSTIKNKMDGK---DGTGYRNVREIYADVRLVF  177 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk--~PMDL~tIk~kL~~~---~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      ..++.|..||..|+.|+.+|||++||+      |+||++|+  +||||+||++||+++   .   |.++++|++||+|||
T Consensus        76 ~~~~~c~~iL~~l~~~~~s~pF~~pV~------~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~---Y~s~~eF~~Dv~Lif  146 (189)
T 2ro1_A           76 ANQRKCERVLLALFCHEPCRPLHQLAT------DSTFSLDQPGGTLDLTLIRARLQEKLSPP---YSSPQEFAQDVGRMF  146 (189)
T ss_dssp             HHHHHHHHHHHHHHHSTTHHHHHSCSC------CTTCSSSCSSCCCCHHHHHHHHHTSSSSC---CSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccCccchhhcCCCC------hhhhccccCCCcccHHHHHHHHhcCCCcc---cCCHHHHHHHHHHHH
Confidence            345689999999999999999999997      68999998  899999999999999   7   999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV  212 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~  212 (395)
                      +||++|| +++.+|.+|..|+++|+++|+++++..
T Consensus       147 ~N~~~yN-~~s~~~~~a~~L~~~Fe~~~~~~~~~~  180 (189)
T 2ro1_A          147 KQFNKLT-EDKADVQSIIGLQRFFETRMNEAFGDT  180 (189)
T ss_dssp             HHHHHHC-CSSCSSHHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHC-CCCHHHHHHHHHHHHHHHHHHHhcCcc
Confidence            9999999 588899999999999999999998753

>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=99.89  E-value=3e-23  Score=201.97  Aligned_cols=98  Identities=27%  Similarity=0.520  Sum_probs=90.3

Q ss_pred             HHHHH-HHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCC
Q 016116          108 FAAIF-RQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE  186 (395)
Q Consensus       108 ~~~il-~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~  186 (395)
                      +..++ ..|+.++.+|||+.||++..  +||||++|++||||+||+.||.++.   |.++.+|.+||+|||.||+.||++
T Consensus       174 l~~i~~~~l~~~~~s~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~Li~~Na~~yN~~  248 (292)
T 3aad_A          174 LDNIVTQKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHK---YQSRESFLDDVNLILANSVKYNGP  248 (292)
T ss_dssp             HHHHHHHTGGGSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHhhhhhhcCcchhHHHhcccccc--cccHHHHcCCcCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHHCCC
Confidence            44444 34788999999999999887  9999999999999999999999999   999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhhCc
Q 016116          187 RDDVHVMAKSLLEKFEEKWLQLLP  210 (395)
Q Consensus       187 ~S~v~~~A~~L~~~Fe~~~~~~~~  210 (395)
                      +|.+|.+|..|+..|+..|..+..
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            999999999999999999987743

>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=3.4e-24  Score=210.24  Aligned_cols=87  Identities=30%  Similarity=0.471  Sum_probs=84.0

Q ss_pred             cCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHH
Q 016116          117 QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS  196 (395)
Q Consensus       117 ~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~  196 (395)
                      .|+.+|||+.||++..  +||||+||++||||+||++||.++.   |.++.+|.+||+|||.||++||+++|.||.+|..
T Consensus       177 ~~~~s~~F~~pvd~~~--~PdY~~iIk~PMDL~tI~~kl~~~~---Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~  251 (311)
T 2r0y_A          177 KVKLSEPFMELVDKDE--LPEYYEIVHSPMALSIVKQNLEIGQ---YSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATT  251 (311)
T ss_dssp             SSCTTGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHHTC---CCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHH
T ss_pred             CCccHHHHhCCCChhh--cccHHHHhCCccCHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            4678999999999987  9999999999999999999999999   9999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhh
Q 016116          197 LLEKFEEKWLQL  208 (395)
Q Consensus       197 L~~~Fe~~~~~~  208 (395)
                      |+..|++.|++.
T Consensus       252 L~~~f~~~~~~~  263 (311)
T 2r0y_A          252 LTNYFNYLIQKE  263 (311)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh
Confidence            999999999874

>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=99.89  E-value=1.4e-23  Score=204.26  Aligned_cols=102  Identities=25%  Similarity=0.517  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      ..+...|..||..|++|+.++||+.||++..  +||||++|++||||+||++||+++.   |.++.+|.+||+|||.||+
T Consensus        46 ~~l~~~~~~il~~l~~~~~a~~F~~pV~~~~--~pdY~~iIk~PmDL~tIk~kl~~~~---Y~s~~~f~~D~~li~~Na~  120 (292)
T 3aad_A           46 VTLSSILESIINDMRDLPNTYPFHTPVNAKV--VKDYYKIITRPMDLQTLRENVRKRL---YPSREEFREHLELIVKNSA  120 (292)
T ss_dssp             HHHHHHHHHHHHHHSSSTTCGGGSSSCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCcchhhcCCCCchh--cccHHHHcCCcCCHHHHHHHhhCCC---cCCHHHHHHHHHHHHHHHH
Confidence            4566789999999999999999999999987  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      +||+++|++|.+|..|.+.|++.|..+
T Consensus       121 ~yN~~~s~i~~~A~~L~~~~~~~~~~~  147 (292)
T 3aad_A          121 TYNGPKHSLTQISQSMLDLCDEKLKEK  147 (292)
T ss_dssp             HHTCSSSHHHHHHTHHHHTTTTTGGGS
T ss_pred             HHcCCchHHHHHHHHHHHHHHhhhhcc
Confidence            999999999999999999999888665

>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=99.86  E-value=1.7e-22  Score=202.12  Aligned_cols=87  Identities=30%  Similarity=0.471  Sum_probs=83.9

Q ss_pred             cCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHHHHHH
Q 016116          117 QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS  196 (395)
Q Consensus       117 ~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~~A~~  196 (395)
                      .|+.+|||+.||++..  +||||+||++||||+||++||.++.   |.++.+|.+||+|||.||++||+++|.||.+|..
T Consensus       227 ~~~~s~~F~~pvd~~~--~PdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~  301 (361)
T 2r10_A          227 KVKLSEPFMELVDKDE--LPEYYEIVHSPMALSIVKQNLEIGQ---YSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATT  301 (361)
T ss_dssp             SSCTTGGGSSCCCTTT--CTHHHHHCSSCCCHHHHHHHHHHTC---CCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHH
T ss_pred             CCcchhcccCCCChhh--cccHHHHhcCcccHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence            3678999999999987  9999999999999999999999999   9999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhh
Q 016116          197 LLEKFEEKWLQL  208 (395)
Q Consensus       197 L~~~Fe~~~~~~  208 (395)
                      |+.+|+..|.+.
T Consensus       302 L~~~f~~~~~~~  313 (361)
T 2r10_A          302 LTNYFNYLIQKE  313 (361)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh
Confidence            999999999874

>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=99.81  E-value=8e-21  Score=189.93  Aligned_cols=99  Identities=19%  Similarity=0.252  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHHHHHcC--CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCC-CHHHHHHHHhchhhh
Q 016116          103 ELKRQFAAIFRQITQH--KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR-NVREIYADVRLVFKN  179 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~--~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~-s~~ef~~Dv~LIf~N  179 (395)
                      .+...|..+|+.+...  ..+++|+.||+...  +||||+||++||||+||++||  ..   |. ++++|.+||+|||.|
T Consensus        78 ~~~~~~~~~l~~l~~~~~~~~~~F~~p~~~~~--~PdY~~iIk~Pmdl~tI~~kl--~~---y~~~~~~f~~D~~li~~N  150 (361)
T 2r10_A           78 KFNRFISFTLDVLIDKYKDIFKDFIKLPSRKF--HPQYYYKIQQPMSINEIKSRD--YE---YEDGPSNFLLDVELLTKN  150 (361)
T ss_dssp             THHHHHHHHHHHHHHHTHHHHGGGSSCCCTTT--CTTHHHHCSSCCCHHHHHTSC--CC---STTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcccHHhcCCCCccc--CCChHhhcCCCcCHHHHHHHh--hc---cCCCHHHHHHHHHHHHHH
Confidence            3445677888887553  46899999999988  999999999999999999998  34   55 899999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      |++||+++|.||.+|..|+++|+..|.+.
T Consensus       151 a~~yN~~~s~i~~~a~~l~~~~~~~~~k~  179 (361)
T 2r10_A          151 CQAYNEYDSLIVKNSMQVVMLIEFEVLKA  179 (361)
T ss_dssp             HHHHBCSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcCCCCCHHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999999999765

>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=99.81  E-value=1.8e-20  Score=183.87  Aligned_cols=95  Identities=19%  Similarity=0.232  Sum_probs=83.2

Q ss_pred             HHHHHHHHHHc--CCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCC-CHHHHHHHHhchhhhhccc
Q 016116          107 QFAAIFRQITQ--HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR-NVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       107 ~~~~il~~l~~--~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~-s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      .|..+|..+..  +..+++|+.||+...  +||||+||++||||+||++||  ..   |. ++++|.+||+|||.||++|
T Consensus        32 ~~~~~L~~~~~~~r~~~~~F~~p~~~~~--~PdY~~iIk~PmDL~tI~~kl--~~---y~~s~~~f~~D~~li~~Na~~y  104 (311)
T 2r0y_A           32 FISFTLDVLIDKYKDIFKDFIKLPSRKF--HPQYYYKIQQPMSINEIKSRD--YE---YEDGPSNFLLDVELLTKNCQAY  104 (311)
T ss_dssp             HHHHHHHHHHHHSHHHHGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHSC--CC---STTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCchhHHhcCCCCccc--CCChHHHcCCCCCHHHHHHHH--hc---ccCCHHHHHHHHHHHHHHHHHc
Confidence            34444444443  347999999999988  999999999999999999998  44   66 8999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          184 NDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      |+++|.||.+|..|+++|++.|.+.
T Consensus       105 N~~~s~i~~~A~~l~~~~~~~~~k~  129 (311)
T 2r0y_A          105 NEYDSLIVKNSMQVVMLIEFEVLKA  129 (311)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999775

>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=99.75  E-value=3.8e-18  Score=149.01  Aligned_cols=97  Identities=15%  Similarity=0.287  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchh
Q 016116          104 LKRQFAAIFRQITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  177 (395)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf  177 (395)
                      +...+..|+..++.+.      .+.+|+..|+..    |+||.  +.||+|.+|++||..+.   |.++++|..||.+||
T Consensus         8 lq~~l~~l~~~v~~~~De~GR~lsd~F~~LPsk~----pdYY~--k~Pi~l~~Ikkri~~~~---Y~sld~f~~D~~lmf   78 (147)
T 3iu6_A            8 IQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVD----PNFPN--KPPLTFDIIRKNVENNR---YRRLDLFQEHMFEVL   78 (147)
T ss_dssp             HHHHHHHHHHHHHTCBCTTSCBGGGGGTTCCSSC----TTSTT--SCCCCHHHHHHHHHTTC---CCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcCCCCCcchHHHhHCCCCC----ccccC--CCCcCHHHHHHHHhcCC---CCCHHHHHHHHHHHH
Confidence            4557788898998875      589999998876    78998  99999999999999999   999999999999999


Q ss_pred             hhhcccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          178 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       178 ~Na~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      .||++||.+||+||.+|..|+.+|.+.+.++.
T Consensus        79 ~NAr~yN~e~S~IyeDAv~Lq~~f~~~r~eL~  110 (147)
T 3iu6_A           79 ERARRMNRTDSEIYEDAVELQQFFIKIRDELC  110 (147)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999997764

>2jns_A Bromodomain-containing protein 4; ET-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.70  E-value=7.3e-18  Score=136.40  Aligned_cols=73  Identities=29%  Similarity=0.563  Sum_probs=69.3

Q ss_pred             hhhcCCCHHHHHHHHHHhccCChHhHHHHHHHHHhcCCCCC-CCCCeEEEeCCCCCHHHHHHHHHHHHHHHHhc
Q 016116          265 QKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFH-ATAQEVDLDMDAQSELTLWRLKVFVQESLKAA  337 (395)
Q Consensus       265 ~~~r~mt~eEK~~L~~~I~~L~~e~L~~vi~II~~~~P~~~-~~~~evElDid~L~~~TL~~L~~yV~~~L~~~  337 (395)
                      ..+++||++||++|+.+|+.||+++|.+||+||++++|.+. ...+|||||||.|++.|||+|++||..||+.+
T Consensus        13 ~~~~~mT~eEK~~Ls~~I~~Lp~e~L~~Vi~II~~~~p~l~~~~~dEIEiDid~L~~~TL~~L~~yV~~~l~~k   86 (90)
T 2jns_A           13 DKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLRELERYVTSCLRKK   86 (90)
T ss_dssp             SSCCCCCHHHHHHHHHHHTTSCHHHHTTHHHHHHTTCGGGTTSCTTSCCCCTTTSCHHHHHHHHHHHHTTSCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCHHHHHHHHHHHHhcCccccCCCCCeEEEeccCCCHHHHHHHHHHHHHHHHhh
Confidence            35799999999999999999999999999999999999986 68899999999999999999999999999876

>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=99.56  E-value=3.8e-15  Score=135.30  Aligned_cols=98  Identities=15%  Similarity=0.289  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      .++.+.+..||..|..++.++||+.+.             ++.||||.||++||+.+.   |.++.+|.+||.|||.||.
T Consensus        74 ~el~~~l~~vl~~L~~~~~s~~~~~y~-------------~k~PmDL~~i~kKl~~~~---Y~s~~eF~~Dv~lIf~n~~  137 (183)
T 3lqh_A           74 KELQISLKQVLTALLNSRTTSHLLRYR-------------QQQPLDLEGVKRKMDQGN---YTSVLEFSDDIVKIIQAAI  137 (183)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHTCC-------------C--CCSHHHHHHHHHTTC---CCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccccHhhhhhh-------------hcCCccHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHh
Confidence            356677899999999999999998732             599999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHhhCcCchHH
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEE  215 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~~~~~~~~~~~  215 (395)
                      .||.+.+.+..++..|+.+|++.+.+++|++...
T Consensus       138 ~~~~~~~e~~~ag~~l~~~f~~~l~~vfpwf~~~  171 (183)
T 3lqh_A          138 NSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVK  171 (183)
T ss_dssp             HHSCCCHHHHHHHHHHHHHHHHHHHHHCTTSCGG
T ss_pred             hccCCChhhhhhhhHHHHHHHHHHHHHCCCCCcc
Confidence            9999999999999999999999999999987654

>2lm0_A AF4/FMR2 family member 1/protein AF-9 chimera; intrinsically disordered, nuclear protein; NMR {Homo sapiens}

Probab=96.03  E-value=0.0078  Score=50.25  Aligned_cols=63  Identities=22%  Similarity=0.339  Sum_probs=54.0

Q ss_pred             cCCCHHHHHHHHHHhccCC-hHhHHHHHHHHHhcCCCCCCCCCeEEEeCCCCCHHHHHHHHHHHH
Q 016116          268 RKMSTEEKKNLGTALTRLS-PEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQ  331 (395)
Q Consensus       268 r~mt~eEK~~L~~~I~~L~-~e~L~~vi~II~~~~P~~~~~~~evElDid~L~~~TL~~L~~yV~  331 (395)
                      .+--.+|.+.|...|..|. .+.|.+|+++|.+. ..+...+..+.+|+.+|+..|+++|+.|+.
T Consensus        57 ~~~y~~~L~~l~~rim~l~d~~~lq~iv~li~~t-G~~~it~~tfDFDLc~LD~~Tv~klq~~l~  120 (125)
T 2lm0_A           57 DKAYLDELVELHRRLMTLRERHILQQIVNLIEET-GHFHITNTTFDFDLCSLDKTTVRKLQSYLE  120 (125)
T ss_dssp             SCSTHHHHHHHHHHHHTCCCCSSHHHHHHHHHTS-CCEEECSSCEEECTTTSCHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHhccccHHHHHHHHHHHHhc-CceeeecccccceeeccCHHHHHHHHHHHH
Confidence            3445588999999999995 56799999999985 366788999999999999999999999974

---

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	395
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	4e-27
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	3e-25
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	1e-23
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	1e-22
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	1e-22
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	5e-22

>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 =  102 bits (256), Expect = 4e-27
 Identities = 29/139 (20%), Positives = 60/139 (43%), Gaps = 8/139 (5%)

Query: 79  HVASIEKQQQDAFHREEAAGRRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDY 138
           H   + +  +    R       +  +      I   +      +PF  PV+ + +   DY
Sbjct: 5   HCDYLNRPHKSIHRRRTDPMVTLSSILES---IINDMRDLPNTYPFHTPVNAKVV--KDY 59

Query: 139 YEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLL 198
           Y++I +PMD  T++  +  +    Y +  E    + L+ KN+  YN  +  +  +++S+L
Sbjct: 60  YKIITRPMDLQTLRENVRKRL---YPSREEFREHLELIVKNSATYNGPKHSLTQISQSML 116

Query: 199 EKFEEKWLQLLPKVMEEEK 217
           +  +EK  +   K+   EK
Sbjct: 117 DLCDEKLKEKEDKLARLEK 135

>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 = 96.9 bits (241), Expect = 3e-25
 Identities = 35/111 (31%), Positives = 57/111 (51%), Gaps = 4/111 (3%)

Query: 102 QELKRQFAAIFRQI-TQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 160
           +EL++        +  Q   + PF  PVD + LG+ DY+++++ PMD STIK K+D    
Sbjct: 5   EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQ- 63

Query: 161 TGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 211
             Y+   +   DV L+F NA  YN +   V+     L E FE++   ++  
Sbjct: 64  --YQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQS 112

>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 = 92.3 bits (229), Expect = 1e-23
 Identities = 33/98 (33%), Positives = 52/98 (53%), Gaps = 5/98 (5%)

Query: 111 IFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY 170
           I  ++  H  AWPF+ PV+ E +   DYY+ I++PMD ST++ K++      Y+ + +  
Sbjct: 11  ILTELQNHAAAWPFLQPVNKEEV--PDYYDFIKEPMDLSTMEIKLESNK---YQKMEDFI 65

Query: 171 ADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
            D RLVF N   YN E    +  A  L + F  K  ++
Sbjct: 66  YDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 103

>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 = 90.1 bits (223), Expect = 1e-22
 Identities = 33/110 (30%), Positives = 51/110 (46%), Gaps = 5/110 (4%)

Query: 99  RRMQELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK 158
           R   +L     +I +Q+  H+ AWPFM PV         YYEVI  PMD  T+  ++  +
Sbjct: 9   RDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEA--PGYYEVIRFPMDLKTMSERLKNR 66

Query: 159 DGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 208
               Y + +   AD++ VF N  +YN    + +  A  L + F  K  + 
Sbjct: 67  Y---YVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEA 113

>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 = 90.0 bits (223), Expect = 1e-22
 Identities = 28/114 (24%), Positives = 51/114 (44%), Gaps = 5/114 (4%)

Query: 113 RQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 172
           +++     +WPF HPV+ + +   DYY+VI  PMD  TI+  +       Y++      D
Sbjct: 20  QKMMAVPDSWPFHHPVNKKFV--PDYYKVIVNPMDLETIRKNISKH---KYQSRESFLDD 74

Query: 173 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKA 226
           V L+  N++KYN         A+ ++    +   +    + + EK     +  A
Sbjct: 75  VNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAA 128

>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 = 87.7 bits (217), Expect = 5e-22
 Identities = 31/103 (30%), Positives = 45/103 (43%), Gaps = 5/103 (4%)

Query: 103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 162
           +L      +  QI  H  AWPFM PV        DYYEVI  P+D  T+  ++  +    
Sbjct: 2   QLYTTLKNLLAQIKSHPSAWPFMEPVKKSEA--PDYYEVIRFPIDLKTMTERLRSRY--- 56

Query: 163 YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 205
           Y   +   AD++ V  N  +YN    +    A +L + F  K 
Sbjct: 57  YVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKL 99

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	395
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.95
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.95
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.94
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.94
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.94
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.93

>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=99.95  E-value=1.2e-28  Score=202.42  Aligned_cols=100  Identities=31%  Similarity=0.504  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      +|...|..||..|.+|+.++||+.||++..  +||||++|++||||+||++||.++.   |.++.+|.+||+|||.||+.
T Consensus         2 ~L~~~l~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~~   76 (102)
T d3d7ca1           2 QLYTTLKNLLAQIKSHPSAWPFMEPVKKSE--APDYYEVIRFPIDLKTMTERLRSRY---YVTRKLFVADLQRVIANCRE   76 (102)
T ss_dssp             HHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCCCCccCCCCChhh--CcCHHHHcCCccCHHHHHHHhccCc---cCCHHHHHHHHHHHHHHHHH
Confidence            578899999999999999999999999887  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHh
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQ  207 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~  207 (395)
                      ||+++|++|.+|..|+++|+++|++
T Consensus        77 yN~~~s~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          77 YNPPDSEYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999998864

>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=99.95  E-value=6.1e-28  Score=201.11  Aligned_cols=100  Identities=33%  Similarity=0.631  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhccc
Q 016116          104 LKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  183 (395)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~Y  183 (395)
                      +...|..||..|++|+.||||+.||++..  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.||+.|
T Consensus         4 ~~~~l~~il~~l~~~~~a~pF~~pvd~~~--~pdY~~vI~~PmdL~tI~~kl~~~~---Y~s~~~f~~Dv~li~~Na~~y   78 (111)
T d1e6ia_           4 HDAAIQNILTELQNHAAAWPFLQPVNKEE--VPDYYDFIKEPMDLSTMEIKLESNK---YQKMEDFIYDARLVFNNCRMY   78 (111)
T ss_dssp             THHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCChhhcCCCCchh--CcCHHHHcCCchhHHHHHHHHHccc---cchHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999987  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          184 NDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       184 N~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      |+++|.++.+|..|++.|+++|+++
T Consensus        79 N~~~s~i~~~A~~l~~~f~~~~~~i  103 (111)
T d1e6ia_          79 NGENTSYYKYANRLEKFFNNKVKEI  103 (111)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999875

>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=99.94  E-value=2e-27  Score=198.90  Aligned_cols=106  Identities=32%  Similarity=0.567  Sum_probs=99.4

Q ss_pred             HHHHHHHHHHHHHHHHcC-CCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhh
Q 016116          101 MQELKRQFAAIFRQITQH-KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  179 (395)
Q Consensus       101 ~~~l~~~~~~il~~l~~~-~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~N  179 (395)
                      ..++.+.|..+|+.|+++ +.|+||..||++...++||||++|++||||+||++||.++.   |.++++|.+||+|||.|
T Consensus         4 p~el~~~l~~~l~~l~~~~p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~---Y~s~~ef~~Dv~li~~N   80 (114)
T d3dwya1           4 PEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQ---YQEPWQYVDDVWLMFNN   80 (114)
T ss_dssp             HHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCcCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCc---cccHHHHHHHHHHHHHH
Confidence            346788999999999987 69999999999886669999999999999999999999999   99999999999999999


Q ss_pred             hcccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 016116          180 AMKYNDERDDVHVMAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       180 a~~YN~~~S~v~~~A~~L~~~Fe~~~~~~~  209 (395)
                      |+.||+++|++|.+|..|+..|++.+..+.
T Consensus        81 a~~yN~~~s~~~~~A~~L~~~f~~~~~~i~  110 (114)
T d3dwya1          81 AWLYNRKTSRVYKFCSKLAEVFEQEIDPVM  110 (114)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999997764

>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=99.94  E-value=2.2e-27  Score=199.78  Aligned_cols=102  Identities=31%  Similarity=0.530  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhc
Q 016116          102 QELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  181 (395)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~  181 (395)
                      .++...|..||..|++|+.++||+.||++..  +||||++|++||||+||++||.++.   |.++++|.+||+|||.||+
T Consensus        12 ~~l~~~l~~il~~l~~~~~a~~F~~pv~~~~--~pdY~~iI~~PmdL~~I~~kl~~~~---Y~s~~ef~~Dv~li~~Na~   86 (118)
T d1wuma1          12 DQLYSTLKSILQQVKSHQSAWPFMEPVKRTE--APGYYEVIRFPMDLKTMSERLKNRY---YVSKKLFMADLQRVFTNCK   86 (118)
T ss_dssp             HHHHHHHHHHHHHHHHSSSCHHHHSCCCSSS--SSSCTTTCSSCCCHHHHHHHHTTTC---CCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCcCcccCCCChhh--CcCHHHHcCChhhHHHHHHHhcccc---cCchHHHHHHHHHHHHHHH
Confidence            3577899999999999999999999999988  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          182 KYNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       182 ~YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      .||+++|.+|.+|..|+.+|++.|++.
T Consensus        87 ~yn~~~s~~~~~A~~l~~~f~~~~~e~  113 (118)
T d1wuma1          87 EYNPPESEYYKCANILEKFFFSKIKEA  113 (118)
T ss_dssp             HHSCTTSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999875

>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=99.94  E-value=4.2e-27  Score=203.51  Aligned_cols=101  Identities=25%  Similarity=0.527  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcc
Q 016116          103 ELKRQFAAIFRQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  182 (395)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~  182 (395)
                      .+...|..|+..|..++.++||..||++..  +||||++|++||||+||++||.++.   |.++++|.+||+|||.||+.
T Consensus        26 ~l~~~l~~il~~l~~~~~s~pF~~Pvd~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~~  100 (139)
T d1eqfa1          26 TLSSILESIINDMRDLPNTYPFHTPVNAKV--VKDYYKIITRPMDLQTLRENVRKRL---YPSREEFREHLELIVKNSAT  100 (139)
T ss_dssp             HHHHHHHHHHHHHHTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCchhhhCCCChhh--ccCHHHHcCChhhHHHHHHHHHcCC---cCCHHHHHHHHHHHHHHHHH
Confidence            466678999999999999999999999988  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 016116          183 YNDERDDVHVMAKSLLEKFEEKWLQL  208 (395)
Q Consensus       183 YN~~~S~v~~~A~~L~~~Fe~~~~~~  208 (395)
                      ||+++|+++.+|..|+..|++.|+++
T Consensus       101 yN~~~s~i~~~A~~L~~~~~~~~~~~  126 (139)
T d1eqfa1         101 YNGPKHSLTQISQSMLDLCDEKLKEK  126 (139)
T ss_dssp             HTCTTSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999876

>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=99.93  E-value=1.2e-26  Score=198.05  Aligned_cols=92  Identities=27%  Similarity=0.535  Sum_probs=86.9

Q ss_pred             HHHHcCCCCCCCCCCCCccccCCCchhhhccCCCChHHHHHHHhCCCCCCCCCHHHHHHHHhchhhhhcccCCCCCHHHH
Q 016116          113 RQITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHV  192 (395)
Q Consensus       113 ~~l~~~~~a~~F~~PVd~~~l~~PdYy~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv~LIf~Na~~YN~~~S~v~~  192 (395)
                      ..++.++.||||+.||++..  +||||++|++||||+||++||.++.   |.|+.+|.+||+|||.||+.||+++|.++.
T Consensus        20 ~~~~~~p~a~pF~~pVd~~~--~PdY~~vIk~PmDL~tI~~kl~~~~---Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~   94 (128)
T d1eqfa2          20 QKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHK---YQSRESFLDDVNLILANSVKYNGPESQYTK   94 (128)
T ss_dssp             HTTTTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHcCCCCChhcCCCCccc--CcCHHHHcCCcccHHHHHHHHHhhc---cccHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            44566789999999999987  9999999999999999999999999   999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhC
Q 016116          193 MAKSLLEKFEEKWLQLL  209 (395)
Q Consensus       193 ~A~~L~~~Fe~~~~~~~  209 (395)
                      +|..|.+.|++.|.++.
T Consensus        95 ~A~~L~~~~~~~l~~~~  111 (128)
T d1eqfa2          95 TAQEIVNVCYQTLTEYD  111 (128)
T ss_dssp             HHHHHHHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHHHHHhH
Confidence            99999999999998763