Citrus Sinensis ID: 020702

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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--
Protein Sequence
MLLALRSSSKMHFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKKLPPNT
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccccEEEEEcccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHccccccHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccHcccccHHHHHHHHHHHHHHHHHccccccccccccHHHcccccHHHHHcccccHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHccccccccccccHHcHccccccHHHHcccccccHHHHHHHHHHHccHHHHHcccccccc
Coil and Loop (DISEMBL)
mllalrssskmhFIGKKLLEGGCKNLSASLLQFFVRQARSFITqhkwawpfmhpvdveglglhdyyeviekpmdfstiknkmdgkdgtgyrNVREIYADVRLVFKNAmkynderdDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVaennpsfhataqevdldmdaQSELTLWRLKVFVQESLKAAsrssgdmggnnnnnnddnnnekdnsnkknknnpkrKKEICDALAKpavkrtkklppnt
Flexible Loop (DISEMBL)
mllalrssskmhFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPmdfstiknkmdgkdgtgyrnVREIYADVRLVFKNAmkynderdDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQkcrkmsteekknlgtaltrlsPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAasrssgdmggnnnnnnddnnnekdnsnkknknnpkrkkeicdalakpavkrtkklppnt
Low Complexity Region (SEG)
MLLALRSSSKMHFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMeeekrqeeeeakaqLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGnnnnnnddnnnekdnsnkknknnpkrkkEICDALAKPAVKRTKKLPPNT
Disordered region (IsUnstruct)
***********HFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP*****************************************************************************EDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQ****************************************************************
Disordered Region (DISOPRED)
********************************FFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWL***********************************************************************************LCKALEI****************LDMDAQSELTLWRLKVFVQ****************************************************************
Disordered Region (DISEMBL)
MLLALRSSSKMHFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVM***************DMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESL********DMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVK*********
Disordered Region (DISPRO)
*********************GCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP*********************************************************RKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAA****************************************DALAK*************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLLALRSSSKMHFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPxxxxxxxxxxxxxxxxxxxxxLTQEAVQTNKxxxxxxxxxxxxxxxxxxxxxVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKKLPPNT
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	322	2.2.26 [Sep-21-2011]
Q84XV2	386	Transcription factor GTE1	yes	no	0.866	0.722	0.604	3e-98
Q9FT54	369	Transcription factor GTE6	no	no	0.692	0.604	0.600	2e-69
Q9LNC4	766	Transcription factor GTE4	no	no	0.642	0.270	0.322	9e-25
Q5TJG6	803	Bromodomain-containing pr	yes	no	0.267	0.107	0.483	2e-20
Q32S26	803	Bromodomain-containing pr	yes	no	0.267	0.107	0.483	2e-20
Q6MGA9	798	Bromodomain-containing pr	yes	no	0.267	0.107	0.483	2e-20
Q7JJ13	798	Bromodomain-containing pr	yes	no	0.267	0.107	0.483	2e-20
P25440	801	Bromodomain-containing pr	yes	no	0.267	0.107	0.483	2e-20
P13709	2038	Homeotic protein female s	yes	no	0.285	0.045	0.458	3e-20
O60885	1362	Bromodomain-containing pr	no	no	0.285	0.067	0.468	4e-20

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

 Score =  358 bits (919), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 176/291 (60%), Positives = 226/291 (77%), Gaps = 12/291 (4%)

Query: 27  SASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKD 86
           S  L++ F    R  I QHKWAWPF+ PVDV+GLGLHDYY+VIEKPMD  TIK KM+  +
Sbjct: 107 SPDLMRQFATMFRQ-IAQHKWAWPFLEPVDVKGLGLHDYYKVIEKPMDLGTIKKKMESSE 165

Query: 87  GTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQ 146
              Y NVREIYADVRLVFKNAM+YN+E++DV+VMA+SLLEKFEEKWL ++PK++EEEK+Q
Sbjct: 166 ---YSNVREIYADVRLVFKNAMRYNEEKEDVYVMAESLLEKFEEKWLLIMPKLVEEEKKQ 222

Query: 147 EEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLG 206
            +EEA+   + QLT EA Q   A++L +EL E+D+QLE LRE+V+Q+CRK+ST+EKK L 
Sbjct: 223 VDEEAEKHANKQLTMEAAQAEMARDLSNELYEIDLQLEKLRESVVQRCRKLSTQEKKGLS 282

Query: 207 TALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASR 266
            AL RLSPEDL KAL++V+E+NPSF A A EV+LD+D Q+++TLWRLKVFVQE+LKAA++
Sbjct: 283 AALGRLSPEDLSKALKMVSESNPSFPAGAPEVELDIDVQTDVTLWRLKVFVQEALKAANK 342

Query: 267 SSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 317
           SSG     NNNN          + + NKNN KR++EI DA+ K ++KR KK
Sbjct: 343 SSGGTNAQNNNNT--------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 =  262 bits (670), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 134/223 (60%), Positives = 171/223 (76%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           ITQHK AWPFMHPV+VEGLGLHDY+EVI+KPMDFSTIKN+M+ KDGTGY++V +IYAD+R
Sbjct: 105 ITQHKCAWPFMHPVNVEGLGLHDYFEVIDKPMDFSTIKNQMEAKDGTGYKHVMQIYADMR 164

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQ 161
           LVF+NAM YN+E  DV+ MAK LLEKFEEKW   LPKV EEEK +EEEE +A  +  L +
Sbjct: 165 LVFENAMNYNEETSDVYSMAKKLLEKFEEKWAHFLPKVQEEEKIREEEEKQAAKEALLAK 224

Query: 162 EAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKAL 221
           EA      +EL +E+   + +LE L   V+++CRK++ EEK+N+G AL +LSP+DL K L
Sbjct: 225 EASHIKTTRELGNEICHANDELEKLMRKVVERCRKITIEEKRNIGLALLKLSPDDLQKVL 284

Query: 222 EIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAA 264
            IVA+ NPSF   A+EV ++MD   E TLWRLK FV+++L  A
Sbjct: 285 GIVAQANPSFQPRAEEVSIEMDILDEPTLWRLKFFVKDALDNA 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 =  114 bits (285), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 118/245 (48%), Gaps = 38/245 (15%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           + +HK  W F  PVDV+GLGL DYY +IE PMD  TIK+ +       Y++ RE   DVR
Sbjct: 432 LMKHKHGWVFNAPVDVKGLGLLDYYTIIEHPMDLGTIKSALMK---NLYKSPREFAEDVR 488

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQ 161
           L F NAM YN E  DVH+MA +LL+ FEE+W      V+E +  +E        +M L  
Sbjct: 489 LTFHNAMTYNPEGQDVHLMAVTLLQIFEERW-----AVIEADYNREMRFVTG-YEMNLPT 542

Query: 162 EAVQTNKAKEL-------RSELNEVD---------------MQLENLRETVIQKC----- 194
             +++     +       R+ ++  D                   + R   ++K      
Sbjct: 543 PTMRSRLGPTMPPPPINVRNTIDRADWSNRQPTTTPGRTPTSATPSGRTPALKKPKANEP 602

Query: 195 --RKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWR 252
             R M+ EEK+ L   L  L P+ L   ++IV + N +     +E+++D+D+    TLW 
Sbjct: 603 NKRDMTYEEKQKLSGHLQNLPPDKLDAIVQIVNKRNTAVKLRDEEIEVDIDSVDPETLWE 662

Query: 253 LKVFV 257
           L  FV
Sbjct: 663 LDRFV 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|Q5TJG6|BRD2_CANFA Bromodomain-containing protein 2 OS=Canis familiaris GN=BRD2 PE=3 SV=1

 Score =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)

Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 368 YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 424

Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             KYN    DV  MA+ L + FE ++ ++
Sbjct: 425 CYKYNPPDHDVVAMARKLQDVFEFRYAKM 453

Canis familiaris (taxid: 9615)

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

 Score =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)

Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 368 YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 424

Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             KYN    DV  MA+ L + FE ++ ++
Sbjct: 425 CYKYNPPDHDVVAMARKLQDVFEFRYAKM 453

Bos taurus (taxid: 9913)

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

 Score =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)

Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 367 YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 423

Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             KYN    DV  MA+ L + FE ++ ++
Sbjct: 424 CYKYNPPDHDVVAMARKLQDVFEFRYAKM 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 =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)

Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 367 YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 423

Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             KYN    DV  MA+ L + FE ++ ++
Sbjct: 424 CYKYNPPDHDVVAMARKLQDVFEFRYAKM 452

May play a role in spermatogenesis or folliculogenesis.

Mus musculus (taxid: 10090)

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

 Score =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)

Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 368 YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 424

Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             KYN    DV  MA+ L + FE ++ ++
Sbjct: 425 CYKYNPPDHDVVAMARKLQDVFEFRYAKM 453

May play a role in spermatogenesis or folliculogenesis.

Homo sapiens (taxid: 9606)

>sp|P13709|FSH_DROME Homeotic protein female sterile OS=Drosophila melanogaster GN=fs(1)h PE=1 SV=2

 Score = 99.8 bits (247), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 44/96 (45%), Positives = 61/96 (63%), Gaps = 4/96 (4%)

Query: 41  FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           F  +H  +AWPF  PVD E LGLHDY+++I+KPMD  T+K KMD ++   Y++  E  AD
Sbjct: 492 FSKKHSGYAWPFYKPVDAEMLGLHDYHDIIKKPMDLGTVKRKMDNRE---YKSAPEFAAD 548

Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           VRL+F N  KYN    DV  M + L + FE ++  +
Sbjct: 549 VRLIFTNCYKYNPPDHDVVAMGRKLQDVFEMRYANI 584

Required maternally for proper expression of other homeotic genes involved in pattern formation, such as Ubx.

Drosophila melanogaster (taxid: 7227)

>sp|O60885|BRD4_HUMAN Bromodomain-containing protein 4 OS=Homo sapiens GN=BRD4 PE=1 SV=2

 Score = 99.0 bits (245), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 45/96 (46%), Positives = 65/96 (67%), Gaps = 4/96 (4%)

Query: 41  FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct: 365 FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGAD 421

Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 422 VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 457

Plays a role in a process governing chromosomal dynamics during mitosis.

Homo sapiens (taxid: 9606)

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	322
224098028	370	global transcription factor group [Popul	0.875	0.762	0.687	1e-101
449452116	378	PREDICTED: transcription factor GTE1-lik	0.807	0.687	0.708	5e-99
356565711	738	PREDICTED: uncharacterized protein LOC10	0.773	0.337	0.707	5e-99
255577689	391	bromodomain-containing protein, putative	0.838	0.690	0.699	1e-97
30686240	386	Transcription factor GTE6 [Arabidopsis t	0.866	0.722	0.604	2e-96
62321808	386	RING3 protein-like [Arabidopsis thaliana	0.866	0.722	0.604	2e-96
42571057	276	Transcription factor GTE6 [Arabidopsis t	0.822	0.960	0.623	4e-96
297826963	386	imbibition-inducible 1 [Arabidopsis lyra	0.866	0.722	0.601	2e-95
359486529	440	PREDICTED: transcription factor GTE1-lik	0.847	0.620	0.670	7e-95
296086052	362	unnamed protein product [Vitis vinifera]	0.847	0.754	0.670	7e-95

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

 Score =  374 bits (959), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 202/294 (68%), Positives = 233/294 (79%), Gaps = 12/294 (4%)

Query: 27  SASLLQFFVRQARSF---ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 83
           +A  +Q  +RQ  +    ITQHKWAWPFM PVDV+GLGLHDYYEVI+KPMDFSTIKN+M+
Sbjct: 83  AAKRMQELMRQFGTILRQITQHKWAWPFMQPVDVKGLGLHDYYEVIDKPMDFSTIKNQME 142

Query: 84  GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE 143
            KDGTGY++VREI ADVRLVFKNAMKYNDER DVHVMAK+LL KFEEKWLQ LPKV EEE
Sbjct: 143 AKDGTGYKSVREICADVRLVFKNAMKYNDERSDVHVMAKTLLGKFEEKWLQFLPKVTEEE 202

Query: 144 KRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKK 203
           KR+EEEEA+AQLDMQL QEA     A++L +EL EVDM LE LRE V+QKCRKMSTEEK+
Sbjct: 203 KRREEEEAEAQLDMQLAQEAAHAKMARDLGNELYEVDMHLEELREMVVQKCRKMSTEEKR 262

Query: 204 NLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKA 263
            LG ALTRLSPEDL KALEIVA+NNP F ATA+EVDLD+DAQSE TLWRLK FV+++L+ 
Sbjct: 263 KLGAALTRLSPEDLTKALEIVAQNNPGFQATAEEVDLDIDAQSETTLWRLKFFVKDALEV 322

Query: 264 ASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 317
             +S+   GG NN             +  N NN KRK+EICDA+AK A KR+KK
Sbjct: 323 QGKSAASAGGRNNTT---------TPSNNNNNNNKRKREICDAIAKTAKKRSKK 367

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  367 bits (941), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 190/268 (70%), Positives = 224/268 (83%), Gaps = 8/268 (2%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           I+QHKWAWPFM PVDVEGLGLHDYYEVI+KPMDFSTIKN+M+ KDGTGY+NVREI +DVR
Sbjct: 108 ISQHKWAWPFMQPVDVEGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKNVREICSDVR 167

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQ 161
           LVFKNAMKYNDER DVHVMAK+LL KFEEKWLQLLPKV EEEKR+E+EEA+A LDMQL Q
Sbjct: 168 LVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREDEEAEALLDMQLAQ 227

Query: 162 EAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKAL 221
           EA Q   A+++ +E+ EVDMQLE LRE V+Q CRK+STEEK+ LG ALT+LSPED+ KAL
Sbjct: 228 EAAQAKMARDISNEIYEVDMQLEELRELVVQNCRKISTEEKRKLGAALTKLSPEDISKAL 287

Query: 222 EIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDD 281
           EIVAENNPSF ATA+EVDLD+DAQSE TLWRLK FV+++L+  ++SS   GG NN N+  
Sbjct: 288 EIVAENNPSFQATAEEVDLDIDAQSESTLWRLKFFVKDALEVHAKSSASTGGGNNQNH-- 345

Query: 282 NNNEKDNSNKKNKNNPKRKKEICDALAK 309
                  ++    +N KRKKEICDA+A+
Sbjct: 346 ------TNSNNINSNNKRKKEICDAIAR 367

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  367 bits (941), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 189/267 (70%), Positives = 218/267 (81%), Gaps = 18/267 (6%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           ITQHKWAWPFM PVD+EGLGLHDYYEVI+KPMDFSTIKN+M+ KDGTGY++VREI ADVR
Sbjct: 480 ITQHKWAWPFMQPVDIEGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKHVREICADVR 539

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQ 161
           LVFKNAMKYNDER DVHVMAK+LL KFEEKWLQLLPKV EEE R+EEEEA+AQL +Q+ Q
Sbjct: 540 LVFKNAMKYNDERSDVHVMAKTLLSKFEEKWLQLLPKVTEEETRREEEEAEAQLALQVAQ 599

Query: 162 EAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKAL 221
           EA Q   A++L +EL EVD+ LE LRE V+++ RKMSTEEK+ LG ALTRLSPEDL KAL
Sbjct: 600 EAAQAKMARDLSNELYEVDVILEELREMVVKRFRKMSTEEKRKLGDALTRLSPEDLSKAL 659

Query: 222 EIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDD 281
           EIVA+NNPSF ATA+EVDLDMDAQSE TLWRLK FV+E+L+   ++SG MGGN N NN  
Sbjct: 660 EIVAQNNPSFQATAEEVDLDMDAQSESTLWRLKFFVKEALEVQGKNSGSMGGNENQNN-- 717

Query: 282 NNNEKDNSNKKNKNNPKRKKEICDALA 308
                           KRK+E+CDA+A
Sbjct: 718 ----------------KRKRELCDAIA 728

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  362 bits (929), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 193/276 (69%), Positives = 227/276 (82%), Gaps = 6/276 (2%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           ITQHKWAWPFM PVDV+GLGLHDYYEVI+KPMDFSTIKN+M+ KDGTGY+NVREI ADVR
Sbjct: 119 ITQHKWAWPFMQPVDVKGLGLHDYYEVIDKPMDFSTIKNQMETKDGTGYKNVREICADVR 178

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQ 161
           LVFKNAMKYNDER DVHVMAK+LL KFEEKWLQLLPKV EEEKR+E EEA+AQLDMQL Q
Sbjct: 179 LVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREMEEAEAQLDMQLAQ 238

Query: 162 EAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKAL 221
           EAV    A+EL +EL E+D  L+ LR+ V+QKCRK+STEEK+ LG ALTRLSPEDL KAL
Sbjct: 239 EAVHAKMARELSNELYEIDTHLDELRDMVVQKCRKISTEEKRKLGAALTRLSPEDLTKAL 298

Query: 222 EIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDD 281
           EIVA+NNP F ATA+EVDLD+DAQ+E TLWRLK FV+++L+   +++       +   ++
Sbjct: 299 EIVAQNNPGFQATAEEVDLDIDAQTESTLWRLKFFVKDALEVQGKNA------ASAGGNN 352

Query: 282 NNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 317
           NNN  + +   N +N KRKKEICDA+AK A KR KK
Sbjct: 353 NNNNSNTTTNNNNSNNKRKKEICDAIAKTAKKRNKK 388

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30686240|ref|NP_181036.2| Transcription factor GTE6 [Arabidopsis thaliana] gi|75148956|sp|Q84XV2.1|GTE1_ARATH RecName: Full=Transcription factor GTE1; AltName: Full=Bromodomain-containing protein GTE1; AltName: Full=Protein GLOBAL TRANSCRIPTION FACTOR GROUP E1; AltName: Full=Protein IMBIBITION-INDUCIBLE 1 gi|27803868|gb|AAO22056.1| IMB1 [Arabidopsis thaliana] gi|110741364|dbj|BAF02232.1| RING3 protein-like [Arabidopsis thaliana] gi|111074406|gb|ABH04576.1| At2g34900 [Arabidopsis thaliana] gi|330253943|gb|AEC09037.1| Transcription factor GTE6 [Arabidopsis thaliana]

 Score =  358 bits (919), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 176/291 (60%), Positives = 226/291 (77%), Gaps = 12/291 (4%)

Query: 27  SASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKD 86
           S  L++ F    R  I QHKWAWPF+ PVDV+GLGLHDYY+VIEKPMD  TIK KM+  +
Sbjct: 107 SPDLMRQFATMFRQ-IAQHKWAWPFLEPVDVKGLGLHDYYKVIEKPMDLGTIKKKMESSE 165

Query: 87  GTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQ 146
              Y NVREIYADVRLVFKNAM+YN+E++DV+VMA+SLLEKFEEKWL ++PK++EEEK+Q
Sbjct: 166 ---YSNVREIYADVRLVFKNAMRYNEEKEDVYVMAESLLEKFEEKWLLIMPKLVEEEKKQ 222

Query: 147 EEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLG 206
            +EEA+   + QLT EA Q   A++L +EL E+D+QLE LRE+V+Q+CRK+ST+EKK L 
Sbjct: 223 VDEEAEKHANKQLTMEAAQAEMARDLSNELYEIDLQLEKLRESVVQRCRKLSTQEKKGLS 282

Query: 207 TALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASR 266
            AL RLSPEDL KAL++V+E+NPSF A A EV+LD+D Q+++TLWRLKVFVQE+LKAA++
Sbjct: 283 AALGRLSPEDLSKALKMVSESNPSFPAGAPEVELDIDVQTDVTLWRLKVFVQEALKAANK 342

Query: 267 SSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 317
           SSG     NNNN          + + NKNN KR++EI DA+ K ++KR KK
Sbjct: 343 SSGGTNAQNNNNT--------GTGEINKNNAKRRREISDAINKASIKRAKK 385

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|62321808|dbj|BAD95432.1| RING3 protein-like [Arabidopsis thaliana]

 Score =  358 bits (918), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 176/291 (60%), Positives = 225/291 (77%), Gaps = 12/291 (4%)

Query: 27  SASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKD 86
           S  L++ F    R  I QHKWAWPF+ PVDV+GLGLHDYY+VIEKPMD  TIK KM+  +
Sbjct: 107 SPDLMRQFATMFRQ-IAQHKWAWPFLEPVDVKGLGLHDYYKVIEKPMDLGTIKKKMESSE 165

Query: 87  GTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQ 146
              Y NVREIYADVRLVFKNAM+YN+E++DV+VMA+SLLEKFEEKWL ++PK++EEEK+Q
Sbjct: 166 ---YSNVREIYADVRLVFKNAMRYNEEKEDVYVMAESLLEKFEEKWLLIMPKLVEEEKKQ 222

Query: 147 EEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLG 206
            +EEA+   + QLT EA Q   A++L +EL E+D+QLE LRE+V+Q+CRK+ST+EKK L 
Sbjct: 223 VDEEAEKHANKQLTMEAAQAEMARDLSNELYEIDLQLEKLRESVVQRCRKLSTQEKKGLS 282

Query: 207 TALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASR 266
            AL RLSPEDL KAL++V+E+NPSF A A EV LD+D Q+++TLWRLKVFVQE+LKAA++
Sbjct: 283 AALGRLSPEDLSKALKMVSESNPSFPAGAPEVGLDIDVQTDVTLWRLKVFVQEALKAANK 342

Query: 267 SSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 317
           SSG     NNNN          + + NKNN KR++EI DA+ K ++KR KK
Sbjct: 343 SSGGTNAQNNNNT--------GTGEINKNNAKRRREISDAINKASIKRAKK 385

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42571057|ref|NP_973602.1| Transcription factor GTE6 [Arabidopsis thaliana] gi|330253942|gb|AEC09036.1| Transcription factor GTE6 [Arabidopsis thaliana]

 Score =  357 bits (916), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 172/276 (62%), Positives = 220/276 (79%), Gaps = 11/276 (3%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           I QHKWAWPF+ PVDV+GLGLHDYY+VIEKPMD  TIK KM+  +   Y NVREIYADVR
Sbjct: 11  IAQHKWAWPFLEPVDVKGLGLHDYYKVIEKPMDLGTIKKKMESSE---YSNVREIYADVR 67

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQ 161
           LVFKNAM+YN+E++DV+VMA+SLLEKFEEKWL ++PK++EEEK+Q +EEA+   + QLT 
Sbjct: 68  LVFKNAMRYNEEKEDVYVMAESLLEKFEEKWLLIMPKLVEEEKKQVDEEAEKHANKQLTM 127

Query: 162 EAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKAL 221
           EA Q   A++L +EL E+D+QLE LRE+V+Q+CRK+ST+EKK L  AL RLSPEDL KAL
Sbjct: 128 EAAQAEMARDLSNELYEIDLQLEKLRESVVQRCRKLSTQEKKGLSAALGRLSPEDLSKAL 187

Query: 222 EIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASRSSGDMGGNNNNNNDD 281
           ++V+E+NPSF A A EV+LD+D Q+++TLWRLKVFVQE+LKAA++SSG     NNNN   
Sbjct: 188 KMVSESNPSFPAGAPEVELDIDVQTDVTLWRLKVFVQEALKAANKSSGGTNAQNNNNT-- 245

Query: 282 NNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 317
                  + + NKNN KR++EI DA+ K ++KR KK
Sbjct: 246 ------GTGEINKNNAKRRREISDAINKASIKRAKK 275

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297826963|ref|XP_002881364.1| imbibition-inducible 1 [Arabidopsis lyrata subsp. lyrata] gi|297327203|gb|EFH57623.1| imbibition-inducible 1 [Arabidopsis lyrata subsp. lyrata]

 Score =  355 bits (911), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 175/291 (60%), Positives = 224/291 (76%), Gaps = 12/291 (4%)

Query: 27  SASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKD 86
           S  L++ F    R  I QHKWAWPF+ PVDV+GLGLHDYY+VIEKPMD  TIK KM+  +
Sbjct: 107 SPDLMRQFATMFRQ-IAQHKWAWPFLEPVDVKGLGLHDYYKVIEKPMDLGTIKKKMESSE 165

Query: 87  GTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQ 146
              Y NVREIYADVRLVFKNAM+YN+E++DV+VMA+SLLEKFEEKWL ++PK++EEEK+Q
Sbjct: 166 ---YSNVREIYADVRLVFKNAMRYNEEKEDVYVMAESLLEKFEEKWLLIMPKLVEEEKKQ 222

Query: 147 EEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKKNLG 206
            +EEA+   + QLT EA Q   A++L +EL E+D+QLE LRE+V+Q+CRK+ST+EKK L 
Sbjct: 223 ADEEAEKHANKQLTLEAAQAEMARDLSNELYEIDLQLERLRESVVQRCRKLSTQEKKGLS 282

Query: 207 TALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKAASR 266
            AL RLSPEDL KAL++V+E+NPSF A A EV+LD+D Q+++TLWRLKVFVQE+LKAA++
Sbjct: 283 AALGRLSPEDLSKALKMVSESNPSFPAGAPEVELDIDVQTDVTLWRLKVFVQEALKAANK 342

Query: 267 SSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICDALAKPAVKRTKK 317
            SG     NNNN          + + NKNN KR++EI DA+ K + KR KK
Sbjct: 343 GSGGTNAQNNNNT--------GTGEINKNNAKRRREISDAINKASTKRAKK 385

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  353 bits (906), Expect = 7e-95,   Method: Compositional matrix adjust.
 Identities = 189/282 (67%), Positives = 223/282 (79%), Gaps = 9/282 (3%)

Query: 27  SASLLQFFVRQARSF---ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 83
           +A  +Q  +RQ  +    ITQHKWAWPFM PVDVEGLGLHDYYEVIEKPMDFSTIKNKM+
Sbjct: 150 AAKRMQELMRQFGTILRQITQHKWAWPFMQPVDVEGLGLHDYYEVIEKPMDFSTIKNKME 209

Query: 84  GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE 143
            KDG GY+NVREI ADVRLVFKNAMKYNDER DVHVMAK+LL KFEEKWLQLLPKV EE+
Sbjct: 210 AKDGAGYKNVREICADVRLVFKNAMKYNDERRDVHVMAKTLLGKFEEKWLQLLPKVAEED 269

Query: 144 KRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKK 203
           KR+EEEEA+AQLDM L QEA     A+++ +EL E+DM L+++RE ++QKCRK STEEK+
Sbjct: 270 KRREEEEAEAQLDMHLAQEAAHAKMARDISNELFEIDMHLDDIREIIVQKCRKTSTEEKR 329

Query: 204 NLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKA 263
            LG AL+RLS EDL KALEIVA++NPSF ATA+EV LD+DAQ E TLWRLK FV+++L+ 
Sbjct: 330 KLGAALSRLSAEDLSKALEIVAQSNPSFQATAEEVHLDIDAQRESTLWRLKFFVKDALEI 389

Query: 264 ASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICD 305
             +SS  MGGNN           +N++    NN KRKKEICD
Sbjct: 390 QGKSSASMGGNNTATT------TNNNHPTTNNNSKRKKEICD 425

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  353 bits (905), Expect = 7e-95,   Method: Compositional matrix adjust.
 Identities = 189/282 (67%), Positives = 223/282 (79%), Gaps = 9/282 (3%)

Query: 27  SASLLQFFVRQARSF---ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMD 83
           +A  +Q  +RQ  +    ITQHKWAWPFM PVDVEGLGLHDYYEVIEKPMDFSTIKNKM+
Sbjct: 72  AAKRMQELMRQFGTILRQITQHKWAWPFMQPVDVEGLGLHDYYEVIEKPMDFSTIKNKME 131

Query: 84  GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE 143
            KDG GY+NVREI ADVRLVFKNAMKYNDER DVHVMAK+LL KFEEKWLQLLPKV EE+
Sbjct: 132 AKDGAGYKNVREICADVRLVFKNAMKYNDERRDVHVMAKTLLGKFEEKWLQLLPKVAEED 191

Query: 144 KRQEEEEAKAQLDMQLTQEAVQTNKAKELRSELNEVDMQLENLRETVIQKCRKMSTEEKK 203
           KR+EEEEA+AQLDM L QEA     A+++ +EL E+DM L+++RE ++QKCRK STEEK+
Sbjct: 192 KRREEEEAEAQLDMHLAQEAAHAKMARDISNELFEIDMHLDDIREIIVQKCRKTSTEEKR 251

Query: 204 NLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQESLKA 263
            LG AL+RLS EDL KALEIVA++NPSF ATA+EV LD+DAQ E TLWRLK FV+++L+ 
Sbjct: 252 KLGAALSRLSAEDLSKALEIVAQSNPSFQATAEEVHLDIDAQRESTLWRLKFFVKDALEI 311

Query: 264 ASRSSGDMGGNNNNNNDDNNNEKDNSNKKNKNNPKRKKEICD 305
             +SS  MGGNN           +N++    NN KRKKEICD
Sbjct: 312 QGKSSASMGGNNTATT------TNNNHPTTNNNSKRKKEICD 347

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	322
TAIR|locus:2044722	386	IMB1 "AT2G34900" [Arabidopsis	0.922	0.769	0.525	4.8e-78
TAIR|locus:2155715	590	GTE7 "AT5G65630" [Arabidopsis	0.263	0.144	0.5	2.6e-27
TAIR|locus:2038565	766	GTE4 "AT1G06230" [Arabidopsis	0.273	0.114	0.538	4.8e-27
TAIR|locus:2030958	487	AT1G17790 "AT1G17790" [Arabido	0.350	0.232	0.411	8.5e-26
UNIPROTKB|H9L2H3	859	LOC100859056 "Uncharacterized	0.285	0.107	0.468	1e-25
UNIPROTKB|O60885	1362	BRD4 "Bromodomain-containing p	0.285	0.067	0.468	7.6e-25
UNIPROTKB|E1BNS3	1367	BRD4 "Uncharacterized protein"	0.285	0.067	0.468	7.7e-25
UNIPROTKB|I3L6E5	1372	BRD4 "Uncharacterized protein"	0.285	0.067	0.468	7.8e-25
MGI|MGI:1888520	1400	Brd4 "bromodomain containing 4	0.285	0.065	0.468	8.2e-25
MGI|MGI:99495	798	Brd2 "bromodomain containing 2	0.267	0.107	0.483	1.4e-24

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

 Score = 785 (281.4 bits), Expect = 4.8e-78, P = 4.8e-78
 Identities = 164/312 (52%), Positives = 215/312 (68%)

Query:     7 SSSKMHFIGKKLLEGGCKNLSA-SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDY 65
             ++SK +  GK+  +G  K++S+  L++ F    R  I QHKWAWPF+ PVDV+GLGLHDY
Sbjct:    88 NNSKGNSAGKEKSKG--KHVSSPDLMRQFATMFRQ-IAQHKWAWPFLEPVDVKGLGLHDY 144

Query:    66 YEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLL 125
             Y+VIEKPMD  TIK KM+  +   Y NVREIYADVRLVFKNAM+YN+E++DV+VMA+SLL
Sbjct:   145 YKVIEKPMDLGTIKKKMESSE---YSNVREIYADVRLVFKNAMRYNEEKEDVYVMAESLL 201

Query:   126 EKFEEKWLQLLPKVMXXXXXXXXXXXXXXLDMQLTQEAVQTNKAKELRSELNEVDMQLEN 185
             EKFEEKWL ++PK++               + QLT EA Q   A++L +EL E+D+QLE 
Sbjct:   202 EKFEEKWLLIMPKLVEEEKKQVDEEAEKHANKQLTMEAAQAEMARDLSNELYEIDLQLEK 261

Query:   186 LRETVIQKCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQEVDLDMDAQ 245
             LRE+V+Q+CRK+ST+EKK L  AL RLSPEDL KAL++V+E+NPSF A A EV+LD+D Q
Sbjct:   262 LRESVVQRCRKLSTQEKKGLSAALGRLSPEDLSKALKMVSESNPSFPAGAPEVELDIDVQ 321

Query:   246 SELTLWRLKVFVQESLKAASRSSGDMGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXEICD 305
             +++TLWRLKVFVQE+LKAA++SSG                                EI D
Sbjct:   322 TDVTLWRLKVFVQEALKAANKSSGGTNAQNNNNTGTGEINKNNAKRRR--------EISD 373

Query:   306 ALAKPAVKRTKK 317
             A+ K ++KR KK
Sbjct:   374 AINKASIKRAKK 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:2155715 GTE7 "AT5G65630" [Arabidopsis thaliana (taxid:3702)]

 Score = 222 (83.2 bits), Expect = 2.6e-27, Sum P(2) = 2.6e-27
 Identities = 44/88 (50%), Positives = 58/88 (65%)

Query:    42 ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
             + +HKWAW F  PVDV GLGLHDY++V++KPMD  T+K  +D   G  Y +  +   DVR
Sbjct:   180 LMKHKWAWVFNTPVDVVGLGLHDYHQVVKKPMDLGTVKLNLD--KGF-YVSPIDFATDVR 236

Query:   102 LVFKNAMKYNDERDDVHVMAKSLLEKFE 129
             L F NAM YN +  DV+ MA  LL+ F+
Sbjct:   237 LTFDNAMTYNPKGQDVYFMADKLLDHFD 264

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 237 (88.5 bits), Expect = 4.8e-27, Sum P(2) = 4.8e-27
 Identities = 49/91 (53%), Positives = 62/91 (68%)

Query:    42 ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
             + +HK  W F  PVDV+GLGL DYY +IE PMD  TIK+ +  K+   Y++ RE   DVR
Sbjct:   432 LMKHKHGWVFNAPVDVKGLGLLDYYTIIEHPMDLGTIKSALM-KNL--YKSPREFAEDVR 488

Query:   102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 132
             L F NAM YN E  DVH+MA +LL+ FEE+W
Sbjct:   489 LTFHNAMTYNPEGQDVHLMAVTLLQIFEERW 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:2030958 AT1G17790 "AT1G17790" [Arabidopsis thaliana (taxid:3702)]

 Score = 221 (82.9 bits), Expect = 8.5e-26, Sum P(2) = 8.5e-26
 Identities = 51/124 (41%), Positives = 73/124 (58%)

Query:    15 GKKLLEGGCKNLSASLLQFFVRQARSFITQ---HKWAWPFMHPVDVEGLGLHDYYEVIEK 71
             GKK   G  K      +Q F +   S +T+   HK AW F  PVD +GLGLHDY+ ++++
Sbjct:   118 GKKSGHGADKGT----VQIF-KNCNSLLTKLMKHKSAWVFNVPVDAKGLGLHDYHNIVKE 172

Query:    72 PMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
             PMD  T+K K+ GK  + Y++  +   DVRL F NA+ YN    DV+  A+ LL  FE+K
Sbjct:   173 PMDLGTVKTKL-GK--SLYKSPLDFAEDVRLTFNNAILYNPIGHDVYRFAELLLNMFEDK 229

Query:   132 WLQL 135
             W+ +
Sbjct:   230 WVSI 233

GO:0003677 "DNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0005515 "protein binding" evidence=IPI

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

 Score = 231 (86.4 bits), Expect = 1.0e-25, Sum P(2) = 1.0e-25
 Identities = 45/96 (46%), Positives = 65/96 (67%)

Query:    41 FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
             F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct:   362 FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDLSTIKSKLENRE---YRDAQEFAAD 418

Query:   100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             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

UNIPROTKB|O60885 BRD4 "Bromodomain-containing protein 4" [Homo sapiens (taxid:9606)]

 Score = 230 (86.0 bits), Expect = 7.6e-25, Sum P(2) = 7.6e-25
 Identities = 45/96 (46%), Positives = 65/96 (67%)

Query:    41 FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
             F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct:   365 FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGAD 421

Query:   100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct:   422 VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 457

GO:0019048 "virus-host interaction" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0007059 "chromosome segregation" 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

GO:0005515 "protein binding" evidence=IPI

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

GO:0000794 "condensed nuclear chromosome" evidence=IDA

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

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

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E1BNS3 BRD4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 230 (86.0 bits), Expect = 7.7e-25, Sum P(2) = 7.7e-25
 Identities = 45/96 (46%), Positives = 65/96 (67%)

Query:    41 FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
             F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct:   365 FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGAD 421

Query:   100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct:   422 VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 457

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

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

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

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

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

GO:0007059 "chromosome segregation" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

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

UNIPROTKB|I3L6E5 BRD4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 230 (86.0 bits), Expect = 7.8e-25, Sum P(2) = 7.8e-25
 Identities = 45/96 (46%), Positives = 65/96 (67%)

Query:    41 FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
             F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct:   365 FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGAD 421

Query:   100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct:   422 VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 457

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

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

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

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

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

GO:0007059 "chromosome segregation" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

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

MGI|MGI:1888520 Brd4 "bromodomain containing 4" [Mus musculus (taxid:10090)]

 Score = 230 (86.0 bits), Expect = 8.2e-25, Sum P(2) = 8.2e-25
 Identities = 45/96 (46%), Positives = 65/96 (67%)

Query:    41 FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
             F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct:   366 FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESRE---YRDAQEFGAD 422

Query:   100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct:   423 VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 458

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

GO:0000790 "nuclear chromatin" evidence=IDA

GO:0000794 "condensed nuclear chromosome" evidence=ISO;IDA

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

GO:0003677 "DNA binding" evidence=IDA

GO:0003682 "chromatin binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0006468 "protein phosphorylation" evidence=IPI

GO:0007059 "chromosome segregation" evidence=IMP

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

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

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

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

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

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

 Score = 232 (86.7 bits), Expect = 1.4e-24, Sum P(2) = 1.4e-24
 Identities = 43/89 (48%), Positives = 60/89 (67%)

Query:    47 WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
             +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct:   367 YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 423

Query:   107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
               KYN    DV  MA+ L + FE ++ ++
Sbjct:   424 CYKYNPPDHDVVAMARKLQDVFEFRYAKM 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

---

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	0.6048	0.8664	0.7227	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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GTE908 global transcription factor group (370 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

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	322
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	7e-42
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	2e-31
smart00297	107	smart00297, BROMO, bromo domain	2e-25
cd04369	99	cd04369, Bromodomain, Bromodomain	7e-25
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	2e-22
pfam00439	84	pfam00439, Bromodomain, Bromodomain	2e-21
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	3e-20
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	8e-19
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	4e-17
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	7e-17
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	5e-16
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	2e-15
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	4e-14
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	5e-13
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	6e-13
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	7e-12
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	4e-11
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	3e-10
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	6e-10
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	6e-09
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	9e-09
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	8e-08
COG5076	371	COG5076, COG5076, Transcription factor involved in	9e-08
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	2e-07
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	1e-06
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	1e-06
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	1e-06
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	2e-06
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	3e-06
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	1e-05
cd05501	102	cd05501, Bromo_SP100C_like, Bromodomain, SP100C_li	4e-04
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	6e-04
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	7e-04
cd05494	114	cd05494, Bromodomain_1, Bromodomain; uncharacteriz	9e-04
cd05508	99	cd05508, Bromo_RACK7, Bromodomain, RACK7_like subf	0.004

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

 Score =  140 bits (354), Expect = 7e-42
 Identities = 46/92 (50%), Positives = 60/92 (65%), Gaps = 3/92 (3%)

Query: 41  FITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADV 100
            + +HKW W F  PVDV  LGL DY+++I+KPMD  T+K K++      Y +  E  ADV
Sbjct: 11  KLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKG---EYSSPEEFAADV 67

Query: 101 RLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 132
           RL F NAM+YN   +DVH MAK LL+ FE +W
Sbjct: 68  RLTFANAMRYNPPGNDVHTMAKELLKIFETRW 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 (284), Expect = 2e-31
 Identities = 47/93 (50%), Positives = 63/93 (67%), Gaps = 4/93 (4%)

Query: 41  FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           F  +HK +AWPF  PVD E LGLHDY+++I+ PMD STIK K+D ++   Y + +E  AD
Sbjct: 13  FSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNRE---YADAQEFAAD 69

Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 132
           VRL+F N  KYN     VH MA+ L + FE++W
Sbjct: 70  VRLMFSNCYKYNPPDHPVHAMARKLQDVFEDRW 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 = 97.3 bits (243), Expect = 2e-25
 Identities = 39/106 (36%), Positives = 57/106 (53%), Gaps = 5/106 (4%)

Query: 30  LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 89
            LQ  ++     +  H  +WPF+ PV  +     DYY++I+KPMD  TIK K++      
Sbjct: 7   KLQELLKAVLDKLDSHPLSWPFLKPVSRKEA--PDYYDIIKKPMDLKTIKKKLENG---K 61

Query: 90  YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           Y +V E  AD  L+F NA  YN    +V+  AK L + FE+K  +L
Sbjct: 62  YSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

Length = 107

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score = 95.9 bits (239), Expect = 7e-25
 Identities = 36/85 (42%), Positives = 50/85 (58%), Gaps = 5/85 (5%)

Query: 48  AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA 107
           + PF+ PVD +     DYYEVI+ PMD STIK K+   +   Y+++ E  ADVRL+F NA
Sbjct: 20  SEPFLEPVDPKEA--PDYYEVIKNPMDLSTIKKKLKNGE---YKSLEEFEADVRLIFSNA 74

Query: 108 MKYNDERDDVHVMAKSLLEKFEEKW 132
             YN     ++  AK L + FE+  
Sbjct: 75  KTYNGPGSPIYKDAKKLEKLFEKLL 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 = 2e-22
 Identities = 36/89 (40%), Positives = 53/89 (59%), Gaps = 5/89 (5%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNK-MDGKDGTGYRNVREIYADVRLV 103
             + WPF+ PVD   L + +Y+ +I+KPMD  TI  K  +G+    Y++ +E   DVRL+
Sbjct: 18  SAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQ----YQSAKEFERDVRLI 73

Query: 104 FKNAMKYNDERDDVHVMAKSLLEKFEEKW 132
           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 = 2e-21
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 5/87 (5%)

Query: 36  RQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVRE 95
            +    + +H  A PF+ PVD E     DYYEVI++PMD STI+ K+       Y+++ E
Sbjct: 2   LEILEDLMEHPLAEPFLEPVDPEEY--PDYYEVIKEPMDLSTIRQKLKSGK---YKSLAE 56

Query: 96  IYADVRLVFKNAMKYNDERDDVHVMAK 122
              DV L+F NA+ YN E  D++  AK
Sbjct: 57  FLKDVELIFSNAITYNGEDSDIYKDAK 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|99929 cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like subfamily, repeat I

 Score = 83.6 bits (207), Expect = 3e-20
 Identities = 38/105 (36%), Positives = 59/105 (56%), Gaps = 3/105 (2%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+ ++     + +HK+AWPF  PVD   L L DY+++I+ PMD  TIK +++      Y
Sbjct: 6   LQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNY---Y 62

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            +  E   D   +F N   YN   DDV +MA++L + F +K  Q+
Sbjct: 63  WSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQM 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|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score = 79.5 bits (197), Expect = 8e-19
 Identities = 35/90 (38%), Positives = 51/90 (56%), Gaps = 5/90 (5%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  HK AWPF+ PVD E     DYY+VI+KPMD ST++ K++      Y  + E  AD++
Sbjct: 13  LKNHKSAWPFLEPVDKEEA--PDYYDVIKKPMDLSTMEEKLENGY---YVTLEEFVADLK 67

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
           L+F N   YN    + +  A  L + F +K
Sbjct: 68  LIFDNCRLYNGPDTEYYKCANKLEKFFWKK 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|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 75.4 bits (186), Expect = 4e-17
 Identities = 30/82 (36%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 48  AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA 107
           A PF+ PVD   L +  Y  +I+KPMD  TI+ K+       Y +V E  AD  L+  N 
Sbjct: 22  ARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKL---KSNVYTSVEEFTADFNLMVDNC 78

Query: 108 MKYNDERDDVHVMAKSLLEKFE 129
           + +N     V  M K L   FE
Sbjct: 79  LTFNGPEHPVSQMGKRLQAAFE 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 = 74.6 bits (184), Expect = 7e-17
 Identities = 35/89 (39%), Positives = 50/89 (56%), Gaps = 3/89 (3%)

Query: 50  PFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK 109
           PF  PV      + +YY++I+ PMD S I+ K+  K    Y +  E  ADVRL+FKN  K
Sbjct: 24  PFHEPV---SPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

Query: 110 YNDERDDVHVMAKSLLEKFEEKWLQLLPK 138
           +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|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily

 Score = 72.5 bits (178), Expect = 5e-16
 Identities = 35/101 (34%), Positives = 53/101 (52%), Gaps = 3/101 (2%)

Query: 30  LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 89
           L Q  +        Q   + PF  PVD + LG+ DY+++++ PMD STI+ K+D   G  
Sbjct: 4   LRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLD--TGQ- 60

Query: 90  YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEE 130
           Y++  +   DV L+F NA  YN +   V+     L E FE+
Sbjct: 61  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|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily

 Score = 70.9 bits (174), Expect = 2e-15
 Identities = 33/90 (36%), Positives = 50/90 (55%), Gaps = 5/90 (5%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           I +HK +WPF+ PV    +   DYY++I+KPMD  TIK K++  +   Y+   E  +D++
Sbjct: 24  IVKHKDSWPFLRPVSKIEVP--DYYDIIKKPMDLGTIKEKLNMGE---YKLAEEFLSDIQ 78

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
           LVF N   YN E   V+     L   F ++
Sbjct: 79  LVFSNCFLYNPEHTSVYKAGTRLQRFFIKR 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|99935 cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BAZ2B_like subfamily

 Score = 66.6 bits (163), Expect = 4e-14
 Identities = 34/91 (37%), Positives = 54/91 (59%), Gaps = 11/91 (12%)

Query: 45  HKWAWPFMHPVD---VEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           H+ AWPF+ PV+   V G     Y ++I+KPMDFSTI+ K++      Y+ + E   DVR
Sbjct: 15  HEDAWPFLEPVNTKLVPG-----YRKIIKKPMDFSTIREKLESG---QYKTLEEFAEDVR 66

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 132
           LVF N   +N++  +V     ++ + FE++W
Sbjct: 67  LVFDNCETFNEDDSEVGRAGHNMRKFFEKRW 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|99943 cd05511, Bromo_TFIID, Bromodomain, TFIID-like subfamily

 Score = 64.2 bits (157), Expect = 5e-13
 Identities = 33/111 (29%), Positives = 51/111 (45%), Gaps = 18/111 (16%)

Query: 48  AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA 107
           +WPF  PV+     + DYY++I++PMD  TI+ K+       Y++  E   D+ L+  N+
Sbjct: 18  SWPFHTPVN--KKKVPDYYKIIKRPMDLQTIRKKISKH---KYQSREEFLEDIELIVDNS 72

Query: 108 MKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQ 158
           + YN         AK +LE             + EE   E EE   QL+  
Sbjct: 73  VLYNGPDSVYTKKAKEMLE-------------LAEELLAEREEKLTQLEKN 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|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily

 Score = 64.4 bits (157), Expect = 6e-13
 Identities = 33/99 (33%), Positives = 50/99 (50%), Gaps = 6/99 (6%)

Query: 50  PFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK 109
           PF  PVD+  L   DY ++I+ PMD  T+K  + G +   Y +  E   DVRL+F N+  
Sbjct: 25  PFRQPVDL--LKYPDYRDIIDTPMDLGTVKETLFGGN---YDDPMEFAKDVRLIFSNSKS 79

Query: 110 YN-DERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQE 147
           Y  ++R  ++ M   L   FEE   +++       KR E
Sbjct: 80  YTPNKRSRIYSMTLRLSALFEEHIKKIISDWKSALKRNE 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|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup

 Score = 60.8 bits (148), Expect = 7e-12
 Identities = 30/87 (34%), Positives = 48/87 (55%), Gaps = 5/87 (5%)

Query: 40  SFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
             +  H++A  F+ PV  +      Y+ V+ +PMD STIK  ++  +GT  R+  E   D
Sbjct: 13  RTLASHRYASVFLKPVTEDIA--PGYHSVVYRPMDLSTIKKNIE--NGT-IRSTAEFQRD 67

Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLE 126
           V L+F+NA+ YN    DV++MA  +  
Sbjct: 68  VLLMFQNAIMYNSSDHDVYLMAVEMQR 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|99937 cd05505, Bromo_WSTF_like, Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like)

 Score = 58.7 bits (142), Expect = 4e-11
 Identities = 32/95 (33%), Positives = 52/95 (54%), Gaps = 9/95 (9%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           I +++++WPF  PV  +     DY +VI  PMD  T++ K        Y +V+E   D++
Sbjct: 12  ILKYRFSWPFREPVTADEA--EDYKKVITNPMDLQTMQTKCSCGS---YSSVQEFLDDMK 66

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL 136
           LVF NA KY +  +  +V+  S + K E+  + LL
Sbjct: 67  LVFSNAEKYYE--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 = 56.5 bits (137), Expect = 3e-10
 Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 7/71 (9%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVH----V 119
           DYY+VI+KP+D   I++K++G     Y+++ ++ +D  L+F NA KYN+    ++     
Sbjct: 38  DYYDVIKKPIDMEKIRSKIEGN---QYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALT 94

Query: 120 MAKSLLEKFEE 130
           + 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 = 55.4 bits (134), Expect = 6e-10
 Identities = 30/85 (35%), Positives = 45/85 (52%), Gaps = 5/85 (5%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L+ F+R     +   K    F  PVD E +   DYYE+I++PMD  TI  K+D      Y
Sbjct: 4   LRLFLRDVLKRLASDKRFNAFTKPVDEEEV--PDYYEIIKQPMDLQTILQKLDTHQ---Y 58

Query: 91  RNVREIYADVRLVFKNAMKYNDERD 115
              ++   D+ L+  NA++YN +RD
Sbjct: 59  LTAKDFLKDIDLIVTNALEYNPDRD 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 = 52.4 bits (126), Expect = 6e-09
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 5/61 (8%)

Query: 51  FMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY 110
           F  PVD+  +   DY + I++PMDFST++ K++ +    YR + +  AD  L+  N + Y
Sbjct: 22  FSEPVDLSEV--PDYLDHIKQPMDFSTMRKKLESQ---RYRTLEDFEADFNLIINNCLAY 76

Query: 111 N 111
           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 = 9e-09
 Identities = 25/61 (40%), Positives = 36/61 (59%), Gaps = 3/61 (4%)

Query: 65  YYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSL 124
           Y  +I+ PMDFST+K K+   D   Y+++ E   D +L+ +NAMKYN      +  AK L
Sbjct: 34  YSSIIKHPMDFSTMKEKIKNND---YQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90

Query: 125 L 125
           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 = 49.4 bits (118), Expect = 8e-08
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 63  HDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAK 122
            DYY++I+KPMD  T+  K+       Y++  E   D+ L++KN + YN +         
Sbjct: 39  PDYYDIIKKPMDLGTMLKKLKNLQ---YKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHA 95

Query: 123 SLLEKFEEKWLQLLP 137
           + ++K  E  L+L+P
Sbjct: 96  NFMKKKAEHLLKLIP 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 = 9e-08
 Identities = 29/97 (29%), Positives = 51/97 (52%), Gaps = 3/97 (3%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 123
           DYYE+I+ PMD  TI+ K+       Y++  E  +D+ L+F N   YN     V+V AK 
Sbjct: 180 DYYEIIKSPMDLLTIQKKLKN---GRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKE 236

Query: 124 LLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLT 160
           L + F +   ++  +++E   +   EE + +  + +T
Sbjct: 237 LEKYFLKLIEEIPEEMLELSIKPGREEREERESVLIT 273

Length = 371

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

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 7/69 (10%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE----RDDVHV 119
           DYY++I +P+D  TI++ +       Y    E+  D +L+F+NA  YN+E     +D ++
Sbjct: 38  DYYKIILEPIDLKTIEHNIRNDK---YATEEELMDDFKLMFRNARHYNEEGSQVYEDANI 94

Query: 120 MAKSLLEKF 128
           + 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: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 123
           DYY+ I+ P+    I+ K+  K+G  Y  + E+ AD+ L+F+NA +YN     ++  A+ 
Sbjct: 38  DYYQEIKNPISLQQIRTKL--KNG-EYETLEELEADLNLMFENAKRYNVPNSRIYKDAEK 94

Query: 124 LLEKFEEK 131
           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|99947 cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like subfamily, specific to animals

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 62  LHDYYEVIEKPMDFSTIKNKM-DGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVM 120
           L +YYE+I KP+DF  IK ++ + K    YR++ ++  DV L+ +NA  +N E   ++  
Sbjct: 37  LPEYYELIRKPVDFKKIKERIRNHK----YRSLEDLEKDVMLLCQNAQTFNLEGSLIYED 92

Query: 121 AKSLLEKFEE 130
           +  L   F+ 
Sbjct: 93  SIVLQSVFKS 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|99950 cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfamily, specific to fungi

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 3/68 (4%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 123
           DYY +I++P+    IK +++G     Y+++ E   D  L+F NA  YN E   V+  A  
Sbjct: 38  DYYVIIKRPIALDQIKRRIEG---RAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVE 94

Query: 124 LLEKFEEK 131
           + + 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|99958 cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like subfamily

 Score = 46.2 bits (110), Expect = 2e-06
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 4/85 (4%)

Query: 44  QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV 103
           Q + A  F +PVD+      DY+  +  PMD  TI+++++ +    YR++  +  DVRL+
Sbjct: 41  QLEIAEYFEYPVDL-RAWYPDYWNRVPVPMDLETIRSRLENR---YYRSLEALRHDVRLI 96

Query: 104 FKNAMKYNDERDDVHVMAKSLLEKF 128
             NA  +N+   ++   AK L +  
Sbjct: 97  LSNAETFNEPNSEIAKKAKRLSDWL 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|99952 cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 123
           DYY++I+ P+  +T+K ++       Y N +E   D+  +  NA  YN +   ++  A  
Sbjct: 39  DYYKIIKNPLSLNTVKKRL-----PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYAL- 92

Query: 124 LLEKF 128
           +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 = 43.5 bits (103), Expect = 1e-05
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 123
           +YYEV+  P+D   I+ K+  ++   Y +V ++ AD  L+  NA  Y       H  A  
Sbjct: 40  EYYEVVSNPIDLLKIQQKLKTEE---YDDVDDLTADFELLINNAKAYYKPDSPEHKDACK 96

Query: 124 LLEKFEE 130
           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 = 38.6 bits (90), Expect = 4e-04
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS 123
           DY + I++PM  + +K +++ +    Y  V     D+RL+F N   +  + D   V    
Sbjct: 32  DYCQGIKEPMWLNKVKERLNER---VYHTVEGFVRDMRLIFHNHKLFYKDDDFGQVGIT- 87

Query: 124 LLEKFEE 130
           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|99953 cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE 113
           +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 = 7e-04
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 5/67 (7%)

Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTG-YRNVREIYADVRLVFKNAMKYNDERDDVHVMAK 122
           DYYE I  P+D STI+ ++     TG Y+      +D+  VF+NA KY   +  +     
Sbjct: 40  DYYERITDPVDLSTIEKQIL----TGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVC 95

Query: 123 SLLEKFE 129
            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

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

 Score = 38.2 bits (89), Expect = 9e-04
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 42 ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKN 80
            +++ AWPF+ PV+    G  DY +VI++PM F T  N
Sbjct: 15 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|99940 cd05508, Bromo_RACK7, Bromodomain, RACK7_like subfamily

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 13/81 (16%)

Query: 50  PFMHPVDVEGLGLHDYYEVIEKPMDFST----IKNKMDGKDGTGYRNVREIYADVRLVFK 105
           PF+ PVD+E     DY + + KPMD ST    ++ K        Y +     AD + +  
Sbjct: 22  PFLKPVDLEQF--PDYAQYVFKPMDLSTLEKNVRKKA-------YGSTDAFLADAKWILH 72

Query: 106 NAMKYNDERDDVHVMAKSLLE 126
           NA+ YN     +   AK++++
Sbjct: 73  NAIIYNGGDHKLTQAAKAIVK 93

RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 99

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	322
KOG1474	640	consensus Transcription initiation factor TFIID, s	100.0
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.96
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.96
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.95
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.95
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.95
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.94
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.94
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.94
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.94
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.94
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.94
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.94
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.94
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.94
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.94
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.94
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.93
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.93
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.93
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.92
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.92
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.91
smart00297	107	BROMO bromo domain.	99.9
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.9
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.9
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.9
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.9
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.9
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.89
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.89
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.87
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.87
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.87
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.86
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.86
KOG1245	1404	consensus Chromatin remodeling complex WSTF-ISWI,	99.72
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.71
COG5076	371	Transcription factor involved in chromatin remodel	99.69
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	99.44
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.38
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	98.98
KOG0955	1051	consensus PHD finger protein BR140/LIN-49 [General	98.97
KOG0008	1563	consensus Transcription initiation factor TFIID, s	98.95
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	98.66
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	98.63
KOG1827	629	consensus Chromatin remodeling complex RSC, subuni	98.58
KOG0008	1563	consensus Transcription initiation factor TFIID, s	98.56
KOG1474	640	consensus Transcription initiation factor TFIID, s	98.55
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	97.93
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	97.69
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	96.81
COG5076	371	Transcription factor involved in chromatin remodel	96.78
KOG0644	1113	consensus Uncharacterized conserved protein, conta	90.68
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	89.72

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

Probab=100.00  E-value=5.2e-34  Score=294.90  Aligned_cols=239  Identities=33%  Similarity=0.486  Sum_probs=172.9

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           28 ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      ...+-+.|..||..|+.|+++|||..|||++.||+||||+||++||||+||+.||+++.   |.++.+|+.||||||.||
T Consensus       220 ~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~---Y~~~~eF~~DVRL~F~Nc  296 (640)
T KOG1474|consen  220 TVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGE---YKSAEEFAADVRLTFDNC  296 (640)
T ss_pred             cHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccc---cCCHHHHHHHHHHHHHHH
Confidence            44566789999999999999999999999999999999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhhCcCchhHHHhhhHHHH---------------------H--Hhhh--hhhhHH
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEA---------------------K--AQLD--MQLTQE  162 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~~~~ee~~~~~ee~---------------------~--~~~~--~~~~~e  162 (322)
                      ++||++|++||.||..|++.|+.+|+.+.............+..                     .  ...+  ...-..
T Consensus       297 m~YNp~g~dV~~Ma~~L~~~Fe~rw~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  376 (640)
T KOG1474|consen  297 MTYNPEGSDVYAMAKKLQEVFEERWASMPLEIEESESAVKEEAGMASSDQIPSNSVEGPRSSSFESRESASEPSSELMSE  376 (640)
T ss_pred             HhcCCCCCHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccccccCcccccchhcccccCcccccccH
Confidence            99999999999999999999999999975443322111000000                     0  0000  000000


Q ss_pred             HhhHHHHHHHhhHHHHHHHhHHHHHH-----------------------------------HHhhhhccCCHHHHHHHHH
Q 020702          163 AVQTNKAKELRSELNEVDMQLENLRE-----------------------------------TVIQKCRKMSTEEKKNLGT  207 (322)
Q Consensus       163 ~~~~~~~~~~~~e~~~l~~~l~~~~~-----------------------------------~~~~k~r~mt~eEK~~L~~  207 (322)
                      .........+......+..++.....                                   ......+.||..|+..|..
T Consensus       377 ~e~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~t~~~~~~l~~  456 (640)
T KOG1474|consen  377 EERKKLLAELKLLLKDVPPQLIALLQRPVSKPPRKIEEELESDKRPLVTGKLIKEKNKKEKAANENKRDMTAPEKAKLKE  456 (640)
T ss_pred             HhhhhhHhhhhcchhhhhHHHHhhhhccccCccccccccccccccccchhhhhhhhhccccccccccccccccccccchh
Confidence            00000011111111111111111000                                   0011246799999999999


Q ss_pred             HhcCC-ChhhHHHHHHHH--HhcCCCCCCCCCeEEEeCCCCC-------------HHHHHHHHHHHHHHHHhcccCCC
Q 020702          208 ALTRL-SPEDLCKALEIV--AENNPSFHATAQEVDLDMDAQS-------------ELTLWRLKVFVQESLKAASRSSG  269 (322)
Q Consensus       208 ~i~~L-~~e~l~~vi~II--~~~~P~~~~~~~evElDid~L~-------------~~TL~~L~~yV~~~L~~~~~~~~  269 (322)
                      .+..| ++..+..+++|+  ....+.+....+++++|++.++             ..|+|++..++...-....+...
T Consensus       457 ~~~~~~~p~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vd~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~s~~~~  534 (640)
T KOG1474|consen  457 LLQNLLPPNKLESIVEILKPEKRQLDLSQNDDEIELDLDSVDGSQSREPSSNPLEIETIRETLKLSTERELELSKASS  534 (640)
T ss_pred             hccCCCCCccccCcccccchhhhcccccccccchhhcccccccccccCCCcccchhhhhhccccchhhHHHHHHHHhh
Confidence            99995 999999999999  5566778788999999999999             99999999888776554444444

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.96  E-value=9.6e-30  Score=207.43  Aligned_cols=105  Identities=36%  Similarity=0.643  Sum_probs=100.8

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           28 ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      +.+++.++..||..|++|+.|+||..|||+..+++||||++|++||||+||++||+++.   |.++.+|.+||+|||.||
T Consensus         3 ~~q~~~~~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~---Y~s~~ef~~D~~li~~Na   79 (107)
T cd05497           3 TNQLQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNY---YWSASECIQDFNTMFTNC   79 (107)
T ss_pred             cHHHHHHHHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHH
Confidence            46888999999999999999999999999998889999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ..||+++|+++.+|..|.+.|++++.++
T Consensus        80 ~~yN~~~s~i~~~A~~l~~~f~~~l~~~  107 (107)
T cd05497          80 YIYNKPGDDVVLMAQTLEKLFLQKLAQM  107 (107)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999999998753

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=99.96  E-value=8.5e-29  Score=202.19  Aligned_cols=104  Identities=31%  Similarity=0.496  Sum_probs=100.4

Q ss_pred             HHHHHHHHHHHHHHHcC-CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           29 SLLQFFVRQARSFITQH-KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~-~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      ++|++.|..+++.|+++ +.|++|..||++..+++|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||
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            57899999999999999 99999999999998889999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      +.||+++|.++.+|..|++.|++.+..+
T Consensus        79 ~~yN~~~s~i~~~a~~l~~~F~~~~~~~  106 (108)
T cd05495          79 WLYNRKTSRVYKYCTKLAEVFEQEIDPV  106 (108)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999998765

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.

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.95  E-value=1.4e-28  Score=203.96  Aligned_cols=106  Identities=28%  Similarity=0.454  Sum_probs=100.5

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      ...+..|..||+.|++|+.++||..||++..  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.||+
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            4678899999999999999999999999876  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCC-CCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702          109 KYNDE-RDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus       109 ~yN~~-~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      .||++ +|.|+.+|..|+..|++++.++.+.+
T Consensus        79 ~yN~~~~s~i~~~a~~L~~~F~~~~~~l~~~~  110 (119)
T cd05496          79 SYTPNKRSRIYSMTLRLSALFEEHIKKIISDW  110 (119)
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99985 99999999999999999999985544

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.

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

Probab=99.95  E-value=7.3e-28  Score=193.05  Aligned_cols=94  Identities=30%  Similarity=0.479  Sum_probs=90.9

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCC
Q 020702           33 FFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYND  112 (322)
Q Consensus        33 ~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~  112 (322)
                      ++|..|++.|++++.++||..||++..  +|+||++|++||||+||++||+++.   |.|+.+|.+||+|||.||.+||+
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            579999999999999999999999876  9999999999999999999999999   99999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHH
Q 020702          113 ERDDVHVMAKSLLEKFEEK  131 (322)
Q Consensus       113 ~~s~v~~~A~~L~~~Fe~~  131 (322)
                      ++|.|+.+|..|++.|.+.
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=99.95  E-value=7e-28  Score=193.51  Aligned_cols=99  Identities=46%  Similarity=0.843  Sum_probs=95.7

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccccc
Q 020702           31 LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  110 (322)
Q Consensus        31 lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~y  110 (322)
                      +++.|..||+.|++++.+++|..||++...++|+|+++|++||||+||++||+++.   |.++.+|.+||++||.||+.|
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            35789999999999999999999999987779999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Q 020702          111 NDERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       111 N~~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      |+++|.++.+|..|.+.|+++|
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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.94  E-value=3e-27  Score=193.27  Aligned_cols=103  Identities=36%  Similarity=0.572  Sum_probs=98.1

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCC---CCCCCCCHHHHHHHHHHHHhc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGK---DGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~---~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      ..++.|..|+..|++|+.++||..||++ .  +|+|+++|++||||+||++||+++   .   |.++.+|.+||+|||+|
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            5677899999999999999999999998 3  999999999999999999999984   6   99999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHhhCcC
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK  138 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~  138 (322)
                      |..||+++|.++.+|..|.+.|++.|..++|.
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.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.94  E-value=1.7e-27  Score=190.92  Aligned_cols=95  Identities=34%  Similarity=0.695  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCC
Q 020702           33 FFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYND  112 (322)
Q Consensus        33 ~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~  112 (322)
                      .+|..||+.|++|+.+++|+.||++..  +|+|+++|++||||+||++||+++.   |.|+.+|..||+|||.||+.||+
T Consensus         3 ~~c~~il~~l~~~~~~~~F~~pv~~~~--~p~Y~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~li~~Na~~yN~   77 (97)
T cd05503           3 ALCETILDEMEAHEDAWPFLEPVNTKL--VPGYRKIIKKPMDFSTIREKLESGQ---YKTLEEFAEDVRLVFDNCETFNE   77 (97)
T ss_pred             HHHHHHHHHHHcCCCchhhcCCCCccc--cCCHHHHhCCCCCHHHHHHHHccCC---CCCHHHHHHHHHHHHHHHHHHCC
Confidence            479999999999999999999999886  9999999999999999999999999   99999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHH
Q 020702          113 ERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       113 ~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      ++|.++.+|..|++.|+++|
T Consensus        78 ~~s~i~~~a~~l~~~f~~~~   97 (97)
T cd05503          78 DDSEVGRAGHNMRKFFEKRW   97 (97)
T ss_pred             CCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999999987

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.94  E-value=2.1e-27  Score=191.75  Aligned_cols=98  Identities=46%  Similarity=0.850  Sum_probs=94.8

Q ss_pred             HHHHHHHHHHHHcC---CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           32 QFFVRQARSFITQH---KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        32 q~~c~~il~~L~~~---~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      +++|..||+.|+++   +.+++|+.||++...++|+||++|++||||+||++||.++.   |.++.+|..||+|||.||+
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   89999999999987789999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHH
Q 020702          109 KYNDERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       109 ~yN~~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      .||+++|.++.+|..|++.|+++|
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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.94  E-value=3.5e-27  Score=189.68  Aligned_cols=97  Identities=29%  Similarity=0.480  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      .+|+..++.++..+. |+.++||..||++..  +||||.+|++||||+||++||+++.   |.++++|.+||+|||.||.
T Consensus         2 ~~l~~~L~~~~~~~~-~~~s~~F~~PV~~~~--~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~Dv~LI~~Na~   75 (99)
T cd05508           2 DQLSKLLKFALERMK-QPGAEPFLKPVDLEQ--FPDYAQYVFKPMDLSTLEKNVRKKA---YGSTDAFLADAKWILHNAI   75 (99)
T ss_pred             hHHHHHHHHHHHHHh-CcCcchhcCCCChhh--CCCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHH
Confidence            478899999999999 999999999999976  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHH
Q 020702          109 KYNDERDDVHVMAKSLLEKFEEK  131 (322)
Q Consensus       109 ~yN~~~s~v~~~A~~L~~~Fe~~  131 (322)
                      .||+++|.++.+|..|.+.|+..
T Consensus        76 ~YN~~~s~i~~~A~~l~~~~~~e   98 (99)
T cd05508          76 IYNGGDHKLTQAAKAIVKICEQE   98 (99)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHhh
Confidence            99999999999999999998764

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.94  E-value=6.7e-27  Score=193.04  Aligned_cols=101  Identities=36%  Similarity=0.585  Sum_probs=96.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      .....|..|++.|+.++.+++|..||+...  +|+||++|++||||+||++||.++.   |.|+.+|.+||+|||.||+.
T Consensus        12 ~~~~~c~~il~~l~~~~~s~~F~~pvd~~~--~pdY~~vI~~PmDL~tI~~kL~~~~---Y~s~~~f~~Dv~LI~~Na~~   86 (115)
T cd05504          12 LNLSALEQLLVEIVKHKDSWPFLRPVSKIE--VPDYYDIIKKPMDLGTIKEKLNMGE---YKLAEEFLSDIQLVFSNCFL   86 (115)
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCCCCccc--cccHHHHhcCcccHHHHHHHHccCC---CCCHHHHHHHHHHHHHHHHH
Confidence            455679999999999999999999999876  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||+++|.++.+|..|++.|++++.++
T Consensus        87 yN~~~s~i~~~A~~l~~~f~~~~~~~  112 (115)
T cd05504          87 YNPEHTSVYKAGTRLQRFFIKRCRKL  112 (115)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999886

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.

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.94  E-value=6.8e-27  Score=189.75  Aligned_cols=100  Identities=29%  Similarity=0.429  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      -++..|..|+..|++|+.++||..||++..  +|+|+++|++||||+||++||+++.   |.++.+|.+||+|||.||..
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            467889999999999999999999999865  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHh
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQ  134 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~  134 (322)
                      ||+++|.|+.+|..|++.|.+.+..
T Consensus        78 yN~~~s~v~~~A~~l~~~~~~~~~~  102 (104)
T cd05507          78 YNSSDHDVYLMAVEMQREVMSQIQQ  102 (104)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999888764

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.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.94  E-value=6.6e-27  Score=189.44  Aligned_cols=100  Identities=32%  Similarity=0.492  Sum_probs=95.7

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      ....++|..|++.|++++.+++|..||++...++|+|+++|++||||+||++||.++.   |.++.+|.+||++||.||+
T Consensus         3 ~~~~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~   79 (103)
T cd05500           3 KHQHKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNV---YTSVEEFTADFNLMVDNCL   79 (103)
T ss_pred             HHHHHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHH
Confidence            3566789999999999999999999999988889999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHH
Q 020702          109 KYNDERDDVHVMAKSLLEKFEEK  131 (322)
Q Consensus       109 ~yN~~~s~v~~~A~~L~~~Fe~~  131 (322)
                      .||+++|.++.+|..|++.|++.
T Consensus        80 ~yN~~~s~~~~~A~~l~~~fe~~  102 (103)
T cd05500          80 TFNGPEHPVSQMGKRLQAAFEKH  102 (103)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHh
Confidence            99999999999999999999975

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.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.94  E-value=5.9e-27  Score=189.32  Aligned_cols=97  Identities=37%  Similarity=0.760  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHc---CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           33 FFVRQARSFITQ---HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        33 ~~c~~il~~L~~---~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      +.|..||+.|++   ++.++||+.||++...++|+||++|++||||++|++||+++.   |.++.+|.+||+|||.||+.
T Consensus         3 ~~c~~Il~~l~~~~~~~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I~~kl~~~~---Y~s~~ef~~D~~li~~N~~~   79 (102)
T cd05499           3 KFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQ---YQSAKEFERDVRLIFKNCYT   79 (102)
T ss_pred             HHHHHHHHHHHcccCCcccchhcCCCCccccCCCCHHHHhcCCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHHHH
Confidence            579999999999   467999999999986669999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHH
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      ||+++|.++.+|..|++.|+++|
T Consensus        80 yn~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          80 FNPEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999987

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.

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.94  E-value=1.4e-26  Score=186.76  Aligned_cols=99  Identities=36%  Similarity=0.607  Sum_probs=95.8

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccccc
Q 020702           31 LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  110 (322)
Q Consensus        31 lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~y  110 (322)
                      ++.+|..|++.|++|+.+++|..||++..  +|+|+++|++||||+||++||.++.   |.|+.+|..||+|||.||+.|
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            56789999999999999999999999987  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHh
Q 020702          111 NDERDDVHVMAKSLLEKFEEKWLQ  134 (322)
Q Consensus       111 N~~~s~v~~~A~~L~~~Fe~~~~~  134 (322)
                      |+++|.++.+|..|++.|++.+++
T Consensus        77 N~~~s~~~~~a~~l~~~f~~~~~~  100 (101)
T cd05509          77 NGPDTEYYKCANKLEKFFWKKLKE  100 (101)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999998875

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.

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.94  E-value=2.9e-26  Score=184.77  Aligned_cols=96  Identities=20%  Similarity=0.316  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCC
Q 020702           33 FFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYND  112 (322)
Q Consensus        33 ~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~  112 (322)
                      +.|+.|+..|.+++.+++|..++  .  ++||||++|++||||+||++||.++.   |.++.+|.+||+|||.||+.||+
T Consensus         5 ~~ce~il~~l~~~~~s~~f~~~p--~--~~pdY~~iIk~PMDL~tI~~kL~~~~---Y~s~~ef~~D~~Lif~N~~~yN~   77 (102)
T cd05501           5 LKCEFLLLKVYCMSKSGFFISKP--Y--YIRDYCQGIKEPMWLNKVKERLNERV---YHTVEGFVRDMRLIFHNHKLFYK   77 (102)
T ss_pred             HHHHHHHHHHHhCcccccccCCC--C--CCCchHHHcCCCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHHHHHcC
Confidence            45999999999999999997632  3  38999999999999999999999999   99999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          113 ERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       113 ~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      ++ .++.+|..|++.|+++|..++
T Consensus        78 ~~-~~~~~a~~L~~~Fek~~~~~f  100 (102)
T cd05501          78 DD-DFGQVGITLEKKFEKNFKEVF  100 (102)
T ss_pred             CC-HHHHHHHHHHHHHHHHHHHHh
Confidence            99 999999999999999999875

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.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.94  E-value=2.9e-26  Score=188.30  Aligned_cols=103  Identities=23%  Similarity=0.391  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHHHHHHcC-CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhc
Q 020702           28 ASLLQFFVRQARSFITQH-KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~-~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      ...++..|..|+..|++| +.+++|..||++..  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.|
T Consensus         5 ~~~~~~~~~~il~~l~~~~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~Li~~N   79 (112)
T cd05510           5 QEEFYESLDKVLNELKTYTEHSTPFLTKVSKRE--APDYYDIIKKPMDLGTMLKKLKNLQ---YKSKAEFVDDLNLIWKN   79 (112)
T ss_pred             HHHHHHHHHHHHHHHHhcCccccchhcCCChhh--cCCHHHHhcCccCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHH
Confidence            467889999999999999 89999999999986  9999999999999999999999999   99999999999999999


Q ss_pred             ccccCCCCC-HHHHHHHHHHHHHHHHHHhh
Q 020702          107 AMKYNDERD-DVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       107 a~~yN~~~s-~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |+.||+++| .++.+|..|++.|+..+..+
T Consensus        80 ~~~yN~~~s~~~~~~A~~l~~~~~~~~~~~  109 (112)
T cd05510          80 CLLYNSDPSHPLRRHANFMKKKAEHLLKLI  109 (112)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence            999999866 67899999999999998876

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.

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

Probab=99.93  E-value=3.9e-26  Score=187.59  Aligned_cols=105  Identities=30%  Similarity=0.491  Sum_probs=100.3

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      ++|+.+|..|++.|+.|+.+++|..||++..  +|+||++|++||||+||++||+++.   |.|+.+|.+||+|||.||.
T Consensus         2 ~~lr~~L~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~vI~~PmdL~tI~~kl~~~~---Y~s~~ef~~Dv~li~~Na~   76 (112)
T cd05528           2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEE--VPDYYEIIKQPMDLQTILQKLDTHQ---YLTAKDFLKDIDLIVTNAL   76 (112)
T ss_pred             hHHHHHHHHHHHHHHhCCCchhhcCCCCccc--cCcHHHHHcCCCCHHHHHHHHcCCC---cCCHHHHHHHHHHHHHHHH
Confidence            4788999999999999999999999999987  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCC----CCHHHHHHHHHHHHHHHHHHhhCcC
Q 020702          109 KYNDE----RDDVHVMAKSLLEKFEEKWLQLLPK  138 (322)
Q Consensus       109 ~yN~~----~s~v~~~A~~L~~~Fe~~~~~i~~~  138 (322)
                      .||++    ||.++.+|..|++.|.+++.+..|.
T Consensus        77 ~yN~~~s~~~s~i~~~A~~L~~~~~~~~~~~~~~  110 (112)
T cd05528          77 EYNPDRDPADKLIRSRACELRDEVHAMIEAELDP  110 (112)
T ss_pred             HHCCCCCccccHHHHHHHHHHHHHHHHHHhcCCC
Confidence            99999    4799999999999999999988664

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

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.93  E-value=9.3e-26  Score=181.14  Aligned_cols=92  Identities=34%  Similarity=0.422  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccccc
Q 020702           31 LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  110 (322)
Q Consensus        31 lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~y  110 (322)
                      |...|..|++.|+.++.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||++|
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            56788999999999999999999999876  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHH
Q 020702          111 NDERDDVHVMAKSLLEK  127 (322)
Q Consensus       111 N~~~s~v~~~A~~L~~~  127 (322)
                      |+++|.++.+|..|...
T Consensus        77 N~~~s~~~~~A~~L~~~   93 (98)
T cd05513          77 NKPDTIYYKAAKKLLHS   93 (98)
T ss_pred             CCCCCHHHHHHHHHHHh
Confidence            99999999999998654

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.

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.93  E-value=9.2e-26  Score=185.45  Aligned_cols=100  Identities=30%  Similarity=0.553  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccccc
Q 020702           31 LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  110 (322)
Q Consensus        31 lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~y  110 (322)
                      |+..++.|++.|++++.+++|..||++..  +|+||++|++||||+||++||.++.   |+++.+|.+||+|||.||..|
T Consensus         1 ~~~~l~~ii~~l~~~~~s~~F~~pv~~~~--~p~Y~~~I~~PmdL~tI~~kl~~~~---Y~s~~ef~~Dv~li~~Na~~y   75 (112)
T cd05511           1 LSFILDEIVNELKNLPDSWPFHTPVNKKK--VPDYYKIIKRPMDLQTIRKKISKHK---YQSREEFLEDIELIVDNSVLY   75 (112)
T ss_pred             CHHHHHHHHHHHHhCCCchhhcCCCChhh--cccHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHH
Confidence            35677899999999999999999999987  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          111 NDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       111 N~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |+++|.++.+|..|...|+..+..+
T Consensus        76 N~~~s~i~~~A~~l~~~~~~~~~~~  100 (112)
T cd05511          76 NGPDSVYTKKAKEMLELAEELLAER  100 (112)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999887

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.

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

Probab=99.92  E-value=1.3e-25  Score=183.17  Aligned_cols=100  Identities=26%  Similarity=0.382  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHHHHcCCC------CCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           31 LQFFVRQARSFITQHKW------AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        31 lq~~c~~il~~L~~~~~------a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      |++.|..|++.|..+..      ++||..||+...  +|+||++|++||||+||++||.++.   |.++.+|..||+|||
T Consensus         2 l~~~~~~il~~v~~~~d~~g~~~s~~F~~~p~~~~--~pdYy~iI~~Pmdl~tI~~kl~~~~---Y~s~~ef~~D~~li~   76 (107)
T cd05516           2 LTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKE--LPEYYELIRKPVDFKKIKERIRNHK---YRSLEDLEKDVMLLC   76 (107)
T ss_pred             HHHHHHHHHHHHHhhhCcCCCEeeHHhhcCCCccc--CCCHHHHcCCCCCHHHHHHHHccCC---CCCHHHHHHHHHHHH
Confidence            67889999999998876      899999998876  9999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      .||+.||++||.|+.+|..|++.|++.+.++
T Consensus        77 ~Na~~yN~~~s~i~~~a~~l~~~f~~~~~~~  107 (107)
T cd05516          77 QNAQTFNLEGSLIYEDSIVLQSVFKSARQKI  107 (107)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999988753

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.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.92  E-value=2.5e-25  Score=178.73  Aligned_cols=91  Identities=29%  Similarity=0.525  Sum_probs=86.9

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccC
Q 020702           32 QFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN  111 (322)
Q Consensus        32 q~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN  111 (322)
                      .-.|+.+++.|+.|+.+++|..||+...  +|+|+++|++||||+||++||.++.   |.++.+|..||+|||.||+.||
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            4578999999999999999999999887  9999999999999999999999999   9999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 020702          112 DERDDVHVMAKSLLEK  127 (322)
Q Consensus       112 ~~~s~v~~~A~~L~~~  127 (322)
                      +++|.+|.+|..|++.
T Consensus        78 ~~~s~~~~~A~~l~~~   93 (98)
T cd05512          78 AKDTIFYRAAVRLRDQ   93 (98)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            9999999999998764

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.

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

Probab=99.91  E-value=6.3e-25  Score=177.83  Aligned_cols=97  Identities=26%  Similarity=0.452  Sum_probs=91.2

Q ss_pred             HHHHHHHHHHHHH------cCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           31 LQFFVRQARSFIT------QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        31 lq~~c~~il~~L~------~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      |++.|..|++.|+      .++.+++|..||+...  +|+||++|++||||+||++||+++.   |.|+.+|..||+|||
T Consensus         1 ~~~~~~~i~~~v~~~~~~~~~~~~~~F~~~p~~~~--~pdYy~iIk~Pmdl~~I~~kl~~~~---Y~s~~~f~~D~~li~   75 (103)
T cd05519           1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKL--YPDYYVIIKRPIALDQIKRRIEGRA---YKSLEEFLEDFHLMF   75 (103)
T ss_pred             CHHHHHHHHHHHHHhcCcCCCchhHHhcCCCCCCC--CcCHHHHcCCCcCHHHHHHHHccCC---CCCHHHHHHHHHHHH
Confidence            5788999999999      4566999999998877  9999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHH
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      .||..||+++|.++.+|..|++.|++++
T Consensus        76 ~Na~~yn~~~s~i~~~A~~l~~~f~~~~  103 (103)
T cd05519          76 ANARTYNQEGSIVYEDAVEMEKAFKKKY  103 (103)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999998763

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.

>smart00297 BROMO bromo domain

Probab=99.90  E-value=8.4e-24  Score=171.02  Aligned_cols=102  Identities=40%  Similarity=0.680  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           28 ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      ...++..|..|+..+.+|+.+++|..||+...  +|+|+++|++||||++|++||+++.   |.++.+|.+||++||.||
T Consensus         5 ~~~~~~~~~~i~~~~~~~~~~~~F~~~~~~~~--~p~Y~~~i~~P~dl~~I~~kl~~~~---Y~s~~ef~~D~~li~~Na   79 (107)
T smart00297        5 QKKLQSLLKAVLDKLDSHRLSWPFLKPVDRKE--APDYYDIIKKPMDLSTIKKKLENGK---YSSVEEFVADVQLMFSNA   79 (107)
T ss_pred             HHHHHHHHHHHHHHHHhCccchhhccCCChhh--ccCHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHH
Confidence            45778899999999999999999999999887  8999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHh
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQ  134 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~  134 (322)
                      +.||+++|.++.+|..|.+.|++.|.+
T Consensus        80 ~~~n~~~s~~~~~a~~l~~~f~~~~~~  106 (107)
T smart00297       80 KTYNGPDSEVYKDAKKLEKFFEKKLRE  106 (107)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999875

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.90  E-value=7e-24  Score=172.36  Aligned_cols=96  Identities=27%  Similarity=0.469  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHHHc------CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHh
Q 020702           32 QFFVRQARSFITQ------HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  105 (322)
Q Consensus        32 q~~c~~il~~L~~------~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~  105 (322)
                      ++.|..|++.|..      ++.+++|..||+...  +|+||++|++||||+||++||.++.   |.++.+|..||+|||.
T Consensus         2 ~~~~~~~~~~i~~~~d~~~~~~a~~F~~~p~~~~--~pdYy~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~l~~~   76 (105)
T cd05515           2 QQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSE--YPDYYDVIKKPIDMEKIRSKIEGNQ---YQSLDDMVSDFVLMFD   76 (105)
T ss_pred             hHHHHHHHHHHHHhhCcCCCcccHHhccCCCccc--CCcHHHHcCCCcCHHHHHHHHccCC---CCCHHHHHHHHHHHHH
Confidence            4568888888876      466899999998877  9999999999999999999999999   9999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHH
Q 020702          106 NAMKYNDERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       106 Na~~yN~~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      ||..||+++|.++.+|..|++.|.+..
T Consensus        77 Na~~yN~~~s~i~~~A~~L~~~~~~~~  103 (105)
T cd05515          77 NACKYNEPDSQIYKDALTLQKVLLETK  103 (105)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999998764

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.

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.90  E-value=4.4e-24  Score=172.97  Aligned_cols=95  Identities=23%  Similarity=0.359  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHHHHcC------CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           31 LQFFVRQARSFITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        31 lq~~c~~il~~L~~~------~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      +|++|..|++.|+.+      +.+++|..+++...  +|+||++|++||||+||++||.++.   |.++.+|..||+|||
T Consensus         1 ~~~~~~~l~~~i~~~~d~~gr~~~~~F~~lp~~~~--~pdYy~vI~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~lm~   75 (103)
T cd05517           1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVL--YPDYYAVIKEPIDLKTIAQRIQSGY---YKSIEDMEKDLDLMV   75 (103)
T ss_pred             ChHHHHHHHHHHHHhhCcCCCChhHHHhcCCCCCC--CCCHHHHcCCCcCHHHHHHHHCcCC---CCCHHHHHHHHHHHH
Confidence            367899999999885      45799999988877  9999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHH
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEE  130 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~  130 (322)
                      .||..||+++|.++.+|..|++.|+.
T Consensus        76 ~Na~~yN~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          76 KNAKTFNEPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999999999975

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.

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.90  E-value=8.6e-24  Score=173.99  Aligned_cols=100  Identities=24%  Similarity=0.351  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHHHcC------CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHh
Q 020702           32 QFFVRQARSFITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  105 (322)
Q Consensus        32 q~~c~~il~~L~~~------~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~  105 (322)
                      .+.|..|++.|+++      +.+.+|..+++...  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.
T Consensus         4 ~~~c~~il~~l~~~~~~~g~~l~~~F~~~p~~~~--~PdYy~iI~~Pmdl~tI~~kl~~~~---Y~s~~~f~~D~~lm~~   78 (113)
T cd05524           4 IAVCQELYDTIRNYKSEDGRILCESFIRVPKRRN--EPEYYEVVSNPIDLLKIQQKLKTEE---YDDVDDLTADFELLIN   78 (113)
T ss_pred             HHHHHHHHHHHHhhcccCCCchhHHHhcCCCccc--CCCHHHHhCCccCHHHHHHHhCcCC---CCCHHHHHHHHHHHHH
Confidence            46799999999964      45678999888665  9999999999999999999999999   9999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          106 NAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       106 Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      ||..||+++|.++.+|..|++.|++.+.++.
T Consensus        79 Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~  109 (113)
T cd05524          79 NAKAYYKPDSPEHKDACKLWELFLSARNEVL  109 (113)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999999988874

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

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.90  E-value=1.5e-23  Score=176.23  Aligned_cols=102  Identities=25%  Similarity=0.353  Sum_probs=95.5

Q ss_pred             HHHHHHHHHHHHHHHH---cCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           28 ASLLQFFVRQARSFIT---QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~---~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      ...++..|..++..|+   +++++++|..||++.. ++|+||++|++||||+||++||.++.   |+++++|..||+|||
T Consensus        22 ~~~~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~-~~p~Y~~iI~~PmdL~tI~~kl~~~~---Y~s~~~f~~Dv~Li~   97 (128)
T cd05529          22 RDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRA-WYPDYWNRVPVPMDLETIRSRLENRY---YRSLEALRHDVRLIL   97 (128)
T ss_pred             CHHHHHHHHHHHHHHHhcccCcccccccCCCCccc-cCCcHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHH
Confidence            5567778889999999   9999999999999882 39999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHH
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEKWL  133 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~  133 (322)
                      .||+.||+++|.++.+|..|.+.|+..+.
T Consensus        98 ~Na~~yN~~~s~i~~~A~~l~~~~~~~l~  126 (128)
T cd05529          98 SNAETFNEPNSEIAKKAKRLSDWLLRILS  126 (128)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999998764

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.

>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III

Probab=99.90  E-value=1.2e-23  Score=170.34  Aligned_cols=91  Identities=27%  Similarity=0.450  Sum_probs=83.0

Q ss_pred             HHHHHHHHcC------CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           36 RQARSFITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        36 ~~il~~L~~~------~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      ..|++.|+.+      +.++||+.||+...  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.
T Consensus         6 ~~l~~~i~~~~~~~g~~~s~pF~~~p~~~~--~PdYy~iI~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~lm~~Na~~   80 (103)
T cd05520           6 WQLYDTIRNARNNQGQLLAEPFLKLPSKRK--YPDYYQEIKNPISLQQIRTKLKNGE---YETLEELEADLNLMFENAKR   80 (103)
T ss_pred             HHHHHHHHhhcCCCCCCccHhhhcCCCccc--CCCHHHHcCCCcCHHHHHHHHccCC---CCCHHHHHHHHHHHHHHHHH
Confidence            4455555553      57999999999876  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHH
Q 020702          110 YNDERDDVHVMAKSLLEKFEEK  131 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~  131 (322)
                      ||+++|.++.+|..|++.|+++
T Consensus        81 yN~~~s~i~~~A~~L~~~f~~~  102 (103)
T cd05520          81 YNVPNSRIYKDAEKLQKLMQAK  102 (103)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999874

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=99.89  E-value=2.6e-23  Score=169.29  Aligned_cols=96  Identities=25%  Similarity=0.354  Sum_probs=86.8

Q ss_pred             HHHHHHHHHHHHHcC------CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           31 LQFFVRQARSFITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        31 lq~~c~~il~~L~~~------~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      |...|..|++.|...      +.++||+.+++...  +|+||++|++||||+||++||.++.   |.++.+|..||.|||
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            455667777777663      45799999988876  9999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHH
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEK  131 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~  131 (322)
                      .||..||+++|.++.+|..|++.|++.
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.

>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV

Probab=99.89  E-value=3.3e-23  Score=167.84  Aligned_cols=94  Identities=27%  Similarity=0.436  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHHc------CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhc
Q 020702           33 FFVRQARSFITQ------HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        33 ~~c~~il~~L~~------~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      +.|..|++.|..      ++.+.+|+.||+...  +||||++|++||||+||+.||.++.   |.++.+|.+||+|||.|
T Consensus         3 ~~~~~l~~~v~~~~d~~gr~~~~~F~~~p~~~~--~pdYy~iIk~Pmdl~tI~~kl~~~~---Y~s~~ef~~D~~li~~N   77 (103)
T cd05518           3 KRMLALFLYVLEYREGSGRRLCDLFMEKPSKKD--YPDYYKIILEPIDLKTIEHNIRNDK---YATEEELMDDFKLMFRN   77 (103)
T ss_pred             HHHHHHHHHHHHhhccCCCcccHHHhcCCCccc--CccHHHHcCCCcCHHHHHHHHCCCC---CCCHHHHHHHHHHHHHH
Confidence            345666666665      467899999999877  9999999999999999999999999   99999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHH
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEK  131 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~  131 (322)
                      |..||+++|.|+.+|..|++.|+++
T Consensus        78 a~~yN~~~s~i~~~A~~le~~~~~~  102 (103)
T cd05518          78 ARHYNEEGSQVYEDANILEKVLKEK  102 (103)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999864

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=2.6e-22  Score=162.87  Aligned_cols=94  Identities=20%  Similarity=0.302  Sum_probs=86.0

Q ss_pred             HHHHHHHHHHHc------CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhc
Q 020702           33 FFVRQARSFITQ------HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        33 ~~c~~il~~L~~------~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      ..+..|++.|++      ++.+++|+.+|+...  +|+||++|++||||+||++||..+.   |.++.+|..||+|||.|
T Consensus         4 ~~~~~i~~~v~~~~d~~g~~l~~~F~~~p~~~~--~pdYy~~I~~Pmdl~tI~~kl~~~~---Y~s~~~f~~D~~li~~N   78 (104)
T cd05522           4 ARIKNILKGLRKERDENGRLLTLHFEKLPDKAR--EPEYYQEISNPISLDDIKKKVKRRK---YKSFDQFLNDLNLMFEN   78 (104)
T ss_pred             HHHHHHHHHHHHHhCcCCCcccHHHhcCCCccc--cCcHHHHhCCCcCHHHHHHHHccCC---CCCHHHHHHHHHHHHHH
Confidence            345667777766      578999999998876  9999999999999999999999999   99999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHH
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEK  131 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~  131 (322)
                      |..||+++|.++.+|..|++.|+..
T Consensus        79 a~~yn~~~s~i~~~A~~l~~~f~~l  103 (104)
T cd05522          79 AKLYNENDSQEYKDAVLLEKEARLL  103 (104)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999863

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.

>cd04369 Bromodomain Bromodomain

Probab=99.87  E-value=3.2e-22  Score=157.42  Aligned_cols=96  Identities=39%  Similarity=0.589  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHHHcC--CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           32 QFFVRQARSFITQH--KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        32 q~~c~~il~~L~~~--~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      ...|..|++.|..+  +.+++|..||++..  +|+|+++|++||||++|+.||.++.   |.++.+|..||++||.||+.
T Consensus         2 ~~~~~~i~~~l~~~~~~~~~~F~~~~~~~~--~~~Y~~~i~~P~~l~~I~~kl~~~~---Y~s~~~f~~D~~li~~Na~~   76 (99)
T cd04369           2 KKKLRSLLDALKKLKRDLSEPFLEPVDPKE--APDYYEVIKNPMDLSTIKKKLKNGE---YKSLEEFEADVRLIFSNAKT   76 (99)
T ss_pred             HHHHHHHHHHHHhhcccccHHHhcCCChhc--CCCHHHHHhCcccHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            45789999999999  99999999999866  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHH
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      ||+++|.++.+|..|...|++.|
T Consensus        77 ~n~~~~~~~~~a~~l~~~~~~~~   99 (99)
T cd04369          77 YNGPGSPIYKDAKKLEKLFEKLL   99 (99)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999999998764

Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They 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=99.87  E-value=2.5e-22  Score=155.51  Aligned_cols=84  Identities=38%  Similarity=0.679  Sum_probs=79.2

Q ss_pred             HHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCC
Q 020702           35 VRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDER  114 (322)
Q Consensus        35 c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~  114 (322)
                      |..|++.|++|+.+++|..||++..  +|+|+++|+.||||++|+.||+++.   |.++.+|..||++||.||+.||+++
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            8999999999999999999997776  9999999999999999999999999   9999999999999999999999999


Q ss_pred             CHHHHHHHH
Q 020702          115 DDVHVMAKS  123 (322)
Q Consensus       115 s~v~~~A~~  123 (322)
                      |.++.+|.+
T Consensus        76 s~~~~~A~~   84 (84)
T PF00439_consen   76 SPIYKAAEK   84 (84)
T ss_dssp             SHHHHHHHH
T ss_pred             CHHHHHhcC
Confidence            999999964

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 ....

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.86  E-value=1.7e-21  Score=159.06  Aligned_cols=99  Identities=16%  Similarity=0.157  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHc-CCCCCCCCCCCCc---ccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           34 FVRQARSFITQ-HKWAWPFMHPVDV---EGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        34 ~c~~il~~L~~-~~~a~~F~~PVd~---~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      .+..++..+.+ -|.++||..||.+   ...++|+|+++|++||||+||++||+++.   |++++||.+||+|||+||..
T Consensus         4 ~L~f~~~~~k~~lp~~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~Dv~LI~~N~~~   80 (109)
T cd05492           4 LLKFIVSRMKSWLPPDTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEK---YTSLEEFKADALLLLHNTAI   80 (109)
T ss_pred             hHHHHHHHHHhcCcccccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            45677788877 6778999999974   33359999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||+++|.++.+|..|.+.....+..+
T Consensus        81 yNg~~s~~~~~A~~l~~d~~~el~Ei  106 (109)
T cd05492          81 FHGADSEQYDAARWLYRDTCHDLREL  106 (109)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999988777666554

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.

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

Probab=99.86  E-value=1.3e-21  Score=159.18  Aligned_cols=95  Identities=21%  Similarity=0.222  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHHHHcC------CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           31 LQFFVRQARSFITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        31 lq~~c~~il~~L~~~------~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      |.+.|..|++.|+..      +.+.+|..+++...  +|+||++|++||||+||++||.+     |.++.+|.+||+|||
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            567788899988874      44679998877766  99999999999999999999985     999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHH
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      .||..||+++|.++.+|..|++.|.+++
T Consensus        75 ~Na~~yN~~~s~i~~~A~~le~~~~~~~  102 (106)
T cd05521          75 WNARLYNTKGSVIYKYALILEKYINDVI  102 (106)
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999999875

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.

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

Probab=99.72  E-value=4.9e-18  Score=186.87  Aligned_cols=98  Identities=34%  Similarity=0.674  Sum_probs=95.0

Q ss_pred             HHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCC
Q 020702           35 VRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDER  114 (322)
Q Consensus        35 c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~  114 (322)
                      |..|+..|+.|..||||++||++..  +|+||+||++||||+||+.|+..+.   |.++.+|..||.|||+||..||.+ 
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            8999999999999999999999998  9999999999999999999999999   999999999999999999999999 


Q ss_pred             CHHHHHHHHHHHHHHHHHHhhCcC
Q 020702          115 DDVHVMAKSLLEKFEEKWLQLLPK  138 (322)
Q Consensus       115 s~v~~~A~~L~~~Fe~~~~~i~~~  138 (322)
                      |.|+.++..|..+|++.|...+|.
T Consensus      1380 s~i~~ag~~l~~ff~~~~~~~~~~ 1403 (1404)
T KOG1245|consen 1380 SEIGRAGTCLRRFFHKRWRKKFPV 1403 (1404)
T ss_pred             hhhhhhcchHHHHHHHHHHhhcCC
Confidence            999999999999999999887653

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.71  E-value=2.5e-17  Score=134.46  Aligned_cols=99  Identities=17%  Similarity=0.176  Sum_probs=89.2

Q ss_pred             HHHHHHHHHHHHHHcCC------CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHH
Q 020702           30 LLQFFVRQARSFITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV  103 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~------~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLI  103 (322)
                      .+|..+..|+..++.|.      ++.+|.+.+.  .  .|+|+.+|+.||||++|++||.+|.   |.++++|..||.+|
T Consensus         3 ~vq~~l~~l~~~V~~~~D~~Gr~~s~~f~~LP~--~--~~~~~~~ik~Pi~l~~Ik~ki~~~~---Y~~ld~~~~D~~lm   75 (110)
T cd05526           3 LVQELLATLFVSVMNHQDEEGRCYSDSLAELPE--L--AVDGVGPKKIPLTLDIIKRNVDKGR---YRRLDKFQEDMFEV   75 (110)
T ss_pred             HHHHHHHHHHHHHHhccCCCCCCchHHHHHCCC--c--ccCchhhhcCCccHHHHHHHHHcCC---cCcHHHHHHHHHHH
Confidence            57788899999999875      4788888665  2  5788999999999999999999999   99999999999999


Q ss_pred             HhcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          104 FKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       104 f~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |.||.+||.+||.+|.+|..|+..|...-.++
T Consensus        76 f~NAr~yN~~~S~iy~dA~eLq~~f~~~rd~~  107 (110)
T cd05526          76 LERARRLSRTDSEIYEDAVELQQFFIKIRDEL  107 (110)
T ss_pred             HHHHHHhCcccCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999876654

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

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

Probab=99.69  E-value=5.6e-17  Score=158.71  Aligned_cols=110  Identities=27%  Similarity=0.384  Sum_probs=93.5

Q ss_pred             cccHHHHHHHHHHHHHHHHc------CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHH
Q 020702           25 NLSASLLQFFVRQARSFITQ------HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYA   98 (322)
Q Consensus        25 ~~~~~~lq~~c~~il~~L~~------~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~   98 (322)
                      ......+.+.|..++..+..      +..+++|..+|+...  +|+||.+|+.||||++|+++|.++.   |+++++|..
T Consensus       137 ~~~~~~~~~~~~~i~~~~~~~~~~~~~~~s~~F~~~p~k~~--~PdYy~iIk~Pm~L~~i~kkl~~~~---Y~s~eef~~  211 (371)
T COG5076         137 KIEDELLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKRE--YPDYYEIIKSPMDLLTIQKKLKNGR---YKSFEEFVS  211 (371)
T ss_pred             cccchhHHHHHHHHHHHHHHhhcccccccccccccCCcccc--CCChheeecchhhHHHHHHHHHhhh---hhhHHHHHH
Confidence            33344444444544444433      467899999998887  9999999999999999999999999   999999999


Q ss_pred             HHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702           99 DVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus        99 DvrLIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      |+.|||.||..||+++|.|+.+|..|+..|...+..+.+..
T Consensus       212 D~~lM~~N~~~yN~~~s~v~~~a~~l~~~~~~~i~~~~~~~  252 (371)
T COG5076         212 DLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEM  252 (371)
T ss_pred             HHHHHHHhhhhccCCCcchhhhhHHHHHHHHHHHHhccccc
Confidence            99999999999999999999999999999999999885443

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

Probab=99.44  E-value=9e-14  Score=143.45  Aligned_cols=101  Identities=33%  Similarity=0.521  Sum_probs=95.5

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      .+......++..|..|..+|||..||+...  +|+||.+|++||||.|++.+|..+.   |..+..|..|+..||.||+.
T Consensus       606 ~~~s~~~~il~~l~~h~~awPf~~Pv~~~e--~pdyy~~I~~pmDl~tM~~~l~~~~---y~~~~~f~ad~~~vf~ncr~  680 (720)
T KOG1472|consen  606 KLFSAIQNILDQLQNHGDAWPFLKPVNKKE--VPDYYDVIKHPMDLRTMQNRLKDNQ---YTEVELFMADVVRVFANCRM  680 (720)
T ss_pred             hhhHHHHhHHhhhhcCCccCCccCcccccc--CCcHHHHhcccccHHHHhhhccccc---hhhHHHHHHHHHHHHhhhhc
Confidence            455677899999999999999999999988  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||++++..+..|-.|...|-.++...
T Consensus       681 yn~~~~~y~k~~~~le~~~~~k~~~~  706 (720)
T KOG1472|consen  681 YNGSDTQYYKCAQALEKFFLFKLNEL  706 (720)
T ss_pred             cCCccchheecccchhhhhcchhhhh
Confidence            99999999999999999998887765

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=99.38  E-value=3.1e-13  Score=111.41  Aligned_cols=81  Identities=22%  Similarity=0.177  Sum_probs=65.5

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCC----CCCCCCHHHHHHHHHHHHhccc
Q 020702           33 FFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKD----GTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        33 ~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~----~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      ..|..++..++.++.+|||..||++...++|+|+++|++||||+||+++|.+..    +..|..-..+..++..+|.||.
T Consensus         6 ~~~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (114)
T cd05494           6 ERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGRRS   85 (114)
T ss_pred             HHHHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHccccccccccccccccccccccccccccC
Confidence            346677778888889999999999977789999999999999999999999862    1225555667777777888877


Q ss_pred             ccCCC
Q 020702          109 KYNDE  113 (322)
Q Consensus       109 ~yN~~  113 (322)
                      .++..
T Consensus        86 ~~~~~   90 (114)
T cd05494          86 PSNIY   90 (114)
T ss_pred             ccccc
Confidence            77653

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

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=98.98  E-value=2.8e-10  Score=93.65  Aligned_cols=41  Identities=20%  Similarity=0.396  Sum_probs=39.3

Q ss_pred             CCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCC
Q 020702           71 KPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDER  114 (322)
Q Consensus        71 ~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~  114 (322)
                      .||||+||++||.+|.   |.++.+|.+||+|||.||..||+++
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            5899999999999999   9999999999999999999999874

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.

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

Probab=98.97  E-value=7.1e-10  Score=119.19  Aligned_cols=100  Identities=27%  Similarity=0.424  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccccc
Q 020702           31 LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY  110 (322)
Q Consensus        31 lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~y  110 (322)
                      ....++.++..+....-...|..|||..+  +|||.++|++||||.|++.+++++.   |.++++|.+|+.+|..||+.|
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            45567788999999999999999999998  9999999999999999999999999   999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          111 NDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       111 N~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |..+...|..|..+++.-...+.+.
T Consensus       641 n~~dtv~~r~av~~~e~~~~~~~~a  665 (1051)
T KOG0955|consen  641 NAKDTVYYRAAVRLRELIKKDFRNA  665 (1051)
T ss_pred             hccCeehHhhhHHHHhhhhhHHHhc
Confidence            9999999999999999988877766

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

Probab=98.95  E-value=8.1e-10  Score=118.94  Aligned_cols=95  Identities=27%  Similarity=0.492  Sum_probs=84.9

Q ss_pred             HHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCC
Q 020702           33 FFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYND  112 (322)
Q Consensus        33 ~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~  112 (322)
                      ..+-.|+.+++.-+.+|+|..||+...  .|+||.+|++||||.+|.+++..+.   |.+.++|..||++|+.||..||+
T Consensus      1385 ~~~d~~vs~~~~ipes~~f~~~v~~k~--~~~yy~kik~pmdl~~i~~n~~~~~---y~s~~e~l~dv~~i~~n~~~~ng 1459 (1563)
T KOG0008|consen 1385 FILDNIVSQMKEIPESWPFHEPVNKKR--VPDYYKKIKNPMDLETILKNIPPHK---YDSRSEFLDDVNLIYVNSVEYNG 1459 (1563)
T ss_pred             hhhhhHHHHHHhcchhcccccccchhh--chHHHHHhcChhhHHHHhhcCCccc---cccHHHHhhhhHhhcccceeecC
Confidence            455677788888899999999999998  9999999999999999999999999   99999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHH
Q 020702          113 ERDDVHVMAKSLLEKFEEKW  132 (322)
Q Consensus       113 ~~s~v~~~A~~L~~~Fe~~~  132 (322)
                      +.+....-|+.+-+.-...+
T Consensus      1460 ~e~~y~~k~~k~~ev~~~~~ 1479 (1563)
T KOG0008|consen 1460 AESAYTKKARKIGEVGLANL 1479 (1563)
T ss_pred             ccccccHHHHHHHHHHHHHH
Confidence            99999888886655544443

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

Probab=98.66  E-value=1.6e-08  Score=104.96  Aligned_cols=81  Identities=27%  Similarity=0.481  Sum_probs=70.5

Q ss_pred             cCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHH
Q 020702           44 QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS  123 (322)
Q Consensus        44 ~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~~~A~~  123 (322)
                      .+..+++|..||+...  .|+||.+|+.||||+|+.+++..+.   |.+.++|+.|+.+||.||.+||.+.+.....-..
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            3788999999999988  9999999999999999999999999   9999999999999999999999976655554444


Q ss_pred             HHHHHH
Q 020702          124 LLEKFE  129 (322)
Q Consensus       124 L~~~Fe  129 (322)
                      +.+.+-
T Consensus       375 v~~~~s  380 (720)
T KOG1472|consen  375 IMNSKS  380 (720)
T ss_pred             hhccCc
Confidence            444443

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

Probab=98.63  E-value=4.8e-08  Score=103.50  Aligned_cols=99  Identities=25%  Similarity=0.384  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHHc------CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhc
Q 020702           33 FFVRQARSFITQ------HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        33 ~~c~~il~~L~~------~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      ..|..|+.....      ++.+..|...+....  +|+||.+|+.|+++..|.+++.++.   |.+..+...|+.++|.|
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            456777777764      445788998877777  9999999999999999999999999   99999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      |..||..||.||..|..|+..|......+.
T Consensus      1102 a~~~~~egs~~y~d~~~l~~~~~~~~~~~~ 1131 (1157)
T KOG0386|consen 1102 ARTYNEEGSRVYEDAIVLQSVFKSARQEIS 1131 (1157)
T ss_pred             hhhhccCCceechhHHHHHHHHhhhHHHHh
Confidence            999999999999999999999998887773

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

Probab=98.58  E-value=7.7e-08  Score=98.63  Aligned_cols=101  Identities=20%  Similarity=0.169  Sum_probs=87.5

Q ss_pred             HHHHHHHHHHHHHHHHcCC------CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHH
Q 020702           28 ASLLQFFVRQARSFITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR  101 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~------~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dvr  101 (322)
                      +..++..+..||..+..+.      ....|.+-.+...  .|+||.+|..||.|..|++|+..+.   |.+.+.|..|+.
T Consensus        50 ~~~~~~~f~~il~~~~~~~d~~gk~~~d~feklp~~~~--~p~yy~~i~~pisl~~ik~kv~k~~---y~~~~~f~~D~~  124 (629)
T KOG1827|consen   50 DPPLIPKFKTILASLLDLKDDEGKQLFDKFEKLPSRKE--FPEYYYVIQQPISLDQIKRKVKKGR---YKRLSFFQLDFL  124 (629)
T ss_pred             ChHHHHHHHHHHHHHHhhccccCcccchhHhhcccccc--CCCcceeecCcccHHHHHHHHHhcc---cccHHHHHHHHH
Confidence            3445555677777776643      4677888878777  8999999999999999999999999   999999999999


Q ss_pred             HHHhcccccCCCCCHHHHHHHHHHHHHHHHHH
Q 020702          102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWL  133 (322)
Q Consensus       102 LIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~  133 (322)
                      +|+.||..||.++|.++.++..|...|.....
T Consensus       125 lm~ena~~~n~~ds~~~~~s~~l~~~~~~~~~  156 (629)
T KOG1827|consen  125 LMTENARLYNRPDSLIYKDSGELEKYFISLED  156 (629)
T ss_pred             HHHHHHHHhcCcchhhhhhhhhhhcchhhhhc
Confidence            99999999999999999999999999987553

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

Probab=98.56  E-value=8.8e-08  Score=103.67  Aligned_cols=99  Identities=25%  Similarity=0.390  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      .++-.+..|+.++...+...+|..||+...  +++||.||+.||||.++++.+....   |.+-++|..|+.+|++|..+
T Consensus      1261 ~~ss~l~~i~n~~~~~~~t~~f~~Pv~~k~--v~dyy~vi~~P~~lq~~kk~v~kr~---y~~r~~fle~~~~~~~ns~~ 1335 (1563)
T KOG0008|consen 1261 SLSSILETIINQARSSPNTYPFPTPVNAKE--VKDYYRVITPPMDLQTQKKLVRKRL---YESREHFLEELPLIVSNSTK 1335 (1563)
T ss_pred             ecccchHHHHHHHhcCCCCcCCCCccchhh--ccchhhccCCCcchHHHHHHHHHHH---HHHHHHHHHHhHHHhhchhh
Confidence            345567889999999999999999999988  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHH
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWL  133 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~  133 (322)
                      ||++.+.+...+..+....-..|.
T Consensus      1336 yng~~~~~t~~~q~mls~~~~~~~ 1359 (1563)
T KOG0008|consen 1336 YNGPLASLTRQQQSMLSLCFEKLK 1359 (1563)
T ss_pred             hcCchHHHHHHHHHHHHHHHHhhc
Confidence            999999999888876665444443

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

Probab=98.55  E-value=1.9e-08  Score=105.10  Aligned_cols=91  Identities=40%  Similarity=0.698  Sum_probs=84.5

Q ss_pred             HHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHH
Q 020702           42 ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMA  121 (322)
Q Consensus        42 L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~~~A  121 (322)
                      +-.|..+|+|..||+.+.+++|+||.+|++|||++||..+++++.   |.+..+..+|+..+|.||..||.++.+|..++
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            346889999999999999999999999999999999999999866   99999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 020702          122 KSLLEKFEEKWLQL  135 (322)
Q Consensus       122 ~~L~~~Fe~~~~~i  135 (322)
                      ..+...|.+.....
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=97.93  E-value=1.9e-06  Score=83.45  Aligned_cols=87  Identities=25%  Similarity=0.251  Sum_probs=76.6

Q ss_pred             HHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCC
Q 020702           36 RQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERD  115 (322)
Q Consensus        36 ~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s  115 (322)
                      ..++..+-+...-..|.-||.+..  .|+|.++|+.|||+.|++.+++-+.   |.+..+|.-|.+++..||..||...+
T Consensus        25 ehhlrkl~sKdp~q~fafplt~~m--ap~y~~iis~Pmd~~t~r~kidd~~---yl~L~~m~~d~kl~~~na~~yn~~~T   99 (418)
T KOG1828|consen   25 EHHLRKLPSKDPKQKFAFPLTDKM--APNYLEIISEPMDRITKRSKIDDTR---YLVLSQMEFDRKLPDGNATLYNLHPT   99 (418)
T ss_pred             HHHHHhccccChhhhhccccchhh--ccchHhhhhcccccccccccCCCcc---ceechhhhhhhcccccchhhhhcCCc
Confidence            445555555666677778888877  8999999999999999999999998   99999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 020702          116 DVHVMAKSLLEK  127 (322)
Q Consensus       116 ~v~~~A~~L~~~  127 (322)
                      .++..|+.|..+
T Consensus       100 v~~~aaKrL~~v  111 (418)
T KOG1828|consen  100 VPIVAAKRLCPV  111 (418)
T ss_pred             cccccccccchh
Confidence            999999988765

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

Probab=97.69  E-value=3.1e-05  Score=75.09  Aligned_cols=82  Identities=13%  Similarity=0.060  Sum_probs=71.5

Q ss_pred             HHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHH
Q 020702           39 RSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVH  118 (322)
Q Consensus        39 l~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~  118 (322)
                      ..++........|..|+-...  .|.|.-+|++|+|++|.+.+..++.   |.| .+|..|..+|+.||++||.+....|
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            334444556677777877766  8999999999999999999999999   999 9999999999999999999999999


Q ss_pred             HHHHHHHH
Q 020702          119 VMAKSLLE  126 (322)
Q Consensus       119 ~~A~~L~~  126 (322)
                      .+|..+.-
T Consensus       291 elank~lh  298 (418)
T KOG1828|consen  291 ELANKQLH  298 (418)
T ss_pred             HHHHhhhh
Confidence            99987655

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

Probab=96.81  E-value=0.0013  Score=55.52  Aligned_cols=67  Identities=13%  Similarity=0.257  Sum_probs=58.7

Q ss_pred             CCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhhCcCchh
Q 020702           72 PMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVME  141 (322)
Q Consensus        72 PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~~~~  141 (322)
                      |.||..|++||+.|.   |+++.+|..||-.|+.-++.-.+....+......+..+|-+.+..++++...
T Consensus        59 p~dL~~V~kkl~~G~---Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~vf~Wf~~  125 (131)
T cd05493          59 PLDLEAVGKKLEAGF---YTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFNS  125 (131)
T ss_pred             cccHHHHHHHHhccc---eehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHhcccccc
Confidence            899999999999999   9999999999999999998887766666666777778899999999887643

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.

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

Probab=96.78  E-value=0.00044  Score=68.02  Aligned_cols=90  Identities=34%  Similarity=0.485  Sum_probs=80.0

Q ss_pred             HHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHH
Q 020702           39 RSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVH  118 (322)
Q Consensus        39 l~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~  118 (322)
                      +.....+..+|+|..|+....  .|+|++.|..+|+++|.+.++..+.   |....+|..|.++++.||..||+.....+
T Consensus       272 i~~~~~~~~~~~~~~~~~~~~--~p~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  346 (371)
T COG5076         272 ITNSQAHVGAWPFLRPVSDEE--VPDYYKDIRDPMDLSTKELKLRNNY---YRPEETFVRDAKLFFDNCVMYNGEVTDYY  346 (371)
T ss_pred             ccccccccccccccccCCccc--ccchhhhhhcccccccchhhhhccc---CCCccccccccchhhhcccccchhhhhhh
Confidence            333455677999999999888  9999999999999999999999999   99999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q 020702          119 VMAKSLLEKFEEKWL  133 (322)
Q Consensus       119 ~~A~~L~~~Fe~~~~  133 (322)
                      ..+..+...|.....
T Consensus       347 ~~~~~~~~~~~~~~~  361 (371)
T COG5076         347 KNANVLEDFVIKKTR  361 (371)
T ss_pred             hhccchhhhHhhhhh
Confidence            888888777766544

>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]

Probab=90.68  E-value=0.23  Score=53.18  Aligned_cols=61  Identities=18%  Similarity=0.377  Sum_probs=52.7

Q ss_pred             ccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHH
Q 020702           68 VIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK  131 (322)
Q Consensus        68 iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~  131 (322)
                      --.-|..|+.|+.+|++..   |++.+.|..||-.|.+||.+|.+-+..+...+..|...|..-
T Consensus      1049 ~fpvpls~evi~~rlEn~y---Yrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~T 1109 (1113)
T KOG0644|consen 1049 RFPVPLSLEVIRSRLENNY---YRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRT 1109 (1113)
T ss_pred             CCCCcccHHHHHHHHHhhh---hhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhhh
Confidence            3556899999999999999   999999999999999999999998887777777777666543

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

Probab=89.72  E-value=0.23  Score=54.67  Aligned_cols=66  Identities=21%  Similarity=0.249  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCCccc---CCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHH--HHHHHHhcccccCCCC
Q 020702           46 KWAWPFMHPVDVEG---LGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYA--DVRLVFKNAMKYNDER  114 (322)
Q Consensus        46 ~~a~~F~~PVd~~~---~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~--DvrLIf~Na~~yN~~~  114 (322)
                      ..+..|..|+++..   +++++|-.+|++|||+...-.+++.+.   |.++.+|..  +++|||.+++.||+..
T Consensus       531 R~~~~~s~Pl~~~~~~ll~~~~~~~~iq~~~~va~~~~k~~e~~---~~~v~~~e~~~~i~lic~~~lli~~~~  601 (1080)
T KOG0732|consen  531 RSSVIFSRPLSTYLKPLLPFQDALEDIQGLMDVASSMAKIEEHL---KLLVRSFESNFAIRLICRPRLLINGGK  601 (1080)
T ss_pred             ccccCCCCCCCcceecccchHHHHHHhhcchhHHhhhhhHHHHh---HHHHHhhhcccchhhhcCcHHhcCCCc
Confidence            34677888887432   225689999999999999999999999   999999999  9999999999999975

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	322
3oni_A	114	Crystal Structure Of The Second Bromodomain Of Huma		7e-20
2i8n_A	114	Solution Structure Of The Second Bromodomain Of Brd		7e-20
2dvv_A	112	Crystal Structure Of The Second Bromodomain Of The		8e-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		2e-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		7e-18
2e7n_A	117	Solution Structure Of The Second Bromodomain From H		9e-18
2dww_A	114	Crystal Structure Of Bromodomain-Containing Protein		1e-17
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
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		1e-14
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		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		4e-13
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		4e-13
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		6e-13
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		3e-12
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		3e-12
2nxb_A	123	Crystal Structure Of Human Bromodomain Containing P		3e-12
3aqa_A	128	Crystal Structure Of The Human Brd2 Bd1 Bromodomain		2e-11
1x0j_A	122	Crystal Structure Analysis Of The N-Terminal Bromod		3e-11
3g0l_A	117	Crystal Structure Of Human Bromodomain Adjacent To		9e-11
2e7o_A	112	Solution Structure Of The Bromodomain From Human Br		1e-10
3dwy_A	119	Crystal Structure Of The Bromodomain Of Human Crebb		2e-10
1jsp_B	121	Nmr Structure Of Cbp Bromodomain In Complex With P5		2e-10
3i3j_A	124	Crystal Structure Of The Bromodomain Of Human Ep300		3e-10
1e6i_A	121	Bromodomain From Gcn5 Complexed With Acetylated H4		4e-09
3u5m_A	207	Crystal Structure Of Trim33 Phd-Bromo In The Free S		6e-09
2yyn_A	135	Crystal Sturcture Of Human Bromodomain Protein Leng		1e-08
3o33_A	184	Crystal Structure Of Trim24 Phd-Bromo In The Free S		1e-08
3lxj_A	136	Crystal Structure Of The Bromodomain Of Human Aaa D		8e-08
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		1e-07
3nxb_A	116	Crystal Structure Of The Bromodomain Of Human Cecr2		1e-07
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		2e-07
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		2e-07
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		2e-07
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		2e-07
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		3e-07
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		3e-07
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		4e-07
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		4e-07
1f68_A	103	Nmr Solution Structure Of The Bromodomain From Huma		2e-06
3d7c_A	112	Crystal Structure Of The Bromodomain Of Human Gcn5,		2e-06
2f6j_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		3e-06
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		4e-06
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		4e-06
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		4e-06
3uv4_A	158	Crystal Structure Of The Second Bromodomain Of Huma		9e-06
2dkw_A	131	Solution Structure Of The Bromodomain Of Human Prot		1e-05
3dai_A	130	Crystal Structure Of The Bromodomain Of The Human A		1e-05
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		2e-05
3hme_A	123	Crystal Structure Of Human Bromodomain Containing 9		2e-05
3hmh_A	155	Crystal Structure Of The Second Bromodomain Of Huma		9e-05
3fkm_X	166	Plasmodium Falciparum Bromodomain-Containing Protei		3e-04
2r10_A	361	Structure Of An Acetylated Rsc4 Tandem Bromodomain		3e-04
2r0v_A	346	Structure Of The Rsc4 Tandem Bromodomain Acetylated		3e-04
2i7k_A	117	Solution Structure Of The Bromodomain Of Human Brd7		5e-04
3tlp_A	150	Crystal Structure Of The Fourth Bromodomain Of Huma		6e-04

>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 = 94.7 bits (234), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)
Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 27  YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 83
Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             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 = 46/97 (47%), Positives = 66/97 (68%), Gaps = 4/97 (4%)
Query: 41  FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct: 14  FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGAD 70
Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL 136
           VRL+F N  KYN    +V  MA+ L + FE ++ ++L
Sbjct: 71  VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKML 107

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 3/89 (3%)
Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 25  YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 81
Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             KYN    DV  MA+ L + FE ++ ++
Sbjct: 82  CYKYNPPDHDVVAMARKLQDVFEFRYAKM 110

>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: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD   LGLHDY+++I+ PMD ST+K KM+ +D   YR+ +E  ADVRL+F N
Sbjct: 21  YAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD---YRDAQEFAADVRLMFSN 77
Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             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 = 93.6 bits (231), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 45/96 (46%), Positives = 65/96 (67%), Gaps = 4/96 (4%)
Query: 41  FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct: 35  FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGAD 91
Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 92  VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 127

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 45/96 (46%), Positives = 65/96 (67%), Gaps = 4/96 (4%)
Query: 41  FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct: 33  FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGAD 89
Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 90  VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 125

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 45/96 (46%), Positives = 65/96 (67%), Gaps = 4/96 (4%)
Query: 41  FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           F  +H  +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  AD
Sbjct: 22  FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESRE---YRDAQEFGAD 78
Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           VRL+F N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 79  VRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 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: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF +PVD + LGLH+YY+V++ PMD  TIK KMD ++   Y++  E  ADVRL+F N
Sbjct: 34  YAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQE---YKDAYEFAADVRLMFMN 90
Query: 107 AMKYNDERDDVHVMAKSLLEKFE 129
             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 = 87.8 bits (216), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 41/89 (46%), Positives = 59/89 (66%), Gaps = 3/89 (3%)
Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD E L LHDY+++I+ PMD ST+K KMDG++   Y + +   ADVRL+F N
Sbjct: 27  YAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGRE---YPDAQGFAADVRLMFSN 83
Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             KYN    +V  MA+ L + FE ++ ++
Sbjct: 84  CYKYNPPDHEVVAMARKLQDVFEMRFAKM 112

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

Iteration: 1
 Score = 87.4 bits (215), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 41/89 (46%), Positives = 59/89 (66%), Gaps = 3/89 (3%)
Query: 47  WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN 106
           +AWPF  PVD E L LHDY+++I+ PMD ST+K KMDG++   Y + +   ADVRL+F N
Sbjct: 32  YAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGRE---YPDAQGFAADVRLMFSN 88
Query: 107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
             KYN    +V  MA+ L + FE ++ ++
Sbjct: 89  CYKYNPPDHEVVAMARKLQDVFEMRFAKM 117

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

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 43/93 (46%), Positives = 60/93 (64%), Gaps = 4/93 (4%)
Query: 41  FITQHK-WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           F  +H  +AWPF  PVDVE LGLHDY ++I+ P D STIK+K++ ++   YR+ +E  AD
Sbjct: 20  FAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPXDXSTIKSKLESRE---YRDAQEFGAD 76
Query: 100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 132
           VRL F N  KYN    +V   A+ L + FE ++
Sbjct: 77  VRLXFSNCYKYNPPDHEVVAXARKLQDVFEXRF 109

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

Iteration: 1
 Score = 77.8 bits (190), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 38/101 (37%), Positives = 58/101 (57%), Gaps = 3/101 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+ +R     + +H++AWPF  PVD   L L DYY++I+ PMD  TIK ++   +   Y
Sbjct: 26  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRL---ENNYY 82
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
            N +E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 83  WNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 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 = 77.4 bits (189), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 38/101 (37%), Positives = 58/101 (57%), Gaps = 3/101 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+ +R     + +H++AWPF  PVD   L L DYY++I+ PMD  TIK ++   +   Y
Sbjct: 22  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRL---ENNYY 78
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
            N +E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 79  WNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 119

>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 = 38/101 (37%), Positives = 58/101 (57%), Gaps = 3/101 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+ +R     + +H++AWPF  PVD   L L DYY++I+ PMD  TIK ++   +   Y
Sbjct: 22  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRL---ENNYY 78
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
            N +E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 79  WNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 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 = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/101 (37%), Positives = 58/101 (57%), Gaps = 3/101 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+ +R     + +H++AWPF  PVD   L L DYY++I+ PMD  TIK ++   +   Y
Sbjct: 42  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRL---ENNYY 98
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
            N +E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 99  WNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 139

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 40/105 (38%), Positives = 57/105 (54%), Gaps = 3/105 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQF  R     + +H ++WPF  PVD   L L DYY +I+ PMD +TIK +++ K    Y
Sbjct: 15  LQFLQRVVLKALWKHGFSWPFQQPVDAVKLKLPDYYTIIKTPMDLNTIKKRLENK---YY 71
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
               E   D   +F N   YN   DD+ VMA++L + F +K  Q+
Sbjct: 72  EKASECIEDFNTMFSNCYLYNKTGDDIVVMAQALEKLFMQKLSQM 116

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 57/101 (56%), Gaps = 3/101 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+  +     + +H++AWPF  PVD   LGL DY+++I++PMD  TIK ++   +   Y
Sbjct: 33  LQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRL---ENNYY 89
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
               E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 90  WAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQK 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 = 72.0 bits (175), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 57/101 (56%), Gaps = 3/101 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+  +     + +H++AWPF  PVD   LGL DY+++I++PMD  TIK ++   +   Y
Sbjct: 33  LQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRL---ENNYY 89
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
               E   D   +F N   YN   DD+ +MA++L + F +K
Sbjct: 90  WAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQK 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 = 71.6 bits (174), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 57/105 (54%), Gaps = 3/105 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+  +     + +H ++WPF  PVD   L L DYY +I+ PMD +TIK +++ K    Y
Sbjct: 14  LQYLQKVVLKDLWKHSFSWPFQRPVDAVKLQLPDYYTIIKNPMDLNTIKKRLENK---YY 70
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
               E   D   +F N   YN   DD+ +MA++L + F +K  Q+
Sbjct: 71  AKASECIEDFNTMFSNCYLYNKPGDDIVLMAQALEKLFMQKLSQM 115

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 36/105 (34%), Positives = 57/105 (54%), Gaps = 3/105 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+        + +H++AWPF  PVD   L L DY+++I+ PMD  TIK ++   +   Y
Sbjct: 22  LQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRL---ENNYY 78
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            +  E   D   +F N   YN   DD+ +MA++L + F +K  Q+
Sbjct: 79  WSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 123

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 36/105 (34%), Positives = 57/105 (54%), Gaps = 3/105 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+        + +H++AWPF  PVD   L L DY+++I+ PMD  TIK ++   +   Y
Sbjct: 20  LQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRL---ENNYY 76
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            +  E   D   +F N   YN   DD+ +MA++L + F +K  Q+
Sbjct: 77  WSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 121

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 36/105 (34%), Positives = 57/105 (54%), Gaps = 3/105 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+        + +H++AWPF  PVD   L L DY+++I+ PMD  TIK ++   +   Y
Sbjct: 18  LQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRL---ENNYY 74
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            +  E   D   +F N   YN   DD+ +MA++L + F +K  Q+
Sbjct: 75  WSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 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 = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 56/111 (50%), Gaps = 3/111 (2%)
Query: 21  GGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKN 80
            G      + LQ+  +     + +H++AWPF  PVD   LGL DY+++I++P D  TIK 
Sbjct: 3   SGSSGRVTNQLQYLHKVVXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKR 62
Query: 81  KMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
           ++   +   Y    E   D    F N   YN   DD+ + A++L + F +K
Sbjct: 63  RL---ENNYYWAASECXQDFNTXFTNCYIYNKPTDDIVLXAQTLEKIFLQK 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: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 54/101 (53%), Gaps = 3/101 (2%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+  +     + +H++AWPF  PVD   LGL DY+++I++P D  TIK ++   +   Y
Sbjct: 7   LQYLHKVVXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRL---ENNYY 63
Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
               E   D    F N   YN   DD+ + A++L + F +K
Sbjct: 64  WAASECXQDFNTXFTNCYIYNKPTDDIVLXAQTLEKIFLQK 104

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 53/88 (60%), Gaps = 5/88 (5%)
Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
           H+ AWPF+ PV+++ +    Y +VI+KPMDFSTI+ K+       Y N+     DVRLVF
Sbjct: 28  HEDAWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREKLSSGQ---YPNLETFALDVRLVF 82
Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKW 132
            N   +N++  D+     ++ + FE+KW
Sbjct: 83  DNCETFNEDDSDIGRAGHNMRKYFEKKW 110

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 53/88 (60%), Gaps = 5/88 (5%)
Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
           H+ AWPF+ PV+++ +    Y +VI+KPMDFSTI+ K+       Y N+     DVRLVF
Sbjct: 25  HEDAWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREKLSSGQ---YPNLETFALDVRLVF 79
Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKW 132
            N   +N++  D+     ++ + FE+KW
Sbjct: 80  DNCETFNEDDSDIGRAGHNMRKYFEKKW 107

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/83 (40%), Positives = 49/83 (59%), Gaps = 5/83 (6%)
Query: 50  PFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG-YRNVREIYADVRLVFKNAM 108
           PF  PVD + LG+ DY+++++ PMD STIK K+D    TG Y+   +   DV L+F NA 
Sbjct: 32  PFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLD----TGQYQEPWQYVDDVWLMFNNAW 87
Query: 109 KYNDERDDVHVMAKSLLEKFEEK 131
            YN +   V+     L E FE++
Sbjct: 88  LYNRKTSRVYKFCSKLAEVFEQE 110

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/83 (40%), Positives = 49/83 (59%), Gaps = 5/83 (6%)
Query: 50  PFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG-YRNVREIYADVRLVFKNAM 108
           PF  PVD + LG+ DY+++++ PMD STIK K+D    TG Y+   +   DV L+F NA 
Sbjct: 34  PFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLD----TGQYQEPWQYVDDVWLMFNNAW 89
Query: 109 KYNDERDDVHVMAKSLLEKFEEK 131
            YN +   V+     L E FE++
Sbjct: 90  LYNRKTSRVYKFCSKLAEVFEQE 112

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 49/83 (59%), Gaps = 5/83 (6%)
Query: 50  PFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG-YRNVREIYADVRLVFKNAM 108
           PF  PVD + LG+ DY+++++ PMD STIK K+D    TG Y+   +   D+ L+F NA 
Sbjct: 37  PFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLD----TGQYQEPWQYVDDIWLMFNNAW 92
Query: 109 KYNDERDDVHVMAKSLLEKFEEK 131
            YN +   V+     L E FE++
Sbjct: 93  LYNRKTSRVYKYCSKLSEVFEQE 115

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 34/97 (35%), Positives = 53/97 (54%), Gaps = 6/97 (6%)
Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  H  AWPF+ PV+ E +   DYY+ I++PMD ST++ K++      Y+ + +   D R
Sbjct: 25  LQNHAAAWPFLQPVNKEEVP--DYYDFIKEPMDLSTMEIKLES---NKYQKMEDFIYDAR 79
Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 138
           LVF N   YN E    +  A   LEKF    ++ +P+
Sbjct: 80  LVFNNCRMYNGENTSYYKYANR-LEKFFNNKVKEIPE 115

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 59/121 (48%), Gaps = 14/121 (11%)
Query: 14  IGKKLLEGGCKNLSAS-----------LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGL 62
           IGK  +E  C NL  S           + Q    +   ++  H+ +  F  PV      +
Sbjct: 54  IGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPA---SI 110
Query: 63  HDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAK 122
            +YY++I+KPMD ST+K K+  K    Y+   +  ADVRL+FKN  ++N+    V V A 
Sbjct: 111 PNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYAD 170
Query: 123 S 123
           +
Sbjct: 171 T 171

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/98 (33%), Positives = 52/98 (53%), Gaps = 4/98 (4%)
Query: 41  FITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADV 100
           F+  H+ +  F  PV    L + DYY++I+ PMD STIK ++  +D + Y    +  AD 
Sbjct: 31  FLYCHEMSLAFQDPV---PLTVPDYYKIIKNPMDLSTIKKRLQ-EDYSMYSKPEDFVADF 86
Query: 101 RLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 138
           RL+F+N  ++N+   +V      L   FEE    L P+
Sbjct: 87  RLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPE 124

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 51/97 (52%), Gaps = 4/97 (4%)
Query: 41  FITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADV 100
           F+  H+ +  F  PV    L + DYY++I+ PMD STIK ++  +D + Y    +  AD 
Sbjct: 92  FLYCHEMSLAFQDPV---PLTVPDYYKIIKNPMDLSTIKKRLQ-EDYSMYSKPEDFVADF 147
Query: 101 RLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP 137
           RL+F+N  ++N+   +V      L   FEE    L P
Sbjct: 148 RLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 184

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L+ F+R     +   K    F  PVD+E +   DY EVI++PMD ST+  K+D      Y
Sbjct: 13  LRLFLRDVTKRLATDKRFNIFSKPVDIEEVS--DYLEVIKEPMDLSTVITKIDKH---NY 67
Query: 91  RNVREIYADVRLVFKNAMKYNDERD 115
              ++   D+ L+  NA++YN ++D
Sbjct: 68  LTAKDFLKDIDLICSNALEYNPDKD 92

>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 = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 51/93 (54%), Gaps = 6/93 (6%)
Query: 40  SFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           + I Q + + PF  PVD+  +   DY ++I+ PMDF T++  +D  +   Y +  E   D
Sbjct: 20  NLIFQCEDSEPFRQPVDL--VEYPDYRDIIDTPMDFGTVRETLDAGN---YDSPLEFCKD 74
Query: 100 VRLVFKNAMKYN-DERDDVHVMAKSLLEKFEEK 131
           +RL+F NA  Y  ++R  ++ M   L   FEEK
Sbjct: 75  IRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEK 107

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 47/83 (56%), Gaps = 5/83 (6%)
Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  HK +WPF+ PVD       +YY++I+ PMD S+++ K+   +G  Y    E   D++
Sbjct: 28  VKAHKDSWPFLEPVDESYAP--NYYQIIKAPMDISSMEKKL---NGGLYCTKEEFVNDMK 82
Query: 102 LVFKNAMKYNDERDDVHVMAKSL 124
            +F+N  KYN E  +   M+ +L
Sbjct: 83  TMFRNCRKYNGESSEYTKMSDNL 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 = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
           HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  AD+  +F
Sbjct: 87  HKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYEKLTEFVADMTKIF 141
Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEK 131
            N   YN      +  A+ L   F +K
Sbjct: 142 DNCRYYNPSDSPFYQCAEVLESFFVQK 168

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
           HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  AD+  +F
Sbjct: 35  HKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYEKLTEFVADMTKIF 89
Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEK 131
            N   YN      +  A+ L   F +K
Sbjct: 90  DNCRYYNPSDSPFYQCAEVLESFFVQK 116

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 5/90 (5%)
Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  AD+ 
Sbjct: 25  LQAHKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYEKLTEFVADMT 79
Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
            +F N   YN      +  A+ L   F +K
Sbjct: 80  AIFDNCRYYNPSDSPFYQCAEVLESFFVQK 109

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
           HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  AD+  +F
Sbjct: 87  HKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYEKLTEFVADMTKIF 141
Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEK 131
            N   YN      +  A+ L   F +K
Sbjct: 142 DNCRYYNPSDSPFYQCAEVLESFFVQK 168

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 54/101 (53%), Gaps = 12/101 (11%)
Query: 29  SLLQFFVRQARSFITQHKWAWPFMHPVD-VEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 87
           S L+  ++Q +S    H+ AWPFM PV   E  G   YYEVI  PMD  T+  ++  +  
Sbjct: 18  STLKSILQQVKS----HQSAWPFMEPVKRTEAPG---YYEVIRFPMDLKTMSERLKNR-- 68
Query: 88  TGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 128
             Y + +   AD++ VF N  +YN    + +  A ++LEKF
Sbjct: 69  -YYVSKKLFMADLQRVFTNCKEYNPPESEYYKCA-NILEKF 107

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 5/90 (5%)
Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  AD+ 
Sbjct: 25  LQAHKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRR---YYEKLTEFVADMT 79
Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
            +F N   YN      +  A+ L   F +K
Sbjct: 80  KIFDNCRYYNPSDSPFYQCAEVLESFFVQK 109

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 54/101 (53%), Gaps = 12/101 (11%)
Query: 29  SLLQFFVRQARSFITQHKWAWPFMHPVD-VEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 87
           S L+  ++Q +S    H+ AWPFM PV   E  G   YYEVI  PMD  T+  ++  +  
Sbjct: 16  STLKSILQQVKS----HQSAWPFMEPVKRTEAPG---YYEVIRFPMDLKTMSERLKNR-- 66
Query: 88  TGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 128
             Y + +   AD++ VF N  +YN    + +  A ++LEKF
Sbjct: 67  -YYVSKKLFMADLQRVFTNCKEYNPPESEYYKCA-NILEKF 105

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 51/92 (55%), Gaps = 6/92 (6%)
Query: 40  SFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           + I Q + + PF  PVD+  L   DY ++I+ PMDF+T++  +   +   Y +  E+  D
Sbjct: 31  NLIFQCEDSEPFRQPVDL--LEYPDYRDIIDTPMDFATVRETL---EAGNYESPMELCKD 85
Query: 100 VRLVFKNAMKYN-DERDDVHVMAKSLLEKFEE 130
           VRL+F N+  Y   +R  ++ M+  L   FEE
Sbjct: 86  VRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEE 117

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY-ADV 100
           I  H  AWPFM PV        DYYEVI  P+D  T+  ++  +    Y   R+++ AD+
Sbjct: 15  IKSHPSAWPFMEPVKKSEAP--DYYEVIRFPIDLKTMTERLRSR----YYVTRKLFVADL 68
Query: 101 RLVFKNAMKYNDERDDVHVMAKSLLEKF 128
           + V  N  +YN   D  +    S LEKF
Sbjct: 69  QRVIANCREYNPP-DSEYCRCASALEKF 95

>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 = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 45/88 (51%), Gaps = 8/88 (9%)
Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIY-ADV 100
           I  H  AWPFM PV  +     DYYEVI  P+D  T+  ++  +    Y   R+++ AD+
Sbjct: 19  IKSHPSAWPFMEPV--KKSEAPDYYEVIRFPIDLKTMTERLRSR----YYVTRKLFVADL 72
Query: 101 RLVFKNAMKYNDERDDVHVMAKSLLEKF 128
           + V  N  +YN   D  +    S LEKF
Sbjct: 73  QRVIANCREYNPP-DSEYCRCASALEKF 99

>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 = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 42/87 (48%), Gaps = 5/87 (5%)
Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
           HK AWPF+ PVD       DYY VI++P D +T + ++  +    Y  + E  AD   +F
Sbjct: 87  HKXAWPFLEPVDPNDAP--DYYGVIKEPXDLATXEERVQRR---YYEKLTEFVADXTKIF 141
Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEK 131
            N   YN      +  A+ L   F +K
Sbjct: 142 DNCRYYNPSDSPFYQCAEVLESFFVQK 168

>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 = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/104 (25%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 28  ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 87
           +S+L+  +   R         +PF  PV+ + +   DYY++I +PMD  T++  +  +  
Sbjct: 49  SSILESIINDMRDLPN----TYPFHTPVNAKVVK--DYYKIITRPMDLQTLRENVRKR-- 100
Query: 88  TGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
             Y +  E    + L+ KN+  YN  +  +  +++S+L+  +EK
Sbjct: 101 -LYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEK 143

>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 = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/104 (25%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 28  ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 87
           +S+L+  +   R         +PF  PV+ + +   DYY++I +PMD  T++  +  +  
Sbjct: 16  SSILESIINDMRDLPN----TYPFHTPVNAKVVK--DYYKIITRPMDLQTLRENVRKR-- 67
Query: 88  TGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
             Y +  E    + L+ KN+  YN  +  +  +++S+L+  +EK
Sbjct: 68  -LYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEK 110

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/104 (25%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 28  ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDG 87
           +S+L+  +   R         +PF  PV+ + +   DYY++I +PMD  T++  +  +  
Sbjct: 28  SSILESIINDMRDLPN----TYPFHTPVNAKVVK--DYYKIITRPMDLQTLRENVRKR-- 79
Query: 88  TGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEK 131
             Y +  E    + L+ KN+  YN  +  +  +++S+L+  +EK
Sbjct: 80  -LYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEK 122

>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 = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 48  AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA 107
           +WPF HPV+ + +   DYY+VI  PMD  TI+  +       Y++      DV L+  N+
Sbjct: 48  SWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKH---KYQSRESFLDDVNLILANS 102
Query: 108 MKYN 111
           +KYN
Sbjct: 103 VKYN 106

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L+ F+R     +   K    F  PV        DY EVI++PMD ST+  K+D  +   Y
Sbjct: 13  LRLFLRDVTKRLATDKRFNIFSKPV-------SDYLEVIKEPMDLSTVITKIDKHN---Y 62
Query: 91  RNVREIYADVRLVFKNAMKYNDERD 115
              ++   D+ L+  NA++YN ++D
Sbjct: 63  LTAKDFLKDIDLICSNALEYNPDKD 87

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L+ F+R     +   K    F  PVD + +   DY  VI++PMD S++ +K+D      Y
Sbjct: 11  LRIFLRNVTHRLAIDKRFRVFTKPVDPDEVP--DYVTVIKQPMDLSSVISKIDLH---KY 65
Query: 91  RNVREIYADVRLVFKNAMKYNDERD 115
             V++   D+ L+  NA++YN +RD
Sbjct: 66  LTVKDYLRDIDLICSNALEYNPDRD 90

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 6/71 (8%)
Query: 51  FMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKY 110
           F  PV ++ +   DY + I+ PMDF+T++ +++ +   GY+N+ E   D  L+  N MKY
Sbjct: 34  FAQPVSLKEVP--DYLDHIKHPMDFATMRKRLEAQ---GYKNLHEFEEDFDLIIDNCMKY 88
Query: 111 NDERDDVHVMA 121
           N  RD V   A
Sbjct: 89  N-ARDTVFYRA 98

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 32/97 (32%), Positives = 50/97 (51%), Gaps = 9/97 (9%)
Query: 30  LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 89
           LL+ F+RQ +       +A+P     D    G   Y  +I+ PMDF T+K+K+   +   
Sbjct: 17  LLEHFLRQLQRKDPHGFFAFPV---TDAIAPG---YSMIIKHPMDFGTMKDKIVANE--- 67
Query: 90  YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLE 126
           Y++V E  AD +L+  NAM YN      + +AK +L 
Sbjct: 68  YKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILH 104

>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 = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 48  AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA 107
           +WPF HPV+ + +   DYY++I  P+D  TI+  +       Y++      DV L+  N+
Sbjct: 45  SWPFHHPVNKKFVP--DYYKMIVNPVDLETIRKNISKH---KYQSRESFLDDVNLILANS 99
Query: 108 MKYN 111
           +KYN
Sbjct: 100 VKYN 103

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +++++    F   VD +     DYY+VI+ P  FS IK K+  K G  Y    E   DV+
Sbjct: 33  LSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPXSFSCIKTKL--KKGQ-YAYPSEFVKDVQ 89
Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKF 128
           L+F N   YN     V +  K++   F
Sbjct: 90  LIFDNCSLYNTSNSVVAITGKNIETYF 116

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 61/119 (51%), Gaps = 10/119 (8%)
Query: 11  MHFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIE 70
           +H++ K L++   K ++ +LL       ++   + K + PFM  VD + L   +YYE++ 
Sbjct: 197 LHYLNK-LVDATEKKINQALLG--ASSPKNLDDKVKLSEPFMELVDKDELP--EYYEIVH 251
Query: 71  KPMDFSTIKNKMD-GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 128
            PM  S +K  ++ G+    Y  + +   D+ LVF+NA  +ND    ++  A +L   F
Sbjct: 252 SPMALSIVKQNLEIGQ----YSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYF 306

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 61/119 (51%), Gaps = 10/119 (8%)
Query: 11  MHFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIE 70
           +H++ K L++   K ++ +LL       ++   + K + PFM  VD + L   +YYE++ 
Sbjct: 182 LHYLNK-LVDATEKKINQALLG--ASSPKNLDDKVKLSEPFMELVDKDELP--EYYEIVH 236
Query: 71  KPMDFSTIKNKMD-GKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKF 128
            PM  S +K  ++ G+    Y  + +   D+ LVF+NA  +ND    ++  A +L   F
Sbjct: 237 SPMALSIVKQNLEIGQ----YSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYF 291

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 65  YYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSL 124
           Y  +I+ PMDFST+K K+   D   Y+++ E+  + +L+  NAM YN      +  AK L
Sbjct: 41  YSMIIKHPMDFSTMKEKIKNND---YQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKL 97
Query: 125 L 125
           L
Sbjct: 98  L 98

>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 = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 7/71 (9%)
Query: 64  DYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDE----RDDVHV 119
           DYY++I +PMD   I++ +      G   + E   D++L+F+NA  YN+E     +D H+
Sbjct: 63  DYYKIILEPMDLKIIEHNIRNDKYAGEEGMIE---DMKLMFRNARHYNEEGSQVYNDAHI 119
Query: 120 MAKSLLEKFEE 130
           + K L EK +E
Sbjct: 120 LEKLLKEKRKE 130

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	322
4alg_A	154	Bromodomain-containing protein 2; signaling protei	2e-42
3p1f_A	119	CREB-binding protein; structural genomics consorti	7e-42
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	1e-40
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	2e-40
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	9e-40
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	2e-39
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	3e-38
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	4e-38
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	4e-36
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	4e-36
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	1e-35
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	5e-35
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	6e-32
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	2e-31
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	4e-31
3d7c_A	112	General control of amino acid synthesis protein 5;	1e-30
3uv4_A	158	Second bromodomain of human transcription initiat	3e-30
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	7e-30
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	7e-30
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	1e-29
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	3e-29
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	3e-23
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	6e-29
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	7e-29
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	2e-22
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-28
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	6e-28
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	8e-28
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	5e-17
2r10_A	361	Chromatin structure-remodeling complex protein RSC	7e-27
2r10_A	361	Chromatin structure-remodeling complex protein RSC	6e-16
2grc_A	129	Probable global transcription activator SNF2L4; br	2e-26
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	2e-26
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	1e-25
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-25
2dat_A	123	Possible global transcription activator SNF2L2; br	9e-25
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-24
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	3e-24
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	6e-24
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	4e-19
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-14
2jns_A	90	Bromodomain-containing protein 4; ET-domain, struc	2e-14
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	9e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>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 =  142 bits (361), Expect = 2e-42
 Identities = 38/123 (30%), Positives = 62/123 (50%), Gaps = 3/123 (2%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+  +     + +H++AWPF  PVD   LGL DY+++I++PMD  TIK +++      Y
Sbjct: 33  LQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNY---Y 89

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEE 150
               E   D   +F N   YN   DD+ +MA++L + F +K   +  +  E      +  
Sbjct: 90  WAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQELVVTIPKNS 149

Query: 151 AKA 153
            K 
Sbjct: 150 HKK 152

>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 =  140 bits (355), Expect = 7e-42
 Identities = 35/110 (31%), Positives = 56/110 (50%), Gaps = 3/110 (2%)

Query: 30  LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 89
           L Q  +    +   Q   + PF  PVD + LG+ DY+++++ PMD STIK K+D      
Sbjct: 12  LRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQ--- 68

Query: 90  YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV 139
           Y+   +   DV L+F NA  YN +   V+     L E FE++   ++  +
Sbjct: 69  YQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 118

>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 =  137 bits (348), Expect = 1e-40
 Identities = 39/105 (37%), Positives = 60/105 (57%), Gaps = 3/105 (2%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ+ +R     + +H++AWPF  PVD   L L DYY++I+ PMD  TIK +++      Y
Sbjct: 22  LQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNY---Y 78

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            N +E   D   +F N   YN   DD+ +MA++L + F +K  +L
Sbjct: 79  WNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINEL 123

>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 =  136 bits (345), Expect = 2e-40
 Identities = 44/97 (45%), Positives = 64/97 (65%), Gaps = 3/97 (3%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
             +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  ADVRL+F
Sbjct: 27  AAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESRE---YRDAQEFGADVRLMF 83

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVME 141
            N  KYN    +V  MA+ L + FE ++ ++  +  E
Sbjct: 84  SNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEE 120

>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 =  135 bits (342), Expect = 9e-40
 Identities = 43/91 (47%), Positives = 62/91 (68%), Gaps = 3/91 (3%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
             +AWPF  PVDVE LGLHDY ++I+ PMD STIK+K++ ++   YR+ +E  ADVRL+F
Sbjct: 40  AAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGADVRLMF 96

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            N  KYN    +V  MA+ L + FE ++ ++
Sbjct: 97  SNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 127

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

 Score =  135 bits (342), Expect = 2e-39
 Identities = 31/148 (20%), Positives = 60/148 (40%), Gaps = 3/148 (2%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
                 Q    +++++    F   VD +     DYY+VI+ PM FS IK K+       Y
Sbjct: 22  WYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQ---Y 78

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEE 150
               E   DV+L+F N   YN     V +  K++   F  + + +       ++++  + 
Sbjct: 79  AYPSEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFNNQLIVMGYNNFILKEKKINDM 138

Query: 151 AKAQLDMQLTQEAVQTNKAKELRSELNE 178
            K   +  +     + ++ +E+    N 
Sbjct: 139 LKLVEEENIKWSKEKEDQIEEIDELENN 166

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

 Score =  131 bits (331), Expect = 3e-38
 Identities = 32/97 (32%), Positives = 51/97 (52%), Gaps = 4/97 (4%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  H+ +  F  PV    L + DYY++I+ PMD STIK ++  +D + Y    +  AD R
Sbjct: 32  LYCHEMSLAFQDPVP---LTVPDYYKIIKNPMDLSTIKKRLQ-EDYSMYSKPEDFVADFR 87

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 138
           L+F+N  ++N+   +V      L   FEE    L P+
Sbjct: 88  LIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPE 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 =  130 bits (329), Expect = 4e-38
 Identities = 34/107 (31%), Positives = 55/107 (51%), Gaps = 6/107 (5%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           I Q + + PF  PVD+  +   DY ++I+ PMDF T++  +D  +   Y +  E   D+R
Sbjct: 22  IFQCEDSEPFRQPVDL--VEYPDYRDIIDTPMDFGTVRETLDAGN---YDSPLEFCKDIR 76

Query: 102 LVFKNAMKYN-DERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQE 147
           L+F NA  Y  ++R  ++ M   L   FEEK  ++       +K  E
Sbjct: 77  LIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKISSDFKIGQKFNE 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 =  125 bits (317), Expect = 4e-36
 Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 6/109 (5%)

Query: 40  SFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD 99
           + I Q + + PF  PVD+  L   DY ++I+ PMDF+T++  ++  +   Y +  E+  D
Sbjct: 31  NLIFQCEDSEPFRQPVDL--LEYPDYRDIIDTPMDFATVRETLEAGN---YESPMELCKD 85

Query: 100 VRLVFKNAMKYN-DERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQE 147
           VRL+F N+  Y   +R  ++ M+  L   FEE    +L       +  +
Sbjct: 86  VRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSDYKSALRFHK 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 =  125 bits (316), Expect = 4e-36
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 5/95 (5%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  H+ AWPF+ PV+++ +    Y +VI+KPMDFSTI+ K+       Y N+     DVR
Sbjct: 25  METHEDAWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREKLSSGQ---YPNLETFALDVR 79

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL 136
           LVF N   +N++  D+     ++ + FE+KW    
Sbjct: 80  LVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTF 114

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

 Score =  124 bits (314), Expect = 1e-35
 Identities = 31/124 (25%), Positives = 56/124 (45%), Gaps = 10/124 (8%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L+ F+R     +   K    F  PV        DY EVI++PMD ST+  K+D  +   Y
Sbjct: 13  LRLFLRDVTKRLATDKRFNIFSKPVS-------DYLEVIKEPMDLSTVITKIDKHN---Y 62

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEE 150
              ++   D+ L+  NA++YN ++D    + +      ++    ++   ++ E  +  EE
Sbjct: 63  LTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEE 122

Query: 151 AKAQ 154
            K  
Sbjct: 123 IKES 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 =  124 bits (313), Expect = 5e-35
 Identities = 32/96 (33%), Positives = 50/96 (52%), Gaps = 4/96 (4%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  H+ +  F  PV    L + DYY++I+ PMD STIK ++  +D + Y    +  AD R
Sbjct: 93  LYCHEMSLAFQDPVP---LTVPDYYKIIKNPMDLSTIKKRLQ-EDYSMYSKPEDFVADFR 148

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP 137
           L+F+N  ++N+   +V      L   FEE    L P
Sbjct: 149 LIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 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 =  114 bits (288), Expect = 6e-32
 Identities = 32/94 (34%), Positives = 50/94 (53%), Gaps = 5/94 (5%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  H  AWPF+ PV+ E +   DYY+ I++PMD ST++ K++      Y+ + +   D R
Sbjct: 25  LQNHAAAWPFLQPVNKEEV--PDYYDFIKEPMDLSTMEIKLESNK---YQKMEDFIYDAR 79

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           LVF N   YN E    +  A  L + F  K  ++
Sbjct: 80  LVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 113

>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 =  113 bits (285), Expect = 2e-31
 Identities = 32/122 (26%), Positives = 60/122 (49%), Gaps = 5/122 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L+ F+R     +   K    F  PVD + +   DY  VI++PMD S++ +K+D      Y
Sbjct: 11  LRIFLRNVTHRLAIDKRFRVFTKPVDPDEV--PDYVTVIKQPMDLSSVISKIDLHK---Y 65

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEE 150
             V++   D+ L+  NA++YN +RD    + +       +    ++ + ++E+  Q  EE
Sbjct: 66  LTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEE 125

Query: 151 AK 152
            +
Sbjct: 126 IQ 127

>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 =  114 bits (286), Expect = 4e-31
 Identities = 30/94 (31%), Positives = 46/94 (48%), Gaps = 5/94 (5%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  HK AWPF+ PVD       DYY VI++PMD +T++ ++  +    Y  + E  AD+ 
Sbjct: 84  LQAHKMAWPFLEPVDPNDA--PDYYGVIKEPMDLATMEERVQRRY---YEKLTEFVADMT 138

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            +F N   YN      +  A+ L   F +K    
Sbjct: 139 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGF 172

>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 =  110 bits (278), Expect = 1e-30
 Identities = 30/105 (28%), Positives = 46/105 (43%), Gaps = 5/105 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L   ++   + I  H  AWPFM PV        DYYEVI  P+D  T+  ++  +    Y
Sbjct: 8   LYTTLKNLLAQIKSHPSAWPFMEPVKKSEA--PDYYEVIRFPIDLKTMTERLRSRY---Y 62

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
              +   AD++ V  N  +YN    +    A +L + F  K  + 
Sbjct: 63  VTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEG 107

>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 =  111 bits (279), Expect = 3e-30
 Identities = 32/154 (20%), Positives = 60/154 (38%), Gaps = 9/154 (5%)

Query: 7   SSSKMHFIGKKLLEGGCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYY 66
            SS +    + L      +   +            +     +WPF HPV+ + +   DYY
Sbjct: 7   HSSGVDLGTENLYFQSMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFV--PDYY 64

Query: 67  EVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLE 126
           +VI  PMD  TI+  +       Y++      DV L+  N++KYN         A+ ++ 
Sbjct: 65  KVIVNPMDLETIRKNISKHK---YQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVN 121

Query: 127 KFEEKWLQLLPKVMEEE----KRQEEEEAKAQLD 156
              +   +    + + E      +E    +A+L+
Sbjct: 122 VCYQTLTEYDEHLTQLEKDICTAKEAALEEAELE 155

>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 =  109 bits (274), Expect = 7e-30
 Identities = 26/102 (25%), Positives = 45/102 (44%), Gaps = 5/102 (4%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           + +      F  PV         Y  +I+ PMDF T+K+K+   +   Y++V E  AD +
Sbjct: 25  LQRKDPHGFFAFPVTDAIA--PGYSMIIKHPMDFGTMKDKIVANE---YKSVTEFKADFK 79

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE 143
           L+  NAM YN      + +AK +L    +   +     ++  
Sbjct: 80  LMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLALKRS 121

>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 =  108 bits (273), Expect = 7e-30
 Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 5/93 (5%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  HK +WPF+ PVD       +YY++I+ PMD S+++ K++G     Y    E   D++
Sbjct: 28  VKAHKDSWPFLEPVDESYA--PNYYQIIKAPMDISSMEKKLNGGL---YCTKEEFVNDMK 82

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQ 134
            +F+N  KYN E  +   M+ +L   F    ++
Sbjct: 83  TMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 115

>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 =  108 bits (272), Expect = 1e-29
 Identities = 26/113 (23%), Positives = 45/113 (39%), Gaps = 5/113 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
               +R+    + +      F  PV +  +   DY + I+KPMDF T+K  ++      Y
Sbjct: 8   FLILLRKTLEQLQEKDTGNIFSEPVPLSEV--PDYLDHIKKPMDFFTMKQNLEAYR---Y 62

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE 143
            N  +   D  L+  N +KYN +    +  A  L E+      Q   +  +  
Sbjct: 63  LNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMG 115

>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 = 3e-29
 Identities = 30/119 (25%), Positives = 54/119 (45%), Gaps = 9/119 (7%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +     +WPF HPV+ + +   DYY+VI  PMD  TI+  +       Y++      DV 
Sbjct: 149 MMAVPDSWPFHHPVNKKFV--PDYYKVIVNPMDLETIRKNISKH---KYQSRESFLDDVN 203

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEK----RQEEEEAKAQLD 156
           L+  N++KYN         A+ ++    +   +    + + EK     +E    +A+L+
Sbjct: 204 LILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELE 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 = 95.8 bits (238), Expect = 3e-23
 Identities = 27/118 (22%), Positives = 55/118 (46%), Gaps = 5/118 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L   +    + +      +PF  PV+ + +   DYY++I +PMD  T++  +  +    Y
Sbjct: 15  LSSILESIINDMRDLPNTYPFHTPVNAKVV--KDYYKIITRPMDLQTLRENVRKRL---Y 69

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEE 148
            +  E    + L+ KN+  YN  +  +  +++S+L+  +EK  +   K+   EK    
Sbjct: 70  PSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINP 127

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

 Score =  106 bits (267), Expect = 6e-29
 Identities = 31/120 (25%), Positives = 50/120 (41%), Gaps = 14/120 (11%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           LQ  + Q    + +   +  F  PV         Y  +I+ PMDFST+K K+   D   Y
Sbjct: 9   LQEALNQLMRQLQRKDPSAFFSFPVTDFIA--PGYSMIIKHPMDFSTMKEKIKNND---Y 63

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEE 150
           +++ E+  + +L+  NAM YN      +  AK LL    +            ++R E   
Sbjct: 64  QSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKIL---------SQERLEHHH 114

>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 =  111 bits (279), Expect = 7e-29
 Identities = 28/110 (25%), Positives = 48/110 (43%), Gaps = 5/110 (4%)

Query: 44  QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV 103
               +WPF HPV+ + +   DYY+VI  PMD  TI+  +       Y++      DV L+
Sbjct: 184 AVPDSWPFHHPVNKKFV--PDYYKVIVNPMDLETIRKNISKH---KYQSRESFLDDVNLI 238

Query: 104 FKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKA 153
             N++KYN         A+ ++    +   +    + + EK     +  A
Sbjct: 239 LANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAA 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 = 93.9 bits (233), Expect = 2e-22
 Identities = 25/110 (22%), Positives = 53/110 (48%), Gaps = 5/110 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L   +    + +      +PF  PV+ + +   DYY++I +PMD  T++  +  +    Y
Sbjct: 48  LSSILESIINDMRDLPNTYPFHTPVNAKVV--KDYYKIITRPMDLQTLRENVRKRL---Y 102

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVM 140
            +  E    + L+ KN+  YN  +  +  +++S+L+  +EK  +   K+ 
Sbjct: 103 PSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLA 152

>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 =  106 bits (266), Expect = 2e-28
 Identities = 31/120 (25%), Positives = 53/120 (44%), Gaps = 5/120 (4%)

Query: 35  VRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVR 94
           V +AR   +  +    FM           DYY++I +PMD   I++ +       Y    
Sbjct: 36  VLEAREPGSGRRLCDLFMVKPSK--KDYPDYYKIILEPMDLKIIEHNIRNDK---YAGEE 90

Query: 95  EIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQ 154
            +  D++L+F+NA  YN+E   V+  A  L +  +EK  +L P   +++     E    Q
Sbjct: 91  GMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKELGPLPDDDDMASPAENLYFQ 150

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

 Score =  104 bits (262), Expect = 6e-28
 Identities = 31/126 (24%), Positives = 53/126 (42%), Gaps = 8/126 (6%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L   +R     +     A  F  PV ++ +   DY + I+ PMDF+T++ +++ +    Y
Sbjct: 14  LTVLLRSVLDQLQDKDPARIFAQPVSLKEV--PDYLDHIKHPMDFATMRKRLEAQG---Y 68

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEE 150
           +N+ E   D  L+  N MKYN      +  A  L ++      Q      E +    EE 
Sbjct: 69  KNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARR---EVDSIGLEEA 125

Query: 151 AKAQLD 156
           +   L 
Sbjct: 126 SGMHLP 131

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

 Score =  109 bits (272), Expect = 8e-28
 Identities = 33/152 (21%), Positives = 58/152 (38%), Gaps = 8/152 (5%)

Query: 32  QFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 91
                  ++   + K + PFM  VD + L   +YYE++  PM  S +K  ++      Y 
Sbjct: 165 LLGASSPKNLDDKVKLSEPFMELVDKDEL--PEYYEIVHSPMALSIVKQNLEIGQ---YS 219

Query: 92  NVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVME---EEKRQEE 148
            + +   D+ LVF+NA  +ND    ++  A +L   F     +     ++   E      
Sbjct: 220 KIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINL 279

Query: 149 EEAKAQLDMQLTQEAVQTNKAKELRSELNEVD 180
           E  K + +  L         A  L     + D
Sbjct: 280 EFDKFEFENYLAIGGGGPAAAGALAISALDND 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 = 79.4 bits (195), Expect = 5e-17
 Identities = 24/160 (15%), Positives = 45/160 (28%), Gaps = 14/160 (8%)

Query: 23  CKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKM 82
                +  L   + + +           F+     +      YY  I++PM  + IK++ 
Sbjct: 29  FNRFISFTLDVLIDKYKDI------FKDFIKLPSRKFH--PQYYYKIQQPMSINEIKSRD 80

Query: 83  DGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEE 142
                           DV L+ KN   YN+    +   +  ++   E + L+        
Sbjct: 81  YEY----EDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNY 136

Query: 143 EKRQEEEEAKAQLDMQLT--QEAVQTNKAKELRSELNEVD 180
               E +        +L    E           S  N  D
Sbjct: 137 LINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDD 176

>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 =  107 bits (268), Expect = 7e-27
 Identities = 27/124 (21%), Positives = 52/124 (41%), Gaps = 5/124 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
                   ++   + K + PFM  VD + L   +YYE++  PM  S +K  ++      Y
Sbjct: 214 ALLGASSPKNLDDKVKLSEPFMELVDKDEL--PEYYEIVHSPMALSIVKQNLEIGQ---Y 268

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEE 150
             + +   D+ LVF+NA  +ND    ++  A +L   F     +     +++   + E  
Sbjct: 269 SKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEIN 328

Query: 151 AKAQ 154
            +  
Sbjct: 329 LEFD 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 = 76.8 bits (188), Expect = 6e-16
 Identities = 24/138 (17%), Positives = 41/138 (29%), Gaps = 8/138 (5%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
                 F+     +      YY  I++PM  + IK++    D            DV L+ 
Sbjct: 95  KDIFKDFIKLPSRKFH--PQYYYKIQQPMSINEIKSR----DYEYEDGPSNFLLDVELLT 148

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLT--QE 162
           KN   YN+    +   +  ++   E + L+            E +        +L    E
Sbjct: 149 KNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATE 208

Query: 163 AVQTNKAKELRSELNEVD 180
                      S  N  D
Sbjct: 209 KKINQALLGASSPKNLDD 226

>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 =  100 bits (251), Expect = 2e-26
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 12/130 (9%)

Query: 24  KNLSASLLQFF--VRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNK 81
            NL+  + +    V + +   +  + +  F+     + L   +YYE+I KP+DF  IK +
Sbjct: 10  PNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKEL--PEYYELIRKPVDFKKIKER 67

Query: 82  MDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVME 141
           +       YR++ ++  DV L+ +NA  +N E   ++  +  L   F         + +E
Sbjct: 68  IRNHK---YRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVR-----QKIE 119

Query: 142 EEKRQEEEEA 151
           +E   E EE+
Sbjct: 120 KEDDSEGEES 129

>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 =  100 bits (250), Expect = 2e-26
 Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 5/91 (5%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
              +  F            DYY +I++P+D  TI  ++       Y+++  +  D+ L+ 
Sbjct: 29  RLISELFQKLPSKVQY--PDYYAIIKEPIDLKTIAQRIQNGS---YKSIHAMAKDIDLLA 83

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           KNA  YN+    V   A S+ + F  K  ++
Sbjct: 84  KNAKTYNEPGSQVFKDANSIKKIFYMKKAEI 114

>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 =  100 bits (250), Expect = 1e-25
 Identities = 34/123 (27%), Positives = 57/123 (46%), Gaps = 20/123 (16%)

Query: 32  QFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR 91
           Q    +   ++  H+ +  F  PV      + +YY++I+KPMD ST+K K+  K    Y+
Sbjct: 83  QRKCERLLLYLYCHELSIEFQEPVP---ASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQ 139

Query: 92  NVREIYADVRLVFKNAMKYNDERDDVHVMA-----------------KSLLEKFEEKWLQ 134
              +  ADVRL+FKN  ++N+    V V A                 K++   FE+K  +
Sbjct: 140 IPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTE 199

Query: 135 LLP 137
           +  
Sbjct: 200 IYS 202

>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 = 5e-25
 Identities = 22/94 (23%), Positives = 39/94 (41%), Gaps = 5/94 (5%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
                 F+           DYYEV+ +P+D   I+ K+  ++   Y +V  + AD +L+F
Sbjct: 26  RLLCELFIRAPKRRNQ--PDYYEVVSQPIDLMKIQQKLKMEE---YDDVNLLTADFQLLF 80

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 138
            NA  Y       +  A  L + +     + + K
Sbjct: 81  NNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQK 114

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

 Score = 95.9 bits (239), Expect = 9e-25
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 5/91 (5%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
            + +  F+     + L   +YYE+I KP+DF  IK ++       YR++ ++  DV L+ 
Sbjct: 34  RQLSEVFIQLPSRKEL--PEYYELIRKPVDFKKIKERIRNH---KYRSLGDLEKDVMLLC 88

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            NA  +N E   ++  +  L   F+      
Sbjct: 89  HNAQTFNLEGSQIYEDSIVLQSVFKSARQSG 119

>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 = 95.9 bits (239), Expect = 1e-24
 Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 5/94 (5%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
              A PF H    +     DYY+ I+ P+    I+ K+  ++   Y  +  +  D+ L+F
Sbjct: 38  QLIAEPFYHLPSKKKY--PDYYQQIKMPISLQQIRTKLKNQE---YETLDHLECDLNLMF 92

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 138
           +NA +YN     ++     L +  + K  +L  +
Sbjct: 93  ENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARR 126

>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 = 94.7 bits (236), Expect = 3e-24
 Identities = 24/99 (24%), Positives = 40/99 (40%), Gaps = 5/99 (5%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
              A P ++    +     DYYE I  P+D  TI+ ++       Y+ V    AD+  VF
Sbjct: 30  QALAAPLLNLPPKKKN--ADYYEKISDPLDLITIEKQILTGY---YKTVEAFDADMLKVF 84

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEE 143
           +NA KY   +  V      L + +     +   ++ E  
Sbjct: 85  RNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQIDEIV 123

>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 = 93.6 bits (233), Expect = 6e-24
 Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 5/91 (5%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
            + +  F+       L   DYY  I+KPMD   I++ M       Y+++  +  D  ++F
Sbjct: 36  RRLSAIFLRLPSRSEL--PDYYLTIKKPMDMEKIRSHMMANK---YQDIDSMVEDFVMMF 90

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            NA  YN+    ++  A  L +   E    L
Sbjct: 91  NNACTYNEPESLIYKDALVLHKVLLETRRDL 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 = 82.6 bits (203), Expect = 4e-19
 Identities = 18/106 (16%), Positives = 34/106 (32%), Gaps = 5/106 (4%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  H+   P                +     +D + I+ ++  K    Y + +E   DV 
Sbjct: 88  LFCHEPCRPLHQLATDS----TFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVG 143

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQE 147
            +FK   K  +++ DV      L   FE +  +            E
Sbjct: 144 RMFKQFNKLTEDKADVQ-SIIGLQRFFETRMNEAFGDTKFSAVLVE 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 = 68.8 bits (168), Expect = 2e-14
 Identities = 16/127 (12%), Positives = 37/127 (29%), Gaps = 12/127 (9%)

Query: 45  HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF 104
             ++               D     + P+ F  I+  ++      YR +      +  V 
Sbjct: 28  RCYSDSLAEIPA------VDPNFPNKPPLTFDIIRKNVENNR---YRRLDLFQEHMFEVL 78

Query: 105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKAQLDMQLTQEAV 164
           + A + N    +++  A  L + F +   +L       E       +     +    E  
Sbjct: 79  ERARRMNRTDSEIYEDAVELQQFFIKIRDELCK---NGEILLSPALSYTTKHLHNDVEKE 135

Query: 165 QTNKAKE 171
           +  K  +
Sbjct: 136 RKEKLPK 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 = 66.9 bits (163), Expect = 2e-14
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 193 KCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFHATAQ-EVDLDMDAQSELTLW 251
           KC+ MS EEK+ L   + +L  E L + + I+    PS   +   E+++D +     TL 
Sbjct: 14  KCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLR 73

Query: 252 RLKVFVQESLKAASR 266
            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 = 53.4 bits (127), Expect = 9e-09
 Identities = 14/89 (15%), Positives = 34/89 (38%), Gaps = 3/89 (3%)

Query: 49  WPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM 108
              +  +       H      ++P+D   +K KMD  +   Y +V E   D+  + + A+
Sbjct: 81  KQVLTALLNSRTTSHLLRYRQQQPLDLEGVKRKMDQGN---YTSVLEFSDDIVKIIQAAI 137

Query: 109 KYNDERDDVHVMAKSLLEKFEEKWLQLLP 137
             +  + ++      +   F  +  ++ P
Sbjct: 138 NSDGGQPEIKKANSMVKSFFIRQMERVFP 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 = 45.2 bits (106), Expect = 2e-05
 Identities = 31/161 (19%), Positives = 57/161 (35%), Gaps = 33/161 (20%)

Query: 73  MDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 132
           MDF T   +   +           Y D+  VF++A   N +  DV  M KS+L K E   
Sbjct: 7   MDFET--GEHQYQ-----------YKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDH 53

Query: 133 LQLLPKVMEEEKR-------QEEEEAKA------QLDMQLTQEAVQT-NKAKELRSELNE 178
           + +    +    R       ++EE  +       +++ +     ++T  +   + + +  
Sbjct: 54  IIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI 113

Query: 179 VDMQLENLRETVIQKCRKMS---TEEKKNLGTALTRLSPED 216
              Q + L     Q   K +    +    L  AL  L P  
Sbjct: 114 --EQRDRLYNDN-QVFAKYNVSRLQPYLKLRQALLELRPAK 151

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	322
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.96
3d7c_A	112	General control of amino acid synthesis protein 5;	99.96
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.95
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.95
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.95
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.95
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.95
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.95
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.95
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.95
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.95
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.95
2dat_A	123	Possible global transcription activator SNF2L2; br	99.95
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.95
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.95
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.95
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.94
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.94
2grc_A	129	Probable global transcription activator SNF2L4; br	99.94
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.94
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.94
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3uv4_A	158	Second bromodomain of human transcription initiat	99.94
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.92
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.92
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.92
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.92
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.91
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.91
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.91
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.9
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.89
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.88
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.87
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.86
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.86
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.82
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.8
2jns_A	90	Bromodomain-containing protein 4; ET-domain, struc	99.71
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.68
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.61
2lm0_A	125	AF4/FMR2 family member 1/protein AF-9 chimera; int	96.6

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

Probab=99.96  E-value=2.5e-29  Score=209.73  Aligned_cols=109  Identities=36%  Similarity=0.647  Sum_probs=103.8

Q ss_pred             ccccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHH
Q 020702           24 KNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV  103 (322)
Q Consensus        24 k~~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLI  103 (322)
                      .+....+|+.+|..||+.|++|+.+|+|..|||+..+++||||++|++||||+||++||+++.   |.++.+|.+||+||
T Consensus        15 ~~r~~~~l~~~~~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~li   91 (127)
T 2oss_A           15 PKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNY---YWNAQECIQDFNTM   91 (127)
T ss_dssp             CCCCCHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHHHhCccchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHHH
Confidence            344567899999999999999999999999999986779999999999999999999999999   99999999999999


Q ss_pred             HhcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          104 FKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       104 f~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |.||+.||+++|.|+.+|..|++.|++.|.++
T Consensus        92 ~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l  123 (127)
T 2oss_A           92 FTNCYIYNKPGDDIVLMAEALEKLFLQKINEL  123 (127)
T ss_dssp             HHHHHHHSCTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHC
Confidence            99999999999999999999999999999887

>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=99.96  E-value=8.5e-29  Score=202.07  Aligned_cols=104  Identities=29%  Similarity=0.427  Sum_probs=100.8

Q ss_pred             cHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhc
Q 020702           27 SASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        27 ~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      ....++..|..|+..|++|+.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.|
T Consensus         4 ~~~~l~~~~~~il~~l~~~~~~~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~Dv~li~~N   78 (112)
T 3d7c_A            4 DPDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSE--APDYYEVIRFPIDLKTMTERLRSRY---YVTRKLFVADLQRVIAN   78 (112)
T ss_dssp             SHHHHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCCchhhcCCCCccc--ccCHHHHccCCcCHHHHHHHHcCCC---CcCHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999876  9999999999999999999999999   99999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |+.||+++|.++.+|..|+..|++.|.++
T Consensus        79 a~~yN~~~s~~~~~A~~L~~~f~~~~~~~  107 (112)
T 3d7c_A           79 CREYNPPDSEYCRCASALEKFFYFKLKEG  107 (112)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHC
Confidence            99999999999999999999999999987

>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=9.2e-29  Score=212.78  Aligned_cols=111  Identities=32%  Similarity=0.586  Sum_probs=105.4

Q ss_pred             cccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           25 NLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        25 ~~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      +....+++.+|..||+.|++++.+|+|..||++..+++|+||++|++||||+||++||+++.   |.++.+|.+||+|||
T Consensus        27 ~r~t~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~---Y~s~~ef~~Dv~Lif  103 (154)
T 4alg_A           27 GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNY---YWAASECMQDFNTMF  103 (154)
T ss_dssp             CCCBHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHHHhCcCchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHH
Confidence            34567999999999999999999999999999997789999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHhhCcC
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK  138 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~  138 (322)
                      .||+.||+++|.|+.+|..|++.|++.|..+.+.
T Consensus       104 ~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~l~~~  137 (154)
T 4alg_A          104 TNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQE  137 (154)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHTTSCSS
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCch
Confidence            9999999999999999999999999999998443

>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=99.95  E-value=1.7e-28  Score=201.73  Aligned_cols=102  Identities=33%  Similarity=0.607  Sum_probs=98.3

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      .....|..|++.|++|+.+++|..||++..  +|+||++|++||||+||++||+++.   |.++++|.+||+|||.||+.
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            456789999999999999999999999987  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      ||+++|.++.+|..|++.|++.|.+++
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            999999999999999999999999874

>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=1.6e-28  Score=202.37  Aligned_cols=108  Identities=31%  Similarity=0.500  Sum_probs=102.8

Q ss_pred             ccHHHHHHHHHHHHHHHHc-CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           26 LSASLLQFFVRQARSFITQ-HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        26 ~~~~~lq~~c~~il~~L~~-~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      .+.+++++.|..++..|++ ++.++||..||++..+++|+||++|++||||+||++||+++.   |.++.+|.+||+|||
T Consensus         7 ~~~~el~~~l~~~l~~l~~~~~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~li~   83 (119)
T 3p1f_A            7 FKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQ---YQEPWQYVDDVWLMF   83 (119)
T ss_dssp             CCHHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhCCCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHH
Confidence            5678999999999999988 789999999999986669999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      .||..||+++|.++.+|..|++.|++.|..++
T Consensus        84 ~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  115 (119)
T 3p1f_A           84 NNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVM  115 (119)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999998874

>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=5.8e-29  Score=205.38  Aligned_cols=104  Identities=42%  Similarity=0.721  Sum_probs=99.4

Q ss_pred             HHHHHHHHHHHHHHcCCC---CCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhc
Q 020702           30 LLQFFVRQARSFITQHKW---AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~---a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      ...+.|..||..|++++.   +|||..||++..+++|+||++|++||||+||++||+++.   |.++.+|.+||+|||.|
T Consensus         9 ~~l~~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~li~~N   85 (120)
T 3jvl_A            9 EQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESRE---YRDAQEFGADVRLMFSN   85 (120)
T ss_dssp             HHHHHHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCC---CCCHHHHHHHHHHHHHH
Confidence            556778999999999876   999999999999899999999999999999999999999   99999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      |+.||+++|.|+.+|..|+..|++.|.++.
T Consensus        86 a~~yN~~~s~~~~~A~~L~~~f~~~~~~~p  115 (120)
T 3jvl_A           86 CYKYNPPDHEVVAMARKLQDVFEMRFAKMP  115 (120)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHCc
Confidence            999999999999999999999999999883

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

Probab=99.95  E-value=1.6e-28  Score=205.63  Aligned_cols=103  Identities=43%  Similarity=0.753  Sum_probs=97.6

Q ss_pred             HHHHHHHHHHHHHcCC---CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           31 LQFFVRQARSFITQHK---WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        31 lq~~c~~il~~L~~~~---~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      ..+.|..||..|++++   ++|||..|||+..+++|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||
T Consensus        23 ~l~~c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~ef~~Dv~li~~Na   99 (130)
T 2ouo_A           23 QLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE---YRDAQEFGADVRLMFSNC   99 (130)
T ss_dssp             HHHHHHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHHHHHHH
Confidence            3467999999999887   4899999999988889999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      +.||+++|.|+.+|..|+..|++.|.++.
T Consensus       100 ~~yN~~~s~i~~~A~~L~~~f~~~~~~lp  128 (130)
T 2ouo_A          100 YKYNPPDHEVVAMARKLQDVFEMRFAKMP  128 (130)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            99999999999999999999999999873

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

Probab=99.95  E-value=6.2e-28  Score=198.59  Aligned_cols=106  Identities=28%  Similarity=0.307  Sum_probs=100.7

Q ss_pred             ccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHh
Q 020702           26 LSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  105 (322)
Q Consensus        26 ~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~  105 (322)
                      .....++..|..||+.|++++.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.
T Consensus         4 ~~~~~l~~~l~~il~~L~~~~~~~~F~~PVd~~~--~pdY~~iIk~PMDL~tI~~kl~~~~---Y~s~~ef~~Dv~Li~~   78 (117)
T 2i7k_A            4 VEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFI--APGYSMIIKHPMDFSTMKEKIKNND---YQSIEELKDNFKLMCT   78 (117)
T ss_dssp             TTHHHHHHHHHHHHHHHHTSSGGGTSSSCCCTTT--SSSHHHHCSCCCCHHHHHHHHTTTS---CCSHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHhCcccHHhcCCCCccc--cCCHHHHhCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHHHHH
Confidence            4456788999999999999999999999999865  9999999999999999999999999   9999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          106 NAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       106 Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      ||+.||+++|.++.+|..|.+.|++.|....
T Consensus        79 Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  109 (117)
T 2i7k_A           79 NAMIYNKPETIYYKAAKKLLHSGMKILSQER  109 (117)
T ss_dssp             HHHHTSCSSSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999998763

>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=1.5e-28  Score=203.87  Aligned_cols=108  Identities=31%  Similarity=0.494  Sum_probs=100.7

Q ss_pred             cHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhc
Q 020702           27 SASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        27 ~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      ....+++.|..||+.|++|+.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|..||+|||.|
T Consensus         7 ~~~~~~~~c~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li~~N   81 (123)
T 3q2e_A            7 VESNWKKQCKELVNLIFQCEDSEPFRQPVDLVE--YPDYRDIIDTPMDFGTVRETLDAGN---YDSPLEFCKDIRLIFSN   81 (123)
T ss_dssp             ---CHHHHHHHHHHHHHTSGGGGGGSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhCCCcHhhcCCCChhh--cCCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHH
Confidence            455789999999999999999999999999986  9999999999999999999999999   99999999999999999


Q ss_pred             ccccCCC-CCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702          107 AMKYNDE-RDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus       107 a~~yN~~-~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      |+.||++ +|.|+.+|..|+..|++.|..+++.+
T Consensus        82 a~~yN~~~~s~i~~~A~~L~~~f~~~~~~~~~~~  115 (123)
T 3q2e_A           82 AKAYTPNKRSKIYSMTLRLSALFEEKMKKISSDF  115 (123)
T ss_dssp             HHHHSCCTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999996 99999999999999999999986543

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

Probab=99.95  E-value=3.3e-28  Score=211.74  Aligned_cols=108  Identities=26%  Similarity=0.387  Sum_probs=99.0

Q ss_pred             cccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           25 NLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        25 ~~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      ......++..|..||..|++++.+++|..||++..+++|+||++|++||||+||++||.++.   |.++.+|.+||+|||
T Consensus        16 ~p~~~~~~~~~~~il~~L~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~---Y~s~~ef~~Dv~Lif   92 (166)
T 3fkm_X           16 FQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQ---YAYPSEFVKDVQLIF   92 (166)
T ss_dssp             -CTTHHHHHHHHHHHHHHTTSTTGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTC---CCSHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHHhCCCChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHH
Confidence            34567888999999999999999999999999987789999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      .||+.||+++|.|+.+|..|.+.|++.|..+
T Consensus        93 ~Na~~yN~~~s~i~~~A~~L~~~f~~~l~~~  123 (166)
T 3fkm_X           93 DNCSLYNTSNSVVAITGKNIETYFNNQLIVM  123 (166)
T ss_dssp             HHHHHSSCTTSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999999999999987

>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=5.9e-28  Score=199.78  Aligned_cols=102  Identities=32%  Similarity=0.613  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccC
Q 020702           32 QFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN  111 (322)
Q Consensus        32 q~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN  111 (322)
                      ...|..||..|++|+.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.||
T Consensus        15 ~~~~~~il~~l~~~~~a~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~~yN   89 (121)
T 1e6i_A           15 DAAIQNILTELQNHAAAWPFLQPVNKEE--VPDYYDFIKEPMDLSTMEIKLESNK---YQKMEDFIYDARLVFNNCRMYN   89 (121)
T ss_dssp             HHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcCCCchhhCCCCChhh--CcCHHHHcCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHHHC
Confidence            4679999999999999999999999876  9999999999999999999999999   9999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702          112 DERDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus       112 ~~~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      +++|.++.+|..|++.|++.|..+ |.|
T Consensus        90 ~~~s~i~~~A~~L~~~f~~~~~~~-p~~  116 (121)
T 1e6i_A           90 GENTSYYKYANRLEKFFNNKVKEI-PEY  116 (121)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHTS-GGG
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHc-ccc
Confidence            999999999999999999999987 554

>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=7.9e-28  Score=199.05  Aligned_cols=101  Identities=26%  Similarity=0.358  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      .++..|..||+.|++++.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.
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            456889999999999999999999999886  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||+++|.++.+|..|++.|++.|..+
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            99999999999999999999999877

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

Probab=99.95  E-value=6.3e-28  Score=200.14  Aligned_cols=106  Identities=24%  Similarity=0.322  Sum_probs=100.0

Q ss_pred             ccHHHHHHHHHHHHHHHHcCC------CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHH
Q 020702           26 LSASLLQFFVRQARSFITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYAD   99 (322)
Q Consensus        26 ~~~~~lq~~c~~il~~L~~~~------~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~D   99 (322)
                      .....++..|..||+.|+.++      .+++|..||+...  +|+||++|++||||+||++||+++.   |.++.+|.+|
T Consensus         9 ~~~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D   83 (123)
T 2dat_A            9 PNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKE--LPEYYELIRKPVDFKKIKERIRNHK---YRSLGDLEKD   83 (123)
T ss_dssp             CCCHHHHHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCTTT--SCHHHHHCSSCCCHHHHHHHHTTTC---CCSHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhhhcccCCeeeHHhcCCCCccc--CCCHHHHcCCCCCHHHHHHHHhCCC---CCCHHHHHHH
Confidence            446788999999999999986      6999999999876  9999999999999999999999999   9999999999


Q ss_pred             HHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       100 vrLIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      |+|||.||+.||+++|.|+.+|..|++.|++.|+++.
T Consensus        84 ~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~p  120 (123)
T 2dat_A           84 VMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQSGP  120 (123)
T ss_dssp             HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHSSS
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999999999999999999873

>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=6e-28  Score=198.13  Aligned_cols=102  Identities=28%  Similarity=0.520  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           28 ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      ...+...|..||+.|++++.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||
T Consensus        14 ~~~~~~~~~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na   88 (116)
T 3nxb_A           14 LDDDFTAMYKVLDVVKAHKDSWPFLEPVDESY--APNYYQIIKAPMDISSMEKKLNGGL---YCTKEEFVNDMKTMFRNC   88 (116)
T ss_dssp             -CCHHHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCCcHhhcCcCChhh--ccChHHHcCCCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHH
Confidence            44567889999999999999999999999986  9999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHh
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQ  134 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~  134 (322)
                      +.||+++|.++.+|..|+..|++.|.+
T Consensus        89 ~~yN~~~s~~~~~A~~L~~~f~~~~~k  115 (116)
T 3nxb_A           89 RKYNGESSEYTKMSDNLERCFHRAMMK  115 (116)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999875

>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=5e-28  Score=203.70  Aligned_cols=106  Identities=29%  Similarity=0.488  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      ..++..|..||..|++++.+++|..||++..  +||||++|++||||+||++||.++.   |.++.+|.+||+|||.||+
T Consensus        20 ~~l~~~~~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~iI~~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na~   94 (135)
T 3mb3_A           20 QAWKKQCEELLNLIFQCEDSEPFRQPVDLLE--YPDYRDIIDTPMDFATVRETLEAGN---YESPMELCKDVRLIFSNSK   94 (135)
T ss_dssp             STHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCChhhcCCCChhh--CCCHHHHhCCCcCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHHH
Confidence            4688999999999999999999999999866  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCC-CCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702          109 KYNDE-RDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus       109 ~yN~~-~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      .||++ +|.|+.+|..|++.|++.|..+++.+
T Consensus        95 ~yN~~~~s~i~~~A~~L~~~f~~~~~~~~~~~  126 (135)
T 3mb3_A           95 AYTPSKRSRIYSMSLRLSAFFEEHISSVLSDY  126 (135)
T ss_dssp             HHSCCTTCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99998 99999999999999999999986543

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

Probab=99.95  E-value=1.8e-27  Score=200.45  Aligned_cols=108  Identities=30%  Similarity=0.520  Sum_probs=100.2

Q ss_pred             cccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcC--CCCCCCCCHHHHHHHHHH
Q 020702           25 NLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG--KDGTGYRNVREIYADVRL  102 (322)
Q Consensus        25 ~~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~--~~~~~Y~s~~ef~~DvrL  102 (322)
                      .++. ..++.|..||..|++|+.+++|..||+..   +|+||++|++||||+||++||++  +.   |.++.+|.+||+|
T Consensus        16 ~m~p-~~~~~c~~il~~L~~~~~s~~F~~Pv~~~---~pdY~~iIk~PmDL~tI~~kL~~~~~~---Y~s~~ef~~Dv~L   88 (135)
T 2yyn_A           16 KLTP-IDKRKCERLLLFLYCHEMSLAFQDPVPLT---VPDYYKIIKNPMDLSTIKKRLQEDYSM---YSKPEDFVADFRL   88 (135)
T ss_dssp             CCCH-HHHHHHHHHHHHHHTSGGGGGGSSCCCTT---STTHHHHCSSCCCHHHHHHHHHSSSCC---CSSHHHHHHHHHH
T ss_pred             CCCH-HHHHHHHHHHHHHHhCccchhhcCCCccc---CCCHHHHcCCCCCHHHHHHHHhccccC---CCCHHHHHHHHHH
Confidence            3444 45678999999999999999999999973   89999999999999999999998  47   9999999999999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702          103 VFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus       103 If~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      ||.||+.||+++|.|+.+|..|+..|++.|.++++.+
T Consensus        89 if~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~  125 (135)
T 2yyn_A           89 IFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPEK  125 (135)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999999999999999998765

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

Probab=99.94  E-value=1.5e-27  Score=200.80  Aligned_cols=109  Identities=26%  Similarity=0.405  Sum_probs=100.3

Q ss_pred             ccccccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHH
Q 020702           22 GCKNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR  101 (322)
Q Consensus        22 ~~k~~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dvr  101 (322)
                      .+..+....++..|..||+.|++|+.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+
T Consensus         5 ~~~~~~~~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~   79 (135)
T 3rcw_A            5 VAMELRLTPLTVLLRSVLDQLQDKDPARIFAQPVSLKE--VPDYLDHIKHPMDFATMRKRLEAQG---YKNLHEFEEDFD   79 (135)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHHTCTTCSSSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHH
T ss_pred             HHHHhcchHHHHHHHHHHHHHHhCCcchhhcCCCChhh--cCCHHHHhCCCCCHHHHHHHHhcCC---CCCHHHHHHHHH
Confidence            34444445688999999999999999999999999986  9999999999999999999999999   999999999999


Q ss_pred             HHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       102 LIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |||.||+.||+++|.+|.+|..|.+.|++.|...
T Consensus        80 li~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~  113 (135)
T 3rcw_A           80 LIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQA  113 (135)
T ss_dssp             HHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999877

>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=2.1e-27  Score=197.14  Aligned_cols=102  Identities=24%  Similarity=0.350  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHHHc------CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHH
Q 020702           30 LLQFFVRQARSFITQ------HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV  103 (322)
Q Consensus        30 ~lq~~c~~il~~L~~------~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLI  103 (322)
                      .+++.|..|++.|+.      |+.+++|..||+...  +|+||++|++||||+||++||+++.   |.++.+|.+||+||
T Consensus        15 ~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li   89 (124)
T 3mb4_A           15 PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSE--LPDYYLTIKKPMDMEKIRSHMMANK---YQDIDSMVEDFVMM   89 (124)
T ss_dssp             HHHHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHhcccCCcccHHhhcCCCccc--cCCHHHHcCCCCCHHHHHHHHHcCC---CCCHHHHHHHHHHH
Confidence            678889999999998      667899999999876  9999999999999999999999999   99999999999999


Q ss_pred             HhcccccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          104 FKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       104 f~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      |.||+.||+++|.|+.+|..|.+.|++.|.++.
T Consensus        90 ~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~  122 (124)
T 3mb4_A           90 FNNACTYNEPESLIYKDALVLHKVLLETRRDLE  122 (124)
T ss_dssp             HHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999873

>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=3.1e-27  Score=195.99  Aligned_cols=101  Identities=27%  Similarity=0.329  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      -++..|..|+..|++++.+++|..||++..  +||||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.
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            467899999999999999999999999886  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||+++|.++.+|..|.+.|++.|.+.
T Consensus        88 yN~~~s~~~~~A~~L~~~~~~~~~~~  113 (123)
T 3hme_A           88 YNRPDTVYYKLAKKILHAGFKMMSKE  113 (123)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHTCHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999987653

>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=2.2e-27  Score=198.48  Aligned_cols=103  Identities=24%  Similarity=0.365  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHHHHcCC-------CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHH
Q 020702           28 ASLLQFFVRQARSFITQHK-------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADV  100 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~-------~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dv  100 (322)
                      +..++..|..||+.|++++       .+++|..||+...  +|+||++|++||||+||++||.++.   |.++.+|.+||
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            4678899999999999875       5899999999776  9999999999999999999999999   99999999999


Q ss_pred             HHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          101 RLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       101 rLIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      +|||.||+.||+++|.|+.+|..|++.|++.|..+
T Consensus        84 ~Li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l  118 (129)
T 2grc_A           84 MLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKI  118 (129)
T ss_dssp             HHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999998

>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=5.3e-27  Score=196.40  Aligned_cols=110  Identities=24%  Similarity=0.384  Sum_probs=100.8

Q ss_pred             cccccccHHHHHHHHHHHHHHHHcCC------CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHH
Q 020702           21 GGCKNLSASLLQFFVRQARSFITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVR   94 (322)
Q Consensus        21 ~~~k~~~~~~lq~~c~~il~~L~~~~------~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~   94 (322)
                      ++.+......+..+|..+++.|....      .++||..||+...  +|+||++|++||||+||++||+++.   |.++.
T Consensus         8 ~~~~~~~~~kl~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~~--~PdY~~iIk~PMdL~tI~~kL~~~~---Y~s~~   82 (130)
T 3k2j_A            8 SSGVDLGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKK--YPDYYQQIKMPISLQQIRTKLKNQE---YETLD   82 (130)
T ss_dssp             --CCSCHHHHHHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTC---CSSHH
T ss_pred             CCCCccchHHHHHHHHHHHHHHHHHhcccCCCccHhhcCCCChhh--CccHHHHcCCCCCHHHHHHHHhcCC---CCCHH
Confidence            34455667788889999999998754      4999999999876  9999999999999999999999999   99999


Q ss_pred             HHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702           95 EIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus        95 ef~~DvrLIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      +|.+||+|||.||+.||+++|.|+.+|..|++.|++.|..+
T Consensus        83 ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l  123 (130)
T 3k2j_A           83 HLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKEL  123 (130)
T ss_dssp             HHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999987

>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=3e-27  Score=196.73  Aligned_cols=106  Identities=25%  Similarity=0.302  Sum_probs=99.2

Q ss_pred             HHHHHHHHHHHHHHHHcCC------CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHH
Q 020702           28 ASLLQFFVRQARSFITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR  101 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~------~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dvr  101 (322)
                      ...++..|..|++.|+.+.      .++||..||+...  +|+||++|++||||+||++||.++.   |.++.+|.+||+
T Consensus         7 ~~~l~~~~~~i~~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~   81 (126)
T 3mqm_A            7 AARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKK--NADYYEKISDPLDLITIEKQILTGY---YKTVEAFDADML   81 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGGG--CTTHHHHCSSCCCHHHHHHHHHHTC---CCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCcCCCChhHHhcCCCCccc--CCCHHHHcCCCCCHHHHHHHHHcCC---CCCHHHHHHHHH
Confidence            4578889999999999864      4999999999886  9999999999999999999999999   999999999999


Q ss_pred             HHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhhCcC
Q 020702          102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK  138 (322)
Q Consensus       102 LIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~  138 (322)
                      |||.||+.||+++|.++.+|..|++.|++.|..+.+.
T Consensus        82 li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~~  118 (126)
T 3mqm_A           82 KVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQ  118 (126)
T ss_dssp             HHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999987443

>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=6e-27  Score=193.37  Aligned_cols=103  Identities=24%  Similarity=0.358  Sum_probs=98.7

Q ss_pred             HHHHHHHHHHHHHHHHcCCC------CCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHH
Q 020702           28 ASLLQFFVRQARSFITQHKW------AWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR  101 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~------a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~Dvr  101 (322)
                      ...++..|..+++.|+.+..      +++|..||+...  +|+||++|++||||+||++||.++.   |.++.+|.+||+
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            56788999999999998766      999999999876  9999999999999999999999999   999999999999


Q ss_pred             HHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       102 LIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |||.||+.||+++|.++.+|..|++.|++.|.++
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            9999999999999999999999999999999987

>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=5.7e-27  Score=192.37  Aligned_cols=102  Identities=22%  Similarity=0.316  Sum_probs=95.8

Q ss_pred             HHHHHHHHHHHHHcC------CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHH
Q 020702           31 LQFFVRQARSFITQH------KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVF  104 (322)
Q Consensus        31 lq~~c~~il~~L~~~------~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf  104 (322)
                      ....|..|+..|+++      +.+++|..||+...  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||
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            356789999999987      46999999999876  9999999999999999999999999   999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 020702          105 KNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  137 (322)
Q Consensus       105 ~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~  137 (322)
                      .||+.||+++|.++.+|..|++.|++.+.++..
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            999999999999999999999999999998844

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

Probab=99.94  E-value=6.9e-27  Score=201.87  Aligned_cols=102  Identities=25%  Similarity=0.500  Sum_probs=92.2

Q ss_pred             HHHHHHHHHHH-HHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           31 LQFFVRQARSF-ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        31 lq~~c~~il~~-L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      +...+..|+.. |+.++.+|||..||++..  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.||+.
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            33445555544 667899999999999886  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQLLP  137 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i~~  137 (322)
                      ||+++|.|+.+|..|...|++.|..+..
T Consensus       105 yN~~~s~i~~~A~~L~~~~~~~l~e~~~  132 (158)
T 3uv4_A          105 YNGPESQYTKTAQEIVNVCYQTLTEYDE  132 (158)
T ss_dssp             HHCTTCHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999998843

>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=1e-25  Score=198.75  Aligned_cols=103  Identities=30%  Similarity=0.526  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcC--CCCCCCCCHHHHHHHHHHHHhc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDG--KDGTGYRNVREIYADVRLVFKN  106 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~--~~~~~Y~s~~ef~~DvrLIf~N  106 (322)
                      ...++.|..||..|+.|+.+++|..||+..   +|+||++|++||||+||++||++  +.   |.++.+|.+||+|||.|
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            466788999999999999999999999864   89999999999999999999998  67   99999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHhhCc
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEKWLQLLP  137 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~  137 (322)
                      |+.||+++|.|+.+|..|++.|++.|.+++|
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

>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=8e-26  Score=197.50  Aligned_cols=101  Identities=30%  Similarity=0.491  Sum_probs=96.5

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           30 LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      ..+..|..||..|+.|+.+++|..||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.
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            456678999999999999999999999876  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||+++|.++.+|..|++.|++.|+.+
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            99999999999999999999998775

>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=99.92  E-value=1.8e-25  Score=191.35  Aligned_cols=108  Identities=24%  Similarity=0.374  Sum_probs=96.2

Q ss_pred             HHHHHHHHHHHHHHcCC-------CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHH
Q 020702           30 LLQFFVRQARSFITQHK-------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRL  102 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~-------~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrL  102 (322)
                      ..+..|..|+..|+++.       .+++|..||+...  +|+||++|++||||+||++||+++.   |.++.+|.+||+|
T Consensus        24 ~~~~~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~ef~~D~~l   98 (150)
T 3tlp_A           24 IRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKD--YPDYYKIILEPMDLKIIEHNIRNDK---YAGEEGMIEDMKL   98 (150)
T ss_dssp             HHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHhcccCCcccHHhcCCCchhh--CcCHHHHhCCCCCHHHHHHHHhcCC---CCCHHHHHHHHHH
Confidence            34567888888887754       4999999999876  9999999999999999999999999   9999999999999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHHHHHHHhhCcCchhH
Q 020702          103 VFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEE  142 (322)
Q Consensus       103 If~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~~~~e  142 (322)
                      ||.||+.||+++|.|+.+|..|++.|++.|..+.+...++
T Consensus        99 i~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~pd~d  138 (150)
T 3tlp_A           99 MFRNARHYNEEGSQVYNDAHILEKLLKEKRKELGPLPDDD  138 (150)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHCCC----
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccCCCChh
Confidence            9999999999999999999999999999999997665433

>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=3e-25  Score=185.66  Aligned_cols=101  Identities=30%  Similarity=0.443  Sum_probs=93.3

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           28 ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      -..++..|..++..|+.++.++||..||++..  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.||
T Consensus         8 l~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na   82 (130)
T 3dai_A            8 FRELRIFLRNVTHRLAIDKRFRVFTKPVDPDE--VPDYVTVIKQPMDLSSVISKIDLHK---YLTVKDYLRDIDLICSNA   82 (130)
T ss_dssp             HHHHHHHHHHHHHHHHTSGGGGGGSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCccHhhcCCCChhh--cCCHHHHcCCCCCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHH
Confidence            45788899999999999999999999999986  9999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHH----HHHHHHHHHHHHHHHH
Q 020702          108 MKYNDERDDV----HVMAKSLLEKFEEKWL  133 (322)
Q Consensus       108 ~~yN~~~s~v----~~~A~~L~~~Fe~~~~  133 (322)
                      +.||+++|++    +..|..|.+.|...+.
T Consensus        83 ~~yN~~~s~~~~~i~~~A~~L~~~~~~~i~  112 (130)
T 3dai_A           83 LEYNPDRDPGDRLIRHRACALRDTAYAIIK  112 (130)
T ss_dssp             HHHCCSSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCChhHHHHHHHHHHHHHHHHHHHH
Confidence            9999999987    5677777777777765

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

Probab=99.91  E-value=2.7e-24  Score=180.17  Aligned_cols=103  Identities=28%  Similarity=0.470  Sum_probs=94.6

Q ss_pred             ccccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHH
Q 020702           24 KNLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV  103 (322)
Q Consensus        24 k~~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLI  103 (322)
                      ......+|+..|..|++.|+.++.++||..|       +||||++|++||||+||++||.++.   |.++.+|.+||+||
T Consensus         6 e~~~~~~L~~~~~~il~~l~~~~~~~~F~~P-------~pdY~~iIk~PmDL~tI~~kl~~~~---Y~s~~~f~~D~~Li   75 (131)
T 2dkw_A            6 SGNTLRELRLFLRDVTKRLATDKRFNIFSKP-------VSDYLEVIKEPMDLSTVITKIDKHN---YLTAKDFLKDIDLI   75 (131)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHSGGGCTTSSC-------CSSCTTSCSSCCCHHHHHHHHHTTC---CCSSHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCccchhhcCc-------CccHHhHcCCCcCHHHHHHHHcCCC---CCCHHHHHHHHHHH
Confidence            3345778999999999999999999999998       7999999999999999999999999   99999999999999


Q ss_pred             HhcccccCCCCCH----HHHHHHHHHHHHHHHHHhhC
Q 020702          104 FKNAMKYNDERDD----VHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       104 f~Na~~yN~~~s~----v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      |.||+.||+++|+    |+..|..|.+.|...++.-+
T Consensus        76 ~~Na~~yN~~~s~~~~~i~~~A~~L~~~~~~~l~~~l  112 (131)
T 2dkw_A           76 CSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAEL  112 (131)
T ss_dssp             HHHHHHSCCCSSTTHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHCCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999996    56899999999998886443

>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=99.91  E-value=2.1e-24  Score=193.80  Aligned_cols=108  Identities=30%  Similarity=0.512  Sum_probs=99.2

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      ...++.|..||..|++|+.+++|..||+..   +|+||++|++||||+||++||+++.++.|.++.+|.+||+|||.||+
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 PVDQRKCERLLLYLYCHELSIEFQEPVPAS---IPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCE  156 (207)
T ss_dssp             HHHHHHHHHHHHHHHTSTTCGGGSSCCCTT---STTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccchhhhhccCChh---hccHhHHhCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHHH
Confidence            456788999999999999999999999873   89999999999999999999998322239999999999999999999


Q ss_pred             ccCC-----------------CCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702          109 KYND-----------------ERDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus       109 ~yN~-----------------~~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      .||+                 ++|.|+.+|..|+..|++.|..++|..
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                 999999999999999999999998863

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

Probab=99.91  E-value=7.4e-25  Score=194.35  Aligned_cols=104  Identities=18%  Similarity=0.198  Sum_probs=95.0

Q ss_pred             cccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccC--CCCChHHHHHHhcCC---CCCCCCCHHHHHHH
Q 020702           25 NLSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIE--KPMDFSTIKNKMDGK---DGTGYRNVREIYAD   99 (322)
Q Consensus        25 ~~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk--~PMDL~tIk~kL~~~---~~~~Y~s~~ef~~D   99 (322)
                      +++... ++.|..||..|+.|+.+|||++||+      |+||++|+  +||||+||++||+++   .   |.++.+|.+|
T Consensus        72 ~m~~~~-~~~c~~iL~~l~~~~~s~pF~~pV~------~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~---Y~s~~eF~~D  141 (189)
T 2ro1_A           72 KLSPAN-QRKCERVLLALFCHEPCRPLHQLAT------DSTFSLDQPGGTLDLTLIRARLQEKLSPP---YSSPQEFAQD  141 (189)
T ss_dssp             SSCHHH-HHHHHHHHHHHHHSTTHHHHHSCSC------CTTCSSSCSSCCCCHHHHHHHHHTSSSSC---CSCHHHHHHH
T ss_pred             CCCHHH-HHHHHHHHhhcccCccchhhcCCCC------hhhhccccCCCcccHHHHHHHHhcCCCcc---cCCHHHHHHH
Confidence            455544 4679999999999999999999998      67999998  899999999999999   7   9999999999


Q ss_pred             HHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702          100 VRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus       100 vrLIf~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      |+|||+||++|| +++.++.+|..|++.|++.|+++++..
T Consensus       142 v~Lif~N~~~yN-~~s~~~~~a~~L~~~Fe~~~~~~~~~~  180 (189)
T 2ro1_A          142 VGRMFKQFNKLT-EDKADVQSIIGLQRFFETRMNEAFGDT  180 (189)
T ss_dssp             HHHHHHHHHHHC-CSSCSSHHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHhcCcc
Confidence            999999999999 588889999999999999999997653

>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=2.8e-24  Score=199.86  Aligned_cols=104  Identities=23%  Similarity=0.451  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           28 ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      ...++..|..||..|++++.+++|..||++..  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.||
T Consensus        12 ~~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~~~~~f~~D~~li~~Na   86 (265)
T 3uv5_A           12 MVTLSSILESIINDMRDLPNTYPFHTPVNAKV--VKDYYKIITRPMDLQTLRENVRKRL---YPSREEFREHLELIVKNS   86 (265)
T ss_dssp             HHHHHHHHHHHHHHHHTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCchhhhCCCChhh--cCCHHHHhCCCCcHHHHHHHHHcCC---CCCHHHHHHHHHHHHhhh
Confidence            45788999999999999999999999999987  9999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      +.||+++|.|+.+|..|...|++.|..+.
T Consensus        87 ~~yN~~~s~i~~~A~~l~~~~~~~~~~~~  115 (265)
T 3uv5_A           87 ATYNGPKHSLTQISQSMLDLCDEKLKEKE  115 (265)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHHHHHHHHTH
T ss_pred             hhcCCCCChHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999998873

>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=99.89  E-value=1.9e-23  Score=194.16  Aligned_cols=101  Identities=26%  Similarity=0.506  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHH-HHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           31 LQFFVRQARSF-ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        31 lq~~c~~il~~-L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      +...|..++.. ++.++.+|||..||++..  +|+||++|++||||+||++||.++.   |.++.+|..||+|||.||+.
T Consensus       137 ~~~il~~i~~~~l~~~~~~~~F~~pv~~~~--~pdY~~iIk~Pmdl~tI~~kl~~~~---Y~~~~~f~~D~~lif~Na~~  211 (265)
T 3uv5_A          137 FSFILDNIVTQKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHK---YQSRESFLDDVNLILANSVK  211 (265)
T ss_dssp             HHHHHHHHHHHTTTTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhhHHHhCCCChhH--hCcHHHHhCCcccHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            34445555543 778999999999999887  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQLL  136 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i~  136 (322)
                      ||+++|.|+.+|..|...|++.|..+.
T Consensus       212 yN~~~s~~~~~A~~l~~~~~~~~~~~~  238 (265)
T 3uv5_A          212 YNGPESQYTKTAQEIVNVCYQTLTEYD  238 (265)
T ss_dssp             HTCTTCHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999883

>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=99.88  E-value=2e-23  Score=196.67  Aligned_cols=102  Identities=24%  Similarity=0.471  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      ..++..|..||+.|+.++.+++|+.||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||+
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            4567899999999999999999999999986  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          109 KYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       109 ~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      .||+++|.++.+|..|.+.|++.|..+
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            999999999999999999999888765

>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=99.87  E-value=1.5e-22  Score=190.78  Aligned_cols=100  Identities=26%  Similarity=0.518  Sum_probs=91.1

Q ss_pred             HHHHHHHHH-HHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccc
Q 020702           31 LQFFVRQAR-SFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMK  109 (322)
Q Consensus        31 lq~~c~~il-~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~  109 (322)
                      +...+..++ ..|+.++.+++|+.||++..  +|+||++|++||||+||++||.++.   |.++.+|..||+|||.||+.
T Consensus       170 ~~~~l~~i~~~~l~~~~~s~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~Li~~Na~~  244 (292)
T 3aad_A          170 FSFILDNIVTQKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHK---YQSRESFLDDVNLILANSVK  244 (292)
T ss_dssp             HHHHHHHHHHHTGGGSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhhhhcCcchhHHHhcccccc--cccHHHHcCCcCCHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHHHH
Confidence            333444444 34788999999999999876  9999999999999999999999999   99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          110 YNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       110 yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||+++|.+|.+|..|...|++.|..+
T Consensus       245 yN~~~s~i~~~A~~L~~~~~~~~~~~  270 (292)
T 3aad_A          245 YNGPESQYTKTAQEIVNVCYQTLTEY  270 (292)
T ss_dssp             HHCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999887

>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=99.86  E-value=1.5e-22  Score=192.28  Aligned_cols=87  Identities=30%  Similarity=0.471  Sum_probs=83.8

Q ss_pred             cCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHH
Q 020702           44 QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS  123 (322)
Q Consensus        44 ~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~~~A~~  123 (322)
                      .|+.+++|+.||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||++||+++|.|+.+|..
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            3678999999999886  9999999999999999999999999   9999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhh
Q 020702          124 LLEKFEEKWLQL  135 (322)
Q Consensus       124 L~~~Fe~~~~~i  135 (322)
                      |+..|++.|.+.
T Consensus       252 L~~~f~~~~~~~  263 (311)
T 2r0y_A          252 LTNYFNYLIQKE  263 (311)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh
Confidence            999999999984

>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=2.6e-22  Score=194.15  Aligned_cols=87  Identities=30%  Similarity=0.471  Sum_probs=83.8

Q ss_pred             cCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHH
Q 020702           44 QHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHVMAKS  123 (322)
Q Consensus        44 ~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~~~A~~  123 (322)
                      .|+.+|+|+.||++..  +|+||++|++||||+||++||+++.   |.++.+|.+||+|||.||+.||+++|.||.+|..
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            3678999999999886  9999999999999999999999999   9999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhh
Q 020702          124 LLEKFEEKWLQL  135 (322)
Q Consensus       124 L~~~Fe~~~~~i  135 (322)
                      |+..|++.|.+.
T Consensus       302 L~~~f~~~~~~~  313 (361)
T 2r10_A          302 LTNYFNYLIQKE  313 (361)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh
Confidence            999999999984

>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=99.82  E-value=8.2e-21  Score=183.71  Aligned_cols=99  Identities=19%  Similarity=0.246  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHHHc--CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCC-CHHHHHHHHHHHHhc
Q 020702           30 LLQFFVRQARSFITQ--HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR-NVREIYADVRLVFKN  106 (322)
Q Consensus        30 ~lq~~c~~il~~L~~--~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~-s~~ef~~DvrLIf~N  106 (322)
                      .+..+|..+|+.+..  +..+++|+.||+...  +||||++|++||||+||++||  +.   |. ++.+|.+||+|||.|
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            346789999999866  356899999999877  999999999999999999998  34   55 899999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |+.||+++|.|+.+|..|++.|++.|.+.
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            99999999999999999999999999875

>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=99.80  E-value=2.3e-20  Score=177.18  Aligned_cols=99  Identities=19%  Similarity=0.246  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHHHHHc--CCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCC-CHHHHHHHHHHHHhc
Q 020702           30 LLQFFVRQARSFITQ--HKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYR-NVREIYADVRLVFKN  106 (322)
Q Consensus        30 ~lq~~c~~il~~L~~--~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~-s~~ef~~DvrLIf~N  106 (322)
                      .++.+|..+|..+..  +..+++|+.||+...  +|+||++|++||||+||++||  +.   |. ++.+|.+||+|||.|
T Consensus        28 ~~~~~~~~~L~~~~~~~r~~~~~F~~p~~~~~--~PdY~~iIk~PmDL~tI~~kl--~~---y~~s~~~f~~D~~li~~N  100 (311)
T 2r0y_A           28 KFNRFISFTLDVLIDKYKDIFKDFIKLPSRKF--HPQYYYKIQQPMSINEIKSRD--YE---YEDGPSNFLLDVELLTKN  100 (311)
T ss_dssp             THHHHHHHHHHHHHHHSHHHHGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHSC--CC---STTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCchhHHhcCCCCccc--CCChHHHcCCCCCHHHHHHHH--hc---ccCCHHHHHHHHHHHHHH
Confidence            455666666666655  347999999999876  999999999999999999999  44   65 899999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          107 AMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       107 a~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |++||+++|.|+.+|..|++.|++.|.+.
T Consensus       101 a~~yN~~~s~i~~~A~~l~~~~~~~~~k~  129 (311)
T 2r0y_A          101 CQAYNEYDSLIVKNSMQVVMLIEFEVLKA  129 (311)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHccCCCCHHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999999999875

>2jns_A Bromodomain-containing protein 4; ET-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.71  E-value=3.5e-18  Score=134.07  Aligned_cols=72  Identities=29%  Similarity=0.567  Sum_probs=68.9

Q ss_pred             hhccCCHHHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCC-CCCCeEEEeCCCCCHHHHHHHHHHHHHHHHhc
Q 020702          193 KCRKMSTEEKKNLGTALTRLSPEDLCKALEIVAENNPSFH-ATAQEVDLDMDAQSELTLWRLKVFVQESLKAA  264 (322)
Q Consensus       193 k~r~mt~eEK~~L~~~i~~L~~e~l~~vi~II~~~~P~~~-~~~~evElDid~L~~~TL~~L~~yV~~~L~~~  264 (322)
                      .+++||++||++|+.+|+.||+++|.+|++||++++|.+. .+++|||||||.|++.|||+|+.||.+||+..
T Consensus        14 ~~~~mT~eEK~~Ls~~I~~Lp~e~L~~Vi~II~~~~p~l~~~~~dEIEiDid~L~~~TL~~L~~yV~~~l~~k   86 (90)
T 2jns_A           14 KCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLRELERYVTSCLRKK   86 (90)
T ss_dssp             SCCCCCHHHHHHHHHHHTTSCHHHHTTHHHHHHTTCGGGTTSCTTSCCCCTTTSCHHHHHHHHHHHHTTSCCC
T ss_pred             CCCCCCHHHHHHHHHHHHHcCHHHHHHHHHHHHhcCccccCCCCCeEEEeccCCCHHHHHHHHHHHHHHHHhh
Confidence            5799999999999999999999999999999999999986 68899999999999999999999999999876

>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=99.68  E-value=1.8e-16  Score=134.27  Aligned_cols=97  Identities=16%  Similarity=0.267  Sum_probs=89.2

Q ss_pred             HHHHHHHHHHHHHHcCC------CCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHH
Q 020702           30 LLQFFVRQARSFITQHK------WAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLV  103 (322)
Q Consensus        30 ~lq~~c~~il~~L~~~~------~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLI  103 (322)
                      .+|..+..|+..++.+.      .+.+|+..++..    |+||.  +.||+|.+|++||..+.   |+++++|..||.+|
T Consensus         7 ~lq~~l~~l~~~v~~~~De~GR~lsd~F~~LPsk~----pdYY~--k~Pi~l~~Ikkri~~~~---Y~sld~f~~D~~lm   77 (147)
T 3iu6_A            7 LIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVD----PNFPN--KPPLTFDIIRKNVENNR---YRRLDLFQEHMFEV   77 (147)
T ss_dssp             HHHHHHHHHHHHHHTCBCTTSCBGGGGGTTCCSSC----TTSTT--SCCCCHHHHHHHHHTTC---CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhcCCCCCcchHHHhHCCCCC----ccccC--CCCcCHHHHHHHHhcCC---CCCHHHHHHHHHHH
Confidence            57888899999999864      478899876654    78998  99999999999999999   99999999999999


Q ss_pred             HhcccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          104 FKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       104 f~Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      |.||..||.+||.||..|..|+..|.+.+.++
T Consensus        78 f~NAr~yN~e~S~IyeDAv~Lq~~f~~~r~eL  109 (147)
T 3iu6_A           78 LERARRMNRTDSEIYEDAVELQQFFIKIRDEL  109 (147)
T ss_dssp             HHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999998887

>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=99.61  E-value=6.1e-16  Score=136.12  Aligned_cols=99  Identities=16%  Similarity=0.260  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           28 ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      ...|+..+..||..|..+..++||+.+.             ++.||||.||++||+.+.   |.++.+|..||++||.||
T Consensus        73 ~~el~~~l~~vl~~L~~~~~s~~~~~y~-------------~k~PmDL~~i~kKl~~~~---Y~s~~eF~~Dv~lIf~n~  136 (183)
T 3lqh_A           73 EKELQISLKQVLTALLNSRTTSHLLRYR-------------QQQPLDLEGVKRKMDQGN---YTSVLEFSDDIVKIIQAA  136 (183)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHTCC-------------C--CCSHHHHHHHHHTTC---CCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccccHhhhhhh-------------hcCCccHHHHHHHHhcCC---CCCHHHHHHHHHHHHHHH
Confidence            3567788899999999999999997731             499999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhhCcCchhH
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEE  142 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~i~~~~~~e  142 (322)
                      ..||.+++.+..++..|...|++.+.+++|.....
T Consensus       137 ~~~~~~~~e~~~ag~~l~~~f~~~l~~vfpwf~~~  171 (183)
T 3lqh_A          137 INSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVK  171 (183)
T ss_dssp             HHHSCCCHHHHHHHHHHHHHHHHHHHHHCTTSCGG
T ss_pred             hhccCCChhhhhhhhHHHHHHHHHHHHHCCCCCcc
Confidence            99999999999999999999999999999987543

>2lm0_A AF4/FMR2 family member 1/protein AF-9 chimera; intrinsically disordered, nuclear protein; NMR {Homo sapiens}

Probab=96.60  E-value=0.0028  Score=51.35  Aligned_cols=62  Identities=23%  Similarity=0.347  Sum_probs=54.1

Q ss_pred             cCCHHHHHHHHHHhcCCC-hhhHHHHHHHHHhcCCCCCCCCCeEEEeCCCCCHHHHHHHHHHHH
Q 020702          196 KMSTEEKKNLGTALTRLS-PEDLCKALEIVAENNPSFHATAQEVDLDMDAQSELTLWRLKVFVQ  258 (322)
Q Consensus       196 ~mt~eEK~~L~~~i~~L~-~e~l~~vi~II~~~~P~~~~~~~evElDid~L~~~TL~~L~~yV~  258 (322)
                      +--.+|-+.|...|..|. .+.|.+|+++|.+. +.+...+..+.||+.+|+..|+++|+.|+.
T Consensus        58 ~~y~~~L~~l~~rim~l~d~~~lq~iv~li~~t-G~~~it~~tfDFDLc~LD~~Tv~klq~~l~  120 (125)
T 2lm0_A           58 KAYLDELVELHRRLMTLRERHILQQIVNLIEET-GHFHITNTTFDFDLCSLDKTTVRKLQSYLE  120 (125)
T ss_dssp             CSTHHHHHHHHHHHHTCCCCSSHHHHHHHHHTS-CCEEECSSCEEECTTTSCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhccccHHHHHHHHHHHHhc-CceeeecccccceeeccCHHHHHHHHHHHH
Confidence            344678889999999995 66799999999995 567789999999999999999999999975

---

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	322
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	2e-25
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	1e-24
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	8e-23
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	9e-23
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	5e-21
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	1e-20

>d1eqfa1 a.29.2.1 (A:1359-1497) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]} Length = 139

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 97.4 bits (242), Expect = 2e-25
 Identities = 27/114 (23%), Positives = 55/114 (48%), Gaps = 5/114 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L   +    + +      +PF  PV+ + +   DYY++I +PMD  T++  +  +    Y
Sbjct: 27  LSSILESIINDMRDLPNTYPFHTPVNAKVV--KDYYKIITRPMDLQTLRENVRKRL---Y 81

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEK 144
            +  E    + L+ KN+  YN  +  +  +++S+L+  +EK  +   K+   EK
Sbjct: 82  PSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEK 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 = 94.3 bits (234), Expect = 1e-24
 Identities = 35/109 (32%), Positives = 55/109 (50%), Gaps = 3/109 (2%)

Query: 30  LLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTG 89
           L Q  +    +   Q   + PF  PVD + LG+ DY+++++ PMD STIK K+D      
Sbjct: 7   LRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQ--- 63

Query: 90  YRNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPK 138
           Y+   +   DV L+F NA  YN +   V+     L E FE++   ++  
Sbjct: 64  YQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQS 112

>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 = 89.6 bits (222), Expect = 8e-23
 Identities = 28/112 (25%), Positives = 49/112 (43%), Gaps = 5/112 (4%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +     +WPF HPV+ + +   DYY+VI  PMD  TI+  +       Y++      DV 
Sbjct: 22  MMAVPDSWPFHHPVNKKFV--PDYYKVIVNPMDLETIRKNISKH---KYQSRESFLDDVN 76

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQLLPKVMEEEKRQEEEEAKA 153
           L+  N++KYN         A+ ++    +   +    + + EK     +  A
Sbjct: 77  LILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAA 128

>d1e6ia_ a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 111

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 88.8 bits (220), Expect = 9e-23
 Identities = 32/94 (34%), Positives = 50/94 (53%), Gaps = 5/94 (5%)

Query: 42  ITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVR 101
           +  H  AWPF+ PV+ E +   DYY+ I++PMD ST++ K++      Y+ + +   D R
Sbjct: 15  LQNHAAAWPFLQPVNKEEV--PDYYDFIKEPMDLSTMEIKLESNK---YQKMEDFIYDAR 69

Query: 102 LVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
           LVF N   YN E    +  A  L + F  K  ++
Sbjct: 70  LVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 103

>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 = 83.9 bits (207), Expect = 5e-21
 Identities = 30/102 (29%), Positives = 45/102 (44%), Gaps = 5/102 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L   ++   + I  H  AWPFM PV        DYYEVI  P+D  T+  ++  +    Y
Sbjct: 3   LYTTLKNLLAQIKSHPSAWPFMEPVKKSEA--PDYYEVIRFPIDLKTMTERLRSRY---Y 57

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKW 132
              +   AD++ V  N  +YN    +    A +L + F  K 
Sbjct: 58  VTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKL 99

>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 = 83.6 bits (206), Expect = 1e-20
 Identities = 30/105 (28%), Positives = 47/105 (44%), Gaps = 5/105 (4%)

Query: 31  LQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGY 90
           L   ++     +  H+ AWPFM PV         YYEVI  PMD  T+  ++  +    Y
Sbjct: 14  LYSTLKSILQQVKSHQSAWPFMEPVKRTEA--PGYYEVIRFPMDLKTMSERLKNRY---Y 68

Query: 91  RNVREIYADVRLVFKNAMKYNDERDDVHVMAKSLLEKFEEKWLQL 135
            + +   AD++ VF N  +YN    + +  A  L + F  K  + 
Sbjct: 69  VSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEA 113

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	322
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.95
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.95
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.95
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=7.9e-29  Score=197.23  Aligned_cols=101  Identities=30%  Similarity=0.451  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhccc
Q 020702           29 SLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAM  108 (322)
Q Consensus        29 ~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~  108 (322)
                      .+|...|..||..|++|+.++||+.||++..  +|+|+++|++||||+||++||.++.   |.++.+|.+||+|||.||+
T Consensus         1 d~L~~~l~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na~   75 (102)
T d3d7ca1           1 DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSE--APDYYEVIRFPIDLKTMTERLRSRY---YVTRKLFVADLQRVIANCR   75 (102)
T ss_dssp             HHHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CCSHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHhCCCCCccCCCCChhh--CcCHHHHcCCccCHHHHHHHhccCc---cCCHHHHHHHHHHHHHHHH
Confidence            3688999999999999999999999999876  9999999999999999999999999   9999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHh
Q 020702          109 KYNDERDDVHVMAKSLLEKFEEKWLQ  134 (322)
Q Consensus       109 ~yN~~~s~v~~~A~~L~~~Fe~~~~~  134 (322)
                      .||+++|+++.+|..|++.|+++|++
T Consensus        76 ~yN~~~s~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          76 EYNPPDSEYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999998864

>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=99.95  E-value=2.9e-28  Score=197.68  Aligned_cols=106  Identities=31%  Similarity=0.497  Sum_probs=101.0

Q ss_pred             cHHHHHHHHHHHHHHHHcC-CCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHh
Q 020702           27 SASLLQFFVRQARSFITQH-KWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  105 (322)
Q Consensus        27 ~~~~lq~~c~~il~~L~~~-~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~  105 (322)
                      +.+++++.|..+|+.|+++ +.|+||..||++...++||||++|++||||+||++||.++.   |.++.+|.+||+|||.
T Consensus         3 ~p~el~~~l~~~l~~l~~~~p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~---Y~s~~ef~~Dv~li~~   79 (114)
T d3dwya1           3 KPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQ---YQEPWQYVDDVWLMFN   79 (114)
T ss_dssp             CHHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCcCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCc---cccHHHHHHHHHHHHH
Confidence            4678999999999999876 79999999999987779999999999999999999999999   9999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          106 NAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       106 Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||+.||+++|+++.+|..|++.|++.+..+
T Consensus        80 Na~~yN~~~s~~~~~A~~L~~~f~~~~~~i  109 (114)
T d3dwya1          80 NAWLYNRKTSRVYKFCSKLAEVFEQEIDPV  109 (114)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999877

>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=3.3e-28  Score=196.46  Aligned_cols=102  Identities=32%  Similarity=0.613  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccC
Q 020702           32 QFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYN  111 (322)
Q Consensus        32 q~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN  111 (322)
                      ...|..||..|++|+.|+||+.||++..  +|+|+++|++||||+||++||.++.   |.++.+|.+||+|||.||+.||
T Consensus         5 ~~~l~~il~~l~~~~~a~pF~~pvd~~~--~pdY~~vI~~PmdL~tI~~kl~~~~---Y~s~~~f~~Dv~li~~Na~~yN   79 (111)
T d1e6ia_           5 DAAIQNILTELQNHAAAWPFLQPVNKEE--VPDYYDFIKEPMDLSTMEIKLESNK---YQKMEDFIYDARLVFNNCRMYN   79 (111)
T ss_dssp             HHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhCCCChhhcCCCCchh--CcCHHHHcCCchhHHHHHHHHHccc---cchHHHHHHHHHHHHHHHHHHC
Confidence            3578999999999999999999999877  9999999999999999999999999   9999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhhCcCc
Q 020702          112 DERDDVHVMAKSLLEKFEEKWLQLLPKV  139 (322)
Q Consensus       112 ~~~s~v~~~A~~L~~~Fe~~~~~i~~~~  139 (322)
                      +++|.++.+|..|++.|++.|..+ |++
T Consensus        80 ~~~s~i~~~A~~l~~~f~~~~~~i-pe~  106 (111)
T d1e6ia_          80 GENTSYYKYANRLEKFFNNKVKEI-PEY  106 (111)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHTS-GGG
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHh-hcc
Confidence            999999999999999999999886 544

>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=1.3e-27  Score=194.89  Aligned_cols=105  Identities=29%  Similarity=0.442  Sum_probs=100.6

Q ss_pred             ccHHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHh
Q 020702           26 LSASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFK  105 (322)
Q Consensus        26 ~~~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~  105 (322)
                      ....+++..|..|+..|++|+.++||+.||++..  +|+||++|++||||+||++||.++.   |.++.+|.+||+|||.
T Consensus         9 ~~~~~l~~~l~~il~~l~~~~~a~~F~~pv~~~~--~pdY~~iI~~PmdL~~I~~kl~~~~---Y~s~~ef~~Dv~li~~   83 (118)
T d1wuma1           9 RDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTE--APGYYEVIRFPMDLKTMSERLKNRY---YVSKKLFMADLQRVFT   83 (118)
T ss_dssp             CSHHHHHHHHHHHHHHHHHSSSCHHHHSCCCSSS--SSSCTTTCSSCCCHHHHHHHHTTTC---CCSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCcCcccCCCChhh--CcCHHHHcCChhhHHHHHHHhcccc---cCchHHHHHHHHHHHH
Confidence            3467899999999999999999999999999877  9999999999999999999999999   9999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          106 NAMKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       106 Na~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      ||+.||+++|.++.+|..|.+.|++.|.+.
T Consensus        84 Na~~yn~~~s~~~~~A~~l~~~f~~~~~e~  113 (118)
T d1wuma1          84 NCKEYNPPESEYYKCANILEKFFFSKIKEA  113 (118)
T ss_dssp             HHHHHSCTTSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999999875

>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=6.9e-27  Score=195.80  Aligned_cols=103  Identities=23%  Similarity=0.465  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcc
Q 020702           28 ASLLQFFVRQARSFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNA  107 (322)
Q Consensus        28 ~~~lq~~c~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na  107 (322)
                      ...++..|..|++.|..++.++||..||++..  +|+||++|++||||+||++||.++.   |.++.+|..||+|||.||
T Consensus        24 ~~~l~~~l~~il~~l~~~~~s~pF~~Pvd~~~--~pdY~~iI~~PmdL~tI~~kl~~~~---Y~s~~~f~~D~~li~~Na   98 (139)
T d1eqfa1          24 MVTLSSILESIINDMRDLPNTYPFHTPVNAKV--VKDYYKIITRPMDLQTLRENVRKRL---YPSREEFREHLELIVKNS   98 (139)
T ss_dssp             HHHHHHHHHHHHHHHHTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTC---CSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCchhhhCCCChhh--ccCHHHHcCChhhHHHHHHHHHcCC---cCCHHHHHHHHHHHHHHH
Confidence            44578899999999999999999999999987  9999999999999999999999999   999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 020702          108 MKYNDERDDVHVMAKSLLEKFEEKWLQL  135 (322)
Q Consensus       108 ~~yN~~~s~v~~~A~~L~~~Fe~~~~~i  135 (322)
                      +.||+++|.++.+|..|...|++.|+++
T Consensus        99 ~~yN~~~s~i~~~A~~L~~~~~~~~~~~  126 (139)
T d1eqfa1          99 ATYNGPKHSLTQISQSMLDLCDEKLKEK  126 (139)
T ss_dssp             HHHTCTTSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999886

>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=9.1e-27  Score=192.50  Aligned_cols=91  Identities=27%  Similarity=0.534  Sum_probs=86.2

Q ss_pred             HHHHcCCCCCCCCCCCCcccCCCCchhhccCCCCChHHHHHHhcCCCCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHH
Q 020702           40 SFITQHKWAWPFMHPVDVEGLGLHDYYEVIEKPMDFSTIKNKMDGKDGTGYRNVREIYADVRLVFKNAMKYNDERDDVHV  119 (322)
Q Consensus        40 ~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~~~~Y~s~~ef~~DvrLIf~Na~~yN~~~s~v~~  119 (322)
                      ..++.++.||||+.||++..  +|+||++|++||||+||++||.++.   |.|+.+|.+||+|||.||+.||+++|.++.
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            34556789999999999877  9999999999999999999999999   999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhh
Q 020702          120 MAKSLLEKFEEKWLQL  135 (322)
Q Consensus       120 ~A~~L~~~Fe~~~~~i  135 (322)
                      +|..|.+.|++.|.++
T Consensus        95 ~A~~L~~~~~~~l~~~  110 (128)
T d1eqfa2          95 TAQEIVNVCYQTLTEY  110 (128)
T ss_dssp             HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999876