Citrus Sinensis ID: 017092

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------
Protein Sequence
MEAMDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKKQGSNSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNNNDNNKNNNNSATNNNKRKREICDAIAKTAKKKKQKASA
Secondary Structure (PSIPRED)
ccccccccccccccccccccccHHHHHHHcccHHHHHccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHccccHHHHHHHHHHHcccccHHHHHHHHHHHHcccHHcHHHHHHHHHHccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHcccccccccccHHHHHHHHHHHHHccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccHHHcccccHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHcccHHHHHccccccccccccccccccccHHHcccHHHHcccccc
Coil and Loop (DISEMBL)
meamdapisnftavhagnpesdvaeVESFTLRVDDIFQKVDKLEERVNEIEQFYLNAskkqgsnskgsstlkdkekerhvpsIRKQQQEASRREKAAEKRMEELIRQFGTILRNITqhkwawpfmqpvdvkglglddyyevidkpmdfsTIKKQMEAKEYKNVREICTDVRLVFKNAmkyndersdVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALksqgnnnnndnnknnnnsatnnnkRKREICDAIAKTAKKKKQKASA
Flexible Loop (DISEMBL)
meamdapisnftavhagnpesdVAEVESFTLRVDDIFQKVDKLEERVNEIEQFylnaskkqgsnskgsstlkdkekerhvpsirkqqqeasrREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMeakeyknvreiCTDVRLVFKNAmkyndersdVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRktsteekrklgaaltrlspedlGKALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSqgnnnnndnnknnnnsatnnnkrkrEICDAIAktakkkkqkasa
Low Complexity Region (SEG)
MEAMDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNAskkqgsnskgssTLKDKEKERHVPSIRKqqqeasrrekaaekrmeeLIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTeeekrreeeeaeaQLDMQLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGnnnnndnnknnnnsatnnnKRKREICDaiaktakkkkqkasa
Disordered region (IsUnstruct)
************************EVESFTLRVDDIFQKVDKLEERVNEIEQFYL************************************************LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLP**************************************LYEVDVHLDELREMLVQ*****************************EIV************************TLWRLKFFVK*************************************************
Disordered Region (DISOPRED)
**********************************************************************************************************QFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVT****************************************************************************LGKALE****************ELDMDAQSESTLWRLKFFV**************************************************
Disordered Region (DISEMBL)
MEAMDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNAS****************************************KRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVT******************************DTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNNNDNNKNNNNSATNNNKRKREICDAIAK***********
Disordered Region (DISPRO)
**********************VAEVESFT*R**DIF*K***********************************************************KRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLP*********************************************************RKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQG******************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAMDAPISNFTAVHAGNPESDVAExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxQGSNSKGSSTLKDKEKERHVPSIRKQxxxxxxxxxxxxxxxxxxxxxFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTxxxxxxxxxxxxxxxxxxxxxDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNNNDNNKNNNNSATNNNKRKREICDAIAKTAKKKKQKASA
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	377	2.2.26 [Sep-21-2011]
Q84XV2	386	Transcription factor GTE1	yes	no	0.904	0.883	0.531	1e-108
Q9FT54	369	Transcription factor GTE6	no	no	0.830	0.848	0.573	6e-87
Q9LNC4	766	Transcription factor GTE4	no	no	0.578	0.284	0.339	3e-31
Q9LXA7	581	Transcription factor GTE2	no	no	0.273	0.177	0.446	3e-24
Q9S7T1	461	Transcription factor GTE3	no	no	0.588	0.481	0.298	7e-23
Q9LK27	813	Transcription factor GTE8	no	no	0.557	0.258	0.299	9e-23
Q93YS6	688	Transcription factor GTE9	no	no	0.575	0.315	0.303	3e-22
Q7Y214	590	Transcription factor GTE7	no	no	0.273	0.174	0.446	8e-21
Q7JJ13	798	Bromodomain-containing pr	yes	no	0.307	0.145	0.379	1e-20
P25440	801	Bromodomain-containing pr	yes	no	0.307	0.144	0.379	1e-20

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

 Score =  390 bits (1002), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 205/386 (53%), Positives = 268/386 (69%), Gaps = 45/386 (11%)

Query: 13  AVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFY--------LNASKK---- 60
           AV  GN ES   E+E+F   VD+I  +V++LE++V E+E FY         N SK     
Sbjct: 23  AVFNGNGES---ELENFGTCVDEITDRVNQLEQKVVEVEHFYSTKDGAAQTNTSKSNSGG 79

Query: 61  ------QGSNSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRN 114
                 Q +NSKG+S  K+K K +HV S                    +L+RQF T+ R 
Sbjct: 80  KKIAISQPNNSKGNSAGKEKSKGKHVSS-------------------PDLMRQFATMFRQ 120

Query: 115 ITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVF 174
           I QHKWAWPF++PVDVKGLGL DYY+VI+KPMD  TIKK+ME+ EY NVREI  DVRLVF
Sbjct: 121 IAQHKWAWPFLEPVDVKGLGLHDYYKVIEKPMDLGTIKKKMESSEYSNVREIYADVRLVF 180

Query: 175 KNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAA 234
           KNAM+YN+E+ DV+VMA++LL KFEEKWL ++PK+ EEEK++ +EEAE   + QL  +AA
Sbjct: 181 KNAMRYNEEKEDVYVMAESLLEKFEEKWLLIMPKLVEEEKKQVDEEAEKHANKQLTMEAA 240

Query: 235 HAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIV 294
            A+MARD SNELYE+D+ L++LRE +VQ+CRK ST+EK+ L AAL RLSPEDL KAL++V
Sbjct: 241 QAEMARDLSNELYEIDLQLEKLRESVVQRCRKLSTQEKKGLSAALGRLSPEDLSKALKMV 300

Query: 295 AQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNNNDNNKNNNNSAT--- 351
           ++SN  F A A EVELD+D Q++ TLWRLK FV++ALK+   ++   N +NNNN+ T   
Sbjct: 301 SESNPSFPAGAPEVELDIDVQTDVTLWRLKVFVQEALKAANKSSGGTNAQNNNNTGTGEI 360

Query: 352 --NNNKRKREICDAIAKTAKKKKQKA 375
             NN KR+REI DAI K + K+ +KA
Sbjct: 361 NKNNAKRRREISDAINKASIKRAKKA 386

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 =  321 bits (822), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 184/321 (57%), Positives = 226/321 (70%), Gaps = 8/321 (2%)

Query: 14  VHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKKQGSNSKGSSTLKD 73
           V  G  +    + E    RVD++ Q VD LE ++ E+E+FY   S    SNS   S  KD
Sbjct: 9   VAGGGLQGFSVDAECIKQRVDEVLQWVDSLEHKLKEVEEFY---SSIGVSNS--GSIGKD 63

Query: 74  KEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGL 133
            EK RHV  IRK QQEA+RRE  A KRM++L+RQFGTI R ITQHK AWPFM PV+V+GL
Sbjct: 64  TEKGRHVVGIRKIQQEAARREAVAAKRMQDLMRQFGTIFRQITQHKCAWPFMHPVNVEGL 123

Query: 134 GLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNAMKYNDERSDVHVM 190
           GL DY+EVIDKPMDFSTIK QMEAK+   YK+V +I  D+RLVF+NAM YN+E SDV+ M
Sbjct: 124 GLHDYFEVIDKPMDFSTIKNQMEAKDGTGYKHVMQIYADMRLVFENAMNYNEETSDVYSM 183

Query: 191 AKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVD 250
           AK LL KFEEKW   LPKV EEEK REEEE +A  +  LA++A+H K  R+  NE+   +
Sbjct: 184 AKKLLEKFEEKWAHFLPKVQEEEKIREEEEKQAAKEALLAKEASHIKTTRELGNEICHAN 243

Query: 251 VHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVEL 310
             L++L   +V++CRK + EEKR +G AL +LSP+DL K L IVAQ+N  FQ  AEEV +
Sbjct: 244 DELEKLMRKVVERCRKITIEEKRNIGLALLKLSPDDLQKVLGIVAQANPSFQPRAEEVSI 303

Query: 311 DMDAQSESTLWRLKFFVKDAL 331
           +MD   E TLWRLKFFVKDAL
Sbjct: 304 EMDILDEPTLWRLKFFVKDAL 324

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 =  136 bits (342), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 86/253 (33%), Positives = 116/253 (45%), Gaps = 35/253 (13%)

Query: 104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNV 163
           + +    +L  + +HK  W F  PVDVKGLGL DYY +I+ PMD  TIK  +    YK+ 
Sbjct: 421 VFKNCSALLERLMKHKHGWVFNAPVDVKGLGLLDYYTIIEHPMDLGTIKSALMKNLYKSP 480

Query: 164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEA 223
           RE   DVRL F NAM YN E  DVH+MA TLL  FEE+W      V E +  RE      
Sbjct: 481 REFAEDVRLTFHNAMTYNPEGQDVHLMAVTLLQIFEERW-----AVIEADYNREMRFVTG 535

Query: 224 QLDMQLAQDAAHAKMARDTSNELYEVDVHLDEL----------------------REMLV 261
             +M L      +++          V   +D                        R   +
Sbjct: 536 -YEMNLPTPTMRSRLGPTMPPPPINVRNTIDRADWSNRQPTTTPGRTPTSATPSGRTPAL 594

Query: 262 QKC-------RKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDA 314
           +K        R  + EEK+KL   L  L P+ L   ++IV + NT  +   EE+E+D+D+
Sbjct: 595 KKPKANEPNKRDMTYEEKQKLSGHLQNLPPDKLDAIVQIVNKRNTAVKLRDEEIEVDIDS 654

Query: 315 QSESTLWRLKFFV 327
               TLW L  FV
Sbjct: 655 VDPETLWELDRFV 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|Q9LXA7|GTE2_ARATH Transcription factor GTE2 OS=Arabidopsis thaliana GN=GTE2 PE=2 SV=2

 Score =  112 bits (281), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 46/103 (44%), Positives = 71/103 (68%)

Query: 97  AEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME 156
           +EK ++ ++   G IL  + +HKW+W F+ PVDV GLGL DY+ ++DKPMD  T+K  +E
Sbjct: 167 SEKVLKSMMTTCGQILVKLMKHKWSWVFLNPVDVVGLGLHDYHRIVDKPMDLGTVKMNLE 226

Query: 157 AKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFE 199
              Y++  +  +DVRL F NAM YN +  DV++MA+ LL++F+
Sbjct: 227 KGLYRSPIDFASDVRLTFTNAMSYNPKGQDVYLMAEKLLSQFD 269

Arabidopsis thaliana (taxid: 3702)

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

 Score =  108 bits (270), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 80/268 (29%), Positives = 122/268 (45%), Gaps = 46/268 (17%)

Query: 96  AAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQM 155
           AA+K   ++++    +L  + +HK  W F  PVDV  LGL DY+ +I +PMD  T+K ++
Sbjct: 111 AADKGTVQILKSCNNLLTKLMKHKSGWIFNTPVDVVTLGLHDYHNIIKEPMDLGTVKTRL 170

Query: 156 EAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKR 215
               YK+  E   DVRL F NAM YN    DV+ MA+ LL  FEEKW   +P  T+ E  
Sbjct: 171 SKSLYKSPLEFAEDVRLTFNNAMLYNPVGHDVYHMAEILLNLFEEKW---VPLETQYELL 227

Query: 216 REEEEAEAQLDMQLAQDAAHAKMARDTSN-ELYEVDVH---------------------- 252
             +++    +D        HA ++ +T N E   +                         
Sbjct: 228 IRKQQPVRDIDF-------HAPVSTNTHNVEALPLPAPTPSLSPPPPPKVVENRTLERAE 280

Query: 253 ----------LDELREMLVQKC---RKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNT 299
                     L  + E LV++    R  + +EKR+L   L  L  + L   ++I+ +   
Sbjct: 281 SMTNPVKPAVLPVVPEKLVEEASANRDLTFDEKRQLSEDLQDLPYDKLEAVVQIIKKRTP 340

Query: 300 GFQATAEEVELDMDAQSESTLWRLKFFV 327
                 +E+ELD+D+    TLW L  FV
Sbjct: 341 ELSQQDDEIELDIDSLDLETLWELFRFV 368

Probable transcription factor that binds to acetylated histone H3.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LK27|GTE8_ARATH Transcription factor GTE8 OS=Arabidopsis thaliana GN=GTE8 PE=2 SV=2

 Score =  108 bits (269), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 73/244 (29%), Positives = 115/244 (47%), Gaps = 34/244 (13%)

Query: 104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNV 163
           L++Q  T+LR +  H  +W F  PVDV  L + DY   I  PMD  T+KK + +  Y + 
Sbjct: 176 LMKQCDTLLRKLWSHPHSWVFQAPVDVVKLNIPDYLTTIKHPMDLGTVKKNLASGVYSSP 235

Query: 164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW-----------LQLLPKVTEE 212
            E   DVRL F NAM YN    DVH+M   L   FE +W           +Q LP VT E
Sbjct: 236 HEFAADVRLTFTNAMTYNPPGHDVHIMGDILSKLFEARWKTIKKKLPPCSMQTLPAVTLE 295

Query: 213 EKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTE-E 271
                 +E +A + +  A+     KMA                +RE + +  +   TE E
Sbjct: 296 PN----DERKAAISVPPAK---KRKMA--------------SPVRESVPEPVKPLMTEVE 334

Query: 272 KRKLGAALTRLSPEDLGKALEIVAQSNT-GFQATAEEVELDMDAQSESTLWRLKFFVKDA 330
           + +LG  L  L  E     ++ + + N+ G +   +E+E+D+D  S+  L  L+  + + 
Sbjct: 335 RHRLGRQLESLLDELPAHIIDFLKKHNSNGGEIAEDEIEIDIDVLSDEVLVTLRNLLDEY 394

Query: 331 LKSQ 334
           ++++
Sbjct: 395 IQNK 398

Arabidopsis thaliana (taxid: 3702)

>sp|Q93YS6|GTE9_ARATH Transcription factor GTE9 OS=Arabidopsis thaliana GN=GTE9 PE=1 SV=1

 Score =  106 bits (264), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 116/231 (50%), Gaps = 14/231 (6%)

Query: 104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNV 163
           L++Q   +L+ +  H++ W F  PVDV  L + DY+ VI+ PMD  T+K ++ +  Y   
Sbjct: 137 LMKQCEALLKRLMSHQYGWVFNTPVDVVKLNILDYFNVIEHPMDLGTVKNKLTSGTYSCP 196

Query: 164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEA 223
            E   DVRL F NAM YN   +DV+VMA TL   FE +W  L  K++  +   E    +A
Sbjct: 197 SEFAADVRLTFSNAMTYNPPGNDVYVMADTLRKFFEVRWKTLEKKLSGTKVHTEPSNLDA 256

Query: 224 QLDMQLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKR-KLGAALTRL 282
             +  +      AK  + T+     VD       E +V   ++  T+E R KLG  L  L
Sbjct: 257 HKEKHIVIPVPMAKKRKTTA-----VDC------ENVVDPAKRVMTDEDRLKLGKDLESL 305

Query: 283 SPEDLGKALEIVAQSNTGFQATA-EEVELDMDAQSESTLWRLKFFVKDALK 332
           + E   + +  +   N+       +E+E+D++  S+  L++L+  + + L+
Sbjct: 306 T-EFPAQLINFLRDHNSNEGGIGDDEIEIDINDLSDHALFQLRDLLDEHLR 355

Arabidopsis thaliana (taxid: 3702)

>sp|Q7Y214|GTE7_ARATH Transcription factor GTE7 OS=Arabidopsis thaliana GN=GTE7 PE=2 SV=1

 Score =  101 bits (252), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 46/103 (44%), Positives = 63/103 (61%)

Query: 97  AEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME 156
           +EK +  ++     IL  + +HKWAW F  PVDV GLGL DY++V+ KPMD  T+K  ++
Sbjct: 162 SEKLLAGMLNTCSQILVKLMKHKWAWVFNTPVDVVGLGLHDYHQVVKKPMDLGTVKLNLD 221

Query: 157 AKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFE 199
              Y +  +  TDVRL F NAM YN +  DV+ MA  LL  F+
Sbjct: 222 KGFYVSPIDFATDVRLTFDNAMTYNPKGQDVYFMADKLLDHFD 264

Arabidopsis thaliana (taxid: 3702)

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

 Score =  100 bits (250), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/124 (37%), Positives = 77/124 (62%), Gaps = 8/124 (6%)

Query: 85  KQQQEASRREKAAEKRMEELIRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEV 141
           +QQ ++S++ K +E+     ++    IL+ +   K   +AWPF +PVD   LGL DY+++
Sbjct: 334 QQQHQSSKKGKLSEQ-----LKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDI 388

Query: 142 IDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
           I  PMD ST+K++ME ++Y++ +E   DVRL+F N  KYN    DV  MA+ L   FE +
Sbjct: 389 IKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFR 448

Query: 202 WLQL 205
           + ++
Sbjct: 449 YAKM 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 (250), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/124 (37%), Positives = 77/124 (62%), Gaps = 8/124 (6%)

Query: 85  KQQQEASRREKAAEKRMEELIRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEV 141
           +QQ ++S++ K +E+     ++    IL+ +   K   +AWPF +PVD   LGL DY+++
Sbjct: 335 QQQHQSSKKGKLSEQ-----LKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDI 389

Query: 142 IDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
           I  PMD ST+K++ME ++Y++ +E   DVRL+F N  KYN    DV  MA+ L   FE +
Sbjct: 390 IKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFR 449

Query: 202 WLQL 205
           + ++
Sbjct: 450 YAKM 453

May play a role in spermatogenesis or folliculogenesis.

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	377
359486529	440	PREDICTED: transcription factor GTE1-lik	0.960	0.822	0.740	1e-146
255577689	391	bromodomain-containing protein, putative	0.989	0.953	0.736	1e-145
297742702	421	unnamed protein product [Vitis vinifera]	0.952	0.852	0.742	1e-139
359484096	377	PREDICTED: transcription factor GTE1-lik	0.946	0.946	0.743	1e-139
147779795	377	hypothetical protein VITISV_019973 [Viti	0.946	0.946	0.743	1e-139
356565711	738	PREDICTED: uncharacterized protein LOC10	0.952	0.486	0.725	1e-139
224098028	370	global transcription factor group [Popul	0.946	0.964	0.720	1e-136
449452116	378	PREDICTED: transcription factor GTE1-lik	0.907	0.904	0.768	1e-135
296086052	362	unnamed protein product [Vitis vinifera]	0.893	0.930	0.701	1e-132
224109720	318	global transcription factor group [Popul	0.816	0.968	0.792	1e-131

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

 Score =  523 bits (1346), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 277/374 (74%), Positives = 315/374 (84%), Gaps = 12/374 (3%)

Query: 1   MEAMDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKK 60
           ME MDA IS+   +  G  + + A+VES   RVDDIF KVDKLE+RVNE+EQFYL ASKK
Sbjct: 52  MEPMDASISDTRNMETGKNQGNAAQVESLKSRVDDIFTKVDKLEQRVNEVEQFYLTASKK 111

Query: 61  QGSNSKGSSTLKDKEK--ERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQH 118
           Q + SKGSS +KDK+K  ERHV S++KQQQ+ASRRE AA KRM+EL+RQFGTILR ITQH
Sbjct: 112 QLNVSKGSSIVKDKDKDKERHVASVKKQQQDASRREAAAAKRMQELMRQFGTILRQITQH 171

Query: 119 KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFK 175
           KWAWPFMQPVDV+GLGL DYYEVI+KPMDFSTIK +MEAK+   YKNVREIC DVRLVFK
Sbjct: 172 KWAWPFMQPVDVEGLGLHDYYEVIEKPMDFSTIKNKMEAKDGAGYKNVREICADVRLVFK 231

Query: 176 NAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAH 235
           NAMKYNDER DVHVMAKTLL KFEEKWLQLLPKV EE+KRREEEEAEAQLDM LAQ+AAH
Sbjct: 232 NAMKYNDERRDVHVMAKTLLGKFEEKWLQLLPKVAEEDKRREEEEAEAQLDMHLAQEAAH 291

Query: 236 AKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVA 295
           AKMARD SNEL+E+D+HLD++RE++VQKCRKTSTEEKRKLGAAL+RLS EDL KALEIVA
Sbjct: 292 AKMARDISNELFEIDMHLDDIREIIVQKCRKTSTEEKRKLGAALSRLSAEDLSKALEIVA 351

Query: 296 QSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNNNDNN-------KNNNN 348
           QSN  FQATAEEV LD+DAQ ESTLWRLKFFVKDAL+ QG ++ +           NN+ 
Sbjct: 352 QSNPSFQATAEEVHLDIDAQRESTLWRLKFFVKDALEIQGKSSASMGGNNTATTTNNNHP 411

Query: 349 SATNNNKRKREICD 362
           +  NN+KRK+EICD
Sbjct: 412 TTNNNSKRKKEICD 425

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  521 bits (1343), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 291/395 (73%), Positives = 326/395 (82%), Gaps = 22/395 (5%)

Query: 1   MEAMDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKK 60
           MEA+ + I +F +   GN      E++ +  RVD++F KVDKLE+RVNE+E FYLN +KK
Sbjct: 1   MEAITSSIPDFGSYDFGNS----VEIDGYKHRVDELFHKVDKLEQRVNEVELFYLNVNKK 56

Query: 61  QGSNSKGSS------TLKDKE-KERH-VPSIRKQQQEASRREKAAEKRMEELIRQFGTIL 112
           Q   S G         +KD   KERH VPSIRKQQQ+AS+RE AA KRM+EL+RQFGTIL
Sbjct: 57  QQQQSGGGGNSKGSSIVKDNNNKERHSVPSIRKQQQDASKREAAASKRMQELMRQFGTIL 116

Query: 113 RNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTD 169
           R ITQHKWAWPFMQPVDVKGLGL DYYEVIDKPMDFSTIK QME K+   YKNVREIC D
Sbjct: 117 RQITQHKWAWPFMQPVDVKGLGLHDYYEVIDKPMDFSTIKNQMETKDGTGYKNVREICAD 176

Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQL 229
           VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRRE EEAEAQLDMQL
Sbjct: 177 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREMEEAEAQLDMQL 236

Query: 230 AQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGK 289
           AQ+A HAKMAR+ SNELYE+D HLDELR+M+VQKCRK STEEKRKLGAALTRLSPEDL K
Sbjct: 237 AQEAVHAKMARELSNELYEIDTHLDELRDMVVQKCRKISTEEKRKLGAALTRLSPEDLTK 296

Query: 290 ALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGN-------NNNNDN 342
           ALEIVAQ+N GFQATAEEV+LD+DAQ+ESTLWRLKFFVKDAL+ QG        NNNN+N
Sbjct: 297 ALEIVAQNNPGFQATAEEVDLDIDAQTESTLWRLKFFVKDALEVQGKNAASAGGNNNNNN 356

Query: 343 NKNNNNSATNNNKRKREICDAIAKTAKKKKQKASA 377
           +    N+  +NNKRK+EICDAIAKTAKK+ +KASA
Sbjct: 357 SNTTTNNNNSNNKRKKEICDAIAKTAKKRNKKASA 391

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  501 bits (1289), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 271/365 (74%), Positives = 308/365 (84%), Gaps = 6/365 (1%)

Query: 2   EAMDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKKQ 61
           E MDA I+N   V  G  + +  +VE F   VDDIF KVDKLE+RVNE+E FYL ASK+Q
Sbjct: 43  EPMDASITNVRNVEIGKHKGNTDQVEGFKSCVDDIFTKVDKLEQRVNEVELFYLTASKRQ 102

Query: 62  GSNSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWA 121
            +  KGSS LKDKE  RHV S +KQQQ+ASRRE AA KRM+EL+RQFGTILR I QHKWA
Sbjct: 103 LNGYKGSSVLKDKE--RHVASAKKQQQDASRREAAAVKRMQELMRQFGTILRQIMQHKWA 160

Query: 122 WPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNAM 178
            PF+ PVDV+GLGL DYYEVIDKPMDFSTIK QMEAK+   YKNVREIC DVRLVFKNAM
Sbjct: 161 GPFLHPVDVEGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKNVREICADVRLVFKNAM 220

Query: 179 KYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKM 238
           KYNDER DVHVMAKTLL KFEEKWLQLLPKV EEEKRREEEEAEAQLDMQLAQ+AAHAKM
Sbjct: 221 KYNDERHDVHVMAKTLLGKFEEKWLQLLPKVAEEEKRREEEEAEAQLDMQLAQEAAHAKM 280

Query: 239 ARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSN 298
           AR+ SNELY++D+HL+E+REM+++KCRK STEEKRKLGAAL+RLS EDL KALEIVAQ+N
Sbjct: 281 AREISNELYDIDMHLEEVREMVIRKCRKMSTEEKRKLGAALSRLSAEDLSKALEIVAQNN 340

Query: 299 TGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNN-NNDNNKNNNNSATNNNKRK 357
             FQATAEEV+LD+DAQ+ESTLWRLKFFVKDAL+ QG ++ +  +N N   +ATNNNKRK
Sbjct: 341 PSFQATAEEVDLDIDAQTESTLWRLKFFVKDALEVQGKSSASKGDNTNTTTTATNNNKRK 400

Query: 358 REICD 362
           +EICD
Sbjct: 401 KEICD 405

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  501 bits (1289), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 270/363 (74%), Positives = 307/363 (84%), Gaps = 6/363 (1%)

Query: 4   MDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKKQGS 63
           MDA I+N   V  G  + +  +VE F   VDDIF KVDKLE+RVNE+E FYL ASK+Q +
Sbjct: 1   MDASITNVRNVEIGKHKGNTDQVEGFKSCVDDIFTKVDKLEQRVNEVELFYLTASKRQLN 60

Query: 64  NSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWP 123
             KGSS LKDKE  RHV S +KQQQ+ASRRE AA KRM+EL+RQFGTILR I QHKWA P
Sbjct: 61  GYKGSSVLKDKE--RHVASAKKQQQDASRREAAAVKRMQELMRQFGTILRQIMQHKWAGP 118

Query: 124 FMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNAMKY 180
           F+ PVDV+GLGL DYYEVIDKPMDFSTIK QMEAK+   YKNVREIC DVRLVFKNAMKY
Sbjct: 119 FLHPVDVEGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKNVREICADVRLVFKNAMKY 178

Query: 181 NDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMAR 240
           NDER DVHVMAKTLL KFEEKWLQLLPKV EEEKRREEEEAEAQLDMQLAQ+AAHAKMAR
Sbjct: 179 NDERHDVHVMAKTLLGKFEEKWLQLLPKVAEEEKRREEEEAEAQLDMQLAQEAAHAKMAR 238

Query: 241 DTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTG 300
           + SNELY++D+HL+E+REM+++KCRK STEEKRKLGAAL+RLS EDL KALEIVAQ+N  
Sbjct: 239 EISNELYDIDMHLEEVREMVIRKCRKMSTEEKRKLGAALSRLSAEDLSKALEIVAQNNPS 298

Query: 301 FQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNN-NNDNNKNNNNSATNNNKRKRE 359
           FQATAEEV+LD+DAQ+ESTLWRLKFFVKDAL+ QG ++ +  +N N   +ATNNNKRK+E
Sbjct: 299 FQATAEEVDLDIDAQTESTLWRLKFFVKDALEVQGKSSASKGDNTNTTTTATNNNKRKKE 358

Query: 360 ICD 362
           ICD
Sbjct: 359 ICD 361

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  500 bits (1288), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 270/363 (74%), Positives = 306/363 (84%), Gaps = 6/363 (1%)

Query: 4   MDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKKQGS 63
           MDA I+N   V  G  + +  +VE F   VDDIF KVDKLE+RVNE+E FYL ASK+Q +
Sbjct: 1   MDASITNVRNVEIGKHKGNTDQVEGFKSCVDDIFTKVDKLEQRVNEVELFYLTASKRQLN 60

Query: 64  NSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWP 123
             KGSS LKDKE  RHV S +KQQQ+ASRRE AA KRM+EL+RQFGTILR I QHKWA P
Sbjct: 61  GYKGSSVLKDKE--RHVASAKKQQQDASRREAAAAKRMQELMRQFGTILRQIMQHKWAGP 118

Query: 124 FMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNAMKY 180
           F+ PVDV+GLGL DYYEVIDKPMDFSTIK QMEAK+   YKNVREIC DVRLVFKNAMKY
Sbjct: 119 FLHPVDVEGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKNVREICADVRLVFKNAMKY 178

Query: 181 NDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMAR 240
           NDER DVHVMAKTLL KFEEKWLQLLPKV EEEKRREEEEAEAQLDMQLAQ+AAHAKMAR
Sbjct: 179 NDERHDVHVMAKTLLGKFEEKWLQLLPKVAEEEKRREEEEAEAQLDMQLAQEAAHAKMAR 238

Query: 241 DTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTG 300
           + SNELY +D+HL+E+REM+++KCRK STEEKRKLGAAL+RLS EDL KALEIVAQ+N  
Sbjct: 239 EISNELYXIDMHLEEVREMVIRKCRKMSTEEKRKLGAALSRLSAEDLSKALEIVAQNNPS 298

Query: 301 FQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNN-NNDNNKNNNNSATNNNKRKRE 359
           FQATAEEV+LD+DAQ+ESTLWRLKFFVKDAL+ QG ++ +  +N N   +ATNNNKRK+E
Sbjct: 299 FQATAEEVDLDIDAQTESTLWRLKFFVKDALEVQGKSSASKGDNTNTTTTATNNNKRKKE 358

Query: 360 ICD 362
           ICD
Sbjct: 359 ICD 361

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  500 bits (1288), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 267/368 (72%), Positives = 303/368 (82%), Gaps = 9/368 (2%)

Query: 1   MEAMDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKK 60
           ME   A IS        N   +  E+E F  RVD+I  KVDKLE++V++IE FY + +K 
Sbjct: 367 METFGASISEARDAATANSNGE-NEIEGFKQRVDEIISKVDKLEQKVHDIENFYSSMNKN 425

Query: 61  QGSNSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKW 120
           Q S  KG+S  KDK+KE+HVPSI+KQQQ+ASRRE AA KRM++L+RQFGTILR ITQHKW
Sbjct: 426 QTSTPKGNSAAKDKDKEKHVPSIKKQQQDASRREAAASKRMQDLMRQFGTILRQITQHKW 485

Query: 121 AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNA 177
           AWPFMQPVD++GLGL DYYEVIDKPMDFSTIK QMEAK+   YK+VREIC DVRLVFKNA
Sbjct: 486 AWPFMQPVDIEGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKHVREICADVRLVFKNA 545

Query: 178 MKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAK 237
           MKYNDERSDVHVMAKTLL+KFEEKWLQLLPKVTEEE RREEEEAEAQL +Q+AQ+AA AK
Sbjct: 546 MKYNDERSDVHVMAKTLLSKFEEKWLQLLPKVTEEETRREEEEAEAQLALQVAQEAAQAK 605

Query: 238 MARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQS 297
           MARD SNELYEVDV L+ELREM+V++ RK STEEKRKLG ALTRLSPEDL KALEIVAQ+
Sbjct: 606 MARDLSNELYEVDVILEELREMVVKRFRKMSTEEKRKLGDALTRLSPEDLSKALEIVAQN 665

Query: 298 NTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNNNDNNKNNNNSATNNNKRK 357
           N  FQATAEEV+LDMDAQSESTLWRLKFFVK+AL+ QG N+ +     N      NNKRK
Sbjct: 666 NPSFQATAEEVDLDMDAQSESTLWRLKFFVKEALEVQGKNSGSMGGNEN-----QNNKRK 720

Query: 358 REICDAIA 365
           RE+CDAIA
Sbjct: 721 RELCDAIA 728

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  491 bits (1265), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 281/390 (72%), Positives = 315/390 (80%), Gaps = 33/390 (8%)

Query: 1   MEAMDAPISNFTAVHAGN-P--ESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFY--- 54
           MEA+   I     V +GN P   SD AE E F   VD+I QKVDKLE+RVNE+EQFY   
Sbjct: 1   MEAISPSI-----VDSGNLPIRNSD-AEAEGFKHSVDEILQKVDKLEQRVNEVEQFYSKN 54

Query: 55  LNASKKQGSNSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRN 114
            +  ++ GS+  GSST+KDK+KERH+P+              A KRM+EL+RQFGTILR 
Sbjct: 55  TSKKQQSGSSKGGSSTVKDKDKERHIPT--------------AAKRMQELMRQFGTILRQ 100

Query: 115 ITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVR 171
           ITQHKWAWPFMQPVDVKGLGL DYYEVIDKPMDFSTIK QMEAK+   YK+VREIC DVR
Sbjct: 101 ITQHKWAWPFMQPVDVKGLGLHDYYEVIDKPMDFSTIKNQMEAKDGTGYKSVREICADVR 160

Query: 172 LVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQ 231
           LVFKNAMKYNDERSDVHVMAKTLL KFEEKWLQ LPKVTEEEKRREEEEAEAQLDMQLAQ
Sbjct: 161 LVFKNAMKYNDERSDVHVMAKTLLGKFEEKWLQFLPKVTEEEKRREEEEAEAQLDMQLAQ 220

Query: 232 DAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKAL 291
           +AAHAKMARD  NELYEVD+HL+ELREM+VQKCRK STEEKRKLGAALTRLSPEDL KAL
Sbjct: 221 EAAHAKMARDLGNELYEVDMHLEELREMVVQKCRKMSTEEKRKLGAALTRLSPEDLTKAL 280

Query: 292 EIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNNNDNNK----NNN 347
           EIVAQ+N GFQATAEEV+LD+DAQSE+TLWRLKFFVKDAL+ QG +  +   +      +
Sbjct: 281 EIVAQNNPGFQATAEEVDLDIDAQSETTLWRLKFFVKDALEVQGKSAASAGGRNNTTTPS 340

Query: 348 NSATNNNKRKREICDAIAKTAKKKKQKASA 377
           N+  NNNKRKREICDAIAKTAKK+ +K S+
Sbjct: 341 NNNNNNNKRKREICDAIAKTAKKRSKKPSS 370

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 =  488 bits (1255), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 269/350 (76%), Positives = 306/350 (87%), Gaps = 8/350 (2%)

Query: 25  EVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKKQGSNSKGSSTLKDKEKERHVPSIR 84
           EV+ F  +VD+IF KVD+LE+ VNEIEQFYL   KKQ + +KGSS +KDK+KERHVPSI+
Sbjct: 18  EVDGFRHQVDEIFLKVDRLEQNVNEIEQFYLTLKKKQPNGNKGSSIVKDKDKERHVPSIK 77

Query: 85  KQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDK 144
           KQQQEA+RRE AA KRM+EL+RQFGTILR I+QHKWAWPFMQPVDV+GLGL DYYEVIDK
Sbjct: 78  KQQQEAARREAAATKRMQELMRQFGTILRQISQHKWAWPFMQPVDVEGLGLHDYYEVIDK 137

Query: 145 PMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
           PMDFSTIK QMEAK+   YKNVREIC+DVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK
Sbjct: 138 PMDFSTIKNQMEAKDGTGYKNVREICSDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 197

Query: 202 WLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVDVHLDELREMLV 261
           WLQLLPKVTEEEKRRE+EEAEA LDMQLAQ+AA AKMARD SNE+YEVD+ L+ELRE++V
Sbjct: 198 WLQLLPKVTEEEKRREDEEAEALLDMQLAQEAAQAKMARDISNEIYEVDMQLEELRELVV 257

Query: 262 QKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDAQSESTLW 321
           Q CRK STEEKRKLGAALT+LSPED+ KALEIVA++N  FQATAEEV+LD+DAQSESTLW
Sbjct: 258 QNCRKISTEEKRKLGAALTKLSPEDISKALEIVAENNPSFQATAEEVDLDIDAQSESTLW 317

Query: 322 RLKFFVKDALK-----SQGNNNNNDNNKNNNNSATNNNKRKREICDAIAK 366
           RLKFFVKDAL+     S      N+ N  N+N+  +NNKRK+EICDAIA+
Sbjct: 318 RLKFFVKDALEVHAKSSASTGGGNNQNHTNSNNINSNNKRKKEICDAIAR 367

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  477 bits (1228), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 259/369 (70%), Positives = 293/369 (79%), Gaps = 32/369 (8%)

Query: 4   MDAPISNFTAVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNASKKQGS 63
           MDA IS+   +  G  + + A+VES   RVDDIF KVDKLE+RVNE+EQFYL ASKKQ +
Sbjct: 1   MDASISDTRNMETGKNQGNAAQVESLKSRVDDIFTKVDKLEQRVNEVEQFYLTASKKQLN 60

Query: 64  NSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWP 123
            SK                      +ASRRE AA KRM+EL+RQFGTILR ITQHKWAWP
Sbjct: 61  VSK----------------------DASRREAAAAKRMQELMRQFGTILRQITQHKWAWP 98

Query: 124 FMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNAMKY 180
           FMQPVDV+GLGL DYYEVI+KPMDFSTIK +MEAK+   YKNVREIC DVRLVFKNAMKY
Sbjct: 99  FMQPVDVEGLGLHDYYEVIEKPMDFSTIKNKMEAKDGAGYKNVREICADVRLVFKNAMKY 158

Query: 181 NDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMAR 240
           NDER DVHVMAKTLL KFEEKWLQLLPKV EE+KRREEEEAEAQLDM LAQ+AAHAKMAR
Sbjct: 159 NDERRDVHVMAKTLLGKFEEKWLQLLPKVAEEDKRREEEEAEAQLDMHLAQEAAHAKMAR 218

Query: 241 DTSNELYEVDVHLDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTG 300
           D SNEL+E+D+HLD++RE++VQKCRKTSTEEKRKLGAAL+RLS EDL KALEIVAQSN  
Sbjct: 219 DISNELFEIDMHLDDIREIIVQKCRKTSTEEKRKLGAALSRLSAEDLSKALEIVAQSNPS 278

Query: 301 FQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNNNDNN-------KNNNNSATNN 353
           FQATAEEV LD+DAQ ESTLWRLKFFVKDAL+ QG ++ +           NN+ +  NN
Sbjct: 279 FQATAEEVHLDIDAQRESTLWRLKFFVKDALEIQGKSSASMGGNNTATTTNNNHPTTNNN 338

Query: 354 NKRKREICD 362
           +KRK+EICD
Sbjct: 339 SKRKKEICD 347

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  474 bits (1221), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 249/314 (79%), Positives = 275/314 (87%), Gaps = 6/314 (1%)

Query: 24  AEVESFTLRVDDIFQKVDKLEERVNEIEQFYLN---ASKKQGSNSKGSSTLKDKEKERHV 80
           A+ E F   VD+IFQKVDKLE+R+N +EQFYL+     +   S   GSS +KDK+KERHV
Sbjct: 4   ADTEGFKHSVDEIFQKVDKLEQRMNGVEQFYLDISKKQQSGSSKGGGSSIVKDKDKERHV 63

Query: 81  PSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYE 140
            SIRKQQQ+AS+RE AA KRM+EL+RQFGTILR ITQHKWAWPFMQPVDVKGL L DYYE
Sbjct: 64  TSIRKQQQDASKREAAAAKRMQELMRQFGTILRQITQHKWAWPFMQPVDVKGLRLHDYYE 123

Query: 141 VIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAK 197
           VIDKPMDFSTIK QMEAK+   YKNVREI  DVRLVFKNAMKYNDERSDVHVMAKTLL K
Sbjct: 124 VIDKPMDFSTIKNQMEAKDGTGYKNVREISADVRLVFKNAMKYNDERSDVHVMAKTLLGK 183

Query: 198 FEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVDVHLDELR 257
           FEEKWLQLLPKVTEEEKRRE+EE EA+LDMQLAQ+AAHAKMARD SNELYEVD+HL+ELR
Sbjct: 184 FEEKWLQLLPKVTEEEKRREDEEVEAKLDMQLAQEAAHAKMARDLSNELYEVDMHLEELR 243

Query: 258 EMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDMDAQSE 317
           +++VQKCRK STEEKRKLG ALTRLSPEDL KALEIVA+SN GFQATAEEV+LD+DAQ+E
Sbjct: 244 DIVVQKCRKMSTEEKRKLGVALTRLSPEDLTKALEIVARSNPGFQATAEEVDLDIDAQTE 303

Query: 318 STLWRLKFFVKDAL 331
           STLWRLKF VKD L
Sbjct: 304 STLWRLKFLVKDVL 317

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	377
TAIR|locus:2044722	386	IMB1 "AT2G34900" [Arabidopsis	0.917	0.896	0.487	2e-81
TAIR|locus:2038565	766	GTE4 "AT1G06230" [Arabidopsis	0.262	0.129	0.515	1.6e-31
TAIR|locus:2155715	590	GTE7 "AT5G65630" [Arabidopsis	0.236	0.150	0.494	1.4e-28
TAIR|locus:2030958	487	AT1G17790 "AT1G17790" [Arabido	0.270	0.209	0.401	3.1e-26
UNIPROTKB|Q5TJG6	803	BRD2 "Bromodomain-containing p	0.421	0.198	0.331	1.7e-25
TAIR|locus:2032692	461	GTE3 "AT1G73150" [Arabidopsis	0.270	0.221	0.441	2.3e-25
ZFIN|ZDB-GENE-990415-248	838	brd2a "bromodomain-containing	0.267	0.120	0.442	3.1e-25
UNIPROTKB|A5D9K6	803	BRD2 "Uncharacterized protein"	0.421	0.198	0.325	4.5e-25
UNIPROTKB|Q32S26	803	BRD2 "Bromodomain-containing p	0.421	0.198	0.325	5.7e-25
UNIPROTKB|O60885	1362	BRD4 "Bromodomain-containing p	0.228	0.063	0.476	1.6e-24

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

 Score = 817 (292.7 bits), Expect = 2.0e-81, P = 2.0e-81
 Identities = 173/355 (48%), Positives = 223/355 (62%)

Query:    13 AVHAGNPESDVAEVESFTLRVDDIFQKVDKLEERVNEIEQFYLNAXXXXXXXXXXXXTLK 72
             AV  GN ES   E+E+F   VD+I  +V++LE++V E+E FY +                
Sbjct:    23 AVFNGNGES---ELENFGTCVDEITDRVNQLEQKVVEVEHFY-STKDGAAQTNTSKSNSG 78

Query:    73 DKEKERHVPSIRKXXXXXXXXXXXXXXXXXXLIRQFGTILRNITQHKWAWPFMQPVDVKG 132
              K+     P+  K                  L+RQF T+ R I QHKWAWPF++PVDVKG
Sbjct:    79 GKKIAISQPNNSKGNSAGKEKSKGKHVSSPDLMRQFATMFRQIAQHKWAWPFLEPVDVKG 138

Query:   133 LGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAK 192
             LGL DYY+VI+KPMD  TIKK+ME+ EY NVREI  DVRLVFKNAM+YN+E+ DV+VMA+
Sbjct:   139 LGLHDYYKVIEKPMDLGTIKKKMESSEYSNVREIYADVRLVFKNAMRYNEEKEDVYVMAE 198

Query:   193 TLLAKFEEKWLQLLPKVTXXXXXXXXXXXXXQLDMQLAQDAAHAKMARDTSNELYEVDVH 252
             +LL KFEEKWL ++PK+                + QL  +AA A+MARD SNELYE+D+ 
Sbjct:   199 SLLEKFEEKWLLIMPKLVEEEKKQVDEEAEKHANKQLTMEAAQAEMARDLSNELYEIDLQ 258

Query:   253 LDELREMLVQKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQATAEEVELDM 312
             L++LRE +VQ+CRK ST+EK+ L AAL RLSPEDL KAL++V++SN  F A A EVELD+
Sbjct:   259 LEKLRESVVQRCRKLSTQEKKGLSAALGRLSPEDLSKALKMVSESNPSFPAGAPEVELDI 318

Query:   313 DAQSESTLWRLKFFVKDALK-----SQGXXXXXXXXXXXXXXXXXXXKRKREICD 362
             D Q++ TLWRLK FV++ALK     S G                   KR+REI D
Sbjct:   319 DVQTDVTLWRLKVFVQEALKAANKSSGGTNAQNNNNTGTGEINKNNAKRRREISD 373

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

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

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

 Score = 265 (98.3 bits), Expect = 1.6e-31, Sum P(2) = 1.6e-31
 Identities = 51/99 (51%), Positives = 62/99 (62%)

Query:   104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNV 163
             + +    +L  + +HK  W F  PVDVKGLGL DYY +I+ PMD  TIK  +    YK+ 
Sbjct:   421 VFKNCSALLERLMKHKHGWVFNAPVDVKGLGLLDYYTIIEHPMDLGTIKSALMKNLYKSP 480

Query:   164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
             RE   DVRL F NAM YN E  DVH+MA TLL  FEE+W
Sbjct:   481 REFAEDVRLTFHNAMTYNPEGQDVHLMAVTLLQIFEERW 519

GO:0003677 "DNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

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

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

GO:0048364 "root development" evidence=IMP

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

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

 Score = 228 (85.3 bits), Expect = 1.4e-28, Sum P(2) = 1.4e-28
 Identities = 44/89 (49%), Positives = 57/89 (64%)

Query:   111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
             IL  + +HKWAW F  PVDV GLGL DY++V+ KPMD  T+K  ++   Y +  +  TDV
Sbjct:   176 ILVKLMKHKWAWVFNTPVDVVGLGLHDYHQVVKKPMDLGTVKLNLDKGFYVSPIDFATDV 235

Query:   171 RLVFKNAMKYNDERSDVHVMAKTLLAKFE 199
             RL F NAM YN +  DV+ MA  LL  F+
Sbjct:   236 RLTFDNAMTYNPKGQDVYFMADKLLDHFD 264

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2030958 AT1G17790 "AT1G17790" [Arabidopsis thaliana (taxid:3702)]

 Score = 224 (83.9 bits), Expect = 3.1e-26, Sum P(2) = 3.1e-26
 Identities = 41/102 (40%), Positives = 62/102 (60%)

Query:   104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNV 163
             + +   ++L  + +HK AW F  PVD KGLGL DY+ ++ +PMD  T+K ++    YK+ 
Sbjct:   132 IFKNCNSLLTKLMKHKSAWVFNVPVDAKGLGLHDYHNIVKEPMDLGTVKTKLGKSLYKSP 191

Query:   164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
              +   DVRL F NA+ YN    DV+  A+ LL  FE+KW+ +
Sbjct:   192 LDFAEDVRLTFNNAILYNPIGHDVYRFAELLLNMFEDKWVSI 233

GO:0003677 "DNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0005515 "protein binding" evidence=IPI

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

 Score = 234 (87.4 bits), Expect = 1.7e-25, Sum P(2) = 1.7e-25
 Identities = 55/166 (33%), Positives = 85/166 (51%)

Query:   111 ILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREIC 167
             IL+ +   K   +AWPF +PVD   LGL DY+++I  PMD ST+K++ME ++Y++ +E  
Sbjct:   356 ILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFA 415

Query:   168 TDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTXXXXXXXXXXXXXQLDM 227
              DVRL+F N  KYN    DV  MA+ L   FE ++     K+               L  
Sbjct:   416 ADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYA----KMPDEPLEPGPLPVSTALPP 471

Query:   228 QLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKR 273
              LA+ ++ +     +S    E D   DE  E   ++   + +EE+R
Sbjct:   472 GLAKSSSESSSEESSSESSSEEDEEEDEEEEEEEEESESSDSEEER 517

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

GO:0003682 "chromatin binding" evidence=ISS

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

GO:0006334 "nucleosome assembly" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

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

TAIR|locus:2032692 GTE3 "AT1G73150" [Arabidopsis thaliana (taxid:3702)]

 Score = 229 (85.7 bits), Expect = 2.3e-25, Sum P(2) = 2.3e-25
 Identities = 45/102 (44%), Positives = 61/102 (59%)

Query:   104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNV 163
             +++    +L  + +HK  W F  PVDV  LGL DY+ +I +PMD  T+K ++    YK+ 
Sbjct:   119 ILKSCNNLLTKLMKHKSGWIFNTPVDVVTLGLHDYHNIIKEPMDLGTVKTRLSKSLYKSP 178

Query:   164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
              E   DVRL F NAM YN    DV+ MA+ LL  FEEKW+ L
Sbjct:   179 LEFAEDVRLTFNNAMLYNPVGHDVYHMAEILLNLFEEKWVPL 220

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0042393 "histone binding" evidence=IPI

ZFIN|ZDB-GENE-990415-248 brd2a "bromodomain-containing 2a" [Danio rerio (taxid:7955)]

 Score = 232 (86.7 bits), Expect = 3.1e-25, Sum P(2) = 3.1e-25
 Identities = 46/104 (44%), Positives = 66/104 (63%)

Query:   105 IRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
             +R   TIL+ +   K   +AWPF +PVDV  LGL DYY++I  PMD STIK++M+ +EY+
Sbjct:   386 LRYCSTILKELLSKKHTAYAWPFYKPVDVSSLGLHDYYDIIMYPMDLSTIKRKMDHREYR 445

Query:   162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
             +  +   DVRL+F N  KYN    DV  MA+ L   FE ++ ++
Sbjct:   446 DALQFAADVRLMFSNCYKYNPPDHDVVAMARRLQDVFEFRFAKM 489

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

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

 Score = 230 (86.0 bits), Expect = 4.5e-25, Sum P(2) = 4.5e-25
 Identities = 54/166 (32%), Positives = 85/166 (51%)

Query:   111 ILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREIC 167
             IL+ +   K   +AWPF +PVD   LGL DY+++I  PMD ST+K++ME ++Y++ +E  
Sbjct:   356 ILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFA 415

Query:   168 TDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTXXXXXXXXXXXXXQLDM 227
              DVRL+F N  KYN    DV  MA+ L   FE ++     K+               L  
Sbjct:   416 ADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYA----KMPDEPLEPGPLPVSTALPP 471

Query:   228 QLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKR 273
              LA+ ++ +     +S    E +   DE  E   ++   + +EE+R
Sbjct:   472 GLAKSSSESSSEESSSESSSEEEEEEDEEEEEEEEESESSDSEEER 517

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

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

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

 Score = 229 (85.7 bits), Expect = 5.7e-25, Sum P(2) = 5.7e-25
 Identities = 54/166 (32%), Positives = 85/166 (51%)

Query:   111 ILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREIC 167
             IL+ +   K   +AWPF +PVD   LGL DY+++I  PMD ST+K++ME ++Y++ +E  
Sbjct:   356 ILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFA 415

Query:   168 TDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTXXXXXXXXXXXXXQLDM 227
              DVRL+F N  KYN    DV  MA+ L   FE ++     K+               L  
Sbjct:   416 ADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYA----KMPDEPLEPGPLPVSTALPP 471

Query:   228 QLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTSTEEKR 273
              LA+ ++ +     +S    E +   DE  E   ++   + +EE+R
Sbjct:   472 GLAKSSSESSSEESSSESSSEEEEEEDEDEEEEEEESESSDSEEER 517

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

GO:0003682 "chromatin binding" evidence=ISS

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

GO:0006334 "nucleosome assembly" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

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

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

 Score = 220 (82.5 bits), Expect = 1.6e-24, Sum P(2) = 1.6e-24
 Identities = 41/86 (47%), Positives = 59/86 (68%)

Query:   120 WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK 179
             +AWPF +PVDV+ LGL DY ++I  PMD STIK ++EA+EY++ +E   DVRL+F N  K
Sbjct:   372 YAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYK 431

Query:   180 YNDERSDVHVMAKTLLAKFEEKWLQL 205
             YN    +V  MA+ L   FE ++ ++
Sbjct:   432 YNPPDHEVVAMARKLQDVFEMRFAKM 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

---

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	0.5310	0.9045	0.8834	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

Fail to connect to STRING server

---

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	377
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	5e-47
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	6e-30
smart00297	107	smart00297, BROMO, bromo domain	5e-28
cd04369	99	cd04369, Bromodomain, Bromodomain	2e-26
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	1e-23
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	6e-23
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	7e-23
pfam00439	84	pfam00439, Bromodomain, Bromodomain	2e-22
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	1e-20
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	1e-19
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	6e-19
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	2e-17
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	7e-17
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	2e-16
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	2e-14
COG5076	371	COG5076, COG5076, Transcription factor involved in	2e-14
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	2e-12
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	4e-12
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	7e-12
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	5e-11
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	1e-10
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	1e-10
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	6e-10
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	1e-09
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	2e-09
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	9e-09
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	1e-08
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	4e-08
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	9e-08
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	1e-07
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	4e-07
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	3e-06
cd05508	99	cd05508, Bromo_RACK7, Bromodomain, RACK7_like subf	6e-06
cd05501	102	cd05501, Bromo_SP100C_like, Bromodomain, SP100C_li	9e-06
cd05517	103	cd05517, Bromo_polybromo_II, Bromodomain, polybrom	2e-05
cd05494	114	cd05494, Bromodomain_1, Bromodomain; uncharacteriz	2e-04

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

 Score =  155 bits (393), Expect = 5e-47
 Identities = 52/97 (53%), Positives = 66/97 (68%)

Query: 106 RQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVRE 165
           +Q GT+LR + +HKW W F  PVDV  LGL DY+++I KPMD  T+KK++E  EY +  E
Sbjct: 3   KQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEE 62

Query: 166 ICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
              DVRL F NAM+YN   +DVH MAK LL  FE +W
Sbjct: 63  FAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETRW 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 =  110 bits (277), Expect = 6e-30
 Identities = 43/87 (49%), Positives = 60/87 (68%), Gaps = 1/87 (1%)

Query: 117 QHK-WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFK 175
           +HK +AWPF +PVD + LGL DY+++I  PMD STIKK+++ +EY + +E   DVRL+F 
Sbjct: 16  KHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFS 75

Query: 176 NAMKYNDERSDVHVMAKTLLAKFEEKW 202
           N  KYN     VH MA+ L   FE++W
Sbjct: 76  NCYKYNPPDHPVHAMARKLQDVFEDRW 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 =  105 bits (264), Expect = 5e-28
 Identities = 42/108 (38%), Positives = 60/108 (55%), Gaps = 2/108 (1%)

Query: 98  EKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA 157
            K  ++L      +L  +  H  +WPF++PV  K     DYY++I KPMD  TIKK++E 
Sbjct: 2   PKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAP--DYYDIIKKPMDLKTIKKKLEN 59

Query: 158 KEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
            +Y +V E   D  L+F NA  YN   S+V+  AK L   FE+K  +L
Sbjct: 60  GKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

Length = 107

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score =  101 bits (253), Expect = 2e-26
 Identities = 42/101 (41%), Positives = 60/101 (59%), Gaps = 4/101 (3%)

Query: 104 LIRQFGTILRNITQHKW--AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
           L ++  ++L  + + K   + PF++PVD K     DYYEVI  PMD STIKK+++  EYK
Sbjct: 1   LKKKLRSLLDALKKLKRDLSEPFLEPVDPKEA--PDYYEVIKNPMDLSTIKKKLKNGEYK 58

Query: 162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
           ++ E   DVRL+F NA  YN   S ++  AK L   FE+  
Sbjct: 59  SLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 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 = 93.9 bits (234), Expect = 1e-23
 Identities = 35/91 (38%), Positives = 54/91 (59%)

Query: 112 LRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVR 171
           L       + WPF+ PVD   L + +Y+ +I KPMD  TI K+++  +Y++ +E   DVR
Sbjct: 12  LMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVR 71

Query: 172 LVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
           L+FKN   +N E +DV++M   L   F +KW
Sbjct: 72  LIFKNCYTFNPEGTDVYMMGHQLEEVFNDKW 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|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score = 91.5 bits (228), Expect = 6e-23
 Identities = 36/99 (36%), Positives = 56/99 (56%), Gaps = 2/99 (2%)

Query: 103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKN 162
            L  Q   +L ++  HK AWPF++PVD +     DYY+VI KPMD ST+++++E   Y  
Sbjct: 1   PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAP--DYYDVIKKPMDLSTMEEKLENGYYVT 58

Query: 163 VREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
           + E   D++L+F N   YN   ++ +  A  L   F +K
Sbjct: 59  LEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKK 97

Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 101

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

 Score = 91.7 bits (228), Expect = 7e-23
 Identities = 40/96 (41%), Positives = 56/96 (58%)

Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
            +L+ + +HK+AWPF QPVD   L L DY+++I  PMD  TIKK++E   Y +  E   D
Sbjct: 12  VVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQD 71

Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
              +F N   YN    DV +MA+TL   F +K  Q+
Sbjct: 72  FNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQM 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|215921 pfam00439, Bromodomain, Bromodomain

 Score = 89.8 bits (223), Expect = 2e-22
 Identities = 37/86 (43%), Positives = 57/86 (66%), Gaps = 2/86 (2%)

Query: 108 FGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREIC 167
              IL ++ +H  A PF++PVD +     DYYEVI +PMD STI++++++ +YK++ E  
Sbjct: 1   CLEILEDLMEHPLAEPFLEPVDPEEY--PDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFL 58

Query: 168 TDVRLVFKNAMKYNDERSDVHVMAKT 193
            DV L+F NA+ YN E SD++  AK 
Sbjct: 59  KDVELIFSNAITYNGEDSDIYKDAKK 84

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

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

 Score = 86.0 bits (213), Expect = 1e-20
 Identities = 36/100 (36%), Positives = 57/100 (57%), Gaps = 1/100 (1%)

Query: 102 EELIRQFGTILRNI-TQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEY 160
           EEL +     L  +  Q   + PF QPVD K LG+ DY++++  PMD STI+++++  +Y
Sbjct: 2   EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQY 61

Query: 161 KNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEE 200
           ++  +   DV L+F NA  YN + S V+     L   FE+
Sbjct: 62  QDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101

Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 108

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

 Score = 82.8 bits (205), Expect = 1e-19
 Identities = 38/93 (40%), Positives = 60/93 (64%), Gaps = 2/93 (2%)

Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
           TIL  +  H+ AWPF++PV+ K +    Y ++I KPMDFSTI++++E+ +YK + E   D
Sbjct: 7   TILDEMEAHEDAWPFLEPVNTKLV--PGYRKIIKKPMDFSTIREKLESGQYKTLEEFAED 64

Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
           VRLVF N   +N++ S+V      +   FE++W
Sbjct: 65  VRLVFDNCETFNEDDSEVGRAGHNMRKFFEKRW 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|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 80.8 bits (200), Expect = 6e-19
 Identities = 31/88 (35%), Positives = 48/88 (54%)

Query: 112 LRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVR 171
           +R++ + K A PF+ PVD   L +  Y  +I KPMD  TI++++++  Y +V E   D  
Sbjct: 13  IRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFN 72

Query: 172 LVFKNAMKYNDERSDVHVMAKTLLAKFE 199
           L+  N + +N     V  M K L A FE
Sbjct: 73  LMVDNCLTFNGPEHPVSQMGKRLQAAFE 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|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily

 Score = 77.1 bits (190), Expect = 2e-17
 Identities = 35/92 (38%), Positives = 53/92 (57%), Gaps = 2/92 (2%)

Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
            +L  I +HK +WPF++PV    +   DYY++I KPMD  TIK+++   EYK   E  +D
Sbjct: 19  QLLVEIVKHKDSWPFLRPVSKIEV--PDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSD 76

Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
           ++LVF N   YN E + V+     L   F ++
Sbjct: 77  IQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKR 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|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily

 Score = 75.6 bits (186), Expect = 7e-17
 Identities = 33/85 (38%), Positives = 49/85 (57%), Gaps = 3/85 (3%)

Query: 123 PFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN- 181
           PF QPVD+  L   DY ++ID PMD  T+K+ +    Y +  E   DVRL+F N+  Y  
Sbjct: 25  PFRQPVDL--LKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTP 82

Query: 182 DERSDVHVMAKTLLAKFEEKWLQLL 206
           ++RS ++ M   L A FEE   +++
Sbjct: 83  NKRSRIYSMTLRLSALFEEHIKKII 107

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|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 35/89 (39%), Positives = 52/89 (58%), Gaps = 6/89 (6%)

Query: 123 PFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKE---YKNVREICTDVRLVFKNAMK 179
           PF +PV      + +YY++I  PMD S I+K+++ K    Y +  E   DVRL+FKN  K
Sbjct: 24  PFHEPV---SPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK 80

Query: 180 YNDERSDVHVMAKTLLAKFEEKWLQLLPK 208
           +N+E S+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|99943 cd05511, Bromo_TFIID, Bromodomain, TFIID-like subfamily

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 34/105 (32%), Positives = 57/105 (54%), Gaps = 9/105 (8%)

Query: 108 FGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREIC 167
              I+  +     +WPF  PV+ K +   DYY++I +PMD  TI+K++   +Y++  E  
Sbjct: 5   LDEIVNELKNLPDSWPFHTPVNKKKV--PDYYKIIKRPMDLQTIRKKISKHKYQSREEFL 62

Query: 168 TDVRLVFKNAMKYNDERS-------DVHVMAKTLLAKFEEKWLQL 205
            D+ L+  N++ YN   S       ++  +A+ LLA+ EEK  QL
Sbjct: 63  EDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELLAEREEKLTQL 107

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

 Score = 73.3 bits (180), Expect = 2e-14
 Identities = 47/175 (26%), Positives = 74/175 (42%), Gaps = 12/175 (6%)

Query: 62  GSNSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWA 121
           G  S   + LK   K+R  P I  + +      KA  K  ++L       LR+       
Sbjct: 117 GLGSLLMAHLKTSVKKRKTPKI--EDELLYADNKAIAKFKKQLF------LRDGRFLSSI 168

Query: 122 WPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN 181
           +              DYYE+I  PMD  TI+K+++   YK+  E  +D+ L+F N   YN
Sbjct: 169 FL----GLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN 224

Query: 182 DERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHA 236
              S V+V AK L   F +   ++  ++ E   +   EE E +  + +    AH 
Sbjct: 225 GPDSSVYVDAKELEKYFLKLIEEIPEEMLELSIKPGREEREERESVLITNSQAHV 279

Length = 371

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

 Score = 62.6 bits (152), Expect = 2e-12
 Identities = 32/84 (38%), Positives = 48/84 (57%), Gaps = 3/84 (3%)

Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           IL  I +++++WPF +PV       +DY +VI  PMD  T++ +     Y +V+E   D+
Sbjct: 8   ILSKILKYRFSWPFREPVTADEA--EDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDM 65

Query: 171 RLVFKNAMKYNDERSDV-HVMAKT 193
           +LVF NA KY +  S V   M KT
Sbjct: 66  KLVFSNAEKYYENGSYVLSCMRKT 89

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|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup

 Score = 62.0 bits (151), Expect = 4e-12
 Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 2/82 (2%)

Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           + R +  H++A  F++PV         Y+ V+ +PMD STIKK +E    ++  E   DV
Sbjct: 11  VYRTLASHRYASVFLKPVTEDIA--PGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDV 68

Query: 171 RLVFKNAMKYNDERSDVHVMAK 192
            L+F+NA+ YN    DV++MA 
Sbjct: 69  LLMFQNAIMYNSSDHDVYLMAV 90

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|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 61.3 bits (149), Expect = 7e-12
 Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 7/109 (6%)

Query: 102 EELIRQFGTI---LRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAK 158
           EE       +   L+  T+H  + PF+  V  +     DYY++I KPMD  T+ K+++  
Sbjct: 6   EEFYESLDKVLNELKTYTEH--STPFLTKVSKREA--PDYYDIIKKPMDLGTMLKKLKNL 61

Query: 159 EYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLP 207
           +YK+  E   D+ L++KN + YN + S         + K  E  L+L+P
Sbjct: 62  QYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHANFMKKKAEHLLKLIP 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|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V

 Score = 58.9 bits (143), Expect = 5e-11
 Identities = 23/58 (39%), Positives = 39/58 (67%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTL 194
           DYY+VI KP+D   I+ ++E  +Y+++ ++ +D  L+F NA KYN+  S ++  A TL
Sbjct: 38  DYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTL 95

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|99944 cd05512, Bromo_brd1_like, Bromodomain; brd1_like subfamily

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 21/58 (36%), Positives = 37/58 (63%), Gaps = 2/58 (3%)

Query: 124 FMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN 181
           F +PVD+  +   DY + I +PMDFST++K++E++ Y+ + +   D  L+  N + YN
Sbjct: 22  FSEPVDLSEV--PDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 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 = 57.4 bits (139), Expect = 1e-10
 Identities = 34/101 (33%), Positives = 56/101 (55%), Gaps = 15/101 (14%)

Query: 98  EKRMEELIRQFGTILRNITQHKWAWP---FMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQ 154
           +K +E+LIRQ   + R      +A+P   F+ P          Y  +I  PMDFST+K++
Sbjct: 3   QKALEQLIRQ---LQRKDPHGFFAFPVTDFIAP---------GYSSIIKHPMDFSTMKEK 50

Query: 155 MEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLL 195
           ++  +Y+++ E   D +L+ +NAMKYN   +  +  AK LL
Sbjct: 51  IKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKLL 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|99951 cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III

 Score = 55.4 bits (134), Expect = 6e-10
 Identities = 20/65 (30%), Positives = 37/65 (56%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DYY+ I  P+    I+ +++  EY+ + E+  D+ L+F+NA +YN   S ++  A+ L  
Sbjct: 38  DYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQK 97

Query: 197 KFEEK 201
             + K
Sbjct: 98  LMQAK 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 = 54.7 bits (132), Expect = 1e-09
 Identities = 30/104 (28%), Positives = 57/104 (54%), Gaps = 8/104 (7%)

Query: 103 ELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME 156
           EL ++   I+  + ++K       A  F+Q    K L   +YYE+I KP+DF  IK+++ 
Sbjct: 1   ELTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKEL--PEYYELIRKPVDFKKIKERIR 58

Query: 157 AKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEE 200
             +Y+++ ++  DV L+ +NA  +N E S ++  +  L + F+ 
Sbjct: 59  NHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKS 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|99949 cd05518, Bromo_polybromo_IV, Bromodomain, polybromo repeat IV

 Score = 54.0 bits (130), Expect = 2e-09
 Identities = 24/65 (36%), Positives = 38/65 (58%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DYY++I +P+D  TI+  +   +Y    E+  D +L+F+NA  YN+E S V+  A  L  
Sbjct: 38  DYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEK 97

Query: 197 KFEEK 201
             +EK
Sbjct: 98  VLKEK 102

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Length = 103

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

 Score = 52.3 bits (126), Expect = 9e-09
 Identities = 24/65 (36%), Positives = 38/65 (58%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DYY +I +P+    IK+++E + YK++ E   D  L+F NA  YN E S V+  A  +  
Sbjct: 38  DYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEK 97

Query: 197 KFEEK 201
            F++K
Sbjct: 98  AFKKK 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|99955 cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-family

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 23/58 (39%), Positives = 31/58 (53%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTL 194
           DYYE I  P+D STI+KQ+    YK      +D+  VF+NA KY   +S +      L
Sbjct: 40  DYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRL 97

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|99958 cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like subfamily

 Score = 51.2 bits (123), Expect = 4e-08
 Identities = 31/115 (26%), Positives = 55/115 (47%), Gaps = 3/115 (2%)

Query: 81  PSIRKQQQEASRREKAAEKRM-EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYY 139
            S   +  +    +        E LI     +L ++ Q + A  F  PVD++     DY+
Sbjct: 5   LSSEWELFDPGWEQPHIRDEERERLISGLDKLLLSL-QLEIAEYFEYPVDLRAW-YPDYW 62

Query: 140 EVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTL 194
             +  PMD  TI+ ++E + Y+++  +  DVRL+  NA  +N+  S++   AK L
Sbjct: 63  NRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRL 117

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

 Score = 49.7 bits (119), Expect = 9e-08
 Identities = 22/62 (35%), Positives = 39/62 (62%), Gaps = 2/62 (3%)

Query: 123 PFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND 182
            F +PVD + +   DYYE+I +PMD  TI ++++  +Y   ++   D+ L+  NA++YN 
Sbjct: 23  AFTKPVDEEEV--PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80

Query: 183 ER 184
           +R
Sbjct: 81  DR 82

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTL 194
           DYY++I  P+  +T+KK++    Y N +E   D+  +  NA  YN + S ++  A  L
Sbjct: 39  DYYKIIKNPLSLNTVKKRL--PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALIL 94

Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 106

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

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 19/62 (30%), Positives = 35/62 (56%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           +YY+ I  P+    IKK+++ ++YK+  +   D+ L+F+NA  YN+  S  +  A  L  
Sbjct: 39  EYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEK 98

Query: 197 KF 198
           + 
Sbjct: 99  EA 100

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|99954 cd05524, Bromo_polybromo_I, Bromodomain, polybromo repeat I

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 20/64 (31%), Positives = 33/64 (51%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           +YYEV+  P+D   I+++++ +EY +V ++  D  L+  NA  Y    S  H  A  L  
Sbjct: 40  EYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWE 99

Query: 197 KFEE 200
            F  
Sbjct: 100 LFLS 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|99940 cd05508, Bromo_RACK7, Bromodomain, RACK7_like subfamily

 Score = 44.3 bits (105), Expect = 6e-06
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 123 PFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND 182
           PF++PVD++     DY + + KPMD ST++K +  K Y +      D + +  NA+ YN 
Sbjct: 22  PFLKPVDLEQF--PDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNG 79

Query: 183 ERSDVHVMAKTLL 195
               +   AK ++
Sbjct: 80  GDHKLTQAAKAIV 92

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

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

 Score = 44.0 bits (104), Expect = 9e-06
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DY + I +PM  + +K+++  + Y  V     D+RL+F N   +  +  D   +  TL  
Sbjct: 32  DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKD-DDFGQVGITLEK 90

Query: 197 KFEE 200
           KFE+
Sbjct: 91  KFEK 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|99948 cd05517, Bromo_polybromo_II, Bromodomain, polybromo repeat II

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 22/65 (33%), Positives = 39/65 (60%)

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DYY VI +P+D  TI +++++  YK++ ++  D+ L+ KNA  +N+  S V+  A  +  
Sbjct: 38  DYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKK 97

Query: 197 KFEEK 201
            F  K
Sbjct: 98  IFTAK 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|99926 cd05494, Bromodomain_1, Bromodomain; uncharacterized subfamily

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 16/42 (38%), Positives = 25/42 (59%)

Query: 112 LRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKK 153
           L+   +++ AWPF++PV+    G  DY +VI +PM F T   
Sbjct: 12  LKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVN 53

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	377
KOG1474	640	consensus Transcription initiation factor TFIID, s	100.0
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.96
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.96
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.96
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.95
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.95
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.95
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.95
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.95
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.94
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.94
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.94
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	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
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.94
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.94
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.93
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
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.92
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.92
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.92
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.91
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.91
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.91
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.91
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.91
smart00297	107	BROMO bromo domain.	99.91
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.9
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.88
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.88
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.88
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.87
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.87
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.78
KOG1245	1404	consensus Chromatin remodeling complex WSTF-ISWI,	99.75
COG5076	371	Transcription factor involved in chromatin remodel	99.72
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	99.66
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.4
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	99.13
KOG0955	1051	consensus PHD finger protein BR140/LIN-49 [General	99.08
KOG0008	1563	consensus Transcription initiation factor TFIID, s	99.02
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	98.93
KOG1827	629	consensus Chromatin remodeling complex RSC, subuni	98.84
KOG0008	1563	consensus Transcription initiation factor TFIID, s	98.83
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	98.82
KOG1474	640	consensus Transcription initiation factor TFIID, s	98.63
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	98.16
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	98.01
COG5076	371	Transcription factor involved in chromatin remodel	97.17
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	96.95
KOG0644	1113	consensus Uncharacterized conserved protein, conta	90.74
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	86.84

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

Probab=100.00  E-value=2.6e-34  Score=304.09  Aligned_cols=234  Identities=35%  Similarity=0.540  Sum_probs=171.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhh
Q 017092           97 AEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKN  176 (377)
Q Consensus        97 ~~~~~~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  176 (377)
                      ..+.+.+++++|..||..|+.|+++|||..|||+..||+||||+||++||||+||+.||.+|.|.++.+|++||||||.|
T Consensus       216 ~~~~~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~Y~~~~eF~~DVRL~F~N  295 (640)
T KOG1474|consen  216 KSKLTVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGEYKSAEEFAADVRLTFDN  295 (640)
T ss_pred             cccccHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccccCCHHHHHHHHHHHHHH
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCCHHHHHHHHHHHHHHHHHHhhCCCCchHHHhhhHHH----------------------HHH-HHh--HHHhH
Q 017092          177 AMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEE----------------------AEA-QLD--MQLAQ  231 (377)
Q Consensus       177 a~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p~~~~~e~~~~~~e----------------------~~~-~~~--~~~~~  231 (377)
                      |++||++|++||.||..|+++|+.+|..+++.+.........+.                      ... ...  .....
T Consensus       296 cm~YNp~g~dV~~Ma~~L~~~Fe~rw~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  375 (640)
T KOG1474|consen  296 CMTYNPEGSDVYAMAKKLQEVFEERWASMPLEIEESESAVKEEAGMASSDQIPSNSVEGPRSSSFESRESASEPSSELMS  375 (640)
T ss_pred             HHhcCCCCCHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccccccCcccccchhcccccCccccccc
Confidence            99999999999999999999999999997654432211000000                      000 000  00000


Q ss_pred             HHHHHHHhhhhhhhhhhhhhhh-----------------------HH--------H----HHHHhhhccCCCHHHHHHHH
Q 017092          232 DAAHAKMARDTSNELYEVDVHL-----------------------DE--------L----REMLVQKCRKTSTEEKRKLG  276 (377)
Q Consensus       232 ~~~~~~~~~~~~~e~~~~~~~l-----------------------~~--------l----~~~~~~~~r~mt~eEK~~L~  276 (377)
                      ..........+...+..+..++                       ..        .    ........+.||..++..|.
T Consensus       376 ~~e~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~t~~~~~~l~  455 (640)
T KOG1474|consen  376 EEERKKLLAELKLLLKDVPPQLIALLQRPVSKPPRKIEEELESDKRPLVTGKLIKEKNKKEKAANENKRDMTAPEKAKLK  455 (640)
T ss_pred             HHhhhhhHhhhhcchhhhhHHHHhhhhccccCccccccccccccccccchhhhhhhhhccccccccccccccccccccch
Confidence            0000000000000000000000                       00        0    00111235789999999999


Q ss_pred             HHhcCC-ChhhHHHHHHHH--HhhCCCCCCCCCeeEEeCcCCC-------------HHHHHHHHHHHHHH
Q 017092          277 AALTRL-SPEDLGKALEIV--AQSNTGFQATAEEVELDMDAQS-------------ESTLWRLKFFVKDA  330 (377)
Q Consensus       277 ~~i~~L-~~e~l~~vi~II--~~~~P~~~~~~~eiEiDid~L~-------------~~TL~~L~~yV~~~  330 (377)
                      ..+..| ++..+..+++|+  ....+.+...++++++|++.++             ..|+|++..++...
T Consensus       456 ~~~~~~~~p~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vd~~~~~~~~~~~~~~e~~~~~~~~~~~~  525 (640)
T KOG1474|consen  456 ELLQNLLPPNKLESIVEILKPEKRQLDLSQNDDEIELDLDSVDGSQSREPSSNPLEIETIRETLKLSTER  525 (640)
T ss_pred             hhccCCCCCccccCcccccchhhhcccccccccchhhcccccccccccCCCcccchhhhhhccccchhhH
Confidence            999994 999999999999  5577778888999999999999             88888888776554

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.96  E-value=4.2e-29  Score=211.26  Aligned_cols=106  Identities=31%  Similarity=0.499  Sum_probs=100.8

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      .++.++|..|+..|++|+.++||..||++..  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||
T Consensus         4 ~~w~~~c~~il~~l~~~~~s~~F~~PVd~~~--~pdY~~iIk~PmDL~tIk~kL~~~~Y~~~~ef~~D~~lif~Na~~yN   81 (119)
T cd05496           4 SDWKKQCKELVNLMWDCEDSEPFRQPVDLLK--YPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT   81 (119)
T ss_pred             HHHHHHHHHHHHHHHhCCccccccCCCChhh--cCcHHHHhCCcccHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            3688899999999999999999999999987  99999999999999999999999999999999999999999999999


Q ss_pred             CC-CCHHHHHHHHHHHHHHHHHHhhCCCC
Q 017092          182 DE-RSDVHVMAKTLLAKFEEKWLQLLPKV  209 (377)
Q Consensus       182 ~~-~s~v~~~A~~L~~~fe~~~~~~~p~~  209 (377)
                      ++ +|.||.+|..|+..|++++..+.+.+
T Consensus        82 ~~~~s~i~~~a~~L~~~F~~~~~~l~~~~  110 (119)
T cd05496          82 PNKRSRIYSMTLRLSALFEEHIKKIISDW  110 (119)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            85 99999999999999999999986544

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

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.96  E-value=9.3e-29  Score=206.11  Aligned_cols=105  Identities=33%  Similarity=0.576  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHHHHHcC-CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhc
Q 017092          102 EELIRQFGTILRNITQH-KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~-~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      .+|.+.|..+++.|+++ +.||+|..||++...++||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.|
T Consensus         2 ~~l~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~y   81 (108)
T cd05495           2 EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLY   81 (108)
T ss_pred             HHHHHHHHHHHHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            37889999999999999 99999999999987779999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          181 NDERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       181 N~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      |+++|.++.+|..|++.|++.+..++
T Consensus        82 N~~~s~i~~~a~~l~~~F~~~~~~~~  107 (108)
T cd05495          82 NRKTSRVYKYCTKLAEVFEQEIDPVM  107 (108)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999988764

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

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.96  E-value=1.1e-28  Score=205.38  Aligned_cols=101  Identities=41%  Similarity=0.635  Sum_probs=95.3

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCC
Q 017092          104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDE  183 (377)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~  183 (377)
                      +.-.+..|+..|++|+.|+||..|||+..+++||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.||++
T Consensus         6 ~~~~~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~   85 (107)
T cd05497           6 LQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKP   85 (107)
T ss_pred             HHHHHHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            33355788999999999999999999987779999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHh
Q 017092          184 RSDVHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       184 ~s~v~~~A~~L~~~fe~~~~~  204 (377)
                      +|.++.+|..|++.|++++.+
T Consensus        86 ~s~i~~~A~~l~~~f~~~l~~  106 (107)
T cd05497          86 GDDVVLMAQTLEKLFLQKLAQ  106 (107)
T ss_pred             CCHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999865

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

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

Probab=99.95  E-value=1.9e-28  Score=200.33  Aligned_cols=95  Identities=31%  Similarity=0.547  Sum_probs=91.9

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCC
Q 017092          105 IRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDER  184 (377)
Q Consensus       105 ~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~  184 (377)
                      ++.|..|++.|++++.++||..||++..  +||||++|++||||+||++||++|.|.|+.+|.+||+|||.||++||++|
T Consensus         2 ~~~c~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~   79 (97)
T cd05505           2 LQKCEEILSKILKYRFSWPFREPVTADE--AEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENG   79 (97)
T ss_pred             HHHHHHHHHHHHhCCCcccccCCCChhh--cccHHHHcCCcCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            4689999999999999999999999877  99999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHH
Q 017092          185 SDVHVMAKTLLAKFEEK  201 (377)
Q Consensus       185 s~v~~~A~~L~~~fe~~  201 (377)
                      |.|+.+|..|++.|.++
T Consensus        80 s~i~~~a~~le~~f~~~   96 (97)
T cd05505          80 SYVLSCMRKTEQCCVNL   96 (97)
T ss_pred             CHHHHHHHHHHHHHHHh
Confidence            99999999999999875

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.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.95  E-value=8.6e-28  Score=196.64  Aligned_cols=96  Identities=40%  Similarity=0.768  Sum_probs=93.5

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCC
Q 017092          105 IRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDER  184 (377)
Q Consensus       105 ~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~  184 (377)
                      +..|..|+..|++++.+++|..||++..  +|+||++|++||||+||++||++|.|.|+.+|.+||+|||.||+.||+++
T Consensus         2 ~~~c~~il~~l~~~~~~~~F~~pv~~~~--~p~Y~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~   79 (97)
T cd05503           2 LALCETILDEMEAHEDAWPFLEPVNTKL--VPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDD   79 (97)
T ss_pred             HHHHHHHHHHHHcCCCchhhcCCCCccc--cCCHHHHhCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            4689999999999999999999999987  99999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHH
Q 017092          185 SDVHVMAKTLLAKFEEKW  202 (377)
Q Consensus       185 s~v~~~A~~L~~~fe~~~  202 (377)
                      |.++.+|..|++.|+.+|
T Consensus        80 s~i~~~a~~l~~~f~~~~   97 (97)
T cd05503          80 SEVGRAGHNMRKFFEKRW   97 (97)
T ss_pred             CHHHHHHHHHHHHHHHhC
Confidence            999999999999999987

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.95  E-value=1e-27  Score=196.77  Aligned_cols=99  Identities=53%  Similarity=0.994  Sum_probs=95.7

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCC
Q 017092          104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDE  183 (377)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~  183 (377)
                      +++.|..||+.|++++.+++|..||++...++|+||++|++||||+||++||++|.|.|+.+|.+||++||.||+.||++
T Consensus         1 ~~~~c~~il~~l~~~~~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yn~~   80 (99)
T cd05506           1 VMKQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPP   80 (99)
T ss_pred             CHHHHHHHHHHHHhCCCCccccCCCCccccCCCCHHHHHcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            47899999999999999999999999886679999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHH
Q 017092          184 RSDVHVMAKTLLAKFEEKW  202 (377)
Q Consensus       184 ~s~v~~~A~~L~~~fe~~~  202 (377)
                      +|.++.+|..|.+.|+++|
T Consensus        81 ~s~i~~~a~~l~~~fe~~w   99 (99)
T cd05506          81 GNDVHTMAKELLKIFETRW   99 (99)
T ss_pred             CCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999987

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.95  E-value=1.2e-27  Score=201.61  Aligned_cols=103  Identities=35%  Similarity=0.609  Sum_probs=98.8

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhc
Q 017092          101 MEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      +...+..|..|+..|+.++.+++|..||+...  +||||++|++||||+||++||.+|.|.|+.+|.+||+|||.||++|
T Consensus        10 ~~~~~~~c~~il~~l~~~~~s~~F~~pvd~~~--~pdY~~vI~~PmDL~tI~~kL~~~~Y~s~~~f~~Dv~LI~~Na~~y   87 (115)
T cd05504          10 GPLNLSALEQLLVEIVKHKDSWPFLRPVSKIE--VPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLY   87 (115)
T ss_pred             CHHHHHHHHHHHHHHHhCCCchhhcCCCCccc--cccHHHHhcCcccHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHH
Confidence            34677899999999999999999999999877  9999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 017092          181 NDERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       181 N~~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      |+++|.++.+|..|+++|+.++.++
T Consensus        88 N~~~s~i~~~A~~l~~~f~~~~~~~  112 (115)
T cd05504          88 NPEHTSVYKAGTRLQRFFIKRCRKL  112 (115)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999876

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=99.95  E-value=2.6e-27  Score=196.17  Aligned_cols=101  Identities=32%  Similarity=0.475  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .+.+.|..|+..|++|+.++||..||+...  +|+||++|++||||+||++||++|.|.++.+|.+||+|||.||..||+
T Consensus         3 ~~~~~~~~il~~l~~~~~a~~F~~pV~~~~--~p~Y~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~   80 (104)
T cd05507           3 AWKKAILLVYRTLASHRYASVFLKPVTEDI--APGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNS   80 (104)
T ss_pred             HHHHHHHHHHHHHHcCCCCHhhcCCCCccc--cCCHHHHhCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            467799999999999999999999999876  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhh
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      ++|.++.+|..|++.|...+..+
T Consensus        81 ~~s~v~~~A~~l~~~~~~~~~~~  103 (104)
T cd05507          81 SDHDVYLMAVEMQREVMSQIQQL  103 (104)
T ss_pred             CCCHHHHHHHHHHHHHHHHhhcc
Confidence            99999999999999998887643

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.94  E-value=6e-27  Score=195.63  Aligned_cols=103  Identities=36%  Similarity=0.634  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhc---CCCCCHHHHHHHHHhhhhhhhh
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA---KEYKNVREICTDVRLVFKNAMK  179 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~---~~Y~s~~ef~~Dv~Lif~Na~~  179 (377)
                      ..++.|..|+..|++|+.++||..||++ .  +|+||++|++||||+||++||++   |.|.++.+|.+||+|||+||+.
T Consensus         4 ~~~~~c~~il~~l~~~~~s~~F~~pv~~-~--~p~Y~~iI~~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~~   80 (109)
T cd05502           4 IDQRKCERLLLELYCHELSLPFHEPVSP-S--VPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYK   80 (109)
T ss_pred             HHHHHHHHHHHHHHhCCCChhhcCCCCC-C--CCCHHHHCCCCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            4577999999999999999999999999 4  99999999999999999999999   5999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhCCC
Q 017092          180 YNDERSDVHVMAKTLLAKFEEKWLQLLPK  208 (377)
Q Consensus       180 YN~~~s~v~~~A~~L~~~fe~~~~~~~p~  208 (377)
                      ||+++|.++.+|..|++.|+++|..++|.
T Consensus        81 yN~~~s~i~~~a~~l~~~f~~~~~~~~p~  109 (109)
T cd05502          81 FNEEDSEVAQAGKELELFFEEQLKEILPD  109 (109)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHCcC
Confidence            99999999999999999999999999873

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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.94  E-value=4e-27  Score=193.15  Aligned_cols=97  Identities=28%  Similarity=0.499  Sum_probs=91.2

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      .++...|..++..|. |+.||||..||++..  +||||.+|++||||+||++||++|.|.++++|.+||+|||.||+.||
T Consensus         2 ~~l~~~L~~~~~~~~-~~~s~~F~~PV~~~~--~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~Na~~YN   78 (99)
T cd05508           2 DQLSKLLKFALERMK-QPGAEPFLKPVDLEQ--FPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN   78 (99)
T ss_pred             hHHHHHHHHHHHHHh-CcCcchhcCCCChhh--CCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            356667888999998 999999999999977  99999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHH
Q 017092          182 DERSDVHVMAKTLLAKFEEK  201 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~  201 (377)
                      +++|.++.+|..|.+.|+..
T Consensus        79 ~~~s~i~~~A~~l~~~~~~e   98 (99)
T cd05508          79 GGDHKLTQAAKAIVKICEQE   98 (99)
T ss_pred             CCCCHHHHHHHHHHHHHHhh
Confidence            99999999999999988753

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.94  E-value=5.4e-27  Score=193.52  Aligned_cols=98  Identities=44%  Similarity=0.876  Sum_probs=94.7

Q ss_pred             HHHHHHHHHHHHcC---CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          105 IRQFGTILRNITQH---KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       105 ~~~~~~il~~l~~~---~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      ++.|..|+..|+++   +.+++|..||++...++|+||++|++||||+||++||.+|.|.|+.+|..||+|||.||+.||
T Consensus         2 ~~~c~~il~~l~~~~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~yn   81 (102)
T cd05498           2 LKFCSGILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYN   81 (102)
T ss_pred             hhHHHHHHHHHHhCCCccccCcccCcCCccccCCCcHHHHccCCCcHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            56899999999999   899999999999877799999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q 017092          182 DERSDVHVMAKTLLAKFEEKW  202 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~  202 (377)
                      +++|.++.+|..|++.|+++|
T Consensus        82 ~~~s~i~~~a~~l~~~fe~~~  102 (102)
T cd05498          82 PPDHPVHAMARKLQDVFEDRW  102 (102)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999987

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.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.94  E-value=9.8e-27  Score=194.95  Aligned_cols=102  Identities=28%  Similarity=0.517  Sum_probs=96.8

Q ss_pred             HHHHHHHHHHHHHHHcC-CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhc
Q 017092          102 EELIRQFGTILRNITQH-KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~-~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      .++...|..|+..|+++ +.|++|..||++..  +||||++|++||||+||++||.+|.|.|+.+|.+||+|||.||+.|
T Consensus         6 ~~~~~~~~~il~~l~~~~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~Li~~N~~~y   83 (112)
T cd05510           6 EEFYESLDKVLNELKTYTEHSTPFLTKVSKRE--APDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLY   83 (112)
T ss_pred             HHHHHHHHHHHHHHHhcCccccchhcCCChhh--cCCHHHHhcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            37888999999999999 89999999999987  9999999999999999999999999999999999999999999999


Q ss_pred             CCCCC-HHHHHHHHHHHHHHHHHHhh
Q 017092          181 NDERS-DVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       181 N~~~s-~v~~~A~~L~~~fe~~~~~~  205 (377)
                      |+++| .++.+|..|++.|+..+..+
T Consensus        84 N~~~s~~~~~~A~~l~~~~~~~~~~~  109 (112)
T cd05510          84 NSDPSHPLRRHANFMKKKAEHLLKLI  109 (112)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence            99766 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.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.94  E-value=9.8e-27  Score=192.42  Aligned_cols=99  Identities=31%  Similarity=0.533  Sum_probs=95.6

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .+.+.|..|++.|++++.+++|..||++...++|+||++|++||||+||++||.+|.|.++.+|..||+|||.||+.||+
T Consensus         4 ~~~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~   83 (103)
T cd05500           4 HQHKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNG   83 (103)
T ss_pred             HHHHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            56789999999999999999999999988777999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHH
Q 017092          183 ERSDVHVMAKTLLAKFEEK  201 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~  201 (377)
                      ++|.++.+|..|++.|++.
T Consensus        84 ~~s~~~~~A~~l~~~fe~~  102 (103)
T cd05500          84 PEHPVSQMGKRLQAAFEKH  102 (103)
T ss_pred             CCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999875

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

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.94  E-value=7.6e-27  Score=192.70  Aligned_cols=98  Identities=36%  Similarity=0.790  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHcC---CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          105 IRQFGTILRNITQH---KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       105 ~~~~~~il~~l~~~---~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      ++.|..||..|+++   +.++||+.||++...++||||++|++||||+||++||++|.|.|+.+|.+||+|||.||+.||
T Consensus         2 ~~~c~~Il~~l~~~~~~~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I~~kl~~~~Y~s~~ef~~D~~li~~N~~~yn   81 (102)
T cd05499           2 LKFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFN   81 (102)
T ss_pred             hHHHHHHHHHHHcccCCcccchhcCCCCccccCCCCHHHHhcCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            46899999999994   579999999999855699999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q 017092          182 DERSDVHVMAKTLLAKFEEKW  202 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~  202 (377)
                      +++|.++.+|..|++.|+.+|
T Consensus        82 ~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          82 PEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999886

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.

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.94  E-value=1.7e-26  Score=189.66  Aligned_cols=98  Identities=21%  Similarity=0.365  Sum_probs=91.5

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCC
Q 017092          105 IRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDER  184 (377)
Q Consensus       105 ~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~  184 (377)
                      ++.|..|+..|++++.|++|..++  ..  +||||++|++||||+||++||.+|.|.|+.+|.+||+|||.||++||+++
T Consensus         4 l~~ce~il~~l~~~~~s~~f~~~p--~~--~pdY~~iIk~PMDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~N~~~yN~~~   79 (102)
T cd05501           4 LLKCEFLLLKVYCMSKSGFFISKP--YY--IRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD   79 (102)
T ss_pred             HHHHHHHHHHHHhCcccccccCCC--CC--CCchHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence            456999999999999999997743  33  99999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhhCC
Q 017092          185 SDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       185 s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                       .++.+|..|++.|+++|..++.
T Consensus        80 -~~~~~a~~L~~~Fek~~~~~f~  101 (102)
T cd05501          80 -DFGQVGITLEKKFEKNFKEVFA  101 (102)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHhc
Confidence             9999999999999999998763

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.

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.94  E-value=1.3e-26  Score=190.93  Aligned_cols=99  Identities=36%  Similarity=0.649  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCC
Q 017092          104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDE  183 (377)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~  183 (377)
                      ++.+|..|++.|++|+.+++|..||++..  +|+||++|++||||+||++||.+|.|.|+.+|..||+|||.||+.||++
T Consensus         2 ~~~~~~~il~~l~~~~~a~~F~~pv~~~~--~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~   79 (101)
T cd05509           2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEE--APDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGP   79 (101)
T ss_pred             hHHHHHHHHHHHHhCCCchhhcCCCChhh--cCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            56789999999999999999999999988  9999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHh
Q 017092          184 RSDVHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       184 ~s~v~~~A~~L~~~fe~~~~~  204 (377)
                      +|.++.+|..|+..|++.+.+
T Consensus        80 ~s~~~~~a~~l~~~f~~~~~~  100 (101)
T cd05509          80 DTEYYKCANKLEKFFWKKLKE  100 (101)
T ss_pred             CCHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999998875

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.

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

Probab=99.93  E-value=2.3e-26  Score=191.44  Aligned_cols=100  Identities=30%  Similarity=0.448  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHHHHHcCCC------CCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhh
Q 017092          103 ELIRQFGTILRNITQHKW------AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKN  176 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~------a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  176 (377)
                      +|.++|..|++.|.++..      ++||..||+...  +||||++|++||||+||++||.+|.|.++.+|..||.|||.|
T Consensus         1 ~l~~~~~~il~~v~~~~d~~g~~~s~~F~~~p~~~~--~pdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~N   78 (107)
T cd05516           1 ELTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKE--LPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQN   78 (107)
T ss_pred             CHHHHHHHHHHHHHhhhCcCCCEeeHHhhcCCCccc--CCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHH
Confidence            367789999999998865      899999999887  999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCCHHHHHHHHHHHHHHHHHHh
Q 017092          177 AMKYNDERSDVHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       177 a~~YN~~~s~v~~~A~~L~~~fe~~~~~  204 (377)
                      |+.||++||.+|.+|..|++.|++.+.+
T Consensus        79 a~~yN~~~s~i~~~a~~l~~~f~~~~~~  106 (107)
T cd05516          79 AQTFNLEGSLIYEDSIVLQSVFKSARQK  106 (107)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999998865

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.

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

Probab=99.93  E-value=4.4e-26  Score=191.06  Aligned_cols=104  Identities=27%  Similarity=0.467  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      ++...|..|+..|++++.+++|..||++..  +||||++|++||||+||++||++|.|.|+.+|.+||+|||.||+.||+
T Consensus         3 ~lr~~L~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~   80 (112)
T cd05528           3 ELRLFLRDVLKRLASDKRFNAFTKPVDEEE--VPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP   80 (112)
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCCCCccc--cCcHHHHHcCCCCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHCC
Confidence            566688999999999999999999999987  999999999999999999999999999999999999999999999999


Q ss_pred             C----CCHHHHHHHHHHHHHHHHHHhhCCC
Q 017092          183 E----RSDVHVMAKTLLAKFEEKWLQLLPK  208 (377)
Q Consensus       183 ~----~s~v~~~A~~L~~~fe~~~~~~~p~  208 (377)
                      +    ||.++.+|..|++.|..++...+|.
T Consensus        81 ~~s~~~s~i~~~A~~L~~~~~~~~~~~~~~  110 (112)
T cd05528          81 DRDPADKLIRSRACELRDEVHAMIEAELDP  110 (112)
T ss_pred             CCCccccHHHHHHHHHHHHHHHHHHhcCCC
Confidence            9    4799999999999999999988774

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

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.93  E-value=7.1e-26  Score=185.42  Aligned_cols=92  Identities=30%  Similarity=0.464  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCC
Q 017092          104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDE  183 (377)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~  183 (377)
                      +...|..|++.|+.++.+++|..||+...  +||||++|++||||+||++||+++.|.|+.+|.+||+|||.||++||++
T Consensus         2 l~~~l~~il~~l~~~~~~~~F~~PV~~~~--~pdY~~vIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~   79 (98)
T cd05513           2 LQKALEQLIRQLQRKDPHGFFAFPVTDFI--APGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKP   79 (98)
T ss_pred             HHHHHHHHHHHHHcCCccccccCcCCccc--cccHHHHHcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            45688999999999999999999999877  9999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 017092          184 RSDVHVMAKTLLAK  197 (377)
Q Consensus       184 ~s~v~~~A~~L~~~  197 (377)
                      +|.+|.+|..|...
T Consensus        80 ~s~~~~~A~~L~~~   93 (98)
T cd05513          80 DTIYYKAAKKLLHS   93 (98)
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999999998654

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=1.5e-25  Score=188.02  Aligned_cols=99  Identities=30%  Similarity=0.539  Sum_probs=95.1

Q ss_pred             HHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCH
Q 017092          107 QFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSD  186 (377)
Q Consensus       107 ~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~  186 (377)
                      .+..|+.+|++++.+++|..||++..  +|+||++|++||||+||++||.+|.|.++.+|.+||+|||.||+.||+++|.
T Consensus         4 ~l~~ii~~l~~~~~s~~F~~pv~~~~--~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~   81 (112)
T cd05511           4 ILDEIVNELKNLPDSWPFHTPVNKKK--VPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSV   81 (112)
T ss_pred             HHHHHHHHHHhCCCchhhcCCCChhh--cccHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            46789999999999999999999987  9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhCC
Q 017092          187 VHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       187 v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      ++.+|..|...|+..+..+..
T Consensus        82 i~~~A~~l~~~~~~~~~~~~~  102 (112)
T cd05511          82 YTKKAKEMLELAEELLAEREE  102 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHhHH
Confidence            999999999999999988743

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.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.92  E-value=1.9e-25  Score=182.98  Aligned_cols=91  Identities=27%  Similarity=0.484  Sum_probs=86.9

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCC
Q 017092          105 IRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDER  184 (377)
Q Consensus       105 ~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~  184 (377)
                      ...|..++++|+.++.+++|..||+...  +||||++|++||||+||++||.+|.|.|+++|..||+|||.||+.||+++
T Consensus         3 ~~~l~~il~~l~~~~~~~~F~~pVd~~~--~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~   80 (98)
T cd05512           3 EVLLRKTLDQLQEKDTAEIFSEPVDLSE--VPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD   80 (98)
T ss_pred             HHHHHHHHHHHHhCCCchhhcCCCCccc--cCCHHHHhcCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            3468899999999999999999999987  99999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHH
Q 017092          185 SDVHVMAKTLLAK  197 (377)
Q Consensus       185 s~v~~~A~~L~~~  197 (377)
                      |.+|.+|..|++.
T Consensus        81 s~~~~~A~~l~~~   93 (98)
T cd05512          81 TIFYRAAVRLRDQ   93 (98)
T ss_pred             CHHHHHHHHHHHh
Confidence            9999999998764

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=99.92  E-value=3e-25  Score=183.55  Aligned_cols=96  Identities=29%  Similarity=0.450  Sum_probs=89.8

Q ss_pred             HHHHHHHHHHHH------cCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhh
Q 017092          105 IRQFGTILRNIT------QHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAM  178 (377)
Q Consensus       105 ~~~~~~il~~l~------~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  178 (377)
                      .+.|..|++.|+      .++.+++|..||+...  +|+||++|++||||+||++||++|.|.|+.+|..||+|||.||+
T Consensus         2 ~~~~~~i~~~v~~~~~~~~~~~~~~F~~~p~~~~--~pdYy~iIk~Pmdl~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~   79 (103)
T cd05519           2 KAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKL--YPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANAR   79 (103)
T ss_pred             HHHHHHHHHHHHHhcCcCCCchhHHhcCCCCCCC--CcCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHH
Confidence            467888888888      4457999999999888  99999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHHHHHHHHH
Q 017092          179 KYNDERSDVHVMAKTLLAKFEEKW  202 (377)
Q Consensus       179 ~YN~~~s~v~~~A~~L~~~fe~~~  202 (377)
                      .||+++|.++.+|..|++.|+.++
T Consensus        80 ~yn~~~s~i~~~A~~l~~~f~~~~  103 (103)
T cd05519          80 TYNQEGSIVYEDAVEMEKAFKKKY  103 (103)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999998764

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

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.92  E-value=8.6e-25  Score=183.65  Aligned_cols=102  Identities=24%  Similarity=0.381  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHHHHcC------CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhh
Q 017092          104 LIRQFGTILRNITQH------KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNA  177 (377)
Q Consensus       104 l~~~~~~il~~l~~~------~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  177 (377)
                      ..+.|..|++.|+++      +.+.+|..+|+...  +||||++|++||||+||++||.++.|.|+.+|.+||+|||.||
T Consensus         3 ~~~~c~~il~~l~~~~~~~g~~l~~~F~~~p~~~~--~PdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na   80 (113)
T cd05524           3 PIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRN--EPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA   80 (113)
T ss_pred             HHHHHHHHHHHHHhhcccCCCchhHHHhcCCCccc--CCCHHHHhCCccCHHHHHHHhCcCCCCCHHHHHHHHHHHHHHH
Confidence            467899999999964      45678999998877  9999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          178 MKYNDERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       178 ~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      +.||+++|.+|.+|..|++.|++.+.++.+
T Consensus        81 ~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~  110 (113)
T cd05524          81 KAYYKPDSPEHKDACKLWELFLSARNEVLS  110 (113)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999999887753

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

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.91  E-value=1e-24  Score=180.94  Aligned_cols=97  Identities=27%  Similarity=0.460  Sum_probs=87.9

Q ss_pred             HHHHHHHHHHHHcC------CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhh
Q 017092          105 IRQFGTILRNITQH------KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAM  178 (377)
Q Consensus       105 ~~~~~~il~~l~~~------~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  178 (377)
                      ++.|..|+..|..+      +.+++|..||+...  +||||++|++||||+||++||.++.|.++.+|.+||.|||.||+
T Consensus         2 ~~~~~~~~~~i~~~~d~~~~~~a~~F~~~p~~~~--~pdYy~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~   79 (105)
T cd05515           2 QQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSE--YPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNAC   79 (105)
T ss_pred             hHHHHHHHHHHHHhhCcCCCcccHHhccCCCccc--CCcHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHH
Confidence            34566666666654      57899999999887  99999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHHHHHHHHHH
Q 017092          179 KYNDERSDVHVMAKTLLAKFEEKWL  203 (377)
Q Consensus       179 ~YN~~~s~v~~~A~~L~~~fe~~~~  203 (377)
                      .||+++|.+|.+|..|++.|.+...
T Consensus        80 ~yN~~~s~i~~~A~~L~~~~~~~~~  104 (105)
T cd05515          80 KYNEPDSQIYKDALTLQKVLLETKR  104 (105)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999987653

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

>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III

Probab=99.91  E-value=2.1e-24  Score=178.36  Aligned_cols=82  Identities=28%  Similarity=0.506  Sum_probs=78.8

Q ss_pred             CCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHHH
Q 017092          118 HKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAK  197 (377)
Q Consensus       118 ~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~~  197 (377)
                      ++.++||..||+...  +||||++|++||||+||+.||.+|.|.++.+|.+||+|||.||+.||+++|.+|.+|..|++.
T Consensus        21 ~~~s~pF~~~p~~~~--~PdYy~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~L~~~   98 (103)
T cd05520          21 QLLAEPFLKLPSKRK--YPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKL   98 (103)
T ss_pred             CCccHhhhcCCCccc--CCCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Confidence            358999999999887  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHH
Q 017092          198 FEEK  201 (377)
Q Consensus       198 fe~~  201 (377)
                      |+++
T Consensus        99 f~~~  102 (103)
T cd05520          99 MQAK  102 (103)
T ss_pred             HHHh
Confidence            9874

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=99.91  E-value=3.8e-24  Score=177.70  Aligned_cols=96  Identities=31%  Similarity=0.397  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHHHHcC------CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhh
Q 017092          104 LIRQFGTILRNITQH------KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNA  177 (377)
Q Consensus       104 l~~~~~~il~~l~~~------~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  177 (377)
                      |...|..|++.|..+      ..++||..+|+...  +||||++|++||||+||++||.+|.|.|+.+|.+||.|||.||
T Consensus         3 l~~~l~~i~~~i~~~kd~~g~~~s~~F~~lp~k~~--~pdYy~~I~~P~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f~Na   80 (106)
T cd05525           3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKK--NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNA   80 (106)
T ss_pred             HHHHHHHHHHHHHHhhccCCCcccHhhccCCCccc--CCchhhhCCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Confidence            455677777777765      35799999999988  9999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCHHHHHHHHHHHHHHHH
Q 017092          178 MKYNDERSDVHVMAKTLLAKFEEK  201 (377)
Q Consensus       178 ~~YN~~~s~v~~~A~~L~~~fe~~  201 (377)
                      +.||+++|.++.+|..|++.|+..
T Consensus        81 ~~yn~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          81 EKYYGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHc
Confidence            999999999999999999999864

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.

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.91  E-value=5.9e-24  Score=182.38  Aligned_cols=99  Identities=28%  Similarity=0.407  Sum_probs=93.2

Q ss_pred             HHHHHHHHHHHHHH---cCCCCCCCCCcCCcc-cCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhh
Q 017092          103 ELIRQFGTILRNIT---QHKWAWPFMQPVDVK-GLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAM  178 (377)
Q Consensus       103 ~l~~~~~~il~~l~---~~~~a~~F~~pVd~~-~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  178 (377)
                      ++...|..++..|+   +++.+++|..||+.. .  +|+||++|++||||+||++||.+|.|+++.+|..||+|||.||+
T Consensus        24 ~~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~~--~p~Y~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~Na~  101 (128)
T cd05529          24 EERERLISGLDKLLLSLQLEIAEYFEYPVDLRAW--YPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAE  101 (128)
T ss_pred             HHHHHHHHHHHHHHhcccCcccccccCCCCcccc--CCcHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence            45667788888888   899999999999998 6  99999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHHHHHHHHHH
Q 017092          179 KYNDERSDVHVMAKTLLAKFEEKWL  203 (377)
Q Consensus       179 ~YN~~~s~v~~~A~~L~~~fe~~~~  203 (377)
                      .||+++|.++.+|..|++.|...+.
T Consensus       102 ~yN~~~s~i~~~A~~l~~~~~~~l~  126 (128)
T cd05529         102 TFNEPNSEIAKKAKRLSDWLLRILS  126 (128)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999998764

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.

>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV

Probab=99.91  E-value=3.1e-24  Score=177.39  Aligned_cols=100  Identities=31%  Similarity=0.438  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhh
Q 017092           99 KRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAM  178 (377)
Q Consensus        99 ~~~~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  178 (377)
                      +++..++..+....+ ...+..+.+|..+|+...  +||||++|++||||+||+.||.+|.|.|+.+|.+||+|||.||+
T Consensus         3 ~~~~~l~~~v~~~~d-~~gr~~~~~F~~~p~~~~--~pdYy~iIk~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~   79 (103)
T cd05518           3 KRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKD--YPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNAR   79 (103)
T ss_pred             HHHHHHHHHHHHhhc-cCCCcccHHHhcCCCccc--CccHHHHcCCCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
Confidence            344455554444422 345678999999999988  99999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHHHHHHHH
Q 017092          179 KYNDERSDVHVMAKTLLAKFEEK  201 (377)
Q Consensus       179 ~YN~~~s~v~~~A~~L~~~fe~~  201 (377)
                      .||+++|.+|.+|..|+++|+++
T Consensus        80 ~yN~~~s~i~~~A~~le~~~~~~  102 (103)
T cd05518          80 HYNEEGSQVYEDANILEKVLKEK  102 (103)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHhc
Confidence            99999999999999999999864

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.

>smart00297 BROMO bromo domain

Probab=99.91  E-value=7.1e-24  Score=175.47  Aligned_cols=101  Identities=43%  Similarity=0.728  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      ..+...|..|+..+.+++.+++|..||+...  +|+||.+|++||||++|++||++|.|.|+.+|.+||++||.||+.||
T Consensus         6 ~~~~~~~~~i~~~~~~~~~~~~F~~~~~~~~--~p~Y~~~i~~P~dl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~~n   83 (107)
T smart00297        6 KKLQSLLKAVLDKLDSHRLSWPFLKPVDRKE--APDYYDIIKKPMDLSTIKKKLENGKYSSVEEFVADVQLMFSNAKTYN   83 (107)
T ss_pred             HHHHHHHHHHHHHHHhCccchhhccCCChhh--ccCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            3567789999999999999999999999988  99999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHh
Q 017092          182 DERSDVHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~~~  204 (377)
                      +++|.++.+|..|...|+..|.+
T Consensus        84 ~~~s~~~~~a~~l~~~f~~~~~~  106 (107)
T smart00297       84 GPDSEVYKDAKKLEKFFEKKLRE  106 (107)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999875

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.90  E-value=4.6e-24  Score=176.36  Aligned_cols=93  Identities=25%  Similarity=0.390  Sum_probs=86.3

Q ss_pred             HHHHHHHHHHHcC------CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhh
Q 017092          106 RQFGTILRNITQH------KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK  179 (377)
Q Consensus       106 ~~~~~il~~l~~~------~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  179 (377)
                      +.|..|+..|+.+      +.+++|..+|+...  +||||++|++||||+||++||.++.|.++.+|..||+|||.||+.
T Consensus         3 ~~~~~l~~~i~~~~d~~gr~~~~~F~~lp~~~~--~pdYy~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~   80 (103)
T cd05517           3 QILEQLLEAVMTATDPSGRLISELFQKLPSKVL--YPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT   80 (103)
T ss_pred             HHHHHHHHHHHHhhCcCCCChhHHHhcCCCCCC--CCCHHHHcCCCcCHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHH
Confidence            4677777777765      46799999999988  999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHH
Q 017092          180 YNDERSDVHVMAKTLLAKFEE  200 (377)
Q Consensus       180 YN~~~s~v~~~A~~L~~~fe~  200 (377)
                      ||+++|.++.+|..|++.|+.
T Consensus        81 yN~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          81 FNEPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             HCCCCCHHHHHHHHHHHHHHh
Confidence            999999999999999999975

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=99.88  E-value=1.1e-22  Score=168.43  Aligned_cols=82  Identities=26%  Similarity=0.376  Sum_probs=79.0

Q ss_pred             CCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHHH
Q 017092          118 HKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAK  197 (377)
Q Consensus       118 ~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~~  197 (377)
                      ++.+++|..+|+...  +|+||++|++||||+||++||.+|.|.++.+|..||.|||.||+.||+++|.++.+|..|++.
T Consensus        22 ~~l~~~F~~~p~~~~--~pdYy~~I~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l~~~   99 (104)
T cd05522          22 RLLTLHFEKLPDKAR--EPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKE   99 (104)
T ss_pred             CcccHHHhcCCCccc--cCcHHHHhCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Confidence            578999999999887  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHH
Q 017092          198 FEEK  201 (377)
Q Consensus       198 fe~~  201 (377)
                      |+..
T Consensus       100 f~~l  103 (104)
T cd05522         100 ARLL  103 (104)
T ss_pred             HHHh
Confidence            9864

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

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

Probab=99.88  E-value=2e-22  Score=167.27  Aligned_cols=96  Identities=25%  Similarity=0.318  Sum_probs=86.7

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhh
Q 017092          104 LIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNA  177 (377)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  177 (377)
                      |.++|..+++.|+...      .+.+|..+|+...  +||||++|++||||+||++||.+  |.++.+|.+||.|||.||
T Consensus         2 l~~~~~~l~~~i~~~~~~~g~~~~~~F~~lp~~~~--~pdYy~iI~~PmdL~tI~~kl~~--Y~s~~ef~~D~~li~~Na   77 (106)
T cd05521           2 LSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKD--YPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNA   77 (106)
T ss_pred             HHHHHHHHHHHHHhhcCcCCCCchHhhhcCCcccc--CccHHHHhcCCCCHHHHHHHHHc--CCCHHHHHHHHHHHHHHH
Confidence            4556777788777654      5679999888877  99999999999999999999998  999999999999999999


Q ss_pred             hhcCCCCCHHHHHHHHHHHHHHHHHH
Q 017092          178 MKYNDERSDVHVMAKTLLAKFEEKWL  203 (377)
Q Consensus       178 ~~YN~~~s~v~~~A~~L~~~fe~~~~  203 (377)
                      +.||+++|.+|.+|..|+++|..++.
T Consensus        78 ~~yN~~~s~i~~~A~~le~~~~~~~~  103 (106)
T cd05521          78 RLYNTKGSVIYKYALILEKYINDVII  103 (106)
T ss_pred             HHHcCCCCHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999998753

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

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

Probab=99.88  E-value=1.5e-22  Score=160.30  Aligned_cols=84  Identities=43%  Similarity=0.726  Sum_probs=79.5

Q ss_pred             HHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHH
Q 017092          108 FGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDV  187 (377)
Q Consensus       108 ~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v  187 (377)
                      |..|+..|++++.+++|..||+...  +|+|+.+|++||||++|+.||++|.|.++.+|..||++||.||+.||+++|.+
T Consensus         1 C~~il~~l~~~~~~~~F~~~~~~~~--~p~y~~~i~~P~dL~~I~~kl~~~~Y~s~~~f~~Dv~~i~~Na~~yn~~~s~~   78 (84)
T PF00439_consen    1 CREILEELMKHPISSPFSKPVDPKE--YPDYYEIIKNPMDLSTIRKKLENGKYKSIEEFEADVRLIFQNARRYNPPDSPI   78 (84)
T ss_dssp             HHHHHHHHHTSTTGGGGSSSTHTTT--STTHHHHSSSS--HHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHHHSCTTSHH
T ss_pred             CHHHHHHHHcCCCchhhcCCCChhh--CCCHHHHHhhccchhhhhHHhhccchhhHHHHHHHHHHHHHHHHHHCCCcCHH
Confidence            8899999999999999999998877  99999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q 017092          188 HVMAKT  193 (377)
Q Consensus       188 ~~~A~~  193 (377)
                      |.+|.+
T Consensus        79 ~~~A~~   84 (84)
T PF00439_consen   79 YKAAEK   84 (84)
T ss_dssp             HHHHHH
T ss_pred             HHHhcC
Confidence            999974

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

>cd04369 Bromodomain Bromodomain

Probab=99.87  E-value=3e-22  Score=161.49  Aligned_cols=95  Identities=42%  Similarity=0.663  Sum_probs=91.0

Q ss_pred             HHHHHHHHHHHcC--CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCC
Q 017092          106 RQFGTILRNITQH--KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDE  183 (377)
Q Consensus       106 ~~~~~il~~l~~~--~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~  183 (377)
                      ..|..|++.+..+  +.+++|..||++..  +|+||.+|++||||++|+.||.+|.|.++.+|.+||++||.||+.||++
T Consensus         3 ~~~~~i~~~l~~~~~~~~~~F~~~~~~~~--~~~Y~~~i~~P~~l~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~~n~~   80 (99)
T cd04369           3 KKLRSLLDALKKLKRDLSEPFLEPVDPKE--APDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP   80 (99)
T ss_pred             HHHHHHHHHHHhhcccccHHHhcCCChhc--CCCHHHHHhCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            5788999999999  99999999999977  9999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHH
Q 017092          184 RSDVHVMAKTLLAKFEEKW  202 (377)
Q Consensus       184 ~s~v~~~A~~L~~~fe~~~  202 (377)
                      +|.++.+|..|...|++.|
T Consensus        81 ~~~~~~~a~~l~~~~~~~~   99 (99)
T cd04369          81 GSPIYKDAKKLEKLFEKLL   99 (99)
T ss_pred             CCHHHHHHHHHHHHHHHhC
Confidence            9999999999999998763

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

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.87  E-value=1.1e-21  Score=163.33  Aligned_cols=98  Identities=16%  Similarity=0.173  Sum_probs=86.5

Q ss_pred             HHHHHHHHHc-CCCCCCCCCcCCcc---cCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCC
Q 017092          108 FGTILRNITQ-HKWAWPFMQPVDVK---GLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDE  183 (377)
Q Consensus       108 ~~~il~~l~~-~~~a~~F~~pVd~~---~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~  183 (377)
                      +..++..+.+ .+.++||..||...   ..++|+|+.+|++||||+||++||++|.|+++++|.+||.|||+||..||++
T Consensus         5 L~f~~~~~k~~lp~~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~N~~~yNg~   84 (109)
T cd05492           5 LKFIVSRMKSWLPPDTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGA   84 (109)
T ss_pred             HHHHHHHHHhcCcccccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            4566777777 57789999999733   3349999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhh
Q 017092          184 RSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       184 ~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      +|.++.+|..|.......+.++
T Consensus        85 ~s~~~~~A~~l~~d~~~el~Ei  106 (109)
T cd05492          85 DSEQYDAARWLYRDTCHDLREL  106 (109)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999988877766654

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

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.78  E-value=7.3e-19  Score=146.09  Aligned_cols=98  Identities=15%  Similarity=0.198  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhh
Q 017092          104 LIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNA  177 (377)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  177 (377)
                      +...+.+|+..+++|.      .+.+|.+.++  .  .|+||.+|+.||||++|++||.+|.|.++++|..||.+||.||
T Consensus         4 vq~~l~~l~~~V~~~~D~~Gr~~s~~f~~LP~--~--~~~~~~~ik~Pi~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NA   79 (110)
T cd05526           4 VQELLATLFVSVMNHQDEEGRCYSDSLAELPE--L--AVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERA   79 (110)
T ss_pred             HHHHHHHHHHHHHhccCCCCCCchHHHHHCCC--c--ccCchhhhcCCccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHH
Confidence            3446677788888774      6899999887  2  5788999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCHHHHHHHHHHHHHHHHHHhh
Q 017092          178 MKYNDERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       178 ~~YN~~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      ++||.+||.+|.+|..|+.+|.....++
T Consensus        80 r~yN~~~S~iy~dA~eLq~~f~~~rd~~  107 (110)
T cd05526          80 RRLSRTDSEIYEDAVELQQFFIKIRDEL  107 (110)
T ss_pred             HHhCcccCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999877655

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

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

Probab=99.75  E-value=1.3e-18  Score=195.75  Aligned_cols=98  Identities=38%  Similarity=0.748  Sum_probs=95.3

Q ss_pred             HHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHH
Q 017092          108 FGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDV  187 (377)
Q Consensus       108 ~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v  187 (377)
                      |..|+..|+.|..||||+.||++..  +||||+||++||||+||+.|+..|.|.++.+|..||.|||.||.+||.+ |.+
T Consensus      1306 ~e~il~e~~~~~~awPFlepVn~~~--vp~Y~~IIk~Pmdl~tir~k~~~~~Y~~~eef~~Di~lvf~Nc~~yN~~-s~i 1382 (1404)
T KOG1245|consen 1306 CEDILHELVVHKAAWPFLEPVNPKE--VPDYYDIIKKPMDLSTIREKLSKGIYPSPEEFATDIELVFDNCETYNED-SEI 1382 (1404)
T ss_pred             HHHHHHHHHHhhhcchhhccCChhh--cccHHHHhcChhHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHhccc-hhh
Confidence            8999999999999999999999999  9999999999999999999999999999999999999999999999999 999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCC
Q 017092          188 HVMAKTLLAKFEEKWLQLLPK  208 (377)
Q Consensus       188 ~~~A~~L~~~fe~~~~~~~p~  208 (377)
                      +.++..|..+|+..|...+|.
T Consensus      1383 ~~ag~~l~~ff~~~~~~~~~~ 1403 (1404)
T KOG1245|consen 1383 GRAGTCLRRFFHKRWRKKFPV 1403 (1404)
T ss_pred             hhhcchHHHHHHHHHHhhcCC
Confidence            999999999999999887763

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

Probab=99.72  E-value=9.3e-18  Score=168.20  Aligned_cols=90  Identities=31%  Similarity=0.446  Sum_probs=85.5

Q ss_pred             CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHHHH
Q 017092          119 KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKF  198 (377)
Q Consensus       119 ~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~~f  198 (377)
                      ..+++|+.+|+...  +|+||.||+.||||++|+++|..+.|.++++|..|+.|||.||.+||+++|.||.+|..|++.|
T Consensus       164 ~~s~~F~~~p~k~~--~PdYy~iIk~Pm~L~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~~  241 (371)
T COG5076         164 FLSSIFLGLPSKRE--YPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYF  241 (371)
T ss_pred             ccccccccCCcccc--CCChheeecchhhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHHHHH
Confidence            57899999999998  9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhCCCCc
Q 017092          199 EEKWLQLLPKVT  210 (377)
Q Consensus       199 e~~~~~~~p~~~  210 (377)
                      ...+..+.+...
T Consensus       242 ~~~i~~~~~~~~  253 (371)
T COG5076         242 LKLIEEIPEEML  253 (371)
T ss_pred             HHHHHhccccch
Confidence            999998866543

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

Probab=99.66  E-value=8.9e-17  Score=168.83  Aligned_cols=142  Identities=28%  Similarity=0.460  Sum_probs=120.8

Q ss_pred             CCCCCCcccCcccCCC---CCccchhhhHHhHHhHHh-hHHHHHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchh
Q 017092           64 NSKGSSTLKDKEKERH---VPSIRKQQQEASRREKAA-EKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYY  139 (377)
Q Consensus        64 ~~~g~s~~~~~~r~r~---~~~~k~~~~~~~~~e~~~-~~~~~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~  139 (377)
                      +++|.++++++.+.++   +|+.+...+.....+... ...+..+...+..++.+|..|..+|||.+||+..+  +||||
T Consensus       563 v~~gl~~~~~~~~~~~~~~iPg~~E~~~~~~~~~~r~~~~~~~~~~s~~~~il~~l~~h~~awPf~~Pv~~~e--~pdyy  640 (720)
T KOG1472|consen  563 VYPGLECFKDGVPQIPPRKIPGFRESGWKPEKESYRQEYKKPGKLFSAIQNILDQLQNHGDAWPFLKPVNKKE--VPDYY  640 (720)
T ss_pred             cccccccccccccccCcccCCCchhhccCcchHHHHhhhcccchhhHHHHhHHhhhhcCCccCCccCcccccc--CCcHH
Confidence            6789999998866554   566655555444333331 13344567788999999999999999999999998  99999


Q ss_pred             hhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          140 EVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       140 ~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      .+|++||||.||+.+|..+.|..+..|++|+..||.||+.||+.++.+|+.|..|...|..++...+.
T Consensus       641 ~~I~~pmDl~tM~~~l~~~~y~~~~~f~ad~~~vf~ncr~yn~~~~~y~k~~~~le~~~~~k~~~~i~  708 (720)
T KOG1472|consen  641 DVIKHPMDLRTMQNRLKDNQYTEVELFMADVVRVFANCRMYNGSDTQYYKCAQALEKFFLFKLNELIL  708 (720)
T ss_pred             HHhcccccHHHHhhhccccchhhHHHHHHHHHHHHhhhhccCCccchheecccchhhhhcchhhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999988876643

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=99.40  E-value=1.9e-13  Score=114.99  Aligned_cols=80  Identities=23%  Similarity=0.281  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcC-------CCCCHHHHHHHHHhhhh
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAK-------EYKNVREICTDVRLVFK  175 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~-------~Y~s~~ef~~Dv~Lif~  175 (377)
                      +.+..|..++..++.++.+|||..||++...++||||++|++||||+||+.+|.++       .|..-..+.+++..++.
T Consensus         3 e~~~~~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (114)
T cd05494           3 EALERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEG   82 (114)
T ss_pred             HHHHHHHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHcccccccccccccccccccccccccc
Confidence            34567888888888899999999999996666999999999999999999999997       35545566677777777


Q ss_pred             hhhhcCC
Q 017092          176 NAMKYND  182 (377)
Q Consensus       176 Na~~YN~  182 (377)
                      ||..+|.
T Consensus        83 ~~~~~~~   89 (114)
T cd05494          83 RRSPSNI   89 (114)
T ss_pred             ccCcccc
Confidence            7777665

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=99.13  E-value=3.8e-11  Score=100.48  Aligned_cols=44  Identities=18%  Similarity=0.307  Sum_probs=40.7

Q ss_pred             ccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCC
Q 017092          142 IDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERS  185 (377)
Q Consensus       142 Ik~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s  185 (377)
                      +-.||||+||++||.+|.|.++.+|.+||+|||.||+.||+++.
T Consensus        61 ~~y~MDL~tIe~RL~ng~Y~tp~~F~~DiklI~~Nc~~ynd~dr  104 (119)
T cd05491          61 KFYNMDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKTIGDRER  104 (119)
T ss_pred             eEeccCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCHHH
Confidence            34699999999999999999999999999999999999998643

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=99.08  E-value=1.4e-10  Score=127.29  Aligned_cols=101  Identities=27%  Similarity=0.418  Sum_probs=93.3

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCC
Q 017092          104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDE  183 (377)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~  183 (377)
                      ..+.+..+++.+...+....|..|||..+  +|||.++|++||||.||+.++++|.|+++++|.+|+.+|..||+.||..
T Consensus       566 ~~kLl~~~l~~lq~kD~~gif~~pvd~~e--~pdy~~iik~pmd~~t~~~kl~s~~y~tle~ieed~~l~~~nc~~yn~~  643 (1051)
T KOG0955|consen  566 FKKLLQKSLDKLQKKDSYGIFAEPVDPSE--LPDYIDIIKKPMDFFTMRLKLESGAYSTLEPIEEDVNLIVSNCMEYNAK  643 (1051)
T ss_pred             HHHHHHHHHHHhhcccccCceeeccChhh--cccHHHHhcCccchhhhhhhccccchhhhhHHHHhHhHhHhHHHHhhcc
Confidence            34456688888888999999999999999  9999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhhC
Q 017092          184 RSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       184 ~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      ++.+|..|..+++.....+...-
T Consensus       644 dtv~~r~av~~~e~~~~~~~~ar  666 (1051)
T KOG0955|consen  644 DTVYYRAAVRLRELIKKDFRNAR  666 (1051)
T ss_pred             CeehHhhhHHHHhhhhhHHHhcc
Confidence            99999999999999888776653

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

Probab=99.02  E-value=2.4e-10  Score=125.27  Aligned_cols=96  Identities=29%  Similarity=0.527  Sum_probs=86.9

Q ss_pred             HHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCH
Q 017092          107 QFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSD  186 (377)
Q Consensus       107 ~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~  186 (377)
                      .+-.|+.+++.-+.+|+|.+||+...  +|+||.+|++||||.||.+++....|.+..+|.+||++|+.||..||+..+.
T Consensus      1386 ~~d~~vs~~~~ipes~~f~~~v~~k~--~~~yy~kik~pmdl~~i~~n~~~~~y~s~~e~l~dv~~i~~n~~~~ng~e~~ 1463 (1563)
T KOG0008|consen 1386 ILDNIVSQMKEIPESWPFHEPVNKKR--VPDYYKKIKNPMDLETILKNIPPHKYDSRSEFLDDVNLIYVNSVEYNGAESA 1463 (1563)
T ss_pred             hhhhHHHHHHhcchhcccccccchhh--chHHHHHhcChhhHHHHhhcCCccccccHHHHhhhhHhhcccceeecCcccc
Confidence            35577888888899999999999999  9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHh
Q 017092          187 VHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       187 v~~~A~~L~~~fe~~~~~  204 (377)
                      +..-|+.+-++....+.+
T Consensus      1464 y~~k~~k~~ev~~~~~~e 1481 (1563)
T KOG0008|consen 1464 YTKKARKIGEVGLANLLE 1481 (1563)
T ss_pred             ccHHHHHHHHHHHHHHHH
Confidence            999988776666555443

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

Probab=98.93  E-value=1.3e-09  Score=117.35  Aligned_cols=100  Identities=30%  Similarity=0.431  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHHcC------CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhh
Q 017092          106 RQFGTILRNITQH------KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK  179 (377)
Q Consensus       106 ~~~~~il~~l~~~------~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  179 (377)
                      +.|..|+.....+      ..+..|...++...  +||||.+|+.||++..|.++|.++.|.+..+...||.++|.||+.
T Consensus      1027 ~~~~~i~~~~~~~~~~~~r~~~~~~~~~~s~k~--~~d~~~~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~na~~ 1104 (1157)
T KOG0386|consen 1027 KQALKIASTSIKYKDSAGRELSEVFLKLPSRKE--YPDYYEIIKKPVAIDKIKKRIENHKYNSLKELEKDFMLLFNNART 1104 (1157)
T ss_pred             HHHHHHHHHHHhcccccccccchhcccCccccc--ccchHHHhcchhhHHHHhhhccccccchHHHHHHHHHhhcchhhh
Confidence            4577788777744      46789999999888  999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          180 YNDERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       180 YN~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      ||..||.||..|..|+.+|......+..
T Consensus      1105 ~~~egs~~y~d~~~l~~~~~~~~~~~~~ 1132 (1157)
T KOG0386|consen 1105 YNEEGSRVYEDAIVLQSVFKSARQEISK 1132 (1157)
T ss_pred             hccCCceechhHHHHHHHHhhhHHHHhc
Confidence            9999999999999999999998888754

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

Probab=98.84  E-value=4.3e-09  Score=109.86  Aligned_cols=97  Identities=28%  Similarity=0.324  Sum_probs=86.9

Q ss_pred             HHHHHHHHHHHHHcCC------CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhh
Q 017092          104 LIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNA  177 (377)
Q Consensus       104 l~~~~~~il~~l~~~~------~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  177 (377)
                      +..++..|+..+..+.      ....|.+.++...  .|+||.+|..||.|..|+.|+..+.|.+.+.|..|+.||+.||
T Consensus        53 ~~~~f~~il~~~~~~~d~~gk~~~d~feklp~~~~--~p~yy~~i~~pisl~~ik~kv~k~~y~~~~~f~~D~~lm~ena  130 (629)
T KOG1827|consen   53 LIPKFKTILASLLDLKDDEGKQLFDKFEKLPSRKE--FPEYYYVIQQPISLDQIKRKVKKGRYKRLSFFQLDFLLMTENA  130 (629)
T ss_pred             HHHHHHHHHHHHHhhccccCcccchhHhhcccccc--CCCcceeecCcccHHHHHHHHHhcccccHHHHHHHHHHHHHHH
Confidence            4446666666666653      5788999999988  9999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCHHHHHHHHHHHHHHHHH
Q 017092          178 MKYNDERSDVHVMAKTLLAKFEEKW  202 (377)
Q Consensus       178 ~~YN~~~s~v~~~A~~L~~~fe~~~  202 (377)
                      +.||.++|.++++|..|...|...-
T Consensus       131 ~~~n~~ds~~~~~s~~l~~~~~~~~  155 (629)
T KOG1827|consen  131 RLYNRPDSLIYKDSGELEKYFISLE  155 (629)
T ss_pred             HHhcCcchhhhhhhhhhhcchhhhh
Confidence            9999999999999999999998754

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

Probab=98.83  E-value=4.6e-09  Score=115.49  Aligned_cols=100  Identities=28%  Similarity=0.467  Sum_probs=91.7

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      -+...+..|++++...+.+.+|..||+...  ++|||.||+.||||.|+++.+....|.+-++|..|+.||++|..+||+
T Consensus      1261 ~~ss~l~~i~n~~~~~~~t~~f~~Pv~~k~--v~dyy~vi~~P~~lq~~kk~v~kr~y~~r~~fle~~~~~~~ns~~yng 1338 (1563)
T KOG0008|consen 1261 SLSSILETIINQARSSPNTYPFPTPVNAKE--VKDYYRVITPPMDLQTQKKLVRKRLYESREHFLEELPLIVSNSTKYNG 1338 (1563)
T ss_pred             ecccchHHHHHHHhcCCCCcCCCCccchhh--ccchhhccCCCcchHHHHHHHHHHHHHHHHHHHHHhHHHhhchhhhcC
Confidence            345567899999999999999999999998  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHh
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~  204 (377)
                      +-+.+...+..+....-..|..
T Consensus      1339 ~~~~~t~~~q~mls~~~~~~~e 1360 (1563)
T KOG0008|consen 1339 PLASLTRQQQSMLSLCFEKLKE 1360 (1563)
T ss_pred             chHHHHHHHHHHHHHHHHhhch
Confidence            9999999998887777666654

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

Probab=98.82  E-value=2.6e-09  Score=113.11  Aligned_cols=82  Identities=27%  Similarity=0.479  Sum_probs=72.8

Q ss_pred             cCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHH
Q 017092          117 QHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA  196 (377)
Q Consensus       117 ~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~  196 (377)
                      .+..+++|..||+...  .|+||.||+-||||+|+.+++..+.|.+.++|+.|+.+||.||..||.+.+.....-..+..
T Consensus       300 ~~~~s~~~~~kvs~~~--a~~y~~i~k~pmdl~t~~~k~~~~~y~~~~~fv~d~~~~~~n~~~~n~ee~~~~~~~~vv~~  377 (720)
T KOG1472|consen  300 RTEHSTPFLEKVSKED--APNYYQIIKAPMDLSTELKKLKSGPYCSKEEFVNDLMLIWRNCEKYNSEESHGLIEFAVIMN  377 (720)
T ss_pred             ccccccccccCCChhh--CcchHHhhhcchHHHHHHHHhccccccchhHHHHHHHHHHhcchhhccccchhhhhhhhhhc
Confidence            3789999999999998  99999999999999999999999999999999999999999999999877766665555555


Q ss_pred             HHHH
Q 017092          197 KFEE  200 (377)
Q Consensus       197 ~fe~  200 (377)
                      -+.-
T Consensus       378 ~~s~  381 (720)
T KOG1472|consen  378 SKSL  381 (720)
T ss_pred             cCcH
Confidence            5543

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

Probab=98.63  E-value=7.9e-09  Score=110.46  Aligned_cols=91  Identities=38%  Similarity=0.676  Sum_probs=84.9

Q ss_pred             HHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHH
Q 017092          115 ITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTL  194 (377)
Q Consensus       115 l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L  194 (377)
                      ...|.++|+|..||+...+++|+||.+|++|||++||..++++..|.+..+..+|+.-+|.||..||..+.+|+.++..+
T Consensus         4 ~~~~~~~~~f~~~v~~v~l~~~~~~~~~~~~~d~~~~~~~~e~n~~~~~~~~~~~f~~~~sn~~~~~~~~~~v~~~~~~~   83 (640)
T KOG1474|consen    4 ARKHKLAWPFLEPVDAVALNLPAYYEIIKRPMDIGTIEKRVENNYYFSASECIADFKTKFSNCYLFNDSGDDVVRMKQSL   83 (640)
T ss_pred             cccccccccccCccchhhccchhhhcccCCCCCchhhhhhhccCccccHhhhhhhccccccchhcccCCccchhhccccc
Confidence            45788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhh
Q 017092          195 LAKFEEKWLQL  205 (377)
Q Consensus       195 ~~~fe~~~~~~  205 (377)
                      ...|.......
T Consensus        84 ~~~~~~~~~~~   94 (640)
T KOG1474|consen   84 EKLFPKKLRSM   94 (640)
T ss_pred             hhhcccccccc
Confidence            99987665544

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

Probab=98.16  E-value=3.9e-07  Score=89.67  Aligned_cols=89  Identities=26%  Similarity=0.257  Sum_probs=77.7

Q ss_pred             HHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHH
Q 017092          110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHV  189 (377)
Q Consensus       110 ~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~  189 (377)
                      .++..+-+...-..|.-||....  .|+|.+||+.|||+.|++.+++.+.|.+..+|..|.+++..||..||..++.++.
T Consensus        26 hhlrkl~sKdp~q~fafplt~~m--ap~y~~iis~Pmd~~t~r~kidd~~yl~L~~m~~d~kl~~~na~~yn~~~Tv~~~  103 (418)
T KOG1828|consen   26 HHLRKLPSKDPKQKFAFPLTDKM--APNYLEIISEPMDRITKRSKIDDTRYLVLSQMEFDRKLPDGNATLYNLHPTVPIV  103 (418)
T ss_pred             HHHHhccccChhhhhccccchhh--ccchHhhhhcccccccccccCCCccceechhhhhhhcccccchhhhhcCCccccc
Confidence            44555555556667777888887  8999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 017092          190 MAKTLLAKFEE  200 (377)
Q Consensus       190 ~A~~L~~~fe~  200 (377)
                      .|+.|..+-..
T Consensus       104 aaKrL~~v~~~  114 (418)
T KOG1828|consen  104 AAKRLCPVRLG  114 (418)
T ss_pred             cccccchhhcc
Confidence            99988766543

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

Probab=98.01  E-value=3.2e-06  Score=83.32  Aligned_cols=82  Identities=12%  Similarity=0.052  Sum_probs=73.2

Q ss_pred             HHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHH
Q 017092          112 LRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMA  191 (377)
Q Consensus       112 l~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A  191 (377)
                      .+++........|.-||-...  +|.|.-+|++|+|++|++.+..++.|.| -+|..|+.||+.||++||.+...+|..|
T Consensus       217 ~~kl~~~~p~~~lnyg~tas~--aP~YSm~Ik~~~~~~Tygdk~~andy~S-~~f~~D~kl~~l~amT~gehsk~yyela  293 (418)
T KOG1828|consen  217 EDKLNRVDPVAYLNYGPTASF--APGYSMTITEVEPPGTYGDKSSANDYES-LSFTQDRKLIALKAVTNGEHSKSYYELA  293 (418)
T ss_pred             HHHhcccCchhhhcccchhhh--cccccccccccCCCcchhhhhhhhhhhh-hhhhcccchhhHHHHhcCCcchHHHHHH
Confidence            345555566778888888777  9999999999999999999999999999 9999999999999999999999999999


Q ss_pred             HHHHH
Q 017092          192 KTLLA  196 (377)
Q Consensus       192 ~~L~~  196 (377)
                      ..+..
T Consensus       294 nk~lh  298 (418)
T KOG1828|consen  294 NKQLH  298 (418)
T ss_pred             Hhhhh
Confidence            88765

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

Probab=97.17  E-value=0.00012  Score=73.85  Aligned_cols=88  Identities=33%  Similarity=0.512  Sum_probs=80.3

Q ss_pred             HHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHH
Q 017092          114 NITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKT  193 (377)
Q Consensus       114 ~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~  193 (377)
                      ....+..+|+|..++....  .|+|++.|..+|+++|.+.++..+.|.....|..|..++|+||..||+....++..+..
T Consensus       274 ~~~~~~~~~~~~~~~~~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  351 (371)
T COG5076         274 NSQAHVGAWPFLRPVSDEE--VPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANV  351 (371)
T ss_pred             ccccccccccccccCCccc--ccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhccc
Confidence            3355667899999999988  99999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHHHHHH
Q 017092          194 LLAKFEEKWL  203 (377)
Q Consensus       194 L~~~fe~~~~  203 (377)
                      +...+.....
T Consensus       352 ~~~~~~~~~~  361 (371)
T COG5076         352 LEDFVIKKTR  361 (371)
T ss_pred             hhhhHhhhhh
Confidence            8888776554

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

Probab=96.95  E-value=0.0011  Score=57.03  Aligned_cols=68  Identities=18%  Similarity=0.331  Sum_probs=57.7

Q ss_pred             CCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHHHHHHHHHhhCCCCchH
Q 017092          145 PMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEE  212 (377)
Q Consensus       145 PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p~~~~~  212 (377)
                      |.||.-|++||+.|.|+++.+|.+||-.|+.-++.=.+....+-+....+..+|-..+..+++++...
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~vf~Wf~~~  126 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFNSE  126 (131)
T ss_pred             cccHHHHHHHHhccceehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHhccccccc
Confidence            89999999999999999999999999999998887666555555556667788999999999887543

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

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

Probab=90.74  E-value=0.21  Score=54.35  Aligned_cols=60  Identities=18%  Similarity=0.379  Sum_probs=52.5

Q ss_pred             ccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 017092          142 IDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK  201 (377)
Q Consensus       142 Ik~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~~fe~~  201 (377)
                      -.-|..|..|..+|++..|++.+.|..||-.|..||.+|.+.+-.+...+..|...|..-
T Consensus      1050 fpvpls~evi~~rlEn~yYrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~T 1109 (1113)
T KOG0644|consen 1050 FPVPLSLEVIRSRLENNYYRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRT 1109 (1113)
T ss_pred             CCCcccHHHHHHHHHhhhhhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhhh
Confidence            456789999999999999999999999999999999999998887777777777776543

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

Probab=86.84  E-value=0.42  Score=53.90  Aligned_cols=64  Identities=22%  Similarity=0.269  Sum_probs=55.4

Q ss_pred             CCCCCCcCCcc---cCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHH--HHHhhhhhhhhcCCCC
Q 017092          121 AWPFMQPVDVK---GLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICT--DVRLVFKNAMKYNDER  184 (377)
Q Consensus       121 a~~F~~pVd~~---~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~--Dv~Lif~Na~~YN~~~  184 (377)
                      +..|..|++..   .+.+++|..+|+.|||+...-.++..+.|.++.+|..  ++.|||.|++.||+..
T Consensus       533 ~~~~s~Pl~~~~~~ll~~~~~~~~iq~~~~va~~~~k~~e~~~~~v~~~e~~~~i~lic~~~lli~~~~  601 (1080)
T KOG0732|consen  533 SVIFSRPLSTYLKPLLPFQDALEDIQGLMDVASSMAKIEEHLKLLVRSFESNFAIRLICRPRLLINGGK  601 (1080)
T ss_pred             ccCCCCCCCcceecccchHHHHHHhhcchhHHhhhhhHHHHhHHHHHhhhcccchhhhcCcHHhcCCCc
Confidence            56677777642   2225699999999999999999999999999999999  9999999999999765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	377
2g4a_A	116	Solution Structure Of A Bromodomain From Ring3 Prot		2e-19
2i8n_A	114	Solution Structure Of The Second Bromodomain Of Brd		2e-19
3oni_A	114	Crystal Structure Of The Second Bromodomain Of Huma		2e-19
2dvv_A	112	Crystal Structure Of The Second Bromodomain Of The		2e-19
2ouo_A	130	Crystal Structure Of The Bromo Domain 2 In Human Br		4e-19
2lsp_B	128	Solution Structures Of Brd4 Second Bromodomain With		5e-19
3jvl_A	120	Crystal Structure Of Bromodomain 2 Of Mouse Brd4 Le		1e-18
2wp1_A	126	Structure Of Brdt Bromodomain 2 Bound To An Acetyla		6e-18
2oo1_A	113	Crystal Structure Of The Bromo Domain 2 Of Human Br		1e-17
2e7n_A	117	Solution Structure Of The Second Bromodomain From H		1e-17
3jvj_A	131	Crystal Structure Of The Bromodomain 1 In Mouse Brd		6e-16
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		6e-16
2oss_A	127	Crystal Structure Of The Bromo Domain 1 In Human Br		7e-16
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		8e-16
2wp2_A	120	Structure Of Brdt Bromodomain Bd1 Bound To A Diacet		1e-15
2dww_A	114	Crystal Structure Of Bromodomain-Containing Protein		1e-15
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		5e-15
2ydw_A	153	Crystal Structure Of The First Bromodomain Of Human		5e-15
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		5e-15
3g0l_A	117	Crystal Structure Of Human Bromodomain Adjacent To		2e-14
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		3e-14
2e7o_A	112	Solution Structure Of The Bromodomain From Human Br		3e-14
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		3e-14
2nxb_A	123	Crystal Structure Of Human Bromodomain Containing P		3e-14
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		9e-14
3aqa_A	128	Crystal Structure Of The Human Brd2 Bd1 Bromodomain		7e-13
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		1e-12
1x0j_A	122	Crystal Structure Analysis Of The N-Terminal Bromod		4e-12
1e6i_A	121	Bromodomain From Gcn5 Complexed With Acetylated H4		5e-12
3dwy_A	119	Crystal Structure Of The Bromodomain Of Human Crebb		7e-12
1jsp_B	121	Nmr Structure Of Cbp Bromodomain In Complex With P5		7e-12
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		1e-11
3i3j_A	124	Crystal Structure Of The Bromodomain Of Human Ep300		2e-11
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		2e-11
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		2e-11
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		2e-11
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		2e-11
2f6j_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		4e-10
3nxb_A	116	Crystal Structure Of The Bromodomain Of Human Cecr2		1e-09
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		1e-09
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		1e-09
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		1e-09
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		2e-09
3uv4_A	158	Crystal Structure Of The Second Bromodomain Of Huma		3e-09
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		3e-09
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		2e-08
3hmh_A	155	Crystal Structure Of The Second Bromodomain Of Huma		4e-08
2yyn_A	135	Crystal Sturcture Of Human Bromodomain Protein Leng		1e-07
3u5m_A	207	Crystal Structure Of Trim33 Phd-Bromo In The Free S		1e-07
3d7c_A	112	Crystal Structure Of The Bromodomain Of Human Gcn5,		2e-07
1f68_A	103	Nmr Solution Structure Of The Bromodomain From Huma		2e-07
3o33_A	184	Crystal Structure Of Trim24 Phd-Bromo In The Free S		2e-07
2r10_A	361	Structure Of An Acetylated Rsc4 Tandem Bromodomain		3e-07
2r0v_A	346	Structure Of The Rsc4 Tandem Bromodomain Acetylated		3e-07
3fkm_X	166	Plasmodium Falciparum Bromodomain-Containing Protei		4e-07
3lxj_A	136	Crystal Structure Of The Bromodomain Of Human Aaa D		2e-06
3dai_A	130	Crystal Structure Of The Bromodomain Of The Human A		3e-06
3hme_A	123	Crystal Structure Of Human Bromodomain Containing 9		6e-06
2r0s_A	285	Crystal Structure Of The Rsc4 Tandem Bromodomain Le		1e-05
2r0y_A	311	Structure Of The Rsc4 Tandem Bromodomain In Complex		1e-05
3tlp_A	150	Crystal Structure Of The Fourth Bromodomain Of Huma		2e-05
3g0j_A	124	Crystal Structure Of The Fifth Bromodomain Of Human		2e-05
3ljw_A	120	Crystal Structure Of The Second Bromodomain Of Huma		3e-05
2yqd_A	120	Solution Structure Of The Fifth Bromodomain From Mo		3e-05
3hmf_A	116	Crystal Structure Of The Second Bromodomain Of Huma		3e-05
2dkw_A	131	Solution Structure Of The Bromodomain Of Human Prot		7e-05
2i7k_A	117	Solution Structure Of The Bromodomain Of Human Brd7		1e-04
2d9e_A	121	Solution Structure Of The Bromodomain Of Peregrin L		1e-04
2ktb_B	121	Solution Structure Of The Second Bromodomain Of Hum		1e-04
3mqm_A	126	Crystal Structure Of The Bromodomain Of Human Ash1l		2e-04
2grc_A	129	1.5 A Structure Of Bromodomain From Human Brg1 Prot		2e-04
3uvd_A	124	Crystal Structure Of The Bromodomain Of Human Trans		2e-04
2h60_A	128	Solution Structure Of Human Brg1 Bromodomain Length		2e-04
2dat_A	123	Solution Structure Of The Bromodomain Of Human SwiS		2e-04
2jns_A	90	Solution Structure Of The Bromodomain-Containing Pr		3e-04
3iu5_A	116	Crystal Structure Of The First Bromodomain Of Human		7e-04

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/104 (40%), Positives = 65/104 (62%), Gaps = 3/104 (2%)
Query: 105 IRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
           ++    IL+ +   K   +AWPF +PVD   LGL DY+++I  PMD ST+K++ME ++Y+
Sbjct: 3   LKHCNVILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYR 62
Query: 162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           + +E   DVRL+F N  KYN    DV  MA+ L   FE ++ ++
Sbjct: 63  DAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKM 106

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/87 (48%), Positives = 60/87 (68%)
Query: 120 WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK 179
           +AWPF +PVDV+ LGL DY ++I  PMD STIK ++EA+EY++ +E   DVRL+F N  K
Sbjct: 21  YAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYK 80
Query: 180 YNDERSDVHVMAKTLLAKFEEKWLQLL 206
           YN    +V  MA+ L   FE ++ ++L
Sbjct: 81  YNPPDHEVVAMARKLQDVFEMRFAKML 107

>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 = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/104 (40%), Positives = 65/104 (62%), Gaps = 3/104 (2%)
Query: 105 IRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
           ++    IL+ +   K   +AWPF +PVD   LGL DY+++I  PMD ST+K++ME ++Y+
Sbjct: 9   LKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYR 68
Query: 162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           + +E   DVRL+F N  KYN    DV  MA+ L   FE ++ ++
Sbjct: 69  DAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKM 112

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/104 (40%), Positives = 65/104 (62%), Gaps = 3/104 (2%)
Query: 105 IRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
           ++    IL+ +   K   +AWPF +PVD   LGL DY+++I  PMD ST+K++ME ++Y+
Sbjct: 7   LKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYR 66
Query: 162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           + +E   DVRL+F N  KYN    DV  MA+ L   FE ++ ++
Sbjct: 67  DAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKM 110

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 41/86 (47%), Positives = 59/86 (68%)
Query: 120 WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK 179
           +AWPF +PVDV+ LGL DY ++I  PMD STIK ++EA+EY++ +E   DVRL+F N  K
Sbjct: 42  YAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYK 101
Query: 180 YNDERSDVHVMAKTLLAKFEEKWLQL 205
           YN    +V  MA+ L   FE ++ ++
Sbjct: 102 YNPPDHEVVAMARKLQDVFEMRFAKM 127

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 41/86 (47%), Positives = 59/86 (68%)
Query: 120 WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK 179
           +AWPF +PVDV+ LGL DY ++I  PMD STIK ++EA+EY++ +E   DVRL+F N  K
Sbjct: 40  YAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYK 99
Query: 180 YNDERSDVHVMAKTLLAKFEEKWLQL 205
           YN    +V  MA+ L   FE ++ ++
Sbjct: 100 YNPPDHEVVAMARKLQDVFEMRFAKM 125

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

Iteration: 1
 Score = 90.9 bits (224), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/86 (46%), Positives = 59/86 (68%)
Query: 120 WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK 179
           +AWPF +PVDV+ LGL DY ++I  PMD STIK ++E++EY++ +E   DVRL+F N  K
Sbjct: 29  YAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYK 88
Query: 180 YNDERSDVHVMAKTLLAKFEEKWLQL 205
           YN    +V  MA+ L   FE ++ ++
Sbjct: 89  YNPPDHEVVAMARKLQDVFEMRFAKM 114

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

Iteration: 1
 Score = 88.2 bits (217), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 40/80 (50%), Positives = 51/80 (63%)
Query: 120 WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK 179
           +AWPF  PVD   LGL +YY+V+  PMD  TIK +M+ +EYK+  E   DVRL+F N  K
Sbjct: 34  YAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYK 93
Query: 180 YNDERSDVHVMAKTLLAKFE 199
           YN    +V  MA+TL   FE
Sbjct: 94  YNPPDHEVVAMARTLQDVFE 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 = 87.4 bits (215), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/104 (39%), Positives = 64/104 (61%), Gaps = 3/104 (2%)
Query: 105 IRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
           +R   +ILR +   K   +AWPF +PVD + L L DY+++I  PMD ST+K++M+ +EY 
Sbjct: 9   LRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYP 68
Query: 162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           + +    DVRL+F N  KYN    +V  MA+ L   FE ++ ++
Sbjct: 69  DAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 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 = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/104 (39%), Positives = 64/104 (61%), Gaps = 3/104 (2%)
Query: 105 IRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
           +R   +ILR +   K   +AWPF +PVD + L L DY+++I  PMD ST+K++M+ +EY 
Sbjct: 14  LRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYP 73
Query: 162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           + +    DVRL+F N  KYN    +V  MA+ L   FE ++ ++
Sbjct: 74  DAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 117

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 38/91 (41%), Positives = 54/91 (59%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +L+ + +H++AWPF QPVD   L L DYY++I  PMD  TIKK++E   Y N +E   D 
Sbjct: 33  VLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDF 92
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN    D+ +MA+ L   F +K
Sbjct: 93  NTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 123

>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 = 81.6 bits (200), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 38/91 (41%), Positives = 54/91 (59%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +L+ + +H++AWPF QPVD   L L DYY++I  PMD  TIKK++E   Y N +E   D 
Sbjct: 49  VLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDF 108
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN    D+ +MA+ L   F +K
Sbjct: 109 NTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 139

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 38/91 (41%), Positives = 54/91 (59%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +L+ + +H++AWPF QPVD   L L DYY++I  PMD  TIKK++E   Y N +E   D 
Sbjct: 29  VLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDF 88
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN    D+ +MA+ L   F +K
Sbjct: 89  NTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 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 = 81.3 bits (199), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 38/91 (41%), Positives = 54/91 (59%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +L+ + +H++AWPF QPVD   L L DYY++I  PMD  TIKK++E   Y N +E   D 
Sbjct: 29  VLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDF 88
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN    D+ +MA+ L   F +K
Sbjct: 89  NTMFTNCYIYNKPGDDIVLMAEALEKLFLQK 119

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

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/96 (40%), Positives = 55/96 (57%)
Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
            +L+ + +H ++WPF QPVD   L L DYY +I  PMD +TIKK++E K Y+   E   D
Sbjct: 21  VVLKALWKHGFSWPFQQPVDAVKLKLPDYYTIIKTPMDLNTIKKRLENKYYEKASECIED 80
Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
              +F N   YN    D+ VMA+ L   F +K  Q+
Sbjct: 81  FNTMFSNCYLYNKTGDDIVVMAQALEKLFMQKLSQM 116

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

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 38/83 (45%), Positives = 54/83 (65%)
Query: 120 WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK 179
           +AWPF +PVDV+ LGL DY ++I  P D STIK ++E++EY++ +E   DVRL F N  K
Sbjct: 27  YAWPFYKPVDVEALGLHDYCDIIKHPXDXSTIKSKLESREYRDAQEFGADVRLXFSNCYK 86
Query: 180 YNDERSDVHVMAKTLLAKFEEKW 202
           YN    +V   A+ L   FE ++
Sbjct: 87  YNPPDHEVVAXARKLQDVFEXRF 109

>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 = 78.6 bits (192), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 55/92 (59%)
Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
            +++ + +H++AWPF QPVD   LGL DY+++I +PMD  TIK+++E   Y    E   D
Sbjct: 39  VVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQD 98
Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
              +F N   YN    D+ +MA+TL   F +K
Sbjct: 99  FNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQK 130

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 55/92 (59%)
Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
            +++ + +H++AWPF QPVD   LGL DY+++I +PMD  TIK+++E   Y    E   D
Sbjct: 39  VVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQD 98
Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
              +F N   YN    D+ +MA+TL   F +K
Sbjct: 99  FNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQK 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 = 78.6 bits (192), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 55/96 (57%)
Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
            +L+++ +H ++WPF +PVD   L L DYY +I  PMD +TIKK++E K Y    E   D
Sbjct: 20  VVLKDLWKHSFSWPFQRPVDAVKLQLPDYYTIIKNPMDLNTIKKRLENKYYAKASECIED 79
Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
              +F N   YN    D+ +MA+ L   F +K  Q+
Sbjct: 80  FNTMFSNCYLYNKPGDDIVLMAQALEKLFMQKLSQM 115

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/92 (40%), Positives = 57/92 (61%), Gaps = 2/92 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           IL  +  H+ AWPF+ PV++K +    Y +VI KPMDFSTI++++ + +Y N+     DV
Sbjct: 21  ILTEMETHEDAWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREKLSSGQYPNLETFALDV 78
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
           RLVF N   +N++ SD+      +   FE+KW
Sbjct: 79  RLVFDNCETFNEDDSDIGRAGHNMRKYFEKKW 110

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

Iteration: 1
 Score = 76.3 bits (186), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 55/97 (56%)
Query: 109 GTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICT 168
             +++ + +H++AWPF QPVD   L L DY+++I  PMD  TIKK++E   Y +  E   
Sbjct: 27  NVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQ 86
Query: 169 DVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           D   +F N   YN    D+ +MA+ L   F +K  Q+
Sbjct: 87  DFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 123

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

Iteration: 1
 Score = 76.3 bits (186), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/92 (40%), Positives = 57/92 (61%), Gaps = 2/92 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           IL  +  H+ AWPF+ PV++K +    Y +VI KPMDFSTI++++ + +Y N+     DV
Sbjct: 18  ILTEMETHEDAWPFLLPVNLKLV--PGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDV 75
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
           RLVF N   +N++ SD+      +   FE+KW
Sbjct: 76  RLVFDNCETFNEDDSDIGRAGHNMRKYFEKKW 107

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

Iteration: 1
 Score = 76.3 bits (186), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 55/97 (56%)
Query: 109 GTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICT 168
             +++ + +H++AWPF QPVD   L L DY+++I  PMD  TIKK++E   Y +  E   
Sbjct: 25  NVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQ 84
Query: 169 DVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           D   +F N   YN    D+ +MA+ L   F +K  Q+
Sbjct: 85  DFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 121

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

Iteration: 1
 Score = 76.3 bits (186), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 55/97 (56%)
Query: 109 GTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICT 168
             +++ + +H++AWPF QPVD   L L DY+++I  PMD  TIKK++E   Y +  E   
Sbjct: 23  NVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQ 82
Query: 169 DVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           D   +F N   YN    D+ +MA+ L   F +K  Q+
Sbjct: 83  DFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQM 119

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

Iteration: 1
 Score = 74.3 bits (181), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 40/96 (41%), Positives = 61/96 (63%), Gaps = 3/96 (3%)
Query: 106 RQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVRE 165
           +Q   +L  I Q + + PF QPVD+  L   DY ++ID PMDF+T+++ +EA  Y++  E
Sbjct: 24  KQCEELLNLIFQCEDSEPFRQPVDL--LEYPDYRDIIDTPMDFATVRETLEAGNYESPME 81
Query: 166 ICTDVRLVFKNAMKYN-DERSDVHVMAKTLLAKFEE 200
           +C DVRL+F N+  Y   +RS ++ M+  L A FEE
Sbjct: 82  LCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEE 117

>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 = 71.6 bits (174), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 34/91 (37%), Positives = 51/91 (56%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           + + + +H++AWPF QPVD   LGL DY+++I +P D  TIK+++E   Y    E   D 
Sbjct: 20  VXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRLENNYYWAASECXQDF 79
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
              F N   YN    D+ + A+TL   F +K
Sbjct: 80  NTXFTNCYIYNKPTDDIVLXAQTLEKIFLQK 110

>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 = 71.2 bits (173), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 38/97 (39%), Positives = 59/97 (60%), Gaps = 3/97 (3%)
Query: 106 RQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVRE 165
           +Q   ++  I Q + + PF QPVD+  +   DY ++ID PMDF T+++ ++A  Y +  E
Sbjct: 13  KQCKELVNLIFQCEDSEPFRQPVDL--VEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLE 70
Query: 166 ICTDVRLVFKNAMKYN-DERSDVHVMAKTLLAKFEEK 201
            C D+RL+F NA  Y  ++RS ++ M   L A FEEK
Sbjct: 71  FCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEK 107

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 34/91 (37%), Positives = 51/91 (56%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           + + + +H++AWPF QPVD   LGL DY+++I +P D  TIK+++E   Y    E   D 
Sbjct: 14  VXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRLENNYYWAASECXQDF 73
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
              F N   YN    D+ + A+TL   F +K
Sbjct: 74  NTXFTNCYIYNKPTDDIVLXAQTLEKIFLQK 104

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 52/92 (56%), Gaps = 2/92 (2%)
Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
            IL  +  H  AWPF+QPV+ + +   DYY+ I +PMD ST++ ++E+ +Y+ + +   D
Sbjct: 20  NILTELQNHAAAWPFLQPVNKEEVP--DYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYD 77
Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
            RLVF N   YN E +  +  A  L   F  K
Sbjct: 78  ARLVFNNCRMYNGENTSYYKYANRLEKFFNNK 109

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%)
Query: 123 PFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND 182
           PF QPVD + LG+ DY++++  PMD STIK++++  +Y+   +   DV L+F NA  YN 
Sbjct: 32  PFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNR 91
Query: 183 ERSDVHVMAKTLLAKFEE 200
           + S V+     L   FE+
Sbjct: 92  KTSRVYKFCSKLAEVFEQ 109

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%)
Query: 123 PFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND 182
           PF QPVD + LG+ DY++++  PMD STIK++++  +Y+   +   DV L+F NA  YN 
Sbjct: 34  PFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNR 93
Query: 183 ERSDVHVMAKTLLAKFEE 200
           + S V+     L   FE+
Sbjct: 94  KTSRVYKFCSKLAEVFEQ 111

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 54/91 (59%), Gaps = 2/91 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +LR++  HK AWPF++PVD       DYY VI +PMD +T++++++ + Y+ + E   D+
Sbjct: 21  VLRSLQAHKMAWPFLEPVDPNDA--PDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADM 78
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN   S  +  A+ L + F +K
Sbjct: 79  TAIFDNCRYYNPSDSPFYQCAEVLESFFVQK 109

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 48/78 (61%)
Query: 123 PFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND 182
           PF QPVD + LG+ DY++++  PMD STIK++++  +Y+   +   D+ L+F NA  YN 
Sbjct: 37  PFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNR 96
Query: 183 ERSDVHVMAKTLLAKFEE 200
           + S V+     L   FE+
Sbjct: 97  KTSRVYKYCSKLSEVFEQ 114

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 54/91 (59%), Gaps = 2/91 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +LR++  HK AWPF++PVD       DYY VI +PMD +T++++++ + Y+ + E   D+
Sbjct: 28  VLRSLQAHKMAWPFLEPVDPNDAP--DYYGVIKEPMDLATMEERVQRRYYEKLTEFVADM 85
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN   S  +  A+ L + F +K
Sbjct: 86  TKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 116

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 54/91 (59%), Gaps = 2/91 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +LR++  HK AWPF++PVD       DYY VI +PMD +T++++++ + Y+ + E   D+
Sbjct: 21  VLRSLQAHKMAWPFLEPVDPNDA--PDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADM 78
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN   S  +  A+ L + F +K
Sbjct: 79  TKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 109

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 54/91 (59%), Gaps = 2/91 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +LR++  HK AWPF++PVD       DYY VI +PMD +T++++++ + Y+ + E   D+
Sbjct: 80  VLRSLQAHKMAWPFLEPVDPNDA--PDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADM 137
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN   S  +  A+ L + F +K
Sbjct: 138 TKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 168

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 54/91 (59%), Gaps = 2/91 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +LR++  HK AWPF++PVD       DYY VI +PMD +T++++++ + Y+ + E   D+
Sbjct: 80  VLRSLQAHKMAWPFLEPVDPNDA--PDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADM 137
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN   S  +  A+ L + F +K
Sbjct: 138 TKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 168

>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 = 62.4 bits (150), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 2/91 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +LR++  HK AWPF++PVD       DYY VI +P D +T +++++ + Y+ + E   D 
Sbjct: 80  VLRSLQAHKXAWPFLEPVDPNDA--PDYYGVIKEPXDLATXEERVQRRYYEKLTEFVADX 137
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEK 201
             +F N   YN   S  +  A+ L + F +K
Sbjct: 138 TKIFDNCRYYNPSDSPFYQCAEVLESFFVQK 168

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 48/84 (57%), Gaps = 2/84 (2%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           +L  +  HK +WPF++PVD       +YY++I  PMD S+++K++    Y    E   D+
Sbjct: 24  VLDVVKAHKDSWPFLEPVDESYAP--NYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDM 81
Query: 171 RLVFKNAMKYNDERSDVHVMAKTL 194
           + +F+N  KYN E S+   M+  L
Sbjct: 82  KTMFRNCRKYNGESSEYTKMSDNL 105

>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 = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/111 (35%), Positives = 56/111 (50%), Gaps = 16/111 (14%)
Query: 108 FGTILRNITQHKW-----AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKN 162
           F  IL NI   K      +WPF  PV+ K +   DYY+VI  PMD  TI+K +   +Y++
Sbjct: 137 FSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQS 194
Query: 163 VREICTDVRLVFKNAMKYNDERSD--------VHVMAKTLLAKFEEKWLQL 205
                 DV L+  N++KYN   S         V+V  +T L +++E   QL
Sbjct: 195 RESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQT-LTEYDEHLTQL 244

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/111 (35%), Positives = 56/111 (50%), Gaps = 16/111 (14%)
Query: 108 FGTILRNITQHKW-----AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKN 162
           F  IL NI   K      +WPF  PV+ K +   DYY+VI  PMD  TI+K +   +Y++
Sbjct: 149 FSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQS 206
Query: 163 VREICTDVRLVFKNAMKYNDERSD--------VHVMAKTLLAKFEEKWLQL 205
                 DV L+  N++KYN   S         V+V  +T L +++E   QL
Sbjct: 207 RESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQT-LTEYDEHLTQL 256

>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 = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/111 (35%), Positives = 56/111 (50%), Gaps = 16/111 (14%)
Query: 108 FGTILRNITQHKW-----AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKN 162
           F  IL NI   K      +WPF  PV+ K +   DYY+VI  PMD  TI+K +   +Y++
Sbjct: 170 FSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQS 227
Query: 163 VREICTDVRLVFKNAMKYNDERSD--------VHVMAKTLLAKFEEKWLQL 205
                 DV L+  N++KYN   S         V+V  +T L +++E   QL
Sbjct: 228 RESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQT-LTEYDEHLTQL 277

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 52/95 (54%), Gaps = 3/95 (3%)
Query: 104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNV 163
           L     +IL+ +  H+ AWPFM+PV  K      YYEVI  PMD  T+ ++++ + Y + 
Sbjct: 16  LYSTLKSILQQVKSHQSAWPFMEPV--KRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSK 73
Query: 164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKF 198
           +    D++ VF N  +YN   S+ +  A  +L KF
Sbjct: 74  KLFMADLQRVFTNCKEYNPPESEYYKCA-NILEKF 107

>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 = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 39/111 (35%), Positives = 56/111 (50%), Gaps = 16/111 (14%)
Query: 108 FGTILRNITQHKW-----AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKN 162
           F  IL NI   K      +WPF  PV+ K +   DYY+VI  PMD  TI+K +   +Y++
Sbjct: 30  FSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQS 87
Query: 163 VREICTDVRLVFKNAMKYNDERSD--------VHVMAKTLLAKFEEKWLQL 205
                 DV L+  N++KYN   S         V+V  +T L +++E   QL
Sbjct: 88  RESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQT-LTEYDEHLTQL 137

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 52/95 (54%), Gaps = 3/95 (3%)
Query: 104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNV 163
           L     +IL+ +  H+ AWPFM+PV  K      YYEVI  PMD  T+ ++++ + Y + 
Sbjct: 14  LYSTLKSILQQVKSHQSAWPFMEPV--KRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSK 71
Query: 164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKF 198
           +    D++ VF N  +YN   S+ +  A  +L KF
Sbjct: 72  KLFMADLQRVFTNCKEYNPPESEYYKCA-NILEKF 105

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
           ++L  +     A  F QPV +K +   DY + I  PMDF+T++K++EA+ YKN+ E   D
Sbjct: 20  SVLDQLQDKDPARIFAQPVSLKEVP--DYLDHIKHPMDFATMRKRLEAQGYKNLHEFEED 77
Query: 170 VRLVFKNAMKYN 181
             L+  N MKYN
Sbjct: 78  FDLIIDNCMKYN 89

>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 = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 44/83 (53%), Gaps = 7/83 (8%)
Query: 108 FGTILRNITQHKW-----AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKN 162
           F  IL NI   K      +WPF  PV+ K +   DYY++I  P+D  TI+K +   +Y++
Sbjct: 27  FSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKMIVNPVDLETIRKNISKHKYQS 84
Query: 163 VREICTDVRLVFKNAMKYNDERS 185
                 DV L+  N++KYN   S
Sbjct: 85  RESFLDDVNLILANSVKYNGPES 107

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 52/104 (50%), Gaps = 5/104 (4%)
Query: 106 RQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME--AKEYKNV 163
           R+   +L  +  H+ +  F  PV    L + DYY++I  PMD STIKK+++     Y   
Sbjct: 23  RKCERLLLFLYCHEMSLAFQDPVP---LTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKP 79
Query: 164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLP 207
            +   D RL+F+N  ++N+  S+V      L   FEE    L P
Sbjct: 80  EDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 123

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 6/91 (6%)
Query: 106 RQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAK---EYKN 162
           R+   +L  +  H+ +  F +PV      + +YY++I KPMD ST+KK+++ K    Y+ 
Sbjct: 84  RKCERLLLYLYCHELSIEFQEPVPA---SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQI 140
Query: 163 VREICTDVRLVFKNAMKYNDERSDVHVMAKT 193
             +   DVRL+FKN  ++N+    V V A T
Sbjct: 141 PDDFVADVRLIFKNCERFNEMMKVVQVYADT 171

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 107 QFGTILRN----ITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKN 162
           Q  T L+N    I  H  AWPFM+PV  K     DYYEVI  P+D  T+ +++ ++ Y  
Sbjct: 7   QLYTTLKNLLAQIKSHPSAWPFMEPV--KKSEAPDYYEVIRFPIDLKTMTERLRSRYYVT 64
Query: 163 VREICTDVRLVFKNAMKYNDERSDVHVMAKTL 194
            +    D++ V  N  +YN   S+    A  L
Sbjct: 65  RKLFVADLQRVIANCREYNPPDSEYCRCASAL 96

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 107 QFGTILRN----ITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKN 162
           Q  T L+N    I  H  AWPFM+PV  K     DYYEVI  P+D  T+ +++ ++ Y  
Sbjct: 3   QLYTTLKNLLAQIKSHPSAWPFMEPV--KKSEAPDYYEVIRFPIDLKTMTERLRSRYYVT 60
Query: 163 VREICTDVRLVFKNAMKYNDERSDVHVMAKTL 194
            +    D++ V  N  +YN   S+    A  L
Sbjct: 61  RKLFVADLQRVIANCREYNPPDSEYCRCASAL 92

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 52/104 (50%), Gaps = 5/104 (4%)
Query: 106 RQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME--AKEYKNV 163
           R+   +L  +  H+ +  F  PV    L + DYY++I  PMD STIKK+++     Y   
Sbjct: 84  RKCERLLLFLYCHEMSLAFQDPV---PLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKP 140
Query: 164 REICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLP 207
            +   D RL+F+N  ++N+  S+V      L   FEE    L P
Sbjct: 141 EDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 184

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 119 KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAM 178
           K + PFM+ VD   L   +YYE++  PM  S +K+ +E  +Y  + +   D+ LVF+NA 
Sbjct: 229 KLSEPFMELVDKDELP--EYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAH 286
Query: 179 KYNDERSDVHVMAKTLLAKF 198
            +ND  + ++  A TL   F
Sbjct: 287 IFNDPSALIYKDATTLTNYF 306

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 119 KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAM 178
           K + PFM+ VD   L   +YYE++  PM  S +K+ +E  +Y  + +   D+ LVF+NA 
Sbjct: 214 KLSEPFMELVDKDELP--EYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAH 271
Query: 179 KYNDERSDVHVMAKTLLAKF 198
            +ND  + ++  A TL   F
Sbjct: 272 IFNDPSALIYKDATTLTNYF 291

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/88 (30%), Positives = 45/88 (51%)
Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           ++ ++++++    F + VD K     DYY+VI  P  FS IK +++  +Y    E   DV
Sbjct: 29  LILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPXSFSCIKTKLKKGQYAYPSEFVKDV 88
Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKF 198
           +L+F N   YN   S V +  K +   F
Sbjct: 89  QLIFDNCSLYNTSNSVVAITGKNIETYF 116

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 48/84 (57%), Gaps = 6/84 (7%)
Query: 105 IRQFGTILRNITQH----KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEY 160
           +R+    LR++T+     K    F +PVD++ +   DY EVI +PMD ST+  +++   Y
Sbjct: 10  LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVS--DYLEVIKEPMDLSTVITKIDKHNY 67
Query: 161 KNVREICTDVRLVFKNAMKYNDER 184
              ++   D+ L+  NA++YN ++
Sbjct: 68  LTAKDFLKDIDLICSNALEYNPDK 91

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 8/84 (9%)
Query: 106 RQFGTILRNITQHKWAWP-----FMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEY 160
           R+    LRN+T H+ A       F +PVD   +   DY  VI +PMD S++  +++  +Y
Sbjct: 9   RELRIFLRNVT-HRLAIDKRFRVFTKPVDPDEVP--DYVTVIKQPMDLSSVISKIDLHKY 65
Query: 161 KNVREICTDVRLVFKNAMKYNDER 184
             V++   D+ L+  NA++YN +R
Sbjct: 66  LTVKDYLRDIDLICSNALEYNPDR 89

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 138 YYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLL 195
           Y  +I  PMDF T+K ++ A EYK+V E   D +L+  NAM YN   +  + +AK +L
Sbjct: 46  YSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKIL 103

>pdb|2R0S|A Chain A, Crystal Structure Of The Rsc4 Tandem Bromodomain Length = 285

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 119 KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAM 178
           K + PF + VD   L   +YYE++  P   S +K+ +E  +Y  + +   D  LVF+NA 
Sbjct: 173 KLSEPFXELVDKDELP--EYYEIVHSPXALSIVKQNLEIGQYSKIYDFIIDXLLVFQNAH 230
Query: 179 KYNDERSDVHVMAKTLLAKF 198
            +ND  + ++  A TL   F
Sbjct: 231 IFNDPSALIYKDATTLTNYF 250

>pdb|2R0Y|A Chain A, Structure Of The Rsc4 Tandem Bromodomain In Complex With An Acetylated H3 Peptide Length = 311

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 119 KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAM 178
           K + PF + VD   L   +YYE++  P   S +K+ +E  +Y  + +   D  LVF+NA 
Sbjct: 179 KLSEPFXELVDKDELP--EYYEIVHSPXALSIVKQNLEIGQYSKIYDFIIDXLLVFQNAH 236
Query: 179 KYNDERSDVHVMAKTLLAKF 198
            +ND  + ++  A TL   F
Sbjct: 237 IFNDPSALIYKDATTLTNYF 256

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DYY++I +PMD   I+  +   +Y     +  D++L+F+NA  YN+E S V+  A  L  
Sbjct: 63  DYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEK 122
Query: 197 KFEEKWLQLLP 207
             +EK  +L P
Sbjct: 123 LLKEKRKELGP 133

>pdb|3G0J|A Chain A, Crystal Structure Of The Fifth Bromodomain Of Human Poly-Bromodomain Containing Protein 1 (Pb1) Length = 124

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 135 LDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERS----DVHVM 190
           L DYY  I KPMD   I+  M A +Y+++  +  D  ++F NA  YN+  S    D  V+
Sbjct: 51  LPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVL 110
Query: 191 AKTLL 195
            K LL
Sbjct: 111 HKVLL 115

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 32/51 (62%)
Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDV 187
           DYY +I +P+D  TI ++++   YK++  +  D+ L+ KNA  YN+  S V
Sbjct: 46  DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQV 96

>pdb|2YQD|A Chain A, Solution Structure Of The Fifth Bromodomain From Mouse Polybromo-1 Length = 120

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 135 LDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERS----DVHVM 190
           L DYY  I KPMD   I+  M A +Y+++  +  D  ++F NA  YN+  S    D  V+
Sbjct: 51  LPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVL 110
Query: 191 AKTLL 195
            K LL
Sbjct: 111 HKVLL 115

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 32/51 (62%)
Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDV 187
           DYY +I +P+D  TI ++++   YK++  +  D+ L+ KNA  YN+  S V
Sbjct: 44  DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQV 94

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 11/84 (13%)
Query: 105 IRQFGTILRNITQH----KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEY 160
           +R+    LR++T+     K    F +PV        DY EVI +PMD ST+  +++   Y
Sbjct: 10  LRELRLFLRDVTKRLATDKRFNIFSKPVS-------DYLEVIKEPMDLSTVITKIDKHNY 62
Query: 161 KNVREICTDVRLVFKNAMKYNDER 184
              ++   D+ L+  NA++YN ++
Sbjct: 63  LTAKDFLKDIDLICSNALEYNPDK 86

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 37/58 (63%)
Query: 138 YYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLL 195
           Y  +I  PMDFST+K++++  +Y+++ E+  + +L+  NAM YN   +  +  AK LL
Sbjct: 41  YSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLL 98

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 124 FMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN 181
           F +PV +  +   DY + I KPMDF T+K+ +EA  Y N  +   D  L+  N +KYN
Sbjct: 28  FSEPVPLSEV--PDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYN 83

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/65 (33%), Positives = 37/65 (56%)
Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DYY +I +P+D  TI ++++   YK++  +  D+ L+ KNA  YN+  S V   A ++  
Sbjct: 47  DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKK 106
Query: 197 KFEEK 201
            F  K
Sbjct: 107 IFYMK 111

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 29/51 (56%)
Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDV 187
           DYYE I  P+D  TI+KQ+    YK V     D+  VF+NA KY   +S V
Sbjct: 47  DYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYYGRKSPV 97

>pdb|2GRC|A Chain A, 1.5 A Structure Of Bromodomain From Human Brg1 Protein, A Central Atpase Of SwiSNF REMODELING COMPLEX Length = 129

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 37/54 (68%)
Query: 135 LDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVH 188
           L +YYE+I KP+DF  IK+++   +Y+++ ++  DV L+ +NA  +N E S ++
Sbjct: 48  LPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIY 101

>pdb|3UVD|A Chain A, Crystal Structure Of The Bromodomain Of Human Transcription Activator Brg1 (Smarca4) In Complex With N-Methyl-2-Pyrrolidone Length = 124

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 37/54 (68%)
Query: 135 LDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVH 188
           L +YYE+I KP+DF  IK+++   +Y+++ ++  DV L+ +NA  +N E S ++
Sbjct: 49  LPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIY 102

>pdb|2H60|A Chain A, Solution Structure Of Human Brg1 Bromodomain Length = 128

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 37/54 (68%)
Query: 135 LDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVH 188
           L +YYE+I KP+DF  IK+++   +Y+++ ++  DV L+ +NA  +N E S ++
Sbjct: 44  LPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIY 97

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/65 (33%), Positives = 41/65 (63%)
Query: 135 LDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTL 194
           L +YYE+I KP+DF  IK+++   +Y+++ ++  DV L+  NA  +N E S ++  +  L
Sbjct: 49  LPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVL 108
Query: 195 LAKFE 199
            + F+
Sbjct: 109 QSVFK 113

>pdb|2JNS|A Chain A, Solution Structure Of The Bromodomain-Containing Protein 4 Et Domain Length = 90

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 263 KCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQ-ATAEEVELDMDAQSESTLW 321
           KC+  S EEKR+L   + +L  E LG+ + I+       + +  +E+E+D +    STL 
Sbjct: 14  KCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLR 73
Query: 322 RLKFFVKDALKSQ 334
            L+ +V   L+ +
Sbjct: 74  ELERYVTSCLRKK 86

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 30/44 (68%)
Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKY 180
           DYYEV+ +P+D   I+++++ +EY +V  +  D +L+F NA  Y
Sbjct: 43  DYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSY 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	377
4alg_A	154	Bromodomain-containing protein 2; signaling protei	9e-48
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	2e-46
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	1e-45
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	2e-45
3p1f_A	119	CREB-binding protein; structural genomics consorti	6e-45
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	2e-44
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	3e-42
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	4e-42
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	4e-42
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	8e-42
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	7e-39
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	1e-37
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	4e-37
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	9e-37
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	2e-36
3d7c_A	112	General control of amino acid synthesis protein 5;	1e-34
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	1e-33
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	2e-33
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	9e-26
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-33
3uv4_A	158	Second bromodomain of human transcription initiat	8e-33
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	3e-32
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	1e-26
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	5e-32
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	8e-32
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	2e-31
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	2e-31
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	3e-31
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	9e-19
2grc_A	129	Probable global transcription activator SNF2L4; br	9e-31
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	3e-29
2r10_A	361	Chromatin structure-remodeling complex protein RSC	4e-29
2r10_A	361	Chromatin structure-remodeling complex protein RSC	1e-17
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-29
2dat_A	123	Possible global transcription activator SNF2L2; br	6e-29
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	4e-28
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-27
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-27
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	4e-25
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	5e-18
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-16
2jns_A	90	Bromodomain-containing protein 4; ET-domain, struc	8e-14
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	2e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06

>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 =  158 bits (401), Expect = 9e-48
 Identities = 41/150 (27%), Positives = 67/150 (44%)

Query: 74  KEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGL 133
                H  S    +       K   +   +L      +++ + +H++AWPF QPVD   L
Sbjct: 3   SHHHHHHSSGLVPRGSHMSNPKKPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKL 62

Query: 134 GLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKT 193
           GL DY+++I +PMD  TIK+++E   Y    E   D   +F N   YN    D+ +MA+T
Sbjct: 63  GLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQT 122

Query: 194 LLAKFEEKWLQLLPKVTEEEKRREEEEAEA 223
           L   F +K   +  +  E      +   + 
Sbjct: 123 LEKIFLQKVASMPQEEQELVVTIPKNSHKK 152

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

 Score =  155 bits (393), Expect = 2e-46
 Identities = 31/160 (19%), Positives = 66/160 (41%)

Query: 83  IRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVI 142
           +      +S RE    +  ++       ++ ++++++    F + VD K     DYY+VI
Sbjct: 1   MHHHHHHSSGRENLYFQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVI 60

Query: 143 DKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
             PM FS IK +++  +Y    E   DV+L+F N   YN   S V +  K +   F  + 
Sbjct: 61  KNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFNNQL 120

Query: 203 LQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMARDT 242
           + +       ++++  +  +   +  +           + 
Sbjct: 121 IVMGYNNFILKEKKINDMLKLVEEENIKWSKEKEDQIEEI 160

>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 =  152 bits (385), Expect = 1e-45
 Identities = 47/129 (36%), Positives = 75/129 (58%), Gaps = 6/129 (4%)

Query: 80  VPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHK---WAWPFMQPVDVKGLGLD 136
           +  +   QQ  +  +     ++ E ++    IL+ +   K   +AWPF +PVDV+ LGL 
Sbjct: 2   MKDVPDSQQHPAPEKS---SKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLH 58

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DY ++I  PMD STIK ++EA+EY++ +E   DVRL+F N  KYN    +V  MA+ L  
Sbjct: 59  DYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQD 118

Query: 197 KFEEKWLQL 205
            FE ++ ++
Sbjct: 119 VFEMRFAKM 127

>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 =  150 bits (382), Expect = 2e-45
 Identities = 46/119 (38%), Positives = 72/119 (60%), Gaps = 3/119 (2%)

Query: 96  AAEKRMEELIRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIK 152
           A   ++ E ++    IL+ +   K   +AWPF +PVDV+ LGL DY ++I  PMD STIK
Sbjct: 2   AMGSKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIK 61

Query: 153 KQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTE 211
            ++E++EY++ +E   DVRL+F N  KYN    +V  MA+ L   FE ++ ++  +  E
Sbjct: 62  SKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEE 120

>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 =  149 bits (379), Expect = 6e-45
 Identities = 39/120 (32%), Positives = 65/120 (54%), Gaps = 3/120 (2%)

Query: 91  SRREKAAEKRMEELIRQFGTILRNI-TQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFS 149
           S R+K    + EEL +     L  +  Q   + PF QPVD + LG+ DY++++  PMD S
Sbjct: 1   SMRKK--IFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLS 58

Query: 150 TIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKV 209
           TIK++++  +Y+   +   DV L+F NA  YN + S V+     L   FE++   ++  +
Sbjct: 59  TIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 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 =  148 bits (377), Expect = 2e-44
 Identities = 40/107 (37%), Positives = 60/107 (56%)

Query: 99  KRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAK 158
           ++  +L      +L+ + +H++AWPF QPVD   L L DYY++I  PMD  TIKK++E  
Sbjct: 17  RQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENN 76

Query: 159 EYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
            Y N +E   D   +F N   YN    D+ +MA+ L   F +K  +L
Sbjct: 77  YYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINEL 123

>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 =  143 bits (362), Expect = 3e-42
 Identities = 41/124 (33%), Positives = 65/124 (52%), Gaps = 3/124 (2%)

Query: 95  KAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQ 154
            A         +Q   ++  I Q + + PF QPVD+  +   DY ++ID PMDF T+++ 
Sbjct: 2   MATNYVESNWKKQCKELVNLIFQCEDSEPFRQPVDL--VEYPDYRDIIDTPMDFGTVRET 59

Query: 155 MEAKEYKNVREICTDVRLVFKNAMKYN-DERSDVHVMAKTLLAKFEEKWLQLLPKVTEEE 213
           ++A  Y +  E C D+RL+F NA  Y  ++RS ++ M   L A FEEK  ++       +
Sbjct: 60  LDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKISSDFKIGQ 119

Query: 214 KRRE 217
           K  E
Sbjct: 120 KFNE 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 =  142 bits (361), Expect = 4e-42
 Identities = 44/134 (32%), Positives = 71/134 (52%), Gaps = 3/134 (2%)

Query: 85  KQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDK 144
             Q     R +A    ++   +Q   +L  I Q + + PF QPVD+  L   DY ++ID 
Sbjct: 3   DHQPRRRLRNRAQSYDIQAWKKQCEELLNLIFQCEDSEPFRQPVDL--LEYPDYRDIIDT 60

Query: 145 PMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN-DERSDVHVMAKTLLAKFEEKWL 203
           PMDF+T+++ +EA  Y++  E+C DVRL+F N+  Y   +RS ++ M+  L A FEE   
Sbjct: 61  PMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHIS 120

Query: 204 QLLPKVTEEEKRRE 217
            +L       +  +
Sbjct: 121 SVLSDYKSALRFHK 134

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

 Score =  142 bits (361), Expect = 4e-42
 Identities = 35/126 (27%), Positives = 58/126 (46%), Gaps = 5/126 (3%)

Query: 90  ASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFS 149
             ++ +   K      R+   +L  +  H+ +  F  PV    L + DYY++I  PMD S
Sbjct: 7   GKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVP---LTVPDYYKIIKNPMDLS 63

Query: 150 TIKKQMEAK--EYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLP 207
           TIKK+++     Y    +   D RL+F+N  ++N+  S+V      L   FEE    L P
Sbjct: 64  TIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 123

Query: 208 KVTEEE 213
           +    +
Sbjct: 124 EKRFPK 129

>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 =  141 bits (358), Expect = 8e-42
 Identities = 39/116 (33%), Positives = 63/116 (54%), Gaps = 2/116 (1%)

Query: 91  SRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFST 150
           S   K  ++   + +     IL  +  H+ AWPF+ PV++K +    Y +VI KPMDFST
Sbjct: 1   SMSVKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVP--GYKKVIKKPMDFST 58

Query: 151 IKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLL 206
           I++++ + +Y N+     DVRLVF N   +N++ SD+      +   FE+KW    
Sbjct: 59  IREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTF 114

>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 =  136 bits (343), Expect = 7e-39
 Identities = 36/138 (26%), Positives = 58/138 (42%), Gaps = 5/138 (3%)

Query: 72  KDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVK 131
              + E              ++ +   K      R+   +L  +  H+ +  F  PV   
Sbjct: 50  DLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVP-- 107

Query: 132 GLGLDDYYEVIDKPMDFSTIKKQMEA--KEYKNVREICTDVRLVFKNAMKYNDERSDVHV 189
            L + DYY++I  PMD STIKK+++     Y    +   D RL+F+N  ++N+  S+V  
Sbjct: 108 -LTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVAN 166

Query: 190 MAKTLLAKFEEKWLQLLP 207
               L   FEE    L P
Sbjct: 167 AGIKLENYFEELLKNLYP 184

>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 =  132 bits (334), Expect = 1e-37
 Identities = 37/136 (27%), Positives = 62/136 (45%), Gaps = 2/136 (1%)

Query: 70  TLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVD 129
            +   E E     +  Q Q             E+       +LR++  HK AWPF++PVD
Sbjct: 39  GILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVD 98

Query: 130 VKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHV 189
                  DYY VI +PMD +T++++++ + Y+ + E   D+  +F N   YN   S  + 
Sbjct: 99  PNDAP--DYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 156

Query: 190 MAKTLLAKFEEKWLQL 205
            A+ L + F +K    
Sbjct: 157 CAEVLESFFVQKLKGF 172

>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 =  129 bits (326), Expect = 4e-37
 Identities = 35/112 (31%), Positives = 56/112 (50%), Gaps = 2/112 (1%)

Query: 94  EKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKK 153
             A   +          IL  +  H  AWPF+QPV+ + +   DYY+ I +PMD ST++ 
Sbjct: 4   NIAQRPKRGPHDAAIQNILTELQNHAAAWPFLQPVNKEEVP--DYYDFIKEPMDLSTMEI 61

Query: 154 QMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           ++E+ +Y+ + +   D RLVF N   YN E +  +  A  L   F  K  ++
Sbjct: 62  KLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 113

>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 =  128 bits (324), Expect = 9e-37
 Identities = 34/117 (29%), Positives = 59/117 (50%), Gaps = 5/117 (4%)

Query: 91  SRREKAAEKRM---EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMD 147
           S RE+   K +   ++       +L  +  HK +WPF++PVD       +YY++I  PMD
Sbjct: 1   SMREEKKTKDLFELDDDFTAMYKVLDVVKAHKDSWPFLEPVDESYAP--NYYQIIKAPMD 58

Query: 148 FSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQ 204
            S+++K++    Y    E   D++ +F+N  KYN E S+   M+  L   F    ++
Sbjct: 59  ISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 115

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

 Score =  127 bits (322), Expect = 2e-36
 Identities = 26/126 (20%), Positives = 53/126 (42%), Gaps = 7/126 (5%)

Query: 99  KRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAK 158
             + EL      + + +   K    F +PV        DY EVI +PMD ST+  +++  
Sbjct: 8   NTLRELRLFLRDVTKRLATDKRFNIFSKPVS-------DYLEVIKEPMDLSTVITKIDKH 60

Query: 159 EYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREE 218
            Y   ++   D+ L+  NA++YN ++     + +      ++    ++    + E  +  
Sbjct: 61  NYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLC 120

Query: 219 EEAEAQ 224
           EE +  
Sbjct: 121 EEIKES 126

>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 =  122 bits (309), Expect = 1e-34
 Identities = 31/107 (28%), Positives = 49/107 (45%), Gaps = 2/107 (1%)

Query: 99  KRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAK 158
           +  ++L      +L  I  H  AWPFM+PV        DYYEVI  P+D  T+ +++ ++
Sbjct: 3   EDPDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAP--DYYEVIRFPIDLKTMTERLRSR 60

Query: 159 EYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
            Y   +    D++ V  N  +YN   S+    A  L   F  K  + 
Sbjct: 61  YYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEG 107

>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 =  120 bits (303), Expect = 1e-33
 Identities = 32/123 (26%), Positives = 52/123 (42%), Gaps = 2/123 (1%)

Query: 91  SRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFST 150
           S  + +AE     + +     LR + +      F  PV         Y  +I  PMDF T
Sbjct: 1   SMLKLSAENESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAP--GYSMIIKHPMDFGT 58

Query: 151 IKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVT 210
           +K ++ A EYK+V E   D +L+  NAM YN   +  + +AK +L    +   +      
Sbjct: 59  MKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLAL 118

Query: 211 EEE 213
           +  
Sbjct: 119 KRS 121

>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 =  124 bits (312), Expect = 2e-33
 Identities = 43/194 (22%), Positives = 81/194 (41%), Gaps = 11/194 (5%)

Query: 42  KLEERVNEIEQFYLNASKKQGSNS---KGSSTLKDKEKER--HVPSIRKQQQEASRREKA 96
             EE    +E    N++   G      + S ++ D   E+         + ++A      
Sbjct: 71  SREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLD 130

Query: 97  AEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME 156
            + ++         + + +     +WPF  PV+ K +   DYY+VI  PMD  TI+K + 
Sbjct: 131 DDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNIS 188

Query: 157 AKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEK-- 214
             +Y++      DV L+  N++KYN   S     A+ ++    +   +    +T+ EK  
Sbjct: 189 KHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDI 248

Query: 215 --RREEEEAEAQLD 226
              +E    EA+L+
Sbjct: 249 CTAKEAALEEAELE 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 =  103 bits (259), Expect = 9e-26
 Identities = 27/119 (22%), Positives = 58/119 (48%), Gaps = 5/119 (4%)

Query: 90  ASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFS 149
             RR       +  ++    +I+ ++      +PF  PV+ K +   DYY++I +PMD  
Sbjct: 4   IHRRRTDPMVTLSSILE---SIINDMRDLPNTYPFHTPVNAKVVK--DYYKIITRPMDLQ 58

Query: 150 TIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPK 208
           T+++ +  + Y +  E    + L+ KN+  YN  +  +  +++++L   +EK  +   K
Sbjct: 59  TLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDK 117

>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 =  120 bits (302), Expect = 3e-33
 Identities = 32/146 (21%), Positives = 60/146 (41%), Gaps = 2/146 (1%)

Query: 74  KEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGL 133
            +      +      +   ++   ++RM+ L           +  +    FM     K  
Sbjct: 2   GDSMISSATSDTGSAKRKSKKNIRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDY 61

Query: 134 GLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKT 193
              DYY++I +PMD   I+  +   +Y     +  D++L+F+NA  YN+E S V+  A  
Sbjct: 62  P--DYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHI 119

Query: 194 LLAKFEEKWLQLLPKVTEEEKRREEE 219
           L    +EK  +L P   +++     E
Sbjct: 120 LEKLLKEKRKELGPLPDDDDMASPAE 145

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

 Score =  119 bits (300), Expect = 8e-33
 Identities = 36/152 (23%), Positives = 62/152 (40%), Gaps = 9/152 (5%)

Query: 78  RHVPSIRKQQQEASRREKAAEKRMEELIRQF-GTILRNITQHKWAWPFMQPVDVKGLGLD 136
            H  S        +   ++ +             + + +     +WPF  PV+ K +   
Sbjct: 4   HHHHSSGVDLGTENLYFQSMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP-- 61

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           DYY+VI  PMD  TI+K +   +Y++      DV L+  N++KYN   S     A+ ++ 
Sbjct: 62  DYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVN 121

Query: 197 KFEEKWLQLLPKVTEEE------KRREEEEAE 222
              +   +    +T+ E      K    EEAE
Sbjct: 122 VCYQTLTEYDEHLTQLEKDICTAKEAALEEAE 153

>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 =  122 bits (306), Expect = 3e-32
 Identities = 39/179 (21%), Positives = 71/179 (39%), Gaps = 7/179 (3%)

Query: 42  KLEERVNEIEQFYLNASKKQGSNSK-----GSSTLKDKEKERHVPSIRKQQQEASRREKA 96
             EE    +E    N++   G          S      EK +       + ++A      
Sbjct: 104 SREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLD 163

Query: 97  AEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME 156
            + ++         + + +     +WPF  PV+ K +   DYY+VI  PMD  TI+K + 
Sbjct: 164 DDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNIS 221

Query: 157 AKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKR 215
             +Y++      DV L+  N++KYN   S     A+ ++    +   +    +T+ EK 
Sbjct: 222 KHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKD 280

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

 Score =  106 bits (266), Expect = 1e-26
 Identities = 28/131 (21%), Positives = 58/131 (44%), Gaps = 2/131 (1%)

Query: 72  KDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVK 131
           K K +           +      +     M  L     +I+ ++      +PF  PV+ K
Sbjct: 16  KKKRRVGTTVHCDYLNRPHKSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAK 75

Query: 132 GLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMA 191
            +   DYY++I +PMD  T+++ +  + Y +  E    + L+ KN+  YN  +  +  ++
Sbjct: 76  VV--KDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQIS 133

Query: 192 KTLLAKFEEKW 202
           +++L   +EK 
Sbjct: 134 QSMLDLCDEKL 144

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

 Score =  116 bits (293), Expect = 5e-32
 Identities = 40/133 (30%), Positives = 61/133 (45%), Gaps = 5/133 (3%)

Query: 94  EKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKK 153
           + A E R+  L     ++L  +     A  F QPV +K +   DY + I  PMDF+T++K
Sbjct: 4   QVAMELRLTPLTVLLRSVLDQLQDKDPARIFAQPVSLKEVP--DYLDHIKHPMDFATMRK 61

Query: 154 QMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEE 213
           ++EA+ YKN+ E   D  L+  N MKYN   +  +  A  L  +      Q      E +
Sbjct: 62  RLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARR---EVD 118

Query: 214 KRREEEEAEAQLD 226
               EE +   L 
Sbjct: 119 SIGLEEASGMHLP 131

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

 Score =  115 bits (290), Expect = 8e-32
 Identities = 29/125 (23%), Positives = 53/125 (42%), Gaps = 11/125 (8%)

Query: 98  EKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA 157
           E     L      ++R + +   +  F  PV         Y  +I  PMDFST+K++++ 
Sbjct: 3   EVEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIA--PGYSMIIKHPMDFSTMKEKIKN 60

Query: 158 KEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRRE 217
            +Y+++ E+  + +L+  NAM YN   +  +  AK LL    +            ++R E
Sbjct: 61  NDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKIL---------SQERLE 111

Query: 218 EEEAE 222
                
Sbjct: 112 HHHHH 116

>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 =  114 bits (288), Expect = 2e-31
 Identities = 28/125 (22%), Positives = 56/125 (44%), Gaps = 2/125 (1%)

Query: 98  EKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA 157
           E    EL      +   +   K    F +PVD   +   DY  VI +PMD S++  +++ 
Sbjct: 5   EDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVP--DYVTVIKQPMDLSSVISKIDL 62

Query: 158 KEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRRE 217
            +Y  V++   D+ L+  NA++YN +R     + +       +    ++ +  +E+  + 
Sbjct: 63  HKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQL 122

Query: 218 EEEAE 222
            EE +
Sbjct: 123 CEEIQ 127

>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 =  114 bits (287), Expect = 2e-31
 Identities = 27/112 (24%), Positives = 46/112 (41%), Gaps = 2/112 (1%)

Query: 102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
              +      L  + +      F +PV +  +   DY + I KPMDF T+K+ +EA  Y 
Sbjct: 6   SGFLILLRKTLEQLQEKDTGNIFSEPVPLSEV--PDYLDHIKKPMDFFTMKQNLEAYRYL 63

Query: 162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEE 213
           N  +   D  L+  N +KYN + +  +  A  L  +      Q   +  +  
Sbjct: 64  NFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMG 115

>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 =  119 bits (300), Expect = 3e-31
 Identities = 38/177 (21%), Positives = 71/177 (40%), Gaps = 5/177 (2%)

Query: 77  ERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLD 136
             +     K     ++   A EK++ + +    +      + K + PFM+ VD   L   
Sbjct: 137 LINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELP-- 194

Query: 137 DYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA 196
           +YYE++  PM  S +K+ +E  +Y  + +   D+ LVF+NA  +ND  + ++  A TL  
Sbjct: 195 EYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTN 254

Query: 197 KFEEKWLQLLPKVTE---EEKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVD 250
            F     +      +   E      E  + + +  LA        A   +    + D
Sbjct: 255 YFNYLIQKEFFPELQDLNERGEINLEFDKFEFENYLAIGGGGPAAAGALAISALDND 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 = 85.1 bits (210), Expect = 9e-19
 Identities = 21/109 (19%), Positives = 40/109 (36%), Gaps = 5/109 (4%)

Query: 98  EKRMEELIRQFGTILRNITQH--KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQM 155
           +  + +  R     L  +          F++    K      YY  I +PM  + IK + 
Sbjct: 23  DWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHP--QYYYKIQQPMSINEIKSR- 79

Query: 156 EAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQ 204
           + +          DV L+ KN   YN+  S +   +  ++   E + L+
Sbjct: 80  DYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLK 128

>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 =  113 bits (284), Expect = 9e-31
 Identities = 33/135 (24%), Positives = 68/135 (50%), Gaps = 7/135 (5%)

Query: 87  QQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPM 146
            ++ S       K+M++++        + +  + +  F+Q    K L   +YYE+I KP+
Sbjct: 2   AEKLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELP--EYYELIRKPV 59

Query: 147 DFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLL 206
           DF  IK+++   +Y+++ ++  DV L+ +NA  +N E S ++  +  L + F     ++ 
Sbjct: 60  DFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKI- 118

Query: 207 PKVTEEEKRREEEEA 221
               E+E   E EE+
Sbjct: 119 ----EKEDDSEGEES 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 =  108 bits (273), Expect = 3e-29
 Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 8/110 (7%)

Query: 102 EELIRQFGTILRNITQHKW------AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQM 155
             L      +L  I           +  F +          DYY +I +P+D  TI +++
Sbjct: 7   AYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYP--DYYAIIKEPIDLKTIAQRI 64

Query: 156 EAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           +   YK++  +  D+ L+ KNA  YN+  S V   A ++   F  K  ++
Sbjct: 65  QNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEI 114

>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 =  114 bits (287), Expect = 4e-29
 Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 2/151 (1%)

Query: 74  KEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGL 133
           +    +     K     ++   A EK++ + +    +      + K + PFM+ VD   L
Sbjct: 184 RNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDEL 243

Query: 134 GLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKT 193
              +YYE++  PM  S +K+ +E  +Y  + +   D+ LVF+NA  +ND  + ++  A T
Sbjct: 244 P--EYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATT 301

Query: 194 LLAKFEEKWLQLLPKVTEEEKRREEEEAEAQ 224
           L   F     +      ++   R E   E  
Sbjct: 302 LTNYFNYLIQKEFFPELQDLNERGEINLEFD 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 = 82.2 bits (202), Expect = 1e-17
 Identities = 23/142 (16%), Positives = 43/142 (30%), Gaps = 5/142 (3%)

Query: 63  SNSKGSSTLKDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHK--W 120
              K       K +E+                   +  + +  R     L  +       
Sbjct: 38  ERPKYLPGKHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDI 97

Query: 121 AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKY 180
              F++    K      YY  I +PM  + IK + + +          DV L+ KN   Y
Sbjct: 98  FKDFIKLPSRKFHP--QYYYKIQQPMSINEIKSR-DYEYEDGPSNFLLDVELLTKNCQAY 154

Query: 181 NDERSDVHVMAKTLLAKFEEKW 202
           N+  S +   +  ++   E + 
Sbjct: 155 NEYDSLIVKNSMQVVMLIEFEV 176

>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 =  108 bits (272), Expect = 5e-29
 Identities = 26/126 (20%), Positives = 49/126 (38%), Gaps = 5/126 (3%)

Query: 86  QQQEASRREKAAEKRMEELIRQFGTILRNITQ---HKWAWPFMQPVDVKGLGLDDYYEVI 142
                S       + +     Q    +R+         A PF      K     DYY+ I
Sbjct: 3   HHHHHSSGVDLGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYP--DYYQQI 60

Query: 143 DKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
             P+    I+ +++ +EY+ +  +  D+ L+F+NA +YN   S ++     L    + K 
Sbjct: 61  KMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKK 120

Query: 203 LQLLPK 208
            +L  +
Sbjct: 121 KELARR 126

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

 Score =  107 bits (270), Expect = 6e-29
 Identities = 29/120 (24%), Positives = 56/120 (46%), Gaps = 8/120 (6%)

Query: 92  RREKAAEKRMEELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKP 145
               +      +L +Q   I+  +  +K       +  F+Q    K L   +YYE+I KP
Sbjct: 2   SSGSSGSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELP--EYYELIRKP 59

Query: 146 MDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           +DF  IK+++   +Y+++ ++  DV L+  NA  +N E S ++  +  L + F+      
Sbjct: 60  VDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQSG 119

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

 Score =  105 bits (265), Expect = 4e-28
 Identities = 34/121 (28%), Positives = 47/121 (38%), Gaps = 8/121 (6%)

Query: 99  KRMEELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIK 152
            R   L + F  I   I  +K       A P +     K     DYYE I  P+D  TI+
Sbjct: 5   ARAARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKKNA--DYYEKISDPLDLITIE 62

Query: 153 KQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEE 212
           KQ+    YK V     D+  VF+NA KY   +S V      L   +     +   ++ E 
Sbjct: 63  KQILTGYYKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQIDEI 122

Query: 213 E 213
            
Sbjct: 123 V 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 =  103 bits (259), Expect = 3e-27
 Identities = 29/118 (24%), Positives = 52/118 (44%), Gaps = 5/118 (4%)

Query: 91  SRREKAAEKRMEELIRQFGTILRNITQ---HKWAWPFMQPVDVKGLGLDDYYEVIDKPMD 147
           S ++      M++ + +    ++N T     + +  F++      L   DYY  I KPMD
Sbjct: 6   SPKKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELP--DYYLTIKKPMD 63

Query: 148 FSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
              I+  M A +Y+++  +  D  ++F NA  YN+  S ++  A  L     E    L
Sbjct: 64  MEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 121

>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 =  103 bits (258), Expect = 3e-27
 Identities = 25/112 (22%), Positives = 48/112 (42%), Gaps = 8/112 (7%)

Query: 103 ELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME 156
           + I     +   I  +K          F++    +     DYYEV+ +P+D   I+++++
Sbjct: 5   DPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQP--DYYEVVSQPIDLMKIQQKLK 62

Query: 157 AKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPK 208
            +EY +V  +  D +L+F NA  Y    S  +  A  L   +     + + K
Sbjct: 63  MEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQK 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 (249), Expect = 4e-25
 Identities = 38/159 (23%), Positives = 69/159 (43%), Gaps = 23/159 (14%)

Query: 72  KDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVK 131
             ++  +          + S++ K A+       R+   +L  +  H+ +  F +PV   
Sbjct: 50  FCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVP-- 107

Query: 132 GLGLDDYYEVIDKPMDFSTIKKQMEAK---EYKNVREICTDVRLVFKNAMKYNDERSDVH 188
              + +YY++I KPMD ST+KK+++ K    Y+   +   DVRL+FKN  ++N+    V 
Sbjct: 108 -ASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQ 166

Query: 189 VMA-----------------KTLLAKFEEKWLQLLPKVT 210
           V A                 K +   FE+K  ++    T
Sbjct: 167 VYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRT 205

>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 = 80.3 bits (197), Expect = 5e-18
 Identities = 21/120 (17%), Positives = 41/120 (34%), Gaps = 8/120 (6%)

Query: 101 MEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAK-- 158
                R+   +L  +  H+   P  Q             +     +D + I+ +++ K  
Sbjct: 74  SPANQRKCERVLLALFCHEPCRPLHQLATDS----TFSLDQPGGTLDLTLIRARLQEKLS 129

Query: 159 -EYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRRE 217
             Y + +E   DV  +FK   K  ++++DV      L   FE +  +            E
Sbjct: 130 PPYSSPQEFAQDVGRMFKQFNKLTEDKADVQ-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 = 73.8 bits (181), Expect = 5e-16
 Identities = 16/112 (14%), Positives = 39/112 (34%), Gaps = 12/112 (10%)

Query: 103 ELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQME 156
            +      +  ++  H+      ++    +   V      ++      P+ F  I+K +E
Sbjct: 7   LIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVD----PNFPNK--PPLTFDIIRKNVE 60

Query: 157 AKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPK 208
              Y+ +      +  V + A + N   S+++  A  L   F +   +L   
Sbjct: 61  NNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCKN 112

>2jns_A Bromodomain-containing protein 4; ET-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 90

 Score = 65.7 bits (160), Expect = 8e-14
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 263 KCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGF-QATAEEVELDMDAQSESTLW 321
           KC+  S EEKR+L   + +L  E LG+ + I+         +  +E+E+D +    STL 
Sbjct: 14  KCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLR 73

Query: 322 RLKFFVKDALKSQ 334
            L+ +V   L+ +
Sbjct: 74  ELERYVTSCLRKK 86

>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 = 61.5 bits (148), Expect = 2e-11
 Identities = 15/118 (12%), Positives = 44/118 (37%), Gaps = 13/118 (11%)

Query: 98  EKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA 157
               +EL      +L  +   +     ++                 +P+D   +K++M+ 
Sbjct: 70  LALEKELQISLKQVLTALLNSRTTSHLLRYRQ-------------QQPLDLEGVKRKMDQ 116

Query: 158 KEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKR 215
             Y +V E   D+  + + A+  +  + ++      + + F  +  ++ P  + ++ R
Sbjct: 117 GNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSR 174

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

 Score = 52.9 bits (126), Expect = 1e-07
 Identities = 54/332 (16%), Positives = 99/332 (29%), Gaps = 90/332 (27%)

Query: 23  VAEV---ESFTLRVDD-IF----QKVDKLEERVNEIEQFYLNASKKQGSNSKGSSTLKDK 74
             +V        ++D  IF    +  +  E  +  +++          S S  SS +K  
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK-- 224

Query: 75  EKERHVPSIRKQQQEASRREKAAEKRMEE-LIRQFGTILRNITQHKWAWPFMQPVDV--K 131
                   +R    +A  R     K  E  L+     +L N+ Q+  AW      ++  K
Sbjct: 225 --------LRIHSIQAELRRLLKSKPYENCLL-----VLLNV-QNAKAW---NAFNLSCK 267

Query: 132 GLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMA 191
            L    + +V D           + A    ++        +         DE        
Sbjct: 268 ILLTTRFKQVTD----------FLSAATTTHISLD--HHSMTL-----TPDE-------V 303

Query: 192 KTLLAKFEEKWLQLLPKVTEEEKRREEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVDV 251
           K+LL K+ +   Q LP            E       +L+  A   +    T +    V+ 
Sbjct: 304 KSLLLKYLDCRPQDLP-----------REVLTTNPRRLSIIAESIRDGLATWDNWKHVN- 351

Query: 252 HLDELREMLVQKCRKTSTEEKRKLGAALTRLS--PEDL---GKALEIVAQSNTGFQATAE 306
             D+L  ++          E RK+     RLS  P         L ++      F     
Sbjct: 352 -CDKLTTIIESSLNVLEPAEYRKM---FDRLSVFPPSAHIPTILLSLI-----WFDVIKS 402

Query: 307 EVELDMDAQSESTLWRLKFFVKDALKSQGNNN 338
           +V + ++          K      ++ Q   +
Sbjct: 403 DVMVVVN----------KLHKYSLVEKQPKES 424

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

 Score = 52.5 bits (125), Expect = 1e-07
 Identities = 47/293 (16%), Positives = 84/293 (28%), Gaps = 88/293 (30%)

Query: 15  HAGNPESDVAEVESFTLRVDDI---FQKVDKLEERVNEIEQFYLNASKKQGSNSKGSSTL 71
           H  + + +  E +    +  DI   F+          +++    +              L
Sbjct: 3   HHHHMDFETGEHQ---YQYKDILSVFEDAFVDNFDCKDVQDMPKSI-------------L 46

Query: 72  KDKEKERHVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVK 131
             +E    +  I   +   S             +R F T+L    Q +    F++ V   
Sbjct: 47  SKEE----IDHIIMSKDAVSG-----------TLRLFWTLLSK--QEEMVQKFVEEV--- 86

Query: 132 GLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVRE-ICTDVRLVFKNAMKYNDERSD---- 186
              L   Y+ +  P+     +  M  + Y   R+ +  D + VF    KYN  R      
Sbjct: 87  ---LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ-VFA---KYNVSRLQPYLK 139

Query: 187 ---------------VHVMA---KTLLA-------KFEEK------WLQLLPKVTEEEKR 215
                          +  +    KT +A       K + K      WL L      +   
Sbjct: 140 LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNL------KNCN 193

Query: 216 REEEEAEAQLDMQLAQDAAHAKMARDTSNELYEVDVHLDELREMLVQKCRKTS 268
             E   E    +    D      +  +SN    +     ELR +L  K  +  
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246

>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 = 49.5 bits (117), Expect = 2e-06
 Identities = 54/257 (21%), Positives = 89/257 (34%), Gaps = 73/257 (28%)

Query: 146 MDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           MDF T   + + + YK       D+  VF++A   N +  DV  M K++L+K E   + +
Sbjct: 7   MDFET--GEHQYQ-YK-------DILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIM 56

Query: 206 LPKVTEEEKR-------REEEEAEAQLDMQLAQD-----AAHAKMARDTS--NELYEVDV 251
                    R       ++EE  +  ++  L  +     +      R  S    +Y    
Sbjct: 57  SKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI--- 113

Query: 252 HLDELREML---VQKCRK---TSTEEKRKLGAALTRLSPEDL---------GK---ALEI 293
              E R+ L    Q   K   +  +   KL  AL  L P            GK   AL+ 
Sbjct: 114 ---EQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALD- 169

Query: 294 VAQS--------------NTGFQATAEEVELDMDAQSESTLWRLKFFVKDALKSQGNNNN 339
           V  S              N     + E V L+M       L +L + +     S+   ++
Sbjct: 170 VCLSYKVQCKMDFKIFWLNLKNCNSPETV-LEM-------LQKLLYQIDPNWTSRS--DH 219

Query: 340 NDNNKNNNNSATNNNKR 356
           + N K   +S     +R
Sbjct: 220 SSNIKLRIHSIQAELRR 236

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	377
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.96
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.96
3d7c_A	112	General control of amino acid synthesis protein 5;	99.96
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.95
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.95
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.95
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.95
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.95
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.95
3p1f_A	119	CREB-binding protein; structural genomics consorti	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
2dat_A	123	Possible global transcription activator SNF2L2; br	99.95
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.95
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.95
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.95
2grc_A	129	Probable global transcription activator SNF2L4; br	99.95
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.95
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.95
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.94
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.94
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.94
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.93
3uv4_A	158	Second bromodomain of human transcription initiat	99.93
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.93
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.93
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	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
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.91
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.9
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.9
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.89
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.88
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.87
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.86
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.81
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.81
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.77
2jns_A	90	Bromodomain-containing protein 4; ET-domain, struc	99.71
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.62
2lm0_A	125	AF4/FMR2 family member 1/protein AF-9 chimera; int	95.69

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

Probab=99.96  E-value=1.5e-29  Score=216.43  Aligned_cols=110  Identities=41%  Similarity=0.774  Sum_probs=102.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHcCC---CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhh
Q 017092           98 EKRMEELIRQFGTILRNITQHK---WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVF  174 (377)
Q Consensus        98 ~~~~~~l~~~~~~il~~l~~~~---~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif  174 (377)
                      ..++.+.++.|..||..|+.++   .+|||..||++..+++||||++|++||||+||++||.+|.|.++.+|.+||+|||
T Consensus        17 ~~~~~~~l~~c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~   96 (130)
T 2ouo_A           17 SSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMF   96 (130)
T ss_dssp             --CHHHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            3455678889999999999987   4899999999987789999999999999999999999999999999999999999


Q ss_pred             hhhhhcCCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          175 KNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       175 ~Na~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      .||++||+++|.+|.+|..|+..|+..|..+..
T Consensus        97 ~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  129 (130)
T 2ouo_A           97 SNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD  129 (130)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            999999999999999999999999999998753

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

Probab=99.96  E-value=5.1e-29  Score=209.36  Aligned_cols=103  Identities=36%  Similarity=0.679  Sum_probs=99.3

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      ..++.|..|+..|++++.+|+|..||++..  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.||+
T Consensus        13 ~~~~~c~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   90 (117)
T 3g0l_A           13 KDLALCSMILTEMETHEDAWPFLLPVNLKL--VPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNE   90 (117)
T ss_dssp             THHHHHHHHHHHHHTSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCcCChhh--cCChHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            467889999999999999999999999987  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      ++|.++.+|..|++.|++.|.+++.
T Consensus        91 ~~s~~~~~A~~L~~~f~~~~~~~~~  115 (117)
T 3g0l_A           91 DDSDIGRAGHNMRKYFEKKWTDTFK  115 (117)
T ss_dssp             SSSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999998753

>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=7.1e-29  Score=206.96  Aligned_cols=103  Identities=30%  Similarity=0.477  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      ..+...|..|+..|++|+.+++|..||++..  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||++||
T Consensus         6 ~~l~~~~~~il~~l~~~~~~~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN   83 (112)
T 3d7c_A            6 DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSE--APDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYN   83 (112)
T ss_dssp             HHHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHcCCCchhhcCCCCccc--ccCHHHHccCCcCHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHC
Confidence            4788999999999999999999999999987  99999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          182 DERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      +++|.++.+|..|++.|++.|.++.
T Consensus        84 ~~~s~~~~~A~~L~~~f~~~~~~~~  108 (112)
T 3d7c_A           84 PPDSEYCRCASALEKFFYFKLKEGG  108 (112)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            9999999999999999999998763

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

Probab=99.95  E-value=1.3e-28  Score=209.86  Aligned_cols=105  Identities=38%  Similarity=0.644  Sum_probs=98.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      ++...|..|+..|++|+.+|+|..||++..+++||||++|++||||+||++||++|.|.++.+|.+||+|||.||++||+
T Consensus        21 ~l~~~~~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~  100 (127)
T 2oss_A           21 QLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNK  100 (127)
T ss_dssp             HHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhCccchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            45667888999999999999999999987566999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      ++|.+|.+|..|++.|++.|.++..
T Consensus       101 ~~s~i~~~A~~L~~~f~~~~~~lp~  125 (127)
T 2oss_A          101 PGDDIVLMAEALEKLFLQKINELPT  125 (127)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            9999999999999999999988753

>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=6.7e-29  Score=209.50  Aligned_cols=107  Identities=41%  Similarity=0.769  Sum_probs=102.1

Q ss_pred             HHHHHHHHHHHHHHHHcCCC---CCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhh
Q 017092          101 MEELIRQFGTILRNITQHKW---AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNA  177 (377)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~~---a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  177 (377)
                      +.+.++.|..||..|.+++.   +|||..||++..+++||||++|++||||+||++||++|.|.++.+|.+||+|||.||
T Consensus         7 ~~~~l~~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na   86 (120)
T 3jvl_A            7 ISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNC   86 (120)
T ss_dssp             SCHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHH
Confidence            34788999999999999886   999999999998889999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          178 MKYNDERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       178 ~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      ++||+++|.++.+|..|+..|+..|..+..
T Consensus        87 ~~yN~~~s~~~~~A~~L~~~f~~~~~~~p~  116 (120)
T 3jvl_A           87 YKYNPPDHEVVAMARKLQDVFEMRFAKMPD  116 (120)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHCcC
Confidence            999999999999999999999999998864

>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=1e-28  Score=207.21  Aligned_cols=101  Identities=30%  Similarity=0.582  Sum_probs=97.7

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      .++.+.|..||..|++++.+++|..||++..  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.||
T Consensus        15 ~~~~~~~~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN   92 (116)
T 3nxb_A           15 DDDFTAMYKVLDVVKAHKDSWPFLEPVDESY--APNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYN   92 (116)
T ss_dssp             CCHHHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCcHhhcCcCChhh--ccChHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            3578899999999999999999999999997  99999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHh
Q 017092          182 DERSDVHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~~~  204 (377)
                      +++|.++.+|..|+..|++.|.+
T Consensus        93 ~~~s~~~~~A~~L~~~f~~~~~k  115 (116)
T 3nxb_A           93 GESSEYTKMSDNLERCFHRAMMK  115 (116)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999875

>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=1.6e-28  Score=208.12  Aligned_cols=105  Identities=36%  Similarity=0.592  Sum_probs=100.8

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .+.+.|..||..|++++.+++|..||++..  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||+.||+
T Consensus        10 ~~~~~c~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   87 (123)
T 3q2e_A           10 NWKKQCKELVNLIFQCEDSEPFRQPVDLVE--YPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTP   87 (123)
T ss_dssp             CHHHHHHHHHHHHHTSGGGGGGSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhCCCcHhhcCCCChhh--cCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            688899999999999999999999999987  999999999999999999999999999999999999999999999999


Q ss_pred             C-CCHHHHHHHHHHHHHHHHHHhhCCCC
Q 017092          183 E-RSDVHVMAKTLLAKFEEKWLQLLPKV  209 (377)
Q Consensus       183 ~-~s~v~~~A~~L~~~fe~~~~~~~p~~  209 (377)
                      + +|.+|.+|..|+..|++.|..+++.+
T Consensus        88 ~~~s~i~~~A~~L~~~f~~~~~~~~~~~  115 (123)
T 3q2e_A           88 NKRSKIYSMTLRLSALFEEKMKKISSDF  115 (123)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6 99999999999999999999986544

>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=1.1e-28  Score=208.51  Aligned_cols=100  Identities=34%  Similarity=0.620  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCC
Q 017092          104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDE  183 (377)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~  183 (377)
                      .+..|..|+..|++|+.+++|..||+...  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||++||++
T Consensus        14 ~~~~~~~il~~l~~~~~a~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~   91 (121)
T 1e6i_A           14 HDAAIQNILTELQNHAAAWPFLQPVNKEE--VPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGE   91 (121)
T ss_dssp             THHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCT
T ss_pred             HHHHHHHHHHHHHcCCCchhhCCCCChhh--CcCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            46789999999999999999999999887  9999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhh
Q 017092          184 RSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       184 ~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      +|.++.+|..|++.|++.|..+
T Consensus        92 ~s~i~~~A~~L~~~f~~~~~~~  113 (121)
T 1e6i_A           92 NTSYYKYANRLEKFFNNKVKEI  113 (121)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHTS
T ss_pred             CCHHHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999887

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

Probab=99.95  E-value=3.8e-28  Score=204.06  Aligned_cols=104  Identities=26%  Similarity=0.337  Sum_probs=99.3

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhc
Q 017092          101 MEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      ...+...|..|++.|++++.+++|..||++..  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++|
T Consensus         6 ~~~l~~~l~~il~~L~~~~~~~~F~~PVd~~~--~pdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Li~~Na~~y   83 (117)
T 2i7k_A            6 QTPLQEALNQLMRQLQRKDPSAFFSFPVTDFI--APGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIY   83 (117)
T ss_dssp             HHHHHHHHHHHHHHHHTSSGGGTSSSCCCTTT--SSSHHHHCSCCCCHHHHHHHHTTTSCCSHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHhCcccHHhcCCCCccc--cCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            34678899999999999999999999999876  9999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          181 NDERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       181 N~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      |+++|.++.+|..|++.|++.|....
T Consensus        84 N~~~s~i~~~A~~L~~~f~~~~~~~~  109 (117)
T 2i7k_A           84 NKPETIYYKAAKKLLHSGMKILSQER  109 (117)
T ss_dssp             SCSSSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999998764

>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=2.8e-28  Score=205.39  Aligned_cols=105  Identities=33%  Similarity=0.569  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHHHHHHc-CCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhc
Q 017092          102 EELIRQFGTILRNITQ-HKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~-~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      .++.+.|..++..|+. ++.+|||..||++..+++||||++|++||||+||++||++|.|.++.+|.+||+|||.||++|
T Consensus        10 ~el~~~l~~~l~~l~~~~~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~y   89 (119)
T 3p1f_A           10 EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLY   89 (119)
T ss_dssp             HHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            4788899999999988 789999999999985569999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          181 NDERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       181 N~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      |+++|.+|.+|..|++.|++.|..++
T Consensus        90 N~~~s~i~~~A~~L~~~f~~~~~~~~  115 (119)
T 3p1f_A           90 NRKTSRVYKFCSKLAEVFEQEIDPVM  115 (119)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999998874

>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=7.2e-29  Score=213.50  Aligned_cols=105  Identities=38%  Similarity=0.607  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      ..+.+.|..||..|+.++.+++|..||++..  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||+.||
T Consensus        20 ~~l~~~~~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN   97 (135)
T 3mb3_A           20 QAWKKQCEELLNLIFQCEDSEPFRQPVDLLE--YPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYT   97 (135)
T ss_dssp             STHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHhCCCChhhcCCCChhh--CCCHHHHhCCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            3688899999999999999999999999977  99999999999999999999999999999999999999999999999


Q ss_pred             CC-CCHHHHHHHHHHHHHHHHHHhhCCC
Q 017092          182 DE-RSDVHVMAKTLLAKFEEKWLQLLPK  208 (377)
Q Consensus       182 ~~-~s~v~~~A~~L~~~fe~~~~~~~p~  208 (377)
                      ++ +|.||.+|..|++.|++.|..+++.
T Consensus        98 ~~~~s~i~~~A~~L~~~f~~~~~~~~~~  125 (135)
T 3mb3_A           98 PSKRSRIYSMSLRLSAFFEEHISSVLSD  125 (135)
T ss_dssp             CCTTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            97 9999999999999999999988654

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

Probab=99.95  E-value=5.2e-28  Score=208.18  Aligned_cols=105  Identities=31%  Similarity=0.526  Sum_probs=99.3

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhc--CCCCCHHHHHHHHHhhhhhhhhc
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA--KEYKNVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~--~~Y~s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      ..++.|..||..|++|+.+++|..||+..   +||||++|++||||+||++||++  +.|.++.+|.+||+|||.||++|
T Consensus        20 ~~~~~c~~il~~L~~~~~s~~F~~Pv~~~---~pdY~~iIk~PmDL~tI~~kL~~~~~~Y~s~~ef~~Dv~Lif~Na~~y   96 (135)
T 2yyn_A           20 IDKRKCERLLLFLYCHEMSLAFQDPVPLT---VPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEF   96 (135)
T ss_dssp             HHHHHHHHHHHHHHTSGGGGGGSSCCCTT---STTHHHHCSSCCCHHHHHHHHHSSSCCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCccchhhcCCCccc---CCCHHHHcCCCCCHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHH
Confidence            35678999999999999999999999973   99999999999999999999998  58999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhhCCCCc
Q 017092          181 NDERSDVHVMAKTLLAKFEEKWLQLLPKVT  210 (377)
Q Consensus       181 N~~~s~v~~~A~~L~~~fe~~~~~~~p~~~  210 (377)
                      |+++|.||.+|..|+..|+..|.+++|...
T Consensus        97 N~~~s~i~~~A~~L~~~f~~~~~~~~~~~~  126 (135)
T 2yyn_A           97 NEPDSEVANAGIKLENYFEELLKNLYPEKR  126 (135)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhccccC
Confidence            999999999999999999999999988654

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

Probab=99.95  E-value=3.8e-28  Score=205.81  Aligned_cols=103  Identities=28%  Similarity=0.437  Sum_probs=98.1

Q ss_pred             HHHHHHHHHHHHHHcCC------CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhh
Q 017092          103 ELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKN  176 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~------~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  176 (377)
                      .+.+.|..|++.|++++      .+++|..||+...  +||||++|++||||+||++||++|.|.++.+|.+||+|||.|
T Consensus        13 ~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~N   90 (123)
T 2dat_A           13 KLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKE--LPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHN   90 (123)
T ss_dssp             HHHHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCTTT--SCHHHHHCSSCCCHHHHHHHHTTTCCCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhcccCCeeeHHhcCCCCccc--CCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence            67889999999999986      6999999999887  999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          177 AMKYNDERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       177 a~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      |++||+++|.+|.+|..|++.|+..|+++++
T Consensus        91 a~~yN~~~s~i~~~A~~L~~~f~~~~~~~ps  121 (123)
T 2dat_A           91 AQTFNLEGSQIYEDSIVLQSVFKSARQSGPS  121 (123)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHcCC
Confidence            9999999999999999999999999998754

>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=5.5e-28  Score=204.30  Aligned_cols=101  Identities=27%  Similarity=0.376  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .+...|..||..|++++.+++|..||++..  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||++||+
T Consensus         7 pl~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~   84 (121)
T 2d9e_A            7 GFLILLRKTLEQLQEKDTGNIFSEPVPLSE--VPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNA   84 (121)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCSSSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHcCCccHhhCCcCCccc--cCCHHHHcCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            466789999999999999999999999987  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhh
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      ++|.+|.+|..|++.|+..|.++
T Consensus        85 ~~s~~~~~A~~L~~~~~~~l~~~  107 (121)
T 2d9e_A           85 KDTIFYRAAVRLREQGGAVLRQA  107 (121)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998876

>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=3.9e-28  Score=213.38  Aligned_cols=107  Identities=35%  Similarity=0.592  Sum_probs=100.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .+...|..|+..|++++.+|+|..||++..+++||||++|++||||+||++||+++.|.++.+|.+||+|||.||++||+
T Consensus        32 ~l~~~~~~il~~l~~~~~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  111 (154)
T 4alg_A           32 QLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNK  111 (154)
T ss_dssp             HHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhCcCchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            45667788999999999999999999999777999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhhCCCC
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQLLPKV  209 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~~p~~  209 (377)
                      ++|.|+.+|..|+++|+..|..+.+..
T Consensus       112 ~~s~i~~~A~~L~~~f~~~~~~l~~~~  138 (154)
T 4alg_A          112 PTDDIVLMAQTLEKIFLQKVASMPQEE  138 (154)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHTTSCSSC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCchh
Confidence            999999999999999999999986543

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

Probab=99.95  E-value=4.1e-28  Score=215.81  Aligned_cols=105  Identities=27%  Similarity=0.436  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      ..+...|..||..|++++.+++|..||++..+++||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||
T Consensus        20 ~~~~~~~~~il~~L~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN   99 (166)
T 3fkm_X           20 KQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLYN   99 (166)
T ss_dssp             HHHHHHHHHHHHHHTTSTTGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHhCCCChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            37888999999999999999999999998877799999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          182 DERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      +++|.|+.+|..|+++|++.|..+.
T Consensus       100 ~~~s~i~~~A~~L~~~f~~~l~~~~  124 (166)
T 3fkm_X          100 TSNSVVAITGKNIETYFNNQLIVMG  124 (166)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            9999999999999999999998873

>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=99.95  E-value=5.9e-28  Score=206.28  Aligned_cols=103  Identities=27%  Similarity=0.428  Sum_probs=98.1

Q ss_pred             HHHHHHHHHHHHHHHcCC-------CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhh
Q 017092          102 EELIRQFGTILRNITQHK-------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVF  174 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~-------~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif  174 (377)
                      ..+.+.|..||+.|++++       .+++|..||+...  +||||++|++||||+||++||.+|.|.++.+|.+||+|||
T Consensus        10 ~~l~~~~~~il~~l~~~~d~~~~~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~   87 (129)
T 2grc_A           10 PNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKE--LPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLC   87 (129)
T ss_dssp             HHHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccccccCeeeHHhcCCCCccc--CCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence            368889999999999875       6899999999877  9999999999999999999999999999999999999999


Q ss_pred             hhhhhcCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          175 KNAMKYNDERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       175 ~Na~~YN~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      .||++||+++|.+|.+|..|++.|++.|..+.
T Consensus        88 ~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~  119 (129)
T 2grc_A           88 QNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIE  119 (129)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            99999999999999999999999999999884

>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=99.95  E-value=1.5e-27  Score=202.36  Aligned_cols=102  Identities=25%  Similarity=0.408  Sum_probs=96.8

Q ss_pred             HHHHHHHHHHHHHHc------CCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhh
Q 017092          103 ELIRQFGTILRNITQ------HKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKN  176 (377)
Q Consensus       103 ~l~~~~~~il~~l~~------~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  176 (377)
                      .+.+.|..|++.|++      ++.+++|..||+...  +||||++|++||||+||++||++|.|.++.+|.+||+|||.|
T Consensus        15 ~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~N   92 (124)
T 3mb4_A           15 PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSE--LPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNN   92 (124)
T ss_dssp             HHHHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHhcccCCcccHHhhcCCCccc--cCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence            567789999999998      567899999999887  999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          177 AMKYNDERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       177 a~~YN~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      |+.||+++|.+|.+|..|++.|++.|.++.
T Consensus        93 a~~yN~~~s~i~~~A~~L~~~f~~~~~~l~  122 (124)
T 3mb4_A           93 ACTYNEPESLIYKDALVLHKVLLETRRDLE  122 (124)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999874

>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=99.95  E-value=1e-27  Score=203.95  Aligned_cols=106  Identities=30%  Similarity=0.359  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHHHHcCC------CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhh
Q 017092          101 MEELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVF  174 (377)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~------~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif  174 (377)
                      ...+.+.|..|++.|.++.      .+|||..||+...  +||||++|++||||+||++||.+|.|.++.+|.+||+|||
T Consensus         7 ~~~l~~~~~~i~~~l~~~~d~~g~~~s~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~   84 (126)
T 3mqm_A            7 AARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKK--NADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVF   84 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGGG--CTTHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCcCCCChhHHhcCCCCccc--CCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            3467778888888888764      5999999999987  9999999999999999999999999999999999999999


Q ss_pred             hhhhhcCCCCCHHHHHHHHHHHHHHHHHHhhCCC
Q 017092          175 KNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPK  208 (377)
Q Consensus       175 ~Na~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p~  208 (377)
                      .||+.||+++|.+|.+|..|++.|++.|.++.+.
T Consensus        85 ~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~~  118 (126)
T 3mqm_A           85 RNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQ  118 (126)
T ss_dssp             HHHHHHHCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999887543

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

Probab=99.94  E-value=1.6e-27  Score=205.04  Aligned_cols=103  Identities=32%  Similarity=0.461  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhc
Q 017092          101 MEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      +..+...|..||+.|++++.+++|..||++..  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.|
T Consensus        11 ~~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~y   88 (135)
T 3rcw_A           11 LTPLTVLLRSVLDQLQDKDPARIFAQPVSLKE--VPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKY   88 (135)
T ss_dssp             CCHHHHHHHHHHHHHHHTCTTCSSSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHhCCcchhhcCCCChhh--cCCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            34678899999999999999999999999987  9999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 017092          181 NDERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       181 N~~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      |+++|.+|.+|..|.+.|+..|...
T Consensus        89 N~~~s~~~~~A~~L~~~~~~~~~~~  113 (135)
T 3rcw_A           89 NARDTVFYRAAVRLRDQGGVVLRQA  113 (135)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999876

>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=1.5e-27  Score=202.21  Aligned_cols=100  Identities=29%  Similarity=0.369  Sum_probs=96.2

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .+...|..|+..|..++.+++|..||++..  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.||+
T Consensus        13 p~~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   90 (123)
T 3hme_A           13 PIQQLLEHFLRQLQRKDPHGFFAFPVTDAI--APGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNR   90 (123)
T ss_dssp             HHHHHHHHHHHHHHTTCTTCSSSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhCCccHhhcCCCChhh--ccCHHHHCCCCCCHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            567789999999999999999999999887  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHh
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~  204 (377)
                      ++|.+|.+|..|.+.|++.|.+
T Consensus        91 ~~s~~~~~A~~L~~~~~~~~~~  112 (123)
T 3hme_A           91 PDTVYYKLAKKILHAGFKMMSK  112 (123)
T ss_dssp             TTSHHHHHHHHHHHHHHHHTCH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998754

>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=1.7e-27  Score=199.74  Aligned_cols=103  Identities=22%  Similarity=0.373  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHHHHcC------CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhh
Q 017092          103 ELIRQFGTILRNITQH------KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKN  176 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~------~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  176 (377)
                      +.++.|..|+..|+++      +.+++|..||+...  +||||++|++||||+||++||++|.|.++.+|.+||+|||.|
T Consensus         5 ~~~~~c~~il~~l~~~~d~~g~~~s~~F~~p~~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~N   82 (116)
T 3iu5_A            5 DPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRN--QPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNN   82 (116)
T ss_dssp             CHHHHHHHHHHHHHHCBCTTCCBGGGGGSSCCCGGG--CHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhccCCCeeeHHhcCCCCccc--CCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence            3577899999999988      46999999999887  999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          177 AMKYNDERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       177 a~~YN~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      |+.||+++|.+|.+|..|++.|+..+.++..
T Consensus        83 a~~yN~~~s~~~~~A~~L~~~f~~~~~~l~~  113 (116)
T 3iu5_A           83 AKSYYKPDSPEYKAACKLWDLYLRTRNEFVQ  113 (116)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999998854

>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=4.1e-27  Score=201.28  Aligned_cols=103  Identities=25%  Similarity=0.394  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHHHHHHcCC------CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhh
Q 017092          101 MEELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVF  174 (377)
Q Consensus       101 ~~~l~~~~~~il~~l~~~~------~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif  174 (377)
                      ...+..+|..+++.|.++.      .++||..||+...  +||||++|++||||+||++||++|.|.++.+|.+||+|||
T Consensus        15 ~~kl~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~~--~PdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~Lif   92 (130)
T 3k2j_A           15 TENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKK--YPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMF   92 (130)
T ss_dssp             HHHHHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhcccCCCccHhhcCCCChhh--CccHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence            3467888888888888764      4999999999887  9999999999999999999999999999999999999999


Q ss_pred             hhhhhcCCCCCHHHHHHHHHHHHHHHHHHhh
Q 017092          175 KNAMKYNDERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       175 ~Na~~YN~~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      .||++||+++|.++.+|..|++.|++.|.++
T Consensus        93 ~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l  123 (130)
T 3k2j_A           93 ENAKRYNVPNSAIYKRVLKLQQVMQAKKKEL  123 (130)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999987

>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=4.1e-27  Score=198.60  Aligned_cols=102  Identities=25%  Similarity=0.380  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHHHHcCCC------CCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhh
Q 017092          102 EELIRQFGTILRNITQHKW------AWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFK  175 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~------a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~  175 (377)
                      ..+...|..++..|..+..      +++|..||+...  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.
T Consensus         7 ~~l~~~~~~ll~~l~~~~d~~g~~~s~~F~~~~~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~   84 (120)
T 3ljw_A            7 AYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQ--YPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAK   84 (120)
T ss_dssp             HHHHHHHHHHHHHHHHCBCTTSCBTTGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccCcCCCcccHHhcCCCCccc--CCChHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHH
Confidence            3567788999999988765      999999999887  99999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCCCHHHHHHHHHHHHHHHHHHhh
Q 017092          176 NAMKYNDERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       176 Na~~YN~~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      ||+.||+++|.+|.+|..|++.|+..|.++
T Consensus        85 Na~~yN~~~s~~~~~A~~L~~~f~~~~~~i  114 (120)
T 3ljw_A           85 NAKTYNEPGSQVFKDANSIKKIFYMKKAEI  114 (120)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999987

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

Probab=99.93  E-value=1.9e-26  Score=201.76  Aligned_cols=104  Identities=27%  Similarity=0.435  Sum_probs=92.1

Q ss_pred             HHHHHHHHHHcC-------CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhh
Q 017092          107 QFGTILRNITQH-------KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK  179 (377)
Q Consensus       107 ~~~~il~~l~~~-------~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  179 (377)
                      +|..|+..|+++       +.+++|..||+...  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.
T Consensus        28 ~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~  105 (150)
T 3tlp_A           28 RMKILFNVVLEAREPGSGRRLCDLFMVKPSKKD--YPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARH  105 (150)
T ss_dssp             HHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcccCCcccHHhcCCCchhh--CcCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            455555555554       45999999999887  999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhCCCCchH
Q 017092          180 YNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEE  212 (377)
Q Consensus       180 YN~~~s~v~~~A~~L~~~fe~~~~~~~p~~~~~  212 (377)
                      ||+++|.||.+|..|++.|++.|.++.+...++
T Consensus       106 yN~~~s~i~~~A~~L~~~f~~~~~~l~~~pd~d  138 (150)
T 3tlp_A          106 YNEEGSQVYNDAHILEKLLKEKRKELGPLPDDD  138 (150)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHCCC----
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHccCCCChh
Confidence            999999999999999999999999998775544

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

Probab=99.93  E-value=2.2e-26  Score=203.00  Aligned_cols=103  Identities=27%  Similarity=0.477  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHH-HHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          103 ELIRQFGTILRN-ITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       103 ~l~~~~~~il~~-l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      .+...|..|+.. |+.++.+|||..||++..  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||
T Consensus        29 ~l~~iL~~i~~~kl~~~~~s~~F~~PVd~~~--~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~yN  106 (158)
T 3uv4_A           29 AFSFILDNIVTQKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYN  106 (158)
T ss_dssp             HHHHHHHHHHHHTTTTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCchhhcCcCChhh--cccHHHHcCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            344455555554 667899999999999987  99999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          182 DERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      +++|.|+.+|..|...|+..|.++..
T Consensus       107 ~~~s~i~~~A~~L~~~~~~~l~e~~~  132 (158)
T 3uv4_A          107 GPESQYTKTAQEIVNVCYQTLTEYDE  132 (158)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999998743

>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=99.93  E-value=5.8e-26  Score=203.11  Aligned_cols=101  Identities=32%  Similarity=0.591  Sum_probs=96.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .....|..||..|+.++.+++|..||++..  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||++||+
T Consensus        72 ~~~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~  149 (174)
T 2ri7_A           72 KDYEGLKRVLRSLQAHKMAWPFLEPVDPND--APDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNP  149 (174)
T ss_dssp             HHHHHHHHHHHHHHTSGGGTTTSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHTTCCCBHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhhhhhhhhhcCCCccc--CCchHHHhCCcCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            456789999999999999999999999987  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhh
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      ++|.+|.+|..|+++|++.|..+
T Consensus       150 ~~s~~~~~A~~L~~~f~~~~~~~  172 (174)
T 2ri7_A          150 SDSPFYQCAEVLESFFVQKLKGF  172 (174)
T ss_dssp             TTSHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999998765

>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=99.93  E-value=2.2e-25  Score=190.63  Aligned_cols=104  Identities=25%  Similarity=0.373  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhh
Q 017092          100 RMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK  179 (377)
Q Consensus       100 ~~~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  179 (377)
                      .+.++...|..++..|..++.++||..||++..  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||+.
T Consensus         7 ~l~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~   84 (130)
T 3dai_A            7 TFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDE--VPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALE   84 (130)
T ss_dssp             HHHHHHHHHHHHHHHHHTSGGGGGGSSCCCTTT--CTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCccHhhcCCCChhh--cCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHH
Confidence            455778899999999999999999999999987  999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHH----HHHHHHHHHHHHHHHHhh
Q 017092          180 YNDERSDV----HVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       180 YN~~~s~v----~~~A~~L~~~fe~~~~~~  205 (377)
                      ||+++|++    +.+|..|++.+...+...
T Consensus        85 yN~~~s~~~~~i~~~A~~L~~~~~~~i~~e  114 (130)
T 3dai_A           85 YNPDRDPGDRLIRHRACALRDTAYAIIKEE  114 (130)
T ss_dssp             HCCSSSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCChhHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999977    678888888888887643

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

Probab=99.92  E-value=1.3e-25  Score=202.81  Aligned_cols=102  Identities=32%  Similarity=0.544  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhc--CCCCCHHHHHHHHHhhhhhhhhc
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA--KEYKNVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~--~~Y~s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      .+.+.|..||..|+.++.+++|..||+..   +|+||++|++||||+||++||++  |.|.++.+|.+||+|||.||++|
T Consensus        81 ~~~~~c~~il~~l~~~~~s~~F~~Pv~~~---~pdY~~iIk~PmdL~tI~~kl~~~~~~Y~s~~ef~~Dv~li~~Na~~y  157 (184)
T 3o36_A           81 IDKRKCERLLLFLYCHEMSLAFQDPVPLT---VPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEF  157 (184)
T ss_dssp             HHHHHHHHHHHHHHHSTTCHHHHSCCCTT---STTHHHHCSSCCCHHHHHHHHHSTTCSCCSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhchhhhhhccccccC---CCchhhhcCCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            56778999999999999999999999964   89999999999999999999998  78999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          181 NDERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       181 N~~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      |+++|.|+.+|..|+.+|++.|.+++|
T Consensus       158 N~~~s~v~~~a~~L~~~f~~~~~~~~P  184 (184)
T 3o36_A          158 NEPDSEVANAGIKLENYFEELLKNLYP  184 (184)
T ss_dssp             SCTTCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhCc
Confidence            999999999999999999999999986

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

Probab=99.91  E-value=3.8e-24  Score=183.07  Aligned_cols=100  Identities=26%  Similarity=0.434  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhh
Q 017092          100 RMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK  179 (377)
Q Consensus       100 ~~~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  179 (377)
                      .+.+|...|..|+..|+.++.++||..|       +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++
T Consensus         9 ~~~~L~~~~~~il~~l~~~~~~~~F~~P-------~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~   81 (131)
T 2dkw_A            9 TLRELRLFLRDVTKRLATDKRFNIFSKP-------VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALE   81 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHSGGGCTTSSC-------CSSCTTSCSSCCCHHHHHHHHHTTCCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCccchhhcCc-------CccHHhHcCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            3457788999999999999999999998       799999999999999999999999999999999999999999999


Q ss_pred             cCCCCCH----HHHHHHHHHHHHHHHHHhhC
Q 017092          180 YNDERSD----VHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       180 YN~~~s~----v~~~A~~L~~~fe~~~~~~~  206 (377)
                      ||+++|+    ++.+|..|.+.|...++.-+
T Consensus        82 yN~~~s~~~~~i~~~A~~L~~~~~~~l~~~l  112 (131)
T 2dkw_A           82 YNPDKDPGDKIIRHRACTLKDTAHAIIAAEL  112 (131)
T ss_dssp             SCCCSSTTHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HCCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999995    57899999999999886544

>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=2.7e-24  Score=197.65  Aligned_cols=104  Identities=31%  Similarity=0.559  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhc---CCCCCHHHHHHHHHhhhhhhhh
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA---KEYKNVREICTDVRLVFKNAMK  179 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~---~~Y~s~~ef~~Dv~Lif~Na~~  179 (377)
                      ...+.|..||..|+.++.+++|..||+. .  +|+||++|++||||+||++||++   |.|.++.+|.+||+|||.||++
T Consensus        81 ~~~~~c~~il~~l~~~~~s~~F~~Pv~~-~--~pdY~~iIk~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li~~Na~~  157 (207)
T 3u5n_A           81 VDQRKCERLLLYLYCHELSIEFQEPVPA-S--IPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCER  157 (207)
T ss_dssp             HHHHHHHHHHHHHHTSTTCGGGSSCCCT-T--STTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccchhhhhccCCh-h--hccHhHHhCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHHHH
Confidence            5677899999999999999999999987 3  99999999999999999999997   7999999999999999999999


Q ss_pred             cCC-----------------CCCHHHHHHHHHHHHHHHHHHhhCCCC
Q 017092          180 YND-----------------ERSDVHVMAKTLLAKFEEKWLQLLPKV  209 (377)
Q Consensus       180 YN~-----------------~~s~v~~~A~~L~~~fe~~~~~~~p~~  209 (377)
                      ||+                 ++|.++.+|..|+.+|+.+|.+++|..
T Consensus       158 yN~~~s~v~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~~~~~~p~~  204 (207)
T 3u5n_A          158 FNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDR  204 (207)
T ss_dssp             HHHHHHHHC----------CCCCHHHHHHHHHHHHHHHHHHHHSTTC
T ss_pred             HCCCcchHHHHHHHHHhcccccCHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            999                 999999999999999999999999863

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

Probab=99.91  E-value=3.2e-24  Score=204.19  Aligned_cols=103  Identities=24%  Similarity=0.510  Sum_probs=99.5

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .+...|..||..|.+++.++||..||++..  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||+
T Consensus        14 ~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   91 (265)
T 3uv5_A           14 TLSSILESIINDMRDLPNTYPFHTPVNAKV--VKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNG   91 (265)
T ss_dssp             HHHHHHHHHHHHHHTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHcCCCchhhhCCCChhh--cCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhhhcCC
Confidence            678899999999999999999999999998  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhhCC
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQLLP  207 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~~p  207 (377)
                      ++|.++.+|..|...|+..|.++.+
T Consensus        92 ~~s~i~~~A~~l~~~~~~~~~~~~~  116 (265)
T 3uv5_A           92 PKHSLTQISQSMLDLCDEKLKEKED  116 (265)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             CCChHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999988743

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

Probab=99.90  E-value=1.4e-24  Score=196.87  Aligned_cols=99  Identities=20%  Similarity=0.251  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhcc--CCCChHHHHHHHhcC---CCCCHHHHHHHHHhhhhhhh
Q 017092          104 LIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVID--KPMDFSTIKKQMEAK---EYKNVREICTDVRLVFKNAM  178 (377)
Q Consensus       104 l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk--~PMDL~tIk~kL~~~---~Y~s~~ef~~Dv~Lif~Na~  178 (377)
                      .++.|..||..|+.|+.+|||.+||+      |+||++|+  +||||+||++||++|   .|.++++|.+||+|||+||+
T Consensus        77 ~~~~c~~iL~~l~~~~~s~pF~~pV~------~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~Y~s~~eF~~Dv~Lif~N~~  150 (189)
T 2ro1_A           77 NQRKCERVLLALFCHEPCRPLHQLAT------DSTFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFN  150 (189)
T ss_dssp             HHHHHHHHHHHHHHSTTHHHHHSCSC------CTTCSSSCSSCCCCHHHHHHHHHTSSSSCCSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccCccchhhcCCCC------hhhhccccCCCcccHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHH
Confidence            35689999999999999999999997      67999998  899999999999999   99999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHHHHHHHHHHhhCCCC
Q 017092          179 KYNDERSDVHVMAKTLLAKFEEKWLQLLPKV  209 (377)
Q Consensus       179 ~YN~~~s~v~~~A~~L~~~fe~~~~~~~p~~  209 (377)
                      +|| +++.++.+|..|+++|+++|.++++..
T Consensus       151 ~yN-~~s~~~~~a~~L~~~Fe~~~~~~~~~~  180 (189)
T 2ro1_A          151 KLT-EDKADVQSIIGLQRFFETRMNEAFGDT  180 (189)
T ss_dssp             HHC-CSSCSSHHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHC-CCCHHHHHHHHHHHHHHHHHHHhcCcc
Confidence            999 588899999999999999999998753

>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=5.6e-24  Score=202.51  Aligned_cols=99  Identities=28%  Similarity=0.497  Sum_probs=92.2

Q ss_pred             HHHHHHHHH-HHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCC
Q 017092          106 RQFGTILRN-ITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDER  184 (377)
Q Consensus       106 ~~~~~il~~-l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~  184 (377)
                      ..|..++.. ++.++.+|||..||+...  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||+++
T Consensus       139 ~il~~i~~~~l~~~~~~~~F~~pv~~~~--~pdY~~iIk~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~lif~Na~~yN~~~  216 (265)
T 3uv5_A          139 FILDNIVTQKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPE  216 (265)
T ss_dssp             HHHHHHHHHTTTTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTT
T ss_pred             HHHHHHHHHHHHhhhhhHHHhCCCChhH--hCcHHHHhCCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            345555544 788999999999999988  99999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhhC
Q 017092          185 SDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       185 s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      |.+|.+|..|...|+..|..+.
T Consensus       217 s~~~~~A~~l~~~~~~~~~~~~  238 (265)
T 3uv5_A          217 SQYTKTAQEIVNVCYQTLTEYD  238 (265)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999874

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

Probab=99.89  E-value=1e-23  Score=203.37  Aligned_cols=102  Identities=25%  Similarity=0.520  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      ..+...|..||..|++++.+++|..||++..  +||||++|++||||+||++||++|.|.++.+|.+||+|||.||++||
T Consensus        46 ~~l~~~~~~il~~l~~~~~a~~F~~pV~~~~--~pdY~~iIk~PmDL~tIk~kl~~~~Y~s~~~f~~D~~li~~Na~~yN  123 (292)
T 3aad_A           46 VTLSSILESIINDMRDLPNTYPFHTPVNAKV--VKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYN  123 (292)
T ss_dssp             HHHHHHHHHHHHHHSSSTTCGGGSSSCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhCCcchhhcCCCCchh--cccHHHHcCCcCCHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHHHc
Confidence            4567789999999999999999999999987  99999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhh
Q 017092          182 DERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      +++|.++.+|..|.+.|++.|..+
T Consensus       124 ~~~s~i~~~A~~L~~~~~~~~~~~  147 (292)
T 3aad_A          124 GPKHSLTQISQSMLDLCDEKLKEK  147 (292)
T ss_dssp             CSSSHHHHHHTHHHHTTTTTGGGS
T ss_pred             CCchHHHHHHHHHHHHHHhhhhcc
Confidence            999999999999999999887664

>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=1e-22  Score=196.28  Aligned_cols=97  Identities=29%  Similarity=0.531  Sum_probs=90.1

Q ss_pred             HHHHH-HHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCH
Q 017092          108 FGTIL-RNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSD  186 (377)
Q Consensus       108 ~~~il-~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~  186 (377)
                      |..++ ..|+.++.+|||..||+...  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||++||+++|.
T Consensus       174 l~~i~~~~l~~~~~s~~F~~pvd~~~--~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s~  251 (292)
T 3aad_A          174 LDNIVTQKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQ  251 (292)
T ss_dssp             HHHHHHHTGGGSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTSH
T ss_pred             HHHHhhhhhhcCcchhHHHhcccccc--cccHHHHcCCcCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            44444 34788999999999999887  9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhC
Q 017092          187 VHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       187 v~~~A~~L~~~fe~~~~~~~  206 (377)
                      +|.+|..|+..|+..|..+.
T Consensus       252 i~~~A~~L~~~~~~~~~~~~  271 (292)
T 3aad_A          252 YTKTAQEIVNVCYQTLTEYD  271 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999998873

>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=99.87  E-value=1.3e-22  Score=196.96  Aligned_cols=87  Identities=32%  Similarity=0.498  Sum_probs=84.0

Q ss_pred             cCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHH
Q 017092          117 QHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA  196 (377)
Q Consensus       117 ~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~  196 (377)
                      .|+.+|+|+.||++..  +||||+||++||||+||++||++|.|.++.+|.+||+|||.||++||+++|.||.+|..|+.
T Consensus       177 ~~~~s~~F~~pvd~~~--~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~  254 (311)
T 2r0y_A          177 KVKLSEPFMELVDKDE--LPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTN  254 (311)
T ss_dssp             SSCTTGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHH
T ss_pred             CCccHHHHhCCCChhh--cccHHHHhCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence            4678999999999987  99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhh
Q 017092          197 KFEEKWLQL  205 (377)
Q Consensus       197 ~fe~~~~~~  205 (377)
                      .|+..|.+.
T Consensus       255 ~f~~~~~~~  263 (311)
T 2r0y_A          255 YFNYLIQKE  263 (311)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHh
Confidence            999999874

>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=2.4e-22  Score=199.07  Aligned_cols=87  Identities=32%  Similarity=0.498  Sum_probs=83.9

Q ss_pred             cCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHHHHHH
Q 017092          117 QHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLA  196 (377)
Q Consensus       117 ~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~~L~~  196 (377)
                      .|+.+|||+.||+...  +||||+||++||||+||++||++|.|.++.+|.+||+|||.||++||+++|.||.+|..|+.
T Consensus       227 ~~~~s~~F~~pvd~~~--~PdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~  304 (361)
T 2r10_A          227 KVKLSEPFMELVDKDE--LPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTN  304 (361)
T ss_dssp             SSCTTGGGSSCCCTTT--CTHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHH
T ss_pred             CCcchhcccCCCChhh--cccHHHHhcCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            3678999999999987  99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhh
Q 017092          197 KFEEKWLQL  205 (377)
Q Consensus       197 ~fe~~~~~~  205 (377)
                      .|+..|.+.
T Consensus       305 ~f~~~~~~~  313 (361)
T 2r10_A          305 YFNYLIQKE  313 (361)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHh
Confidence            999999874

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

Probab=99.81  E-value=1.1e-20  Score=187.16  Aligned_cols=98  Identities=23%  Similarity=0.252  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHHHHcC--CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCC-CHHHHHHHHHhhhhhhhhc
Q 017092          104 LIRQFGTILRNITQH--KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK-NVREICTDVRLVFKNAMKY  180 (377)
Q Consensus       104 l~~~~~~il~~l~~~--~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~-s~~ef~~Dv~Lif~Na~~Y  180 (377)
                      +...|..+|+.+.+.  ..+++|+.||+...  +||||+||++||||+||++||  +.|. ++.+|.+||+|||.||++|
T Consensus        79 ~~~~~~~~l~~l~~~~~~~~~~F~~p~~~~~--~PdY~~iIk~Pmdl~tI~~kl--~~y~~~~~~f~~D~~li~~Na~~y  154 (361)
T 2r10_A           79 FNRFISFTLDVLIDKYKDIFKDFIKLPSRKF--HPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAY  154 (361)
T ss_dssp             HHHHHHHHHHHHHHHTHHHHGGGSSCCCTTT--CTTHHHHCSSCCCHHHHHTSC--CCSTTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcccHHhcCCCCccc--CCChHhhcCCCcCHHHHHHHh--hccCCCHHHHHHHHHHHHHHHhhc
Confidence            344677788887653  46899999999988  999999999999999999998  5555 8999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhh
Q 017092          181 NDERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       181 N~~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      |+++|.||.+|..|+++|+..|.+.
T Consensus       155 N~~~s~i~~~a~~l~~~~~~~~~k~  179 (361)
T 2r10_A          155 NEYDSLIVKNSMQVVMLIEFEVLKA  179 (361)
T ss_dssp             BCSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999865

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

Probab=99.81  E-value=2.1e-20  Score=181.48  Aligned_cols=94  Identities=23%  Similarity=0.258  Sum_probs=82.7

Q ss_pred             HHHHHHHHHc--CCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCC-CHHHHHHHHHhhhhhhhhcCCCC
Q 017092          108 FGTILRNITQ--HKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK-NVREICTDVRLVFKNAMKYNDER  184 (377)
Q Consensus       108 ~~~il~~l~~--~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~-s~~ef~~Dv~Lif~Na~~YN~~~  184 (377)
                      |..+|..+..  +..+++|+.||+...  +||||+||++||||+||++||  +.|. ++.+|.+||+|||.||++||+++
T Consensus        33 ~~~~L~~~~~~~r~~~~~F~~p~~~~~--~PdY~~iIk~PmDL~tI~~kl--~~y~~s~~~f~~D~~li~~Na~~yN~~~  108 (311)
T 2r0y_A           33 ISFTLDVLIDKYKDIFKDFIKLPSRKF--HPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAYNEYD  108 (311)
T ss_dssp             HHHHHHHHHHHSHHHHGGGSSCCCTTT--CHHHHHHCSSCCCHHHHHHSC--CCSTTHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHcCCchhHHhcCCCCccc--CCChHHHcCCCCCHHHHHHHH--hcccCCHHHHHHHHHHHHHHHHHccCCC
Confidence            3344444443  347899999999888  999999999999999999999  5565 89999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhh
Q 017092          185 SDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       185 s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      |.||.+|..|++.|+..|.+.
T Consensus       109 s~i~~~A~~l~~~~~~~~~k~  129 (311)
T 2r0y_A          109 SLIVKNSMQVVMLIEFEVLKA  129 (311)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999875

>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=99.77  E-value=2.4e-18  Score=148.51  Aligned_cols=98  Identities=16%  Similarity=0.245  Sum_probs=89.5

Q ss_pred             HHHHHHHHHHHHHHcCC------CCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhh
Q 017092          103 ELIRQFGTILRNITQHK------WAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKN  176 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~------~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  176 (377)
                      .+...+..|+..++++.      .+.+|+..|+..    |+||.  +.||+|.+|++||..|.|.++++|..||.+||.|
T Consensus         7 ~lq~~l~~l~~~v~~~~De~GR~lsd~F~~LPsk~----pdYY~--k~Pi~l~~Ikkri~~~~Y~sld~f~~D~~lmf~N   80 (147)
T 3iu6_A            7 LIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVD----PNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLER   80 (147)
T ss_dssp             HHHHHHHHHHHHHHTCBCTTSCBGGGGGTTCCSSC----TTSTT--SCCCCHHHHHHHHHTTCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhcCCCCCcchHHHhHCCCCC----ccccC--CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            35567888888998874      689999988776    78998  9999999999999999999999999999999999


Q ss_pred             hhhcCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          177 AMKYNDERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       177 a~~YN~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      |++||.+||.||.+|..|+.+|...+.++.
T Consensus        81 Ar~yN~e~S~IyeDAv~Lq~~f~~~r~eL~  110 (147)
T 3iu6_A           81 ARRMNRTDSEIYEDAVELQQFFIKIRDELC  110 (147)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999988764

>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=4.8e-18  Score=135.90  Aligned_cols=74  Identities=30%  Similarity=0.581  Sum_probs=69.6

Q ss_pred             hhccCCCHHHHHHHHHHhcCCChhhHHHHHHHHHhhCCCCC-CCCCeeEEeCcCCCHHHHHHHHHHHHHHHHhcC
Q 017092          262 QKCRKTSTEEKRKLGAALTRLSPEDLGKALEIVAQSNTGFQ-ATAEEVELDMDAQSESTLWRLKFFVKDALKSQG  335 (377)
Q Consensus       262 ~~~r~mt~eEK~~L~~~i~~L~~e~l~~vi~II~~~~P~~~-~~~~eiEiDid~L~~~TL~~L~~yV~~~L~~~g  335 (377)
                      ..+++||++||++|+.+|+.||+++|.+|++||++++|.+. .+++|||||||.|++.|||+|++||.+||+.+.
T Consensus        13 ~~~~~mT~eEK~~Ls~~I~~Lp~e~L~~Vi~II~~~~p~l~~~~~dEIEiDid~L~~~TL~~L~~yV~~~l~~k~   87 (90)
T 2jns_A           13 DKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLRELERYVTSCLRKKR   87 (90)
T ss_dssp             SSCCCCCHHHHHHHHHHHTTSCHHHHTTHHHHHHTTCGGGTTSCTTSCCCCTTTSCHHHHHHHHHHHHTTSCCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCHHHHHHHHHHHHhcCccccCCCCCeEEEeccCCCHHHHHHHHHHHHHHHHhhc
Confidence            45899999999999999999999999999999999999987 578999999999999999999999999998753

>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=99.62  E-value=6.7e-16  Score=138.74  Aligned_cols=98  Identities=14%  Similarity=0.304  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcC
Q 017092          102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYN  181 (377)
Q Consensus       102 ~~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN  181 (377)
                      .++...+..||..|..++.++||+.+             .++.||||.||++||+.|.|.|+.+|.+||.|||.||..||
T Consensus        74 ~el~~~l~~vl~~L~~~~~s~~~~~y-------------~~k~PmDL~~i~kKl~~~~Y~s~~eF~~Dv~lIf~n~~~~~  140 (183)
T 3lqh_A           74 KELQISLKQVLTALLNSRTTSHLLRY-------------RQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSD  140 (183)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHTC-------------CC--CCSHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHhccccHhhhhh-------------hhcCCccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhcc
Confidence            36677899999999999999999773             15999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhhCCCCchH
Q 017092          182 DERSDVHVMAKTLLAKFEEKWLQLLPKVTEE  212 (377)
Q Consensus       182 ~~~s~v~~~A~~L~~~fe~~~~~~~p~~~~~  212 (377)
                      .+++.+..++..|..+|++.++.++|++...
T Consensus       141 ~~~~e~~~ag~~l~~~f~~~l~~vfpwf~~~  171 (183)
T 3lqh_A          141 GGQPEIKKANSMVKSFFIRQMERVFPWFSVK  171 (183)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHCTTSCGG
T ss_pred             CCChhhhhhhhHHHHHHHHHHHHHCCCCCcc
Confidence            9999999999999999999999999987653

>2lm0_A AF4/FMR2 family member 1/protein AF-9 chimera; intrinsically disordered, nuclear protein; NMR {Homo sapiens}

Probab=95.69  E-value=0.016  Score=47.77  Aligned_cols=63  Identities=17%  Similarity=0.309  Sum_probs=53.7

Q ss_pred             cCCCHHHHHHHHHHhcCCC-hhhHHHHHHHHHhhCCCCCCCCCeeEEeCcCCCHHHHHHHHHHHH
Q 017092          265 RKTSTEEKRKLGAALTRLS-PEDLGKALEIVAQSNTGFQATAEEVELDMDAQSESTLWRLKFFVK  328 (377)
Q Consensus       265 r~mt~eEK~~L~~~i~~L~-~e~l~~vi~II~~~~P~~~~~~~eiEiDid~L~~~TL~~L~~yV~  328 (377)
                      .+--.+|-+.|...|..|. .+.|.+|+++|.+. +.+..++..+.+|+-+|+..|+++|+.|+.
T Consensus        57 ~~~y~~~L~~l~~rim~l~d~~~lq~iv~li~~t-G~~~it~~tfDFDLc~LD~~Tv~klq~~l~  120 (125)
T 2lm0_A           57 DKAYLDELVELHRRLMTLRERHILQQIVNLIEET-GHFHITNTTFDFDLCSLDKTTVRKLQSYLE  120 (125)
T ss_dssp             SCSTHHHHHHHHHHHHTCCCCSSHHHHHHHHHTS-CCEEECSSCEEECTTTSCHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHhccccHHHHHHHHHHHHhc-CceeeecccccceeeccCHHHHHHHHHHHH
Confidence            3445678889999999995 56799999999974 467788999999999999999999999864

---

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	377
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	2e-31
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	5e-27
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	3e-26
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	3e-24
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	6e-24
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	7e-24

>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 =  113 bits (285), Expect = 2e-31
 Identities = 30/136 (22%), Positives = 65/136 (47%), Gaps = 5/136 (3%)

Query: 79  HVPSIRKQQQEASRREKAAEKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDY 138
           H   + +  +   RR       +  ++    +I+ ++      +PF  PV+ K +   DY
Sbjct: 5   HCDYLNRPHKSIHRRRTDPMVTLSSILE---SIINDMRDLPNTYPFHTPVNAKVVK--DY 59

Query: 139 YEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKF 198
           Y++I +PMD  T+++ +  + Y +  E    + L+ KN+  YN  +  +  +++++L   
Sbjct: 60  YKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLC 119

Query: 199 EEKWLQLLPKVTEEEK 214
           +EK  +   K+   EK
Sbjct: 120 DEKLKEKEDKLARLEK 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 =  101 bits (253), Expect = 5e-27
 Identities = 36/108 (33%), Positives = 59/108 (54%), Gaps = 1/108 (0%)

Query: 102 EELIRQFGTILRNI-TQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEY 160
           EEL +     L  +  Q   + PF QPVD + LG+ DY++++  PMD STIK++++  +Y
Sbjct: 5   EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQY 64

Query: 161 KNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPK 208
           +   +   DV L+F NA  YN + S V+     L   FE++   ++  
Sbjct: 65  QEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQS 112

>d1e6ia_ a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 111

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 99.2 bits (247), Expect = 3e-26
 Identities = 34/96 (35%), Positives = 54/96 (56%), Gaps = 2/96 (2%)

Query: 110 TILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTD 169
            IL  +  H  AWPF+QPV+ + +   DYY+ I +PMD ST++ ++E+ +Y+ + +   D
Sbjct: 10  NILTELQNHAAAWPFLQPVNKEEV--PDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYD 67

Query: 170 VRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
            RLVF N   YN E +  +  A  L   F  K  ++
Sbjct: 68  ARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 103

>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 = 94.3 bits (234), Expect = 3e-24
 Identities = 31/113 (27%), Positives = 54/113 (47%), Gaps = 2/113 (1%)

Query: 111 ILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDV 170
           + + +     +WPF  PV+ K +   DYY+VI  PMD  TI+K +   +Y++      DV
Sbjct: 18  VTQKMMAVPDSWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQSRESFLDDV 75

Query: 171 RLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQLLPKVTEEEKRREEEEAEA 223
            L+  N++KYN   S     A+ ++    +   +    +T+ EK     +  A
Sbjct: 76  NLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAA 128

>d3d7ca1 a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.8 bits (230), Expect = 6e-24
 Identities = 31/101 (30%), Positives = 47/101 (46%), Gaps = 2/101 (1%)

Query: 102 EELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYK 161
           ++L      +L  I  H  AWPFM+PV        DYYEVI  P+D  T+ +++ ++ Y 
Sbjct: 1   DQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEA--PDYYEVIRFPIDLKTMTERLRSRYYV 58

Query: 162 NVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKW 202
             +    D++ V  N  +YN   S+    A  L   F  K 
Sbjct: 59  TRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKL 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 = 93.2 bits (231), Expect = 7e-24
 Identities = 32/108 (29%), Positives = 54/108 (50%), Gaps = 2/108 (1%)

Query: 98  EKRMEELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEA 157
            +  ++L     +IL+ +  H+ AWPFM+PV         YYEVI  PMD  T+ ++++ 
Sbjct: 8   PRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEA--PGYYEVIRFPMDLKTMSERLKN 65

Query: 158 KEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAKTLLAKFEEKWLQL 205
           + Y + +    D++ VF N  +YN   S+ +  A  L   F  K  + 
Sbjct: 66  RYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEA 113

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	377
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.96
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.95
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.95
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.94
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	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=99.96  E-value=5.3e-29  Score=202.44  Aligned_cols=100  Identities=31%  Similarity=0.511  Sum_probs=96.8

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      +|...|..|+..|.+|+.++||..||++..  +||||++|++||||+||++||.+|.|.|+.+|.+||+|||.||+.||+
T Consensus         2 ~L~~~l~~il~~l~~~~~s~~F~~pv~~~~--~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~   79 (102)
T d3d7ca1           2 QLYTTLKNLLAQIKSHPSAWPFMEPVKKSE--APDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNP   79 (102)
T ss_dssp             HHHHHHHHHHHHHHHSGGGGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSC
T ss_pred             hHHHHHHHHHHHHHhCCCCCccCCCCChhh--CcCHHHHcCCccCHHHHHHHhccCccCCHHHHHHHHHHHHHHHHHHCC
Confidence            678899999999999999999999999887  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHh
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQ  204 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~  204 (377)
                      ++|.++.+|..|++.|+++|++
T Consensus        80 ~~s~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          80 PDSEYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999998864

>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=3.8e-28  Score=200.28  Aligned_cols=99  Identities=34%  Similarity=0.633  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCC
Q 017092          105 IRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDER  184 (377)
Q Consensus       105 ~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~  184 (377)
                      .+.|..||..|++|+.||||..||++..  +|+||++|++||||+||++||.+|.|.|+.+|.+||+|||.||+.||+++
T Consensus         5 ~~~l~~il~~l~~~~~a~pF~~pvd~~~--~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~   82 (111)
T d1e6ia_           5 DAAIQNILTELQNHAAAWPFLQPVNKEE--VPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGEN   82 (111)
T ss_dssp             HHHHHHHHHHHHHSTTCGGGSSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHhCCCChhhcCCCCchh--CcCHHHHcCCchhHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHCCCC
Confidence            5789999999999999999999999987  99999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhh
Q 017092          185 SDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       185 s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      |.++.+|..|++.|+++|..+
T Consensus        83 s~i~~~A~~l~~~f~~~~~~i  103 (111)
T d1e6ia_          83 TSYYKYANRLEKFFNNKVKEI  103 (111)
T ss_dssp             SHHHHHHHHHHHHHHHHHHTS
T ss_pred             CHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999875

>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=6.2e-28  Score=199.90  Aligned_cols=106  Identities=33%  Similarity=0.559  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHHHHHHcC-CCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhh
Q 017092          101 MEELIRQFGTILRNITQH-KWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMK  179 (377)
Q Consensus       101 ~~~l~~~~~~il~~l~~~-~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  179 (377)
                      ..++.+.|..+++.|+++ +.|+||..||++...++||||++|++||||+||++||.+|.|.|+.+|.+||+|||.||+.
T Consensus         4 p~el~~~l~~~l~~l~~~~p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~   83 (114)
T d3dwya1           4 PEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWL   83 (114)
T ss_dssp             HHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCcCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCccccHHHHHHHHHHHHHHHHH
Confidence            347888999999999987 6999999999988666999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHhhC
Q 017092          180 YNDERSDVHVMAKTLLAKFEEKWLQLL  206 (377)
Q Consensus       180 YN~~~s~v~~~A~~L~~~fe~~~~~~~  206 (377)
                      ||+++|.++.+|..|++.|++.+..+.
T Consensus        84 yN~~~s~~~~~A~~L~~~f~~~~~~i~  110 (114)
T d3dwya1          84 YNRKTSRVYKFCSKLAEVFEQEIDPVM  110 (114)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999998764

>d1eqfa1 a.29.2.1 (A:1359-1497) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=4.3e-27  Score=201.35  Aligned_cols=101  Identities=25%  Similarity=0.532  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      .+...|..|+..|..++.++||..||++..  +||||++|++||||+||++||.+|.|.|+.+|.+||+|||.||+.||+
T Consensus        26 ~l~~~l~~il~~l~~~~~s~pF~~Pvd~~~--~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~  103 (139)
T d1eqfa1          26 TLSSILESIINDMRDLPNTYPFHTPVNAKV--VKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNG  103 (139)
T ss_dssp             HHHHHHHHHHHHHHTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHcCCCchhhhCCCChhh--ccCHHHHcCChhhHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHHCC
Confidence            456678999999999999999999999988  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhh
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      ++|.++.+|..|...|++.|.++
T Consensus       104 ~~s~i~~~A~~L~~~~~~~~~~~  126 (139)
T d1eqfa1         104 PKHSLTQISQSMLDLCDEKLKEK  126 (139)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999876

>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=9.9e-28  Score=199.87  Aligned_cols=101  Identities=32%  Similarity=0.534  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCC
Q 017092          103 ELIRQFGTILRNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYND  182 (377)
Q Consensus       103 ~l~~~~~~il~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~  182 (377)
                      ++...|..|+..|++|+.++||..||++..  +||||++|++||||+||++||.+|.|.++.+|.+||+|||.||+.||+
T Consensus        13 ~l~~~l~~il~~l~~~~~a~~F~~pv~~~~--~pdY~~iI~~PmdL~~I~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yn~   90 (118)
T d1wuma1          13 QLYSTLKSILQQVKSHQSAWPFMEPVKRTE--APGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNP   90 (118)
T ss_dssp             HHHHHHHHHHHHHHHSSSCHHHHSCCCSSS--SSSCTTTCSSCCCHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhCCCcCcccCCCChhh--CcCHHHHcCChhhHHHHHHHhcccccCchHHHHHHHHHHHHHHHHHCC
Confidence            578899999999999999999999999987  999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhh
Q 017092          183 ERSDVHVMAKTLLAKFEEKWLQL  205 (377)
Q Consensus       183 ~~s~v~~~A~~L~~~fe~~~~~~  205 (377)
                      ++|.++.+|..|++.|.+.|++.
T Consensus        91 ~~s~~~~~A~~l~~~f~~~~~e~  113 (118)
T d1wuma1          91 PESEYYKCANILEKFFFSKIKEA  113 (118)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999875

>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=6.3e-27  Score=197.63  Aligned_cols=91  Identities=30%  Similarity=0.550  Sum_probs=86.8

Q ss_pred             HHHHcCCCCCCCCCcCCcccCCCCchhhhccCCCChHHHHHHHhcCCCCCHHHHHHHHHhhhhhhhhcCCCCCHHHHHHH
Q 017092          113 RNITQHKWAWPFMQPVDVKGLGLDDYYEVIDKPMDFSTIKKQMEAKEYKNVREICTDVRLVFKNAMKYNDERSDVHVMAK  192 (377)
Q Consensus       113 ~~l~~~~~a~~F~~pVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~v~~~A~  192 (377)
                      ..++.++.||||..||++..  +||||++|++||||+||++||.+|.|.|+.+|.+||+|||.||+.||+++|.++.+|.
T Consensus        20 ~~~~~~p~a~pF~~pVd~~~--~PdY~~vIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~   97 (128)
T d1eqfa2          20 QKMMAVPDSWPFHHPVNKKF--VPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQ   97 (128)
T ss_dssp             HTTTTSTTCGGGTSCCCTTT--STTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHcCCCCChhcCCCCccc--CcCHHHHcCCcccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence            45667789999999999987  9999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 017092          193 TLLAKFEEKWLQL  205 (377)
Q Consensus       193 ~L~~~fe~~~~~~  205 (377)
                      .|.+.|+..+.++
T Consensus        98 ~L~~~~~~~l~~~  110 (128)
T d1eqfa2          98 EIVNVCYQTLTEY  110 (128)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999998876