Psyllid ID: psy245

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560------
Protein Sequence
MELSKIGAIILYRTLVKIWKVAKAGTRSIDPKSMDEKDFALSNGGEPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPASSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCLRKKPRKPN
Secondary Structure (PSIPRED)
cccccccHHHccccHHEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHccccccccccccEEEccccccHHHHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHEEEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccHHHcccccccHHHHHHHHHHHHHHHccccccccccccHHHcccccHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHccccccHHHccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHcHHHHcHHcccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHcccccHHHHHHEEEEEccccccccccccEEEEEHHcccHHHHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
MELSKIGAIILYRTLVKIWKVAkagtrsidpksmdekdfalsnggeppareeprlepvngivqpptvppphrpgrntnqLAFISKNVlkpvmkhqhawpfhqpvdaidlnlpFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTncyvynkpgeDVVVMAQTLEKLFLTKVSARResgrqikkpnrgsdegsftTQLATSVtsvgdqgsyakpkltESLKYCNEILKELFSKkhssyawpfykpvdaawlglndyheiikkpmdlgtvkAKMDAreyksskefADDVRLIFTncykynppdhDVVAMAKKLQDVFETKiakapddvpivssssmvptltvnknnigrwspdsssdstdsEADERARKLISlqdqvtpkpataaqrkkppttplsapqpassvkkparppaktpvkrkappmpnksvsaqhtqpapvmndesdeesskpmsyfekqelsldinklpgkklgRVVHIIQsrepslrdsnpdeieidfetlkpsTLRELEKYVATCLRKKPRKPN
Flexible Loop (DISEMBL)
MELSKIGAIILYRTLVKIWKVAkagtrsidpksmdeKDFALSNGGEPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKvsarresgrqikkpnrgsdegsfttqlatsvtsvgdqgsyakpKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREyksskefaddvRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIakapddvpivssssmvptltvnknnigrwspdsssdstdSEADERARKLislqdqvtpkpataaqrkkppttplsapqpassvkkparppaktpvkrkappmpnksvsaqhtqpapvmNDESDEESSKPMSYFEKQELSLDinklpgkklgRVVHIIqsrepslrdsnpdeIEIDfetlkpstlreLEKYVatclrkkprkpn
Low Complexity Region (SEG)
MELSKIGAIILYRTLVKIWKVAKAGTRSIDPKSMDEKDFALSNGGeppareeprlepVNGIVQpptvppphrpGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRWspdsssdstdsEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPASSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCLRKKPRKPN
Disordered region (IsUnstruct)
****KIGAIILYRTLVKIWKVAKA*******************************************************LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV*******************************************LTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKM********KEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKA************************************************************************************************************************************************KKLGRVVHII****************************ELEKYVATC*********
Disordered Region (DISOPRED)
************************************************************************************KNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGS****************SYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK***************************************************************************************************************************************************************************IDFETLKPSTLRELEKYVAT***K******
Disordered Region (DISEMBL)
MELSKIGAIILYRTLVKIWKVAKAGTRSIDPKSMDEKDFALSNGGEPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVS*********************TTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRW****************ARKLISLQDQ****************************************************************************YFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCLRKKPRKPN
Disordered Region (DISPRO)
*ELSKIGAIILYRTLVKIWKVAK**************************************************GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR***************************************KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKA***************************************************************************************************************************SKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCLRKK*****
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MELSKIGAIILYRTLVKIWKVAKAGTRSIDPKSMDEKDFALSNGGEPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPASSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCLRKKPRKPN
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	566	2.2.26 [Sep-21-2011]
Q4R8Y1	947	Bromodomain testis-specif	N/A	N/A	0.530	0.316	0.498	1e-78
Q58F21	947	Bromodomain testis-specif	yes	N/A	0.537	0.321	0.492	2e-78
Q91Y44	956	Bromodomain testis-specif	yes	N/A	0.528	0.312	0.529	7e-78
D4A7T3	952	Bromodomain testis-specif	yes	N/A	0.533	0.317	0.507	1e-76
F1QW93	918	Bromodomain testis-specif	no	N/A	0.579	0.357	0.481	7e-72
F7DRV9	933	Bromodomain testis-specif	yes	N/A	0.528	0.320	0.503	6e-66
P13709	2038	Homeotic protein female s	yes	N/A	0.234	0.065	0.582	2e-52
P25440	801	Bromodomain-containing pr	no	N/A	0.272	0.192	0.582	2e-49
Q6MGA9	798	Bromodomain-containing pr	yes	N/A	0.272	0.192	0.576	5e-49
Q32S26	803	Bromodomain-containing pr	no	N/A	0.272	0.191	0.576	5e-49

>sp|Q4R8Y1|BRDT_MACFA Bromodomain testis-specific protein OS=Macaca fascicularis GN=BRDT PE=2 SV=3

 Score =  294 bits (753), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 161/323 (49%), Positives = 213/323 (65%), Gaps = 23/323 (7%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           K+TE L++C+EILKE+ +KKH SYAWPFY PVD   LGL++Y++I+K PMDLGT+K KMD
Sbjct: 268 KVTEQLRHCSEILKEMLAKKHFSYAWPFYNPVDVNALGLHNYYDIVKNPMDLGTIKEKMD 327

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP----DDVPIV 373
            +EYK + +FA DVRL+F NCYKYNPPDH+VV MA+ LQDVFET  +K P    + +P+ 
Sbjct: 328 NQEYKDAYKFAADVRLMFMNCYKYNPPDHEVVTMARMLQDVFETHFSKIPVEPVESMPLC 387

Query: 374 SSSSMVPTLTVNKNNIGRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPP 433
              + + T T  + N    S + +S S DSE DER ++L  LQ+Q+           + P
Sbjct: 388 YIKTDI-TETTGRENTNEASSEGNS-SGDSE-DERVQRLAKLQEQLKAVHQQLQVLSQVP 444

Query: 434 TTPLSAPQPA-----------SSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMN 482
              L+  +             +S + P +   +  +K K+     K    Q+     +  
Sbjct: 445 FRKLNKKKEKSKKEKKKEKVNNSNENPRKMCEQMRLKEKSKRNQPKKRKQQY-----IGQ 499

Query: 483 DESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETL 542
              DE+++KPM+Y EK++LSL+INKLPG KLGRVVHIIQSREPSL +SNPDEIEIDFETL
Sbjct: 500 KSEDEDNAKPMNYDEKRQLSLNINKLPGDKLGRVVHIIQSREPSLSNSNPDEIEIDFETL 559

Query: 543 KPSTLRELEKYVATCLRKKPRKP 565
           K STLRELEKYV+ CLRK+P KP
Sbjct: 560 KASTLRELEKYVSACLRKRPLKP 582

May play a role in the transcriptional regulation of spermatogenesis. Seems to have a structural ATP-independent role in the reorganization of acetylated chromatin.
Macaca fascicularis (taxid: 9541)

>sp|Q58F21|BRDT_HUMAN Bromodomain testis-specific protein OS=Homo sapiens GN=BRDT PE=1 SV=4

 Score =  293 bits (751), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 157/319 (49%), Positives = 208/319 (65%), Gaps = 15/319 (4%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           K+TE L++C+EILKE+ +KKH SYAWPFY PVD   LGL++Y++++K PMDLGT+K KMD
Sbjct: 268 KVTEQLRHCSEILKEMLAKKHFSYAWPFYNPVDVNALGLHNYYDVVKNPMDLGTIKEKMD 327

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP----DDVPIV 373
            +EYK + +FA DVRL+F NCYKYNPPDH+VV MA+ LQDVFET  +K P    + +P+ 
Sbjct: 328 NQEYKDAYKFAADVRLMFMNCYKYNPPDHEVVTMARMLQDVFETHFSKIPIEPVESMPLC 387

Query: 374 SSSSMVPTLTVNKNNIGRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPP 433
              + + T T  + N    S  S  +S+D   DER ++L  LQ+Q+           + P
Sbjct: 388 YIKTDI-TETTGRENTNEAS--SEGNSSDDSEDERVKRLAKLQEQLKAVHQQLQVLSQVP 444

Query: 434 TTPLS-------APQPASSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESD 486
              L+         +    V      P K   + +      ++   +  Q    +  E D
Sbjct: 445 FRKLNKKKEKSKKEKKKEKVNNSNENPRKMCEQMRLKEKSKRNQPKKRKQQFIGLKSE-D 503

Query: 487 EESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPST 546
           E+++KPM+Y EK++LSL+INKLPG KLGRVVHIIQSREPSL +SNPDEIEIDFETLK ST
Sbjct: 504 EDNAKPMNYDEKRQLSLNINKLPGDKLGRVVHIIQSREPSLSNSNPDEIEIDFETLKAST 563

Query: 547 LRELEKYVATCLRKKPRKP 565
           LRELEKYV+ CLRK+P KP
Sbjct: 564 LRELEKYVSACLRKRPLKP 582

May play a role in the transcriptional regulation of spermatogenesis. Seems to have a structural ATP-independent role in the reorganization of acetylated chromatin.

Homo sapiens (taxid: 9606)

>sp|Q91Y44|BRDT_MOUSE Bromodomain testis-specific protein OS=Mus musculus GN=Brdt PE=1 SV=3

 Score =  291 bits (746), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 170/321 (52%), Positives = 207/321 (64%), Gaps = 22/321 (6%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           K+TE LK+C+EILKE+ +KKH  YAWPFY PVDA  LGL++Y++++K PMDLGT+K KMD
Sbjct: 267 KVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMD 326

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSS 377
            +EYK + EFA DVRL+F NCYKYNPPDH+VVAMA+ LQDVFE   AK PD+ PI S  +
Sbjct: 327 NQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVFELHFAKIPDE-PIESMHA 385

Query: 378 MVPTLTVNKNNI-----GRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKP 432
               LT N            +    + S DSE DER + L  LQ+Q+    A   Q +  
Sbjct: 386 C--HLTTNSAQALSRESSSEASSGDASSEDSE-DERVQHLAKLQEQLN---AVHQQLQVL 439

Query: 433 PTTPLSAPQPASSVKKPARPPAKTPVK------RKAPPMPNKSVSAQHTQPAPVMNDESD 486
              PL         +K  R P +  V       RK P    +   A+  QP         
Sbjct: 440 SQVPLRK--LKKKNEKSKRAPKRKKVNNRDENPRKKPKQMKQKEKAKINQPKKKKPLLKS 497

Query: 487 EE--SSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKP 544
           EE  ++KPM+Y EK++LSLDINKLPG KLGR+VHIIQSREPSLR+SNPDEIEIDFETLK 
Sbjct: 498 EEEDNAKPMNYDEKRQLSLDINKLPGDKLGRIVHIIQSREPSLRNSNPDEIEIDFETLKA 557

Query: 545 STLRELEKYVATCLRKKPRKP 565
           STLRELEKYV  CLRK+  KP
Sbjct: 558 STLRELEKYVLACLRKRSLKP 578

May play a role in the transcriptional regulation of spermatogenesis. Seems to have a structural ATP-independent role in the reorganization of acetylated chromatin.

Mus musculus (taxid: 10090)

>sp|D4A7T3|BRDT_RAT Bromodomain testis-specific protein OS=Rattus norvegicus GN=Brdt PE=1 SV=1

 Score =  287 bits (735), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 162/319 (50%), Positives = 204/319 (63%), Gaps = 17/319 (5%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           K+TE LK+C+EILKE+ +KKH  YAWPFY PVD   LGL++Y++I+K PMDLGT+K KMD
Sbjct: 267 KVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDVDALGLHNYYDIVKNPMDLGTIKGKMD 326

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSS 377
            +EYK + EFA DVRL+F NCYKYNPPDH+VV MA+ LQDVFE   AK PD+ P+ S  +
Sbjct: 327 KQEYKDACEFAADVRLMFMNCYKYNPPDHEVVTMARMLQDVFEMHFAKIPDE-PVESMRA 385

Query: 378 MVPTLTVNK---NNIGRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPT 434
              T    K         +      S DSE DER ++L  LQ+Q+    A   Q +    
Sbjct: 386 CHLTTNSAKALSRESSSEASSGDCSSEDSE-DERVQRLAKLQEQLN---AVHQQLQVLSQ 441

Query: 435 TPLSAPQPASSVKKPARPPAKTPVKRKAPP-------MPNKSVSAQHTQPAPVMNDESDE 487
            PL         +K  R P +  V R   P          +   +   +    +    +E
Sbjct: 442 VPLRK--LKKKNEKSKRAPKRKKVNRDENPKKKAKQMKQKEKAKSNQPKKKKPLLKLEEE 499

Query: 488 ESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTL 547
           +++KPM+Y EK++LSLDINKLPG KLGR+VHIIQSREPSLR+SNPDEIEIDFETLK STL
Sbjct: 500 DNAKPMNYDEKRQLSLDINKLPGDKLGRIVHIIQSREPSLRNSNPDEIEIDFETLKASTL 559

Query: 548 RELEKYVATCLRKKPRKPN 566
           RELEKYV  CLRK+  KP+
Sbjct: 560 RELEKYVLACLRKRSLKPH 578

Testis-specific chromatin protein that specifically binds histone H4 acetylated at 'Lys-5' and 'Lys-8' (H4K5ac and H4K8ac, respectively) and plays a key role in spermatogenesis. Required in late pachytene spermatocytes: plays a role in meiotic and post-meiotic cells by binding to acetylated histones at the promoter of specific meiotic and post-meiotic genes, facilitating their activation at the appropriate time. In the post-meiotic phase of spermatogenesis, binds to hyperacetylated histones and participates in their general removal from DNA. Also acts as a component of the splicing machinery in pachytene spermatocytes and round spermatids and participates in 3'-UTR truncation of specific mRNAs in post-meiotic spermatids. Required for chromocenter organization, a structure comprised of peri-centromeric heterochromatin.

Rattus norvegicus (taxid: 10116)

>sp|F1QW93|BRDT_DANRE Bromodomain testis-specific protein OS=Danio rerio GN=brdt PE=2 SV=2

 Score =  271 bits (694), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 171/355 (48%), Positives = 226/355 (63%), Gaps = 27/355 (7%)

Query: 214 KVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKEL 273
           K+ +RR SGR IK P +   E     Q+              + KL+E LKYCN ILKE+
Sbjct: 236 KLFSRRGSGRPIKPPCKDLPESPPQHQVGR------------RTKLSERLKYCNAILKEM 283

Query: 274 FSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRL 333
           FSKKHS+YAWPFYKPVDA  LGL DYHEII +PMD+ T+K KM+AREY  + +FA D+RL
Sbjct: 284 FSKKHSAYAWPFYKPVDAETLGLLDYHEIIHQPMDMSTIKKKMEAREYTDALQFAADMRL 343

Query: 334 IFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD---VPIVSSSSMV------PTLTV 384
           +F+NCYKYNPP H+VV+MA+KLQDVFE + +K PD+      VSS + V         + 
Sbjct: 344 MFSNCYKYNPPGHEVVSMARKLQDVFEFRFSKIPDEPKNANPVSSHNRVKKERARSPSSS 403

Query: 385 NKNNIGRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPAS 444
             ++    SP++SSD+ + + +ERA +L SL++Q     A   Q +    TPLS     S
Sbjct: 404 ESSDSESSSPENSSDTEEEDEEERAHRLASLEEQQL--KAVREQLQLLTQTPLSKILKRS 461

Query: 445 SVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESDEESSKPMSYFEKQELSLD 504
           S  K +     T +     P  N  +  + ++      D  +E ++ PMSY EK++LSLD
Sbjct: 462 SSSKSSGCKVCTMMNSLKKPKFNSVLRRKESRAC----DSEEEMNTLPMSYEEKRQLSLD 517

Query: 505 INKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCLR 559
           INKLPG KLG+VV+II++REP LRD++P+EIEIDFETLKPSTLR LE YV  CLR
Sbjct: 518 INKLPGDKLGKVVNIIKAREPLLRDTDPEEIEIDFETLKPSTLRALECYVVGCLR 572

Testis-specific chromatin protein that specifically binds histone H4 acetylated at 'Lys-5' and 'Lys-8' (H4K5ac and H4K8ac, respectively) and plays a key role in spermatogenesis. Required in late pachytene spermatocytes: plays a role in meiotic and post-meiotic cells by binding to acetylated histones at the promoter of specific meiotic and post-meiotic genes, facilitating their activation at the appropriate time. In the post-meiotic phase of spermatogenesis, binds to hyperacetylated histones and participates in their general removal from DNA.

Danio rerio (taxid: 7955)

>sp|F7DRV9|BRDT_XENTR Bromodomain testis-specific protein OS=Xenopus tropicalis GN=brdt PE=3 SV=1

 Score =  252 bits (643), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 156/310 (50%), Positives = 196/310 (63%), Gaps = 11/310 (3%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           ++ E LK+CN IL E+ SKKH+ YAWPFYK V      L D  + IK PMDL T++ KM+
Sbjct: 279 QICEQLKHCNNILNEMMSKKHAEYAWPFYKTVIPT--SLLDCSDAIKHPMDLATIRDKME 336

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSS 377
              YK +++FA DVRL+F N YKYNPPD++VV MA+K+QDVFE   AK PDD P+ ++ S
Sbjct: 337 NGLYKDTQDFASDVRLMFMNSYKYNPPDNEVVNMARKMQDVFEGMFAKIPDD-PL-ATQS 394

Query: 378 MVPTLTVNKNNIGRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTPL 437
           MV     +       S  S   S+    DERA+ L  LQ+Q+    A   Q K    TP+
Sbjct: 395 MVERYKTSTEESSS-SSSSEQSSSSDSEDERAQHLALLQEQLR---AVQEQLKALTETPI 450

Query: 438 -SAPQPASSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESDEESSKPMSYF 496
            S  QP S+V        K  VK   P          +      ++   +EE  KPMSY 
Sbjct: 451 FSKIQPKSAVG--VYDKYKQWVKCIEPMGKLLKRKKNYDAKKKKLHVSDEEEDVKPMSYD 508

Query: 497 EKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVAT 556
           EK++LSLDINKLPG+KLGR+VHIIQSREPSL+DSNP+EIEIDFETLK STLR LEKYV  
Sbjct: 509 EKRQLSLDINKLPGEKLGRIVHIIQSREPSLKDSNPNEIEIDFETLKQSTLRHLEKYVMV 568

Query: 557 CLRKKPRKPN 566
           CLRK+P+KP+
Sbjct: 569 CLRKRPKKPS 578

Testis-specific chromatin protein that specifically binds histone H4 acetylated at 'Lys-5' and 'Lys-8' (H4K5ac and H4K8ac, respectively) and plays a key role in spermatogenesis. Required in late pachytene spermatocytes: plays a role in meiotic and post-meiotic cells by binding to acetylated histones at the promoter of specific meiotic and post-meiotic genes, facilitating their activation at the appropriate time. In the post-meiotic phase of spermatogenesis, binds to hyperacetylated histones and participates in their general removal from DNA.

Xenopus tropicalis (taxid: 8364)

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

 Score =  207 bits (526), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/170 (58%), Positives = 110/170 (64%), Gaps = 37/170 (21%)

Query: 46  EPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVD 105
           EPP R EP +EPVNGIVQPP +PP  RPGRNTNQL ++ K V+K + KH  +WPF QPVD
Sbjct: 5   EPPPRYEPPVEPVNGIVQPPVIPPAERPGRNTNQLQYLIKTVMKVIWKHHFSWPFQQPVD 64

Query: 106 AIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIK 165
           A  LNLP                                     DYHK+IK PMD+GTIK
Sbjct: 65  AKKLNLP-------------------------------------DYHKIIKQPMDMGTIK 87

Query: 166 KRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
           KRLEN YYWS KE I DFNTMF NCYVYNKPGEDVVVMAQTLEK+FL K+
Sbjct: 88  KRLENNYYWSAKETIQDFNTMFNNCYVYNKPGEDVVVMAQTLEKVFLQKI 137

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

Drosophila melanogaster (taxid: 7227)

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

 Score =  197 bits (501), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 99/170 (58%), Positives = 121/170 (71%), Gaps = 16/170 (9%)

Query: 218 RRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKK 277
           RRESGR IK P +   +     Q            S  K KL+E LK+CN ILKEL SKK
Sbjct: 317 RRESGRPIKPPRKDLPDSQQQHQ------------SSKKGKLSEQLKHCNGILKELLSKK 364

Query: 278 HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN 337
           H++YAWPFYKPVDA+ LGL+DYH+IIK PMDL TVK KM+ R+Y+ ++EFA DVRL+F+N
Sbjct: 365 HAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSN 424

Query: 338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD----VPIVSSSSMVPTLT 383
           CYKYNPPDHDVVAMA+KLQDVFE + AK PD+     P+  S++M P L 
Sbjct: 425 CYKYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTAMPPGLA 474

May play a role in spermatogenesis or folliculogenesis.

Homo sapiens (taxid: 9606)

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

 Score =  196 bits (498), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 98/170 (57%), Positives = 121/170 (71%), Gaps = 16/170 (9%)

Query: 218 RRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKK 277
           RRESGR IK P +   +     Q            S  K KL+E LK+CN ILKEL SKK
Sbjct: 316 RRESGRPIKPPRKDLPDSQQQHQ------------SSKKGKLSEQLKHCNGILKELLSKK 363

Query: 278 HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN 337
           H++YAWPFYKPVDA+ LGL+DYH+IIK PMDL TVK KM+ R+Y+ ++EFA DVRL+F+N
Sbjct: 364 HAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSN 423

Query: 338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD----VPIVSSSSMVPTLT 383
           CYKYNPPDHDVVAMA+KLQDVFE + AK PD+     P+  S+++ P L 
Sbjct: 424 CYKYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTALPPGLA 473

May play a role in spermatogenesis or folliculogenesis.

Rattus norvegicus (taxid: 10116)

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

 Score =  196 bits (497), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 98/170 (57%), Positives = 121/170 (71%), Gaps = 16/170 (9%)

Query: 218 RRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKK 277
           RRESGR IK P +   +     Q            S  K KL+E LK+CN ILKEL SKK
Sbjct: 317 RRESGRPIKPPRKDLPDSQQQHQ------------SSKKGKLSEQLKHCNGILKELLSKK 364

Query: 278 HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN 337
           H++YAWPFYKPVDA+ LGL+DYH+IIK PMDL TVK KM+ R+Y+ ++EFA DVRL+F+N
Sbjct: 365 HAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSN 424

Query: 338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD----VPIVSSSSMVPTLT 383
           CYKYNPPDHDVVAMA+KLQDVFE + AK PD+     P+  S+++ P L 
Sbjct: 425 CYKYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTALPPGLA 474

Bos taurus (taxid: 9913)

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	566
326936210	697	PREDICTED: bromodomain-containing protei	0.819	0.665	0.434	1e-117
348505480	513	PREDICTED: bromodomain-containing protei	0.754	0.832	0.456	1e-110
410903440	546	PREDICTED: bromodomain-containing protei	0.752	0.780	0.401	1e-99
321456065	754	hypothetical protein DAPPUDRAFT_302185 [	0.588	0.441	0.519	9e-89
170036200	848	conserved hypothetical protein [Culex qu	0.583	0.389	0.477	1e-84
1588281	509	RING3 protein	0.461	0.512	0.510	1e-84
148725668	664	novel protein (zgc:77289) [Danio rerio]	0.602	0.513	0.503	2e-84
47086635	664	bromodomain-containing protein 3 [Danio	0.602	0.513	0.501	2e-84
402855238	899	PREDICTED: bromodomain testis-specific p	0.832	0.523	0.385	3e-84
391337779	802	PREDICTED: bromodomain testis-specific p	0.591	0.417	0.513	6e-84

>gi|326936210|ref|XP_003214150.1| PREDICTED: bromodomain-containing protein 4-like, partial [Meleagris gallopavo]

 Score =  429 bits (1102), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 260/599 (43%), Positives = 337/599 (56%), Gaps = 135/599 (22%)

Query: 64  PPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQH 123
           PP    P++P R TNQL ++ K VLK + KHQ AWPF QPVDA+ LNLP           
Sbjct: 47  PPETSNPNKPKRQTNQLQYLLKVVLKTLWKHQFAWPFQQPVDAVKLNLP----------- 95

Query: 124 WVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDF 183
                                     DY+K+IK PMD+GTIKKRLEN YYW+ +E I DF
Sbjct: 96  --------------------------DYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDF 129

Query: 184 NTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVS-------------------ARRESGRQ 224
           NTMFTNCY+YNKPG+D+V+MA+ LEKLFL K+S                   AR+E+G  
Sbjct: 130 NTMFTNCYIYNKPGDDIVLMAEALEKLFLQKISEMTQEETEIVIAQTKGRGRARKEAGMA 189

Query: 225 IKKPNRGSDEGSFTTQLATS-----------------------------VTSVGDQGSYA 255
           +     G   G F  +L T                               T +G +   +
Sbjct: 190 LSHIIHGFANGDFFPRLQTKKGVKRKADTTTPTTIDPIHESSSLPTEPKSTKLGPRRESS 249

Query: 256 KP--------------------KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLG 295
           +P                    K++E LKYC+ I+KE+F+KKH++YAWPFYKPVD   LG
Sbjct: 250 RPVKPPKKDVPDSQQHMVEKSSKVSEQLKYCSGIIKEMFAKKHAAYAWPFYKPVDVEALG 309

Query: 296 LNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKL 355
           L+DY +IIK PMDL T+K+K++ REY+ ++EFA DVRL+F+NCYKYNP DH+VVAMA+KL
Sbjct: 310 LHDYCDIIKHPMDLSTIKSKLENREYRDAQEFAADVRLMFSNCYKYNPADHEVVAMARKL 369

Query: 356 QDVFETKIAKAPD--DVPIVSSSSMVPTLTVNKNNIGRWSPDSSSDSTDSEA------DE 407
           QDVFE + AK PD  + P++ +SS V      K      S  SS  S+DS++      +E
Sbjct: 370 QDVFEMRFAKMPDEPEEPVIPASSPVVVPPPTKVVPPSSSDSSSDSSSDSDSSSDDSEEE 429

Query: 408 RARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPA--------------------SSVK 447
           RA++L  LQ+Q+       A   +P        +                      S  K
Sbjct: 430 RAQRLAELQEQLKAVHEQLAALSQPQQNKPKKKEKDKKEKKKEKHKKKEELEDSKKSKAK 489

Query: 448 KPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESDEESSKPMSYFEKQELSLDINK 507
           +P    AK      +     + V+ ++++P P    E +EE  KPMSY EK++LSLDINK
Sbjct: 490 EPPSKKAKKSNSNSSTSSKKEPVTVKNSKPPPAYESE-EEEKCKPMSYEEKRQLSLDINK 548

Query: 508 LPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCLRKKPRKPN 566
           LPG+KLGRVVHIIQSREPSL++SNPDEIEIDFETLKPSTLRELE+YV +CLRKK RKP 
Sbjct: 549 LPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLRELERYVTSCLRKK-RKPQ 606

Source: Meleagris gallopavo

Species: Meleagris gallopavo

Genus: Meleagris

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348505480|ref|XP_003440289.1| PREDICTED: bromodomain-containing protein 3-like [Oreochromis niloticus]

 Score =  406 bits (1043), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 233/510 (45%), Positives = 297/510 (58%), Gaps = 83/510 (16%)

Query: 67  VPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVL 126
           V  P++PGR TNQL ++   V+K + +HQ AWPF+QPVDA+ L LP              
Sbjct: 20  VTNPNKPGRRTNQLQYMQNIVIKSLWRHQFAWPFYQPVDAVALGLP-------------- 65

Query: 127 SMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTM 186
                                  DYHK+I  PMD+GTIKKRLEN YYWS  E + DFNTM
Sbjct: 66  -----------------------DYHKIITSPMDMGTIKKRLENNYYWSASECLQDFNTM 102

Query: 187 FTNCYVYNKPGEDVVVMAQTLEKLFLTKVS------------ARRESGRQIKKP-NRGSD 233
           FTNCY+YNKP +D+V+MA  LEK++L KV+            A +  G++   P +R   
Sbjct: 103 FTNCYIYNKPTDDIVLMALALEKIYLQKVAQMPQSEVEIVPHAAKGKGKKSSTPESRKKR 162

Query: 234 EGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAW 293
           E S  ++  +       Q +     L+E LKYCN ILKE+ SKKHS+YAWPFYKPVDA  
Sbjct: 163 ESS--SRAKSDFEEESSQQNTEPCGLSEQLKYCNHILKEMLSKKHSAYAWPFYKPVDAEA 220

Query: 294 LGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAK 353
           L L+DYH+IIK PMDL TVK KMDA EY+ ++ FA DVRLIF+NCYKYNP  HDVV  A+
Sbjct: 221 LQLHDYHDIIKYPMDLSTVKKKMDAGEYQDAQAFAADVRLIFSNCYKYNPAHHDVVIKAR 280

Query: 354 KLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRWSPDSSSDSTDSEADERARKLI 413
           KLQ +FE + AK PD+   V+S +                    S      A+ER  +L 
Sbjct: 281 KLQGIFEQRFAKMPDEHVEVTSQA------------------GGSLEKPESAEERTTRLA 322

Query: 414 SLQDQVTPKPATAAQRKKPPTTPLSA--PQPASSVKKPARPPAKTPVKRKAPPMPNKSVS 471
            LQ+QV       A + K     L+A    P S  KK      K   ++    M ++  S
Sbjct: 323 ELQEQV------GADQLKAVHGQLAALSEAPVSKPKKKKENDKKDNSRQNVGVMNSRCTS 376

Query: 472 ---AQHTQPAPVMNDESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLR 528
              A+++      N+   E+ S PM+Y EK +LSLDIN+LPG KLG VVHIIQSREPS+ 
Sbjct: 377 NSCARYSWKGS--NEWESEDESLPMTYDEKHQLSLDINRLPGMKLGHVVHIIQSREPSVC 434

Query: 529 DSNPDEIEIDFETLKPSTLRELEKYVATCL 558
           ++NPDEIEIDFETLKPSTLR LE+YV +CL
Sbjct: 435 NTNPDEIEIDFETLKPSTLRALEQYVKSCL 464

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|410903440|ref|XP_003965201.1| PREDICTED: bromodomain-containing protein 2-like [Takifugu rubripes]

 Score =  370 bits (949), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 227/566 (40%), Positives = 295/566 (52%), Gaps = 140/566 (24%)

Query: 64  PPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQH 123
           PP V  P +PGR TNQL ++   V+K + +H +AWPF++PVDA+ L L            
Sbjct: 16  PPEVENPDKPGRRTNQLQYMQNIVVKSLWRHHYAWPFYEPVDAVGLGLA----------- 64

Query: 124 WVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDF 183
                                     DYHK+I  PMDLGTIKKRLEN YYW+  E + DF
Sbjct: 65  --------------------------DYHKIITSPMDLGTIKKRLENNYYWTASECLQDF 98

Query: 184 NTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRES----------GRQIKKPNRGSD 233
           NTMFTNCY+YNKP +D+V+MA TLEK+FL KV+   +           G+  K    G +
Sbjct: 99  NTMFTNCYIYNKPTDDIVLMALTLEKIFLQKVAQMPQEEVEVLPYVAKGKGKKGNASGKN 158

Query: 234 EGSFTTQ-----------LATSVTSV-GDQ---------------GSYAKPK-------- 258
             S TT            L+T+ +S  G+Q               GS + P         
Sbjct: 159 NASVTTAPSTLSSPPRAGLSTTTSSADGEQAALPKQTSTGGSPTAGSGSSPSQNQRSLRK 218

Query: 259 -----------------------LTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLG 295
                                  L+E LK+CN ILKE+ SKKH++YAWPFY+PVDA  L 
Sbjct: 219 SGRVNNQPKKTVEEKEPPKPEHGLSERLKFCNVILKEMLSKKHAAYAWPFYEPVDAVALQ 278

Query: 296 LNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKL 355
           LNDYH+IIK PMDL TVK K+D  EY ++  FA DV+LIF+NCYKYNP   +VVA AKKL
Sbjct: 279 LNDYHDIIKHPMDLSTVKRKLDRGEYPNADSFAADVQLIFSNCYKYNPSHLEVVAHAKKL 338

Query: 356 QDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRWSPDSSSDSTDSEADERARKLISL 415
           Q VFE   AK PD+    + +    T    K+++                +E A +L  L
Sbjct: 339 QGVFEKSFAKIPDE---PTGTGQAQTAAFGKSDL---------------TEEGATRLAEL 380

Query: 416 QDQVTPKPATAAQRKKPPTTPLSAPQPASSVKKPARPPAKTPVKRKAPPMPNKSVSAQHT 475
           Q+QV   P   A   + P            V K  R   ++   R+    P     +   
Sbjct: 381 QEQVKAVPDHLAAISEVP------------VNKRKRKDDESKTDRQTRGSPTSDPGS--- 425

Query: 476 QPAPVMNDESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEI 535
            P  +   + D +   P++Y EK +LSLDIN+LPGKKLGRVV IIQ+ EPS+ ++NPDEI
Sbjct: 426 -PCKLKTWDPDNKCL-PLTYEEKHQLSLDINRLPGKKLGRVVQIIQTLEPSMCETNPDEI 483

Query: 536 EIDFETLKPSTLRELEKYVATCLRKK 561
           EIDFE LKPSTLR L++YV  CL +K
Sbjct: 484 EIDFEVLKPSTLRRLQQYVKKCLHQK 509

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|321456065|gb|EFX67182.1| hypothetical protein DAPPUDRAFT_302185 [Daphnia pulex]

 Score =  334 bits (856), Expect = 9e-89,   Method: Compositional matrix adjust.
 Identities = 204/393 (51%), Positives = 235/393 (59%), Gaps = 60/393 (15%)

Query: 193 YNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQG 252
           Y+ PG  V+  A  +      K+S+RRESGRQIKK             L  ++       
Sbjct: 300 YDSPGGMVLHSAGKV-----AKISSRRESGRQIKK---------VVKDLPDTLPQ---HH 342

Query: 253 SYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTV 312
           S  + KL ES K CNEILKELFSKKHS YAWPFYKPVDA  LGL+DYH+IIKKPMDLGTV
Sbjct: 343 SKPRDKLRESTKACNEILKELFSKKHSGYAWPFYKPVDAGLLGLHDYHDIIKKPMDLGTV 402

Query: 313 KAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPI 372
           KAKMD REY+S+ EFA DVR+IFTNCYKYNPPDHDVVAMA+KLQDVFE + AK PDD P 
Sbjct: 403 KAKMDGREYRSAAEFASDVRMIFTNCYKYNPPDHDVVAMARKLQDVFEMRYAKIPDDGPD 462

Query: 373 VSSSSMVPTLTVNKNNIGRWSPDSSSD-------------STDSEADERARKLISLQDQV 419
           V   S           IG     S SD             S DS  DER RKL+  Q+Q+
Sbjct: 463 VEGES-----------IGGDDKSSGSDMESGSESDSDGSDSDDSAHDERDRKLMQFQEQL 511

Query: 420 TPKPATAAQRKKPPTTPLSAPQPASSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAP 479
                   Q +       SA +     K            +  P   +K  ++  T+ A 
Sbjct: 512 -----RIMQEQLRSLMEDSARRRRKREKTKKDLKRDVIKDKAGPTTASKPRNSASTKSAV 566

Query: 480 VMN--------------DESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREP 525
                            D  DE+++KPMSY EK++LSLDINKLPG KLGRVVHIIQSREP
Sbjct: 567 TAPPGKKKPAPPPAGAFDSEDEDNAKPMSYDEKRQLSLDINKLPGDKLGRVVHIIQSREP 626

Query: 526 SLRDSNPDEIEIDFETLKPSTLRELEKYVATCL 558
           SLRDSNPDEIEIDFETLKPSTLRELE YVA+CL
Sbjct: 627 SLRDSNPDEIEIDFETLKPSTLRELESYVASCL 659

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170036200|ref|XP_001845953.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167878751|gb|EDS42134.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score =  320 bits (820), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 206/431 (47%), Positives = 244/431 (56%), Gaps = 101/431 (23%)

Query: 214 KVSARRESGRQIKKPNRGSD------EGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCN 267
           K++ RRESGRQ   P + +       +GS   Q               K KL+++LK CN
Sbjct: 365 KIATRRESGRQEIAPFQSASYPISPYQGSAAAQ----------NPPKNKEKLSDALKSCN 414

Query: 268 EILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEF 327
           EILKELFSKKHS YAWPFYKPVDA  LGL+DYH+IIKKPMDLGTVK KMD REYKS+ EF
Sbjct: 415 EILKELFSKKHSGYAWPFYKPVDAELLGLHDYHDIIKKPMDLGTVKRKMDNREYKSANEF 474

Query: 328 ADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKN 387
           A DVRLIFTNCYKYNPPDHDVVAM +KLQDVFE ++A  PD+     ++++ P  +   +
Sbjct: 475 AADVRLIFTNCYKYNPPDHDVVAMGRKLQDVFEMRLANIPDE----PANNITPNQSKESD 530

Query: 388 NIGRWSPDSSSDSTDS----------------EADERARKLIS--------------LQD 417
           +      D + +++DS                E  ER RKL                 + 
Sbjct: 531 SSSSSDSDVTEENSDSDEECNQKLKILEKQLFEMQERMRKLAEEASLKKKAKKKMKDKKK 590

Query: 418 QVTP-----KPATAAQRKKP---------PTTPLSAPQPASSVKKPARPPA---KTPVKR 460
             TP     KP        P         P T L+ PQ +S    P  PPA   KT  K 
Sbjct: 591 STTPGSSDAKPGMEVHANPPHPVAAKVLHPVTALAQPQISSVA--PTIPPAAATKTKTKG 648

Query: 461 KAPP--------------------------MPNKSVSAQHTQPAPVMN-DESDEESSKPM 493
           +  P                           PNK   +Q      V N D  +E+++KPM
Sbjct: 649 QRAPKAGATPNAPAKRAKGAGAAGAGGAGRGPNKKKGSQA-----VTNFDSEEEDTAKPM 703

Query: 494 SYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKY 553
           SY EK++LSLDINKLPG KLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELE Y
Sbjct: 704 SYDEKRQLSLDINKLPGDKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELESY 763

Query: 554 VATCLRKKPRK 564
           VA+CLRKK  K
Sbjct: 764 VASCLRKKTHK 774

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|1588281|prf||2208296A RING3 protein

 Score =  320 bits (819), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 164/321 (51%), Positives = 207/321 (64%), Gaps = 60/321 (18%)

Query: 64  PPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQH 123
           PP V  P +PGR TNQL ++ K V+K + KHQ AWPF QPVDA+ L LP           
Sbjct: 16  PPEVSNPKKPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLP----------- 64

Query: 124 WVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDF 183
                                     DYHK+IK PMD+GTIK+RLEN YYW+  E + DF
Sbjct: 65  --------------------------DYHKIIKQPMDMGTIKRRLENNYYWAASECMQDF 98

Query: 184 NTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQI---------------KKP 228
           NTMFTNCY+YNKP +D+V+MAQTLEK+FL KV++  +  +++               K  
Sbjct: 99  NTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQELVVTTAAPPAQPLAKKKGV 158

Query: 229 NRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKP 288
            R +D  +       + T++   GS A P    SL+ CN ILKEL SKKH++YAWPFYKP
Sbjct: 159 KRKADTTT------PTPTAILAPGSPASP--PGSLEPCNGILKELLSKKHAAYAWPFYKP 210

Query: 289 VDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDV 348
           VDA+ LGL+DYH+IIK PMDL TVK KM+ R+Y+ ++EFA DVRL+F+NCYKYNPPDHDV
Sbjct: 211 VDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDV 270

Query: 349 VAMAKKLQDVFETKIAKAPDD 369
           VAMA+KLQDVFE + AK PD+
Sbjct: 271 VAMARKLQDVFEFRYAKMPDE 291

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|148725668|emb|CAN87976.1| novel protein (zgc:77289) [Danio rerio]

 Score =  320 bits (819), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 192/381 (50%), Positives = 239/381 (62%), Gaps = 40/381 (10%)

Query: 213 TKVSARRES-GRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILK 271
           +KV +RRES GR IK P +  ++G               Q    K KL + LKYC+ ILK
Sbjct: 256 SKVISRRESTGRPIKPPKKDLEDGDV------------QQPGNKKSKLNDHLKYCDTILK 303

Query: 272 ELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDV 331
           E+ SKKH++YAWPFYKPVDA  L L+DYHEIIK+PMDL TVK KMD+REY  ++ FA DV
Sbjct: 304 EMLSKKHAAYAWPFYKPVDAEALELHDYHEIIKQPMDLSTVKKKMDSREYPDAQNFAADV 363

Query: 332 RLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMV-PTLTVNKNNIG 390
           RL+F+NCYKYNPPDH+VVAMA+KLQDVFE K AK PD+    SS + V  T  V+K+   
Sbjct: 364 RLMFSNCYKYNPPDHEVVAMARKLQDVFEMKFAKMPDEPAEPSSPNAVSATAVVSKSTGS 423

Query: 391 RWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPASSVK--- 447
             S   SS S+    +ERA +L  LQ+Q+       A   + P +     +     +   
Sbjct: 424 SESSADSSSSSSDSEEERATRLAELQEQLKAVHEQLAALSQGPVSKPKKKKEKKEKEKKK 483

Query: 448 --------------------KPARPPAKTPVKRKAPPMPNKSVSAQHTQPA---PVMNDE 484
                               K  +P  +TP K+ +   PN + + +  +        N E
Sbjct: 484 KDKEKDKDKNKVKAEEDKKAKSTQPNKQTPQKKTSARKPNSTSTTRQAKKGGKPGAANYE 543

Query: 485 SDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKP 544
           SDEE S PMSY EK++LSLDIN+LPG+KLGRVVHIIQSREPSLRDSNPDEIEIDFETLKP
Sbjct: 544 SDEEESLPMSYDEKRQLSLDINRLPGEKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKP 603

Query: 545 STLRELEKYVATCLRKKPRKP 565
           STLRELE+YV +CL+KK RKP
Sbjct: 604 STLRELERYVKSCLQKKQRKP 624

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|47086635|ref|NP_997867.1| bromodomain-containing protein 3 [Danio rerio] gi|41944567|gb|AAH65949.1| Bromodomain containing 3b [Danio rerio]

 Score =  319 bits (818), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 191/381 (50%), Positives = 239/381 (62%), Gaps = 40/381 (10%)

Query: 213 TKVSARRES-GRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILK 271
           +KV +RRES GR IK P +  ++G               Q    K KL + LKYC+ ILK
Sbjct: 256 SKVISRRESTGRPIKPPKKDLEDGDV------------QQPGNKKSKLNDHLKYCDTILK 303

Query: 272 ELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDV 331
           E+ SKKH++YAWPFYKPVDA  L L+DYHEIIK+PMDL TVK KMD+REY  ++ FA D+
Sbjct: 304 EMLSKKHAAYAWPFYKPVDAEALELHDYHEIIKQPMDLSTVKKKMDSREYPDAQNFAADI 363

Query: 332 RLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMV-PTLTVNKNNIG 390
           RL+F+NCYKYNPPDH+VVAMA+KLQDVFE K AK PD+    SS + V  T  V+K+   
Sbjct: 364 RLMFSNCYKYNPPDHEVVAMARKLQDVFEMKFAKMPDEPAEPSSPNAVSATAVVSKSTGS 423

Query: 391 RWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPASSVK--- 447
             S   SS S+    +ERA +L  LQ+Q+       A   + P +     +     +   
Sbjct: 424 SESSADSSSSSSDSEEERATRLAELQEQLKAVHEQLAALSQGPVSKPKKKKEKKEKEKKK 483

Query: 448 --------------------KPARPPAKTPVKRKAPPMPNKSVSAQHTQPA---PVMNDE 484
                               K  +P  +TP K+ +   PN + + +  +        N E
Sbjct: 484 KDKEKDKDKNKVKAEEDKKAKSTQPNKQTPQKKTSARKPNSTSTTRQAKKGGKPGAANYE 543

Query: 485 SDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKP 544
           SDEE S PMSY EK++LSLDIN+LPG+KLGRVVHIIQSREPSLRDSNPDEIEIDFETLKP
Sbjct: 544 SDEEESLPMSYDEKRQLSLDINRLPGEKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKP 603

Query: 545 STLRELEKYVATCLRKKPRKP 565
           STLRELE+YV +CL+KK RKP
Sbjct: 604 STLRELERYVKSCLQKKQRKP 624

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|402855238|ref|XP_003892238.1| PREDICTED: bromodomain testis-specific protein isoform 4 [Papio anubis] gi|402855240|ref|XP_003892239.1| PREDICTED: bromodomain testis-specific protein isoform 5 [Papio anubis]

 Score =  319 bits (817), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 216/560 (38%), Positives = 302/560 (53%), Gaps = 89/560 (15%)

Query: 61  IVQPPTVPPPH----RPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIF 116
           IV PP  PP +    + GR TNQL ++ K VLK + KH  +WPF +PVDA+ L LP    
Sbjct: 11  IVNPP--PPEYINTKKNGRLTNQLQYLQKVVLKDLWKHSFSWPFQRPVDAVKLKLP---- 64

Query: 117 RFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRL-----ENF 171
                         +  +L+A AL     + +Q   ++ +    +G  K+R+     +N 
Sbjct: 65  ------------PGDDIVLMAQALEK---LFMQKLSQMPQEEQVVGG-KERIKKGTQQNI 108

Query: 172 YYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRG 231
             +S KE  S   T      V+ +     V    +L  L + + ++   S + + +  +G
Sbjct: 109 AVFSAKEKSSPNATE----KVFKQQAIPSVFSKTSLSPLNVAQGASVNSSSQTVVQVTKG 164

Query: 232 SDEGSFTTQLATSVTSVGDQGS-------------------------------YAKPKLT 260
               + TT  ATSV     + S                                   K+T
Sbjct: 165 VKRKADTTTPATSVVKASSEFSPTFTEKSVTLPPIKENMPKNVLPDSQQQYNVVKSVKVT 224

Query: 261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDARE 320
           E L++C+EILKE+ +KKH SYAWPFY PVD   LGL++Y++I+K PMDLGT+K KMD +E
Sbjct: 225 EQLRHCSEILKEMLAKKHFSYAWPFYNPVDVNALGLHNYYDIVKNPMDLGTIKEKMDNQE 284

Query: 321 YKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP----DDVPIVSSS 376
           YK + +FA DVRL+F NCYKYNPPDH+VV MA+ LQDVFET  +K P    + +P+    
Sbjct: 285 YKDAYKFAADVRLMFMNCYKYNPPDHEVVTMARMLQDVFETHFSKIPVEPVESMPLCYIK 344

Query: 377 SMVPTLTVNKNNIGRWSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTP 436
           + + T T  + N    S + +S S DSE DER ++L  LQ+Q+           + P   
Sbjct: 345 TDI-TETTGRENTNEASSEGNS-SGDSE-DERVQRLAKLQEQLKAVHQQLQVLSQVPFRK 401

Query: 437 LSAPQPA-----------SSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDES 485
           L+  +             +S + P +   +  +K K+     K    Q+     +     
Sbjct: 402 LNKKKEKSKKEKKKEKVNNSNENPRKMCEQMRLKEKSKRNQPKKRKQQY-----IGQKSE 456

Query: 486 DEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPS 545
           DE+++KPM+Y EK++LSL+INKLPG KLGRVVHIIQSREPSL +SNPDEIEIDFETLK S
Sbjct: 457 DEDNAKPMNYDEKRQLSLNINKLPGDKLGRVVHIIQSREPSLSNSNPDEIEIDFETLKAS 516

Query: 546 TLRELEKYVATCLRKKPRKP 565
           TLRELEKYV+ CLRK+P KP
Sbjct: 517 TLRELEKYVSACLRKRPLKP 536

Source: Papio anubis

Species: Papio anubis

Genus: Papio

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|391337779|ref|XP_003743242.1| PREDICTED: bromodomain testis-specific protein-like [Metaseiulus occidentalis]

 Score =  318 bits (814), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 190/370 (51%), Positives = 243/370 (65%), Gaps = 35/370 (9%)

Query: 214 KVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKEL 273
           K+S RRESGR IKKP +   E +  +++              + K+TE LKYCN I+KEL
Sbjct: 360 KISTRRESGRPIKKPVKDIPESAQHSKVK-------------RGKMTEKLKYCNSIIKEL 406

Query: 274 FSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRL 333
           F+KKHS+YAWPFY  VD   LGL+DY++II +PMDLGT+K KM+ REY++  +F +DVRL
Sbjct: 407 FAKKHSAYAWPFYTAVDVEGLGLHDYYDIITQPMDLGTIKTKMERREYRNPDDFCNDVRL 466

Query: 334 IFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRWS 393
           +F NCYKYNP DH+VV MA+KLQDVFE K+ K P++ PI +SS+   +   +++ +   S
Sbjct: 467 VFMNCYKYNPADHEVVKMARKLQDVFEMKLTKMPNE-PIPASSASSDSDEASESEVA--S 523

Query: 394 PDSSSDSTDSEADERARKLISLQDQ---VTPKPATAAQRKKPPTTPLSAPQPASSVKKPA 450
            + S    DSEA ER RKL  LQDQ   VT + +  A + +  +            K+ A
Sbjct: 524 AEDSDSGDDSEA-ERERKLQQLQDQLKRVTEEISALAAQSRSSSKKKKKKSQKEKDKEKA 582

Query: 451 RPPAKTPVKRKAPPMPNKSVSA------------QHTQPAPVMNDESDEESSKPMSYFEK 498
           + P+K+ VKR+     N + +             + T  A    D  DE+S+KPMSY EK
Sbjct: 583 KSPSKSRVKREMNKATNNNNNNNNNNTAKPKRQKRETAVARGDFDSEDEDSAKPMSYDEK 642

Query: 499 QELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCL 558
           ++LSLDINKLPG KLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELE YVA+CL
Sbjct: 643 RQLSLDINKLPGDKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELESYVASCL 702

Query: 559 ---RKKPRKP 565
               KKPRKP
Sbjct: 703 ARNAKKPRKP 712

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	566
UNIPROTKB|F1S033	726	BRD3 "Uncharacterized protein"	0.452	0.352	0.427	5.4e-128
UNIPROTKB|Q15059	726	BRD3 "Bromodomain-containing p	0.452	0.352	0.437	6.7e-126
MGI|MGI:1914632	726	Brd3 "bromodomain containing 3	0.434	0.338	0.445	1.4e-125
RGD|1308925	742	Brd3 "bromodomain containing 3	0.402	0.307	0.467	7.5e-125
FB|FBgn0004656	2038	fs(1)h "female sterile (1) hom	0.280	0.078	0.624	1.6e-124
MGI|MGI:99495	798	Brd2 "bromodomain containing 2	0.455	0.323	0.412	1.7e-124
RGD|1303324	798	Brd2 "bromodomain containing 2	0.457	0.324	0.407	3.9e-124
MGI|MGI:1891374	956	Brdt "bromodomain, testis-spec	0.535	0.316	0.520	4.5e-113
RGD|1306678	952	Brdt "bromodomain, testis-spec	0.533	0.317	0.520	4.5e-113
UNIPROTKB|E1BCG9	629	Bt.104862 "Uncharacterized pro	0.542	0.488	0.522	1.2e-112

UNIPROTKB|F1S033 BRD3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 494 (179.0 bits), Expect = 5.4e-128, Sum P(4) = 5.4e-128
 Identities = 120/281 (42%), Positives = 161/281 (57%)

Query:   214 KVSARRESG-RQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKE 272
             KV ARRESG R IK P +  ++G    Q A      G +G     +L+E L++C+ IL+E
Sbjct:   274 KVVARRESGGRPIKPPKKDLEDGE-VPQHA------GKKG-----RLSEHLRHCDSILRE 321

Query:   273 LFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVR 332
             + SKKH++YAWPFYKPVDA  L L+DYH+IIK PMDL TVK KMD+REY  ++ FA D+R
Sbjct:   322 MLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKKKMDSREYPDAQGFAADIR 381

Query:   333 LIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTL-TVNKNN-IG 390
             L+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK PD+ P+ + +   P    V+K     
Sbjct:   382 LMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE-PVEAPALPAPAAPVVSKGTESS 440

Query:   391 RWXXXXXXXXXXXEADE-RARKLISLQDQVTP-KPATAAQRKKPPTTPLSAPQPASSVKK 448
             R            +++E RA +L  LQ+Q+       AA  + P   P    +     KK
Sbjct:   441 RSSEESSSDSGSSDSEEERATRLAELQEQLKAVHEQLAALSQAPVNKPKRKKEKKEKKKK 500

Query:   449 PA-------RPPAKTPVKRKAPPMPNKSVSAQHTQPAPVMN 482
                      R  AK+  ++KA   P    + Q   PA   N
Sbjct:   501 DKDKDKDKERHKAKSEEEKKAKAAPPAKQAQQKKAPAKKAN 541

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

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

GO:0003682 "chromatin binding" evidence=IEA

UNIPROTKB|Q15059 BRD3 "Bromodomain-containing protein 3" [Homo sapiens (taxid:9606)]

 Score = 494 (179.0 bits), Expect = 6.7e-126, Sum P(4) = 6.7e-126
 Identities = 123/281 (43%), Positives = 159/281 (56%)

Query:   214 KVSARRESG-RQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKE 272
             KV ARRESG R IK P +  ++G    Q A      G +G     KL+E L+YC+ IL+E
Sbjct:   274 KVVARRESGGRPIKPPKKDLEDGE-VPQHA------GKKG-----KLSEHLRYCDSILRE 321

Query:   273 LFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVR 332
             + SKKH++YAWPFYKPVDA  L L+DYH+IIK PMDL TVK KMD REY  ++ FA DVR
Sbjct:   322 MLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVR 381

Query:   333 LIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLT-VNKN-NIG 390
             L+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK PD+ P+ + +   P    V+K     
Sbjct:   382 LMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE-PVEAPALPAPAAPMVSKGAESS 440

Query:   391 RWXXXXXXXXXXXEADE-RARKLISLQDQVTP-KPATAAQRKKPPTTPLSAPQPASSVKK 448
             R            +++E RA +L  LQ+Q+       AA  + P   P    +     KK
Sbjct:   441 RSSEESSSDSGSSDSEEERATRLAELQEQLKAVHEQLAALSQAPVNKPKKKKEKKEKEKK 500

Query:   449 PA---RPPAKTPVK----RKAPPMPNKSVSAQHTQPAPVMN 482
                  +   K  VK    +KA   P    + Q   PA   N
Sbjct:   501 KKDKEKEKEKHKVKAEEEKKAKVAPPAKQAQQKKAPAKKAN 541

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

GO:0016568 "chromatin modification" evidence=IEA

GO:0005634 "nucleus" evidence=NAS

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

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

GO:0003682 "chromatin binding" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:1914632 Brd3 "bromodomain containing 3" [Mus musculus (taxid:10090)]

 Score = 494 (179.0 bits), Expect = 1.4e-125, Sum P(4) = 1.4e-125
 Identities = 118/265 (44%), Positives = 155/265 (58%)

Query:   214 KVSARRESG-RQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKE 272
             KV ARRESG R IK P +  ++G    Q A      G +G     KL+E L++C+ IL+E
Sbjct:   273 KVVARRESGGRPIKPPKKDLEDGE-VPQHA------GKKG-----KLSEHLRHCDSILRE 320

Query:   273 LFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVR 332
             + SKKH++YAWPFYKPVDA  L L+DYH+IIK PMDL TVK KMD+REY  ++ FA D+R
Sbjct:   321 MLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDSREYPDAQGFAADIR 380

Query:   333 LIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLT-VNKN-NIG 390
             L+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK PD+ P+ + +   PT   V+K     
Sbjct:   381 LMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE-PMEAPALPAPTAPIVSKGAESS 439

Query:   391 RWXXXXXXXXXXXEADE-RARKLISLQDQVTP-KPATAAQRKKPPTTPLSAPQPASSVKK 448
             R            +++E RA +L  LQ+Q+       AA  + P   P    +     KK
Sbjct:   440 RSSEESSSDSGSSDSEEERATRLAELQEQLKAVHEQLAALSQAPVNKPKKKKEKKEKEKK 499

Query:   449 PA-RPPAKTPVKRKAPPMPNKSVSA 472
                +   K   K KA     K   A
Sbjct:   500 KKDKDKDKEKEKHKAKSEEEKKAKA 524

GO:0003682 "chromatin binding" evidence=ISO

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0016568 "chromatin modification" evidence=IEA

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

RGD|1308925 Brd3 "bromodomain containing 3" [Rattus norvegicus (taxid:10116)]

 Score = 483 (175.1 bits), Expect = 7.5e-125, Sum P(5) = 7.5e-125
 Identities = 116/248 (46%), Positives = 152/248 (61%)

Query:   214 KVSARRESG-RQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKE 272
             KV ARRESG R IK P +  ++G    Q A      G +G     KL+E L++C+ IL+E
Sbjct:   274 KVVARRESGGRPIKPPKKDLEDGE-VPQHA------GKKG-----KLSEHLRHCDSILRE 321

Query:   273 LFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVR 332
             + SKKH++YAWPFYKPVDA  L L+DYH+IIK PMDL TVK KMD+REY  ++ FA D+R
Sbjct:   322 MLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDSREYPDAQGFAADIR 381

Query:   333 LIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLT-VNKN-NIG 390
             L+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK PD+ P+   +   PT   V+K     
Sbjct:   382 LMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE-PMEVPALPAPTAPIVSKGAESS 440

Query:   391 RWXXXXXXXXXXXEADE-RARKLISLQDQVTPKPATAAQRKKPPTTPLSA--PQPASSVK 447
             R            +++E RA +L  LQ+Q T   A   Q     +  L A   Q A+  +
Sbjct:   441 RSSEESSSDSGSSDSEEERATRLAELQEQ-TGCGAFQDQLLNVSSVQLKAVHEQLAALSQ 499

Query:   448 KPARPPAK 455
              P + P K
Sbjct:   500 APKKAPTK 507

GO:0003682 "chromatin binding" evidence=ISO

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

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

FB|FBgn0004656 fs(1)h "female sterile (1) homeotic" [Drosophila melanogaster (taxid:7227)]

 Score = 504 (182.5 bits), Expect = 1.6e-124, Sum P(4) = 1.6e-124
 Identities = 108/173 (62%), Positives = 126/173 (72%)

Query:   214 KVSARRESGRQIKKPNRGSDEGSFTTQLATS-VTSVGD--QGSYA-------KPKLTESL 263
             K++ RRES RQ     +GS  G   + L  S V  +G    G  A       K KL+++L
Sbjct:   425 KIATRRESNRQ-DLTFQGS--GYNMSPLGVSGVPGLGGLVAGGVAGVAVAKNKEKLSDAL 481

Query:   264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKS 323
             K CNEILKELFSKKHS YAWPFYKPVDA  LGL+DYH+IIKKPMDLGTVK KMD REYKS
Sbjct:   482 KSCNEILKELFSKKHSGYAWPFYKPVDAEMLGLHDYHDIIKKPMDLGTVKRKMDNREYKS 541

Query:   324 SKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSS 376
             + EFA DVRLIFTNCYKYNPPDHDVVAM +KLQDVFE + A  PD+ P+ +++
Sbjct:   542 APEFAADVRLIFTNCYKYNPPDHDVVAMGRKLQDVFEMRYANIPDE-PVANAA 593

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

GO:0003677 "DNA binding" evidence=NAS

GO:0004672 "protein kinase activity" evidence=NAS

GO:0007362 "terminal region determination" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IMP

GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IMP

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

 Score = 483 (175.1 bits), Expect = 1.7e-124, Sum P(4) = 1.7e-124
 Identities = 116/281 (41%), Positives = 155/281 (55%)

Query:   218 RRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKK 277
             RRESGR IK P +   +     Q            S  K KL+E LK+CN ILKEL SKK
Sbjct:   316 RRESGRPIKPPRKDLPDSQQQHQ------------SSKKGKLSEQLKHCNGILKELLSKK 363

Query:   278 HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN 337
             H++YAWPFYKPVDA+ LGL+DYH+IIK PMDL TVK KM+ R+Y+ ++EFA DVRL+F+N
Sbjct:   364 HAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSN 423

Query:   338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV----PIVSSSSMVPTLTVNKNNIGRWX 393
             CYKYNPPDHDVVAMA+KLQDVFE + AK PD+     P+  S+++ P LT  K++     
Sbjct:   424 CYKYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTALPPGLT--KSSSESSS 481

Query:   394 XXXXXXXXXXEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSA--PQPASSVKKPAR 451
                       E +E        + + +      A R       L A   Q A+  + P  
Sbjct:   482 EESSSESSSEEEEEEEEDEDEEESESSDSEEERAHRLAELQEQLRAVHEQLAALSQGPIS 541

Query:   452 PPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESDEESSKP 492
              P +   KR+      K  + +H     +  D+    + +P
Sbjct:   542 KPKR---KREKKEKKKKRKAEKHRGRIGIDEDDKGPRAPRP 579

GO:0003682 "chromatin binding" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006334 "nucleosome assembly" evidence=ISO

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

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

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

GO:0016568 "chromatin modification" evidence=IEA

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

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

 Score = 480 (174.0 bits), Expect = 3.9e-124, Sum P(4) = 3.9e-124
 Identities = 115/282 (40%), Positives = 156/282 (55%)

Query:   218 RRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKK 277
             RRESGR IK P +   +     Q            S  K KL+E LK+CN ILKEL SKK
Sbjct:   316 RRESGRPIKPPRKDLPDSQQQHQ------------SSKKGKLSEQLKHCNGILKELLSKK 363

Query:   278 HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN 337
             H++YAWPFYKPVDA+ LGL+DYH+IIK PMDL TVK KM+ R+Y+ ++EFA DVRL+F+N
Sbjct:   364 HAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSN 423

Query:   338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV----PIVSSSSMVPTLTVNKNNIGRWX 393
             CYKYNPPDHDVVAMA+KLQDVFE + AK PD+     P+  S+++ P L   K++     
Sbjct:   424 CYKYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTALPPGLA--KSSSESSS 481

Query:   394 XXXXXXXXXXEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSA--PQPASSVKKPAR 451
                       E +E   +    + + +      A R       L A   Q A+  + P  
Sbjct:   482 EESSSESSSEEEEEEDEEDEEEESESSDSEEERAHRLAELQEQLRAVHEQLAALSQGPIS 541

Query:   452 PPAKTPVKRKAPPMPNKSVSAQHTQPAPVMNDESDEESSKPM 493
              P +   KR+      K  + +H     +  D+    + +P+
Sbjct:   542 KPKR---KREKKEKKKKRKAEKHRGRIGIDEDDKGPRAPRPL 580

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

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

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

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

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

GO:0016568 "chromatin modification" evidence=IEA

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

MGI|MGI:1891374 Brdt "bromodomain, testis-specific" [Mus musculus (taxid:10090)]

 Score = 771 (276.5 bits), Expect = 4.5e-113, Sum P(3) = 4.5e-113
 Identities = 165/317 (52%), Positives = 205/317 (64%)

Query:   258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
             K+TE LK+C+EILKE+ +KKH  YAWPFY PVDA  LGL++Y++++K PMDLGT+K KMD
Sbjct:   267 KVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMD 326

Query:   318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSS 377
              +EYK + EFA DVRL+F NCYKYNPPDH+VVAMA+ LQDVFE   AK PD+ PI S  +
Sbjct:   327 NQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVFELHFAKIPDE-PIESMHA 385

Query:   378 MVPTLTVNKNN-IGRWXXXXXXXXXXXEAD---ERARKLISLQDQVTPKPATAAQRKKPP 433
                 LT N    + R              D   ER + L  LQ+Q+           + P
Sbjct:   386 C--HLTTNSAQALSRESSSEASSGDASSEDSEDERVQHLAKLQEQLNAVHQQLQVLSQVP 443

Query:   434 TTPLSAPQPASSVKKPARPPAKTPVK--RKAPPMPNKSVSAQHTQPA---PVMNDESDEE 488
                L      S  + P R       +  RK P    +   A+  QP    P++  E +E+
Sbjct:   444 LRKLKKKNEKSK-RAPKRKKVNNRDENPRKKPKQMKQKEKAKINQPKKKKPLLKSE-EED 501

Query:   489 SSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLR 548
             ++KPM+Y EK++LSLDINKLPG KLGR+VHIIQSREPSLR+SNPDEIEIDFETLK STLR
Sbjct:   502 NAKPMNYDEKRQLSLDINKLPGDKLGRIVHIIQSREPSLRNSNPDEIEIDFETLKASTLR 561

Query:   549 ELEKYVATCLRKKPRKP 565
             ELEKYV  CLRK+  KP
Sbjct:   562 ELEKYVLACLRKRSLKP 578

GO:0001207 "histone displacement" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0006338 "chromatin remodeling" evidence=IDA

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

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0007126 "meiosis" evidence=IEA

GO:0007140 "male meiosis" evidence=IMP

GO:0007141 "male meiosis I" evidence=IMP

GO:0007283 "spermatogenesis" evidence=IMP

GO:0008380 "RNA splicing" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0042393 "histone binding" evidence=ISO;IDA

GO:0043484 "regulation of RNA splicing" evidence=IMP

GO:0051039 "positive regulation of transcription during meiosis" evidence=IMP

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

RGD|1306678 Brdt "bromodomain, testis-specific" [Rattus norvegicus (taxid:10116)]

 Score = 768 (275.4 bits), Expect = 4.5e-113, Sum P(3) = 4.5e-113
 Identities = 166/319 (52%), Positives = 208/319 (65%)

Query:   258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
             K+TE LK+C+EILKE+ +KKH  YAWPFY PVD   LGL++Y++I+K PMDLGT+K KMD
Sbjct:   267 KVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDVDALGLHNYYDIVKNPMDLGTIKGKMD 326

Query:   318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSS 377
              +EYK + EFA DVRL+F NCYKYNPPDH+VV MA+ LQDVFE   AK PD+ P+ S  +
Sbjct:   327 KQEYKDACEFAADVRLMFMNCYKYNPPDHEVVTMARMLQDVFEMHFAKIPDE-PVESMRA 385

Query:   378 MVPTLTVNKNN-IGRWXXXXXXX---XXXXEADERARKLISLQDQVTPKPATAAQRKKPP 433
                 LT N    + R                 DER ++L  LQ+Q+           + P
Sbjct:   386 C--HLTTNSAKALSRESSSEASSGDCSSEDSEDERVQRLAKLQEQLNAVHQQLQVLSQVP 443

Query:   434 TTPLSAPQPASSVKKPARPPA---KTPVKRKAPPMPNKSVSAQHTQPA---PVMNDESDE 487
                L      S  + P R      + P K+KA  M  K   A+  QP    P++  E +E
Sbjct:   444 LRKLKKKNEKSK-RAPKRKKVNRDENP-KKKAKQMKQKE-KAKSNQPKKKKPLLKLE-EE 499

Query:   488 ESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTL 547
             +++KPM+Y EK++LSLDINKLPG KLGR+VHIIQSREPSLR+SNPDEIEIDFETLK STL
Sbjct:   500 DNAKPMNYDEKRQLSLDINKLPGDKLGRIVHIIQSREPSLRNSNPDEIEIDFETLKASTL 559

Query:   548 RELEKYVATCLRKKPRKPN 566
             RELEKYV  CLRK+  KP+
Sbjct:   560 RELEKYVLACLRKRSLKPH 578

GO:0001207 "histone displacement" evidence=ISS

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0006338 "chromatin remodeling" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0007140 "male meiosis" evidence=ISS

GO:0007141 "male meiosis I" evidence=ISS

GO:0007283 "spermatogenesis" evidence=ISS

GO:0008380 "RNA splicing" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0042393 "histone binding" evidence=IEA

GO:0043484 "regulation of RNA splicing" evidence=ISS

GO:0051039 "positive regulation of transcription during meiosis" evidence=ISS

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

UNIPROTKB|E1BCG9 Bt.104862 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 761 (272.9 bits), Expect = 1.2e-112, Sum P(3) = 1.2e-112
 Identities = 166/318 (52%), Positives = 205/318 (64%)

Query:   258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
             K+TE L++C+EILKE+  KKH SYAWPFY PVD   LGL++Y++I+K PMDLGT+KAKMD
Sbjct:   272 KVTEQLRHCSEILKEMLGKKHLSYAWPFYNPVDVNALGLHNYYDIVKTPMDLGTIKAKMD 331

Query:   318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSS 377
              +EYK + EFA DVRL+F NCYKYNPPDH+VV MA+ LQDVFE   AK PD+ P V S  
Sbjct:   332 NQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVTMARMLQDVFEMHFAKIPDE-P-VESMP 389

Query:   378 MVPTLTVNKNNIGRWXXXXXXXXXXXEAD---ERARKLISLQDQVTPKPATAAQRKKPPT 434
             +    T     +GR              D   ER ++L  LQ+Q+           + P 
Sbjct:   390 VCYVKTDTTKTLGRESSSEASSEDNSSGDSEDERVQRLAKLQEQLQAVHQQLQVLSQVPF 449

Query:   435 TPLSAPQPASSVKKPARP---PAKTPVKR-KAPPMPNKSVSAQHTQPAP-VMNDES-DEE 488
               L      S  +K         + P K+ K   +  KS      +  P V   +S DE+
Sbjct:   450 RKLKRKNEKSKREKKKEKIDNRDENPRKKFKQMKLKEKSKRNLPKKKKPQVFTMKSEDED 509

Query:   489 SSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLR 548
             ++KPM+Y EK++LSLDINKLPG KLGRVVHIIQSREPSLR+SNPDEIEIDFETLK STLR
Sbjct:   510 NAKPMNYDEKRQLSLDINKLPGDKLGRVVHIIQSREPSLRNSNPDEIEIDFETLKSSTLR 569

Query:   549 ELEKYVATCLRKKPRKPN 566
             EL+KYVA CLRK+  KPN
Sbjct:   570 ELQKYVAGCLRKRSLKPN 587

GO:0042393 "histone binding" evidence=IEA

GO:0006338 "chromatin remodeling" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q91Y44	BRDT_MOUSE	No assigned EC number	0.5295	0.5282	0.3127	yes	N/A
D4A7T3	BRDT_RAT	No assigned EC number	0.5078	0.5335	0.3172	yes	N/A
F7DRV9	BRDT_XENTR	No assigned EC number	0.5032	0.5282	0.3204	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	566
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	6e-60
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	1e-55
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	2e-42
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	1e-37
smart00297	107	smart00297, BROMO, bromo domain	2e-35
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	1e-32
cd04369	99	cd04369, Bromodomain, Bromodomain	9e-32
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	7e-28
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	7e-26
smart00297	107	smart00297, BROMO, bromo domain	1e-25
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	4e-24
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	4e-24
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	6e-24
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	1e-23
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	2e-21
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	3e-21
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	4e-21
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	9e-21
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	1e-20
cd04369	99	cd04369, Bromodomain, Bromodomain	2e-20
pfam00439	84	pfam00439, Bromodomain, Bromodomain	2e-20
COG5076	371	COG5076, COG5076, Transcription factor involved in	4e-18
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	6e-18
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	2e-17
COG5076	371	COG5076, COG5076, Transcription factor involved in	4e-17
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	3e-16
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	7e-16
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	2e-15
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	3e-15
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	3e-15
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	3e-14
pfam00439	84	pfam00439, Bromodomain, Bromodomain	8e-14
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	1e-12
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	1e-12
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	4e-12
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	4e-11
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	7e-11
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	1e-10
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	2e-10
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	2e-10
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	2e-10
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	8e-10
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	1e-09
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	2e-09
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	2e-09
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	2e-09
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	3e-09
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	2e-08
cd05501	102	cd05501, Bromo_SP100C_like, Bromodomain, SP100C_li	2e-08
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	5e-08
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	5e-08
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	8e-08
cd05508	99	cd05508, Bromo_RACK7, Bromodomain, RACK7_like subf	2e-07
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	3e-07
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	3e-07
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	4e-07
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	6e-07
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	7e-07
cd05494	114	cd05494, Bromodomain_1, Bromodomain; uncharacteriz	2e-06
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	4e-06
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	4e-06
cd05501	102	cd05501, Bromo_SP100C_like, Bromodomain, SP100C_li	9e-06
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	1e-05
cd05517	103	cd05517, Bromo_polybromo_II, Bromodomain, polybrom	1e-05
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	4e-05
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	7e-05
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	1e-04
cd05517	103	cd05517, Bromo_polybromo_II, Bromodomain, polybrom	1e-04
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	9e-04
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	0.001
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.004

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

 Score =  193 bits (493), Expect = 6e-60
 Identities = 72/101 (71%), Positives = 85/101 (84%)

Query: 262 SLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREY 321
            LK+C+ ILKELFSKKH +YAWPFYKPVD   LGL+DYH+IIK PMDL T+K K+D REY
Sbjct: 1   QLKFCSGILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREY 60

Query: 322 KSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETK 362
             ++EFA DVRL+F+NCYKYNPPDH V AMA+KLQDVFE +
Sbjct: 61  ADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101

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

 Score =  182 bits (463), Expect = 1e-55
 Identities = 78/142 (54%), Positives = 90/142 (63%), Gaps = 37/142 (26%)

Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
           R+TNQL ++ K VLK + KH+ AWPF QPVDA+ LNLP                      
Sbjct: 1   RHTNQLQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLP---------------------- 38

Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                          DYHK+IK PMDLGTIKKRLEN YYWS  E I DFNTMFTNCY+YN
Sbjct: 39  ---------------DYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYN 83

Query: 195 KPGEDVVVMAQTLEKLFLTKVS 216
           KPG+DVV+MAQTLEKLFL K++
Sbjct: 84  KPGDDVVLMAQTLEKLFLQKLA 105

Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 107

>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score =  147 bits (372), Expect = 2e-42
 Identities = 54/100 (54%), Positives = 68/100 (68%)

Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
           LK+C E+LKEL   KHS+Y WPF  PVD   L + +Y  IIKKPMDLGT+  K+   +Y+
Sbjct: 2   LKFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQ 61

Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETK 362
           S+KEF  DVRLIF NCY +NP   DV  M  +L++VF  K
Sbjct: 62  SAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101

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|99938 cd05506, Bromo_plant1, Bromodomain, uncharacterized subfamily specific to plants

 Score =  133 bits (338), Expect = 1e-37
 Identities = 53/100 (53%), Positives = 66/100 (66%), Gaps = 3/100 (3%)

Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
           +K C  +L++L   K     W F  PVD   LGL DY +IIKKPMDLGTVK K++  EY 
Sbjct: 2   MKQCGTLLRKLMKHKWG---WVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYS 58

Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETK 362
           S +EFA DVRL F N  +YNPP +DV  MAK+L  +FET+
Sbjct: 59  SPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETR 98

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|197636 smart00297, BROMO, bromo domain

 Score =  128 bits (324), Expect = 2e-35
 Identities = 45/107 (42%), Positives = 62/107 (57%), Gaps = 3/107 (2%)

Query: 261 ESLKYCNEILKELFSKKHSS-YAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAR 319
           +  K   E+LK +  K  S   +WPF KPV        DY++IIKKPMDL T+K K++  
Sbjct: 3   KLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAP--DYYDIIKKPMDLKTIKKKLENG 60

Query: 320 EYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKA 366
           +Y S +EF  D  L+F+N   YN PD +V   AKKL+  FE K+ + 
Sbjct: 61  KYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

Length = 107

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

 Score =  120 bits (303), Expect = 1e-32
 Identities = 51/106 (48%), Positives = 66/106 (62%), Gaps = 4/106 (3%)

Query: 260 TESLKYC-NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA 318
           T  L+Y    +LK L+  K    AWPF +PVDA  L L DYH+IIK PMDLGT+K +++ 
Sbjct: 3   TNQLQYLLKVVLKALWKHKF---AWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLEN 59

Query: 319 REYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIA 364
             Y S+ E   D   +FTNCY YN P  DVV MA+ L+ +F  K+A
Sbjct: 60  NYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLA 105

Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 107

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score =  117 bits (296), Expect = 9e-32
 Identities = 43/101 (42%), Positives = 56/101 (55%), Gaps = 3/101 (2%)

Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
            K    +L  L   K    + PF +PVD       DY+E+IK PMDL T+K K+   EYK
Sbjct: 2   KKKLRSLLDALKKLKRD-LSEPFLEPVDP--KEAPDYYEVIKNPMDLSTIKKKLKNGEYK 58

Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI 363
           S +EF  DVRLIF+N   YN P   +   AKKL+ +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|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score =  106 bits (268), Expect = 7e-28
 Identities = 41/98 (41%), Positives = 59/98 (60%), Gaps = 5/98 (5%)

Query: 268 EILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEF 327
           ++L  L  K H S AWPF +PVD       DY+++IKKPMDL T++ K++   Y + +EF
Sbjct: 8   KVLDSL--KNHKS-AWPFLEPVDKEEAP--DYYDVIKKPMDLSTMEEKLENGYYVTLEEF 62

Query: 328 ADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
             D++LIF NC  YN PD +    A KL+  F  K+ +
Sbjct: 63  VADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKE 100

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

 Score =  101 bits (254), Expect = 7e-26
 Identities = 48/136 (35%), Positives = 62/136 (45%), Gaps = 41/136 (30%)

Query: 79  QLAFISKNVLKPVMKHQH---AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPIL 135
           QL F S  +LK +   +H   AWPF++PVD   L L                        
Sbjct: 1   QLKFCSG-ILKELFSKKHKAYAWPFYKPVDPEALGLH----------------------- 36

Query: 136 LAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNK 195
                         DYH +IKHPMDL TIKK+L+N  Y   +E  +D   MF+NCY YN 
Sbjct: 37  --------------DYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNP 82

Query: 196 PGEDVVVMAQTLEKLF 211
           P   V  MA+ L+ +F
Sbjct: 83  PDHPVHAMARKLQDVF 98

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 =  101 bits (253), Expect = 1e-25
 Identities = 46/140 (32%), Positives = 61/140 (43%), Gaps = 39/140 (27%)

Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
           +   +L  + K VL  +  H  +WPF +PV                          E P 
Sbjct: 3   KLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRK-----------------------EAP- 38

Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                          DY+ +IK PMDL TIKK+LEN  Y S +E ++DFN MF+N   YN
Sbjct: 39  ---------------DYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

Query: 195 KPGEDVVVMAQTLEKLFLTK 214
            P  +V   A+ LEK F  K
Sbjct: 84  GPDSEVYKDAKKLEKFFEKK 103

Length = 107

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

 Score = 96.5 bits (241), Expect = 4e-24
 Identities = 41/131 (31%), Positives = 58/131 (44%), Gaps = 39/131 (29%)

Query: 85  KNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPV 144
           K VL  +  H+ AWPF +PVD  +                                  P 
Sbjct: 7   KKVLDSLKNHKSAWPFLEPVDKEE---------------------------------AP- 32

Query: 145 LIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMA 204
                DY+ VIK PMDL T++++LEN YY + +E ++D   +F NC +YN P  +    A
Sbjct: 33  -----DYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCA 87

Query: 205 QTLEKLFLTKV 215
             LEK F  K+
Sbjct: 88  NKLEKFFWKKL 98

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

>gnl|CDD|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 96.6 bits (241), Expect = 4e-24
 Identities = 40/97 (41%), Positives = 53/97 (54%), Gaps = 3/97 (3%)

Query: 264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKS 323
           K+    ++ L   K    A PF  PVD   L +  Y  IIKKPMDLGT++ K+ +  Y S
Sbjct: 7   KFLLSSIRSL---KRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTS 63

Query: 324 SKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFE 360
            +EF  D  L+  NC  +N P+H V  M K+LQ  FE
Sbjct: 64  VEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAFE 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|99938 cd05506, Bromo_plant1, Bromodomain, uncharacterized subfamily specific to plants

 Score = 95.9 bits (239), Expect = 6e-24
 Identities = 44/129 (34%), Positives = 58/129 (44%), Gaps = 37/129 (28%)

Query: 86  NVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVL 145
            +L+ +MKH+  W F+ PVD + L LP                                 
Sbjct: 7   TLLRKLMKHKWGWVFNAPVDVVALGLP--------------------------------- 33

Query: 146 IILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQ 205
               DY  +IK PMDLGT+KK+LE   Y S +E  +D    F N   YN PG DV  MA+
Sbjct: 34  ----DYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAK 89

Query: 206 TLEKLFLTK 214
            L K+F T+
Sbjct: 90  ELLKIFETR 98

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|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 95.4 bits (238), Expect = 1e-23
 Identities = 40/110 (36%), Positives = 63/110 (57%), Gaps = 10/110 (9%)

Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDARE-- 320
            + C  +L EL+  + S    PF++PV      + +Y++IIK PMDL  ++ K+  +   
Sbjct: 6   QRKCERLLLELYCHELSL---PFHEPVSP---SVPNYYKIIKTPMDLSLIRKKLQPKSPQ 59

Query: 321 -YKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKA-PD 368
            Y S +EF  DVRL+F NCYK+N  D +V    K+L+  FE ++ +  PD
Sbjct: 60  HYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKEILPD 109

Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 109

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

 Score = 89.0 bits (221), Expect = 2e-21
 Identities = 35/87 (40%), Positives = 51/87 (58%)

Query: 277 KHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFT 336
           K    + PF +PVD   LG+ DY +I+K PMDL T++ K+D  +Y+   ++ DDV L+F 
Sbjct: 17  KQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFD 76

Query: 337 NCYKYNPPDHDVVAMAKKLQDVFETKI 363
           N + YN     V     KL +VFE +I
Sbjct: 77  NAWLYNRKTSRVYKYCTKLAEVFEQEI 103

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|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 88.7 bits (220), Expect = 3e-21
 Identities = 40/107 (37%), Positives = 59/107 (55%), Gaps = 11/107 (10%)

Query: 266 CNEILKELFSKKHSSYAWPFYKPV---DAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
            +++L EL  K ++ ++ PF   V   +A      DY++IIKKPMDLGT+  K+   +YK
Sbjct: 12  LDKVLNEL--KTYTEHSTPFLTKVSKREAP-----DYYDIIKKPMDLGTMLKKLKNLQYK 64

Query: 323 SSKEFADDVRLIFTNCYKYNP-PDHDVVAMAKKLQDVFETKIAKAPD 368
           S  EF DD+ LI+ NC  YN  P H +   A  ++   E  +   PD
Sbjct: 65  SKAEFVDDLNLIWKNCLLYNSDPSHPLRRHANFMKKKAEHLLKLIPD 111

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|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score = 88.1 bits (219), Expect = 4e-21
 Identities = 45/128 (35%), Positives = 58/128 (45%), Gaps = 40/128 (31%)

Query: 87  VLKPVMKHQH---AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVP 143
           VLK +MK +H    WPF  PVD + LN+P                               
Sbjct: 8   VLKELMKPKHSAYNWPFLDPVDPVALNIP------------------------------- 36

Query: 144 VLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVM 203
                 +Y  +IK PMDLGTI K+L+N  Y S KE   D   +F NCY +N  G DV +M
Sbjct: 37  ------NYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMM 90

Query: 204 AQTLEKLF 211
              LE++F
Sbjct: 91  GHQLEEVF 98

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

 Score = 87.3 bits (217), Expect = 9e-21
 Identities = 36/97 (37%), Positives = 60/97 (61%), Gaps = 3/97 (3%)

Query: 269 ILKELFSK-KHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEF 327
           IL E+ ++ K+   +WPF+ PV+   +   DY++IIK+PMDL T++ K+   +Y+S +EF
Sbjct: 4   ILDEIVNELKNLPDSWPFHTPVNKKKV--PDYYKIIKRPMDLQTIRKKISKHKYQSREEF 61

Query: 328 ADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIA 364
            +D+ LI  N   YN PD      AK++ ++ E  +A
Sbjct: 62  LEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELLA 98

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

 Score = 87.5 bits (217), Expect = 1e-20
 Identities = 40/104 (38%), Positives = 59/104 (56%), Gaps = 5/104 (4%)

Query: 261 ESLKYCNEILKELFS--KKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA 318
                    L++L     KH   +WPF +PV      + DY++IIKKPMDLGT+K K++ 
Sbjct: 8   HHGPLNLSALEQLLVEIVKHKD-SWPFLRPVSKI--EVPDYYDIIKKPMDLGTIKEKLNM 64

Query: 319 REYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETK 362
            EYK ++EF  D++L+F+NC+ YNP    V     +LQ  F  +
Sbjct: 65  GEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKR 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|99922 cd04369, Bromodomain, Bromodomain

 Score = 85.9 bits (213), Expect = 2e-20
 Identities = 35/92 (38%), Positives = 50/92 (54%), Gaps = 1/92 (1%)

Query: 125 VLSMYIEYPILLAFALTVPV-LIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDF 183
           +L    +    L+     PV      DY++VIK+PMDL TIKK+L+N  Y S +E  +D 
Sbjct: 8   LLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADV 67

Query: 184 NTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
             +F+N   YN PG  +   A+ LEKLF   +
Sbjct: 68  RLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 99

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

>gnl|CDD|215921 pfam00439, Bromodomain, Bromodomain

 Score = 85.5 bits (212), Expect = 2e-20
 Identities = 40/89 (44%), Positives = 53/89 (59%), Gaps = 5/89 (5%)

Query: 266 CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSK 325
           C EIL++L        A PF +PVD       DY+E+IK+PMDL T++ K+ + +YKS  
Sbjct: 1   CLEILEDLMEHPL---AEPFLEPVDPE--EYPDYYEVIKEPMDLSTIRQKLKSGKYKSLA 55

Query: 326 EFADDVRLIFTNCYKYNPPDHDVVAMAKK 354
           EF  DV LIF+N   YN  D D+   AKK
Sbjct: 56  EFLKDVELIFSNAITYNGEDSDIYKDAKK 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|227408 COG5076, COG5076, Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

 Score = 86.0 bits (213), Expect = 4e-18
 Identities = 51/230 (22%), Positives = 82/230 (35%), Gaps = 15/230 (6%)

Query: 142 VPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVV 201
            P     ++  +     M    I   +++     G  A  + +        Y+   ++  
Sbjct: 39  APEEEGSKNLFQKQLKRMPKEYITSIVDD--REPGSMANVNDDLENVGGITYSPFEKNRP 96

Query: 202 VMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTE 261
                    F   V    ES                T+        + D+       L  
Sbjct: 97  ES-----LRFDEIVFLAIESVTPESGLGSLLMAHLKTSVKKRKTPKIEDE------LLYA 145

Query: 262 SLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREY 321
             K   +  K+LF +     +  F            DY+EIIK PMDL T++ K+    Y
Sbjct: 146 DNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYP--DYYEIIKSPMDLLTIQKKLKNGRY 203

Query: 322 KSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVP 371
           KS +EF  D+ L+F NC  YN PD  V   AK+L+  F   I + P+++ 
Sbjct: 204 KSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEML 253

Length = 371

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

 Score = 79.0 bits (195), Expect = 6e-18
 Identities = 39/100 (39%), Positives = 60/100 (60%), Gaps = 5/100 (5%)

Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
           L  C  IL E+  + H   AWPF +PV+   +    Y +IIKKPMD  T++ K+++ +YK
Sbjct: 2   LALCETILDEM--EAHED-AWPFLEPVNTKLV--PGYRKIIKKPMDFSTIREKLESGQYK 56

Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETK 362
           + +EFA+DVRL+F NC  +N  D +V      ++  FE +
Sbjct: 57  TLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFFEKR 96

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|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily

 Score = 78.3 bits (193), Expect = 2e-17
 Identities = 41/103 (39%), Positives = 54/103 (52%), Gaps = 6/103 (5%)

Query: 264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKS 323
           K C E++  ++  + S    PF +PVD   L   DY +II  PMDLGTVK  +    Y  
Sbjct: 8   KQCKELVNLMWDCEDSE---PFRQPVDL--LKYPDYRDIIDTPMDLGTVKETLFGGNYDD 62

Query: 324 SKEFADDVRLIFTNCYKYNPPDHD-VVAMAKKLQDVFETKIAK 365
             EFA DVRLIF+N   Y P     + +M  +L  +FE  I K
Sbjct: 63  PMEFAKDVRLIFSNSKSYTPNKRSRIYSMTLRLSALFEEHIKK 105

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

 Score = 82.9 bits (205), Expect = 4e-17
 Identities = 63/211 (29%), Positives = 91/211 (43%), Gaps = 33/211 (15%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+++IK PMDL TI+K+L+N  Y S +E +SD N MF NC +YN P   V V A+ LEK
Sbjct: 180 DYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEK 239

Query: 210 LFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEI 269
            FL  +    E   ++       +                                    
Sbjct: 240 YFLKLIEEIPEEMLELSIKPGREEREER-------------------------------E 268

Query: 270 LKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFAD 329
              + + +    AWPF +PV      + DY++ I+ PMDL T + K+    Y+  + F  
Sbjct: 269 SVLITNSQAHVGAWPFLRPVSDE--EVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVR 326

Query: 330 DVRLIFTNCYKYNPPDHDVVAMAKKLQDVFE 360
           D +L F NC  YN    D    A  L+D   
Sbjct: 327 DAKLFFDNCVMYNGEVTDYYKNANVLEDFVI 357

Length = 371

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

 Score = 74.1 bits (182), Expect = 3e-16
 Identities = 34/97 (35%), Positives = 52/97 (53%), Gaps = 5/97 (5%)

Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
           L+ C EIL ++   + S   WPF +PV A      DY ++I  PMDL T++ K     Y 
Sbjct: 2   LQKCEEILSKILKYRFS---WPFREPVTAD--EAEDYKKVITNPMDLQTMQTKCSCGSYS 56

Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVF 359
           S +EF DD++L+F+N  KY      V++  +K +   
Sbjct: 57  SVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKTEQCC 93

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

 Score = 73.5 bits (181), Expect = 7e-16
 Identities = 39/107 (36%), Positives = 58/107 (54%), Gaps = 10/107 (9%)

Query: 263 LKYC-NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREY 321
           L+    ++LK L S K  +    F KPVD     + DY+EIIK+PMDL T+  K+D  +Y
Sbjct: 4   LRLFLRDVLKRLASDKRFN---AFTKPVDEE--EVPDYYEIIKQPMDLQTILQKLDTHQY 58

Query: 322 KSSKEFADDVRLIFTNCYKYNPPDHD----VVAMAKKLQDVFETKIA 364
            ++K+F  D+ LI TN  +YNP        + + A +L+D     I 
Sbjct: 59  LTAKDFLKDIDLIVTNALEYNPDRDPADKLIRSRACELRDEVHAMIE 105

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

 Score = 72.0 bits (177), Expect = 2e-15
 Identities = 36/128 (28%), Positives = 57/128 (44%), Gaps = 39/128 (30%)

Query: 87  VLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLI 146
           +L  ++KH+ +WPF +PV  I+                                 VP   
Sbjct: 20  LLVEIVKHKDSWPFLRPVSKIE---------------------------------VP--- 43

Query: 147 ILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQT 206
              DY+ +IK PMDLGTIK++L    Y   +E +SD   +F+NC++YN     V      
Sbjct: 44  ---DYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTR 100

Query: 207 LEKLFLTK 214
           L++ F+ +
Sbjct: 101 LQRFFIKR 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|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 71.6 bits (176), Expect = 3e-15
 Identities = 35/126 (27%), Positives = 54/126 (42%), Gaps = 37/126 (29%)

Query: 86  NVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVL 145
           + ++ + + + A PF  PVD + LN+P                                 
Sbjct: 11  SSIRSLKRLKDARPFLVPVDPVKLNIP--------------------------------- 37

Query: 146 IILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQ 205
                Y  +IK PMDLGTI+++L++  Y S +E  +DFN M  NC  +N P   V  M +
Sbjct: 38  ----HYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGK 93

Query: 206 TLEKLF 211
            L+  F
Sbjct: 94  RLQAAF 99

BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 103

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

 Score = 71.2 bits (175), Expect = 3e-15
 Identities = 27/65 (41%), Positives = 37/65 (56%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+ +IK P+ L  IK+R+E   Y S +E + DF+ MF N   YN+ G  V   A  +EK
Sbjct: 38  DYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEK 97

Query: 210 LFLTK 214
            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|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 68.5 bits (168), Expect = 3e-14
 Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 3/76 (3%)

Query: 143 PVLIILQDYHKVIKHPMDLGTIKKRLE---NFYYWSGKEAISDFNTMFTNCYVYNKPGED 199
           PV   + +Y+K+IK PMDL  I+K+L+     +Y S +E ++D   MF NCY +N+   +
Sbjct: 28  PVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSE 87

Query: 200 VVVMAQTLEKLFLTKV 215
           V    + LE  F  ++
Sbjct: 88  VAQAGKELELFFEEQL 103

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|215921 pfam00439, Bromodomain, Bromodomain

 Score = 66.7 bits (163), Expect = 8e-14
 Identities = 22/57 (38%), Positives = 34/57 (59%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQT 206
           DY++VIK PMDL TI+++L++  Y S  E + D   +F+N   YN    D+   A+ 
Sbjct: 28  DYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKDVELIFSNAITYNGEDSDIYKDAKK 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|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 64.4 bits (157), Expect = 1e-12
 Identities = 25/61 (40%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNK-PGEDVVVMAQTLE 208
           DY+ +IK PMDLGT+ K+L+N  Y S  E + D N ++ NC +YN  P   +   A  ++
Sbjct: 40  DYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHANFMK 99

Query: 209 K 209
           K
Sbjct: 100 K 100

SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 112

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

 Score = 63.9 bits (156), Expect = 1e-12
 Identities = 34/91 (37%), Positives = 50/91 (54%), Gaps = 9/91 (9%)

Query: 269 ILKELFSKKHSSYAWPFYKPV--DAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKE 326
           + + L S +++S    F KPV  D A      YH ++ +PMDL T+K  ++    +S+ E
Sbjct: 11  VYRTLASHRYAS---VFLKPVTEDIA----PGYHSVVYRPMDLSTIKKNIENGTIRSTAE 63

Query: 327 FADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           F  DV L+F N   YN  DHDV  MA ++Q 
Sbjct: 64  FQRDVLLMFQNAIMYNSSDHDVYLMAVEMQR 94

In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 104

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

 Score = 62.4 bits (152), Expect = 4e-12
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 285 FYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPP 344
           F +PVD +   + DY + IK+PMD  T++ K++++ Y++ ++F  D  LI  NC  YN  
Sbjct: 22  FSEPVDLS--EVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAK 79

Query: 345 DHDVVAMAKKLQD 357
           D      A +L+D
Sbjct: 80  DTIFYRAAVRLRD 92

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|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V

 Score = 59.6 bits (145), Expect = 4e-11
 Identities = 25/63 (39%), Positives = 37/63 (58%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+ VIK P+D+  I+ ++E   Y S  + +SDF  MF N   YN+P   +   A TL+K
Sbjct: 38  DYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQK 97

Query: 210 LFL 212
           + L
Sbjct: 98  VLL 100

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Length = 105

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

 Score = 58.9 bits (143), Expect = 7e-11
 Identities = 26/66 (39%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY+++IKKP+D+  +++K++  +Y+S  +   D  L+F N  KYN PD  +   A  LQ 
Sbjct: 38  DYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQK 97

Query: 358 VF-ETK 362
           V  ETK
Sbjct: 98  VLLETK 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 = 105

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

 Score = 58.2 bits (141), Expect = 1e-10
 Identities = 27/57 (47%), Positives = 34/57 (59%)

Query: 299 YHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKL 355
           Y  IIK PMD  T+K K+   +Y+S +EF DD +L+  N  KYN PD      AKKL
Sbjct: 34  YSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90

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

 Score = 57.7 bits (140), Expect = 2e-10
 Identities = 24/66 (36%), Positives = 38/66 (57%)

Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY+ IIK+P+ L  +K +++ R YKS +EF +D  L+F N   YN     V   A +++ 
Sbjct: 38  DYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEK 97

Query: 358 VFETKI 363
            F+ K 
Sbjct: 98  AFKKKY 103

SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 103

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

 Score = 57.8 bits (140), Expect = 2e-10
 Identities = 26/66 (39%), Positives = 36/66 (54%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+K+I  P+DL TI+  + N  Y + +E + DF  MF N   YN+ G  V   A  LEK
Sbjct: 38  DYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEK 97

Query: 210 LFLTKV 215
           +   K 
Sbjct: 98  VLKEKR 103

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

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

 Score = 58.1 bits (141), Expect = 2e-10
 Identities = 24/76 (31%), Positives = 35/76 (46%)

Query: 137 AFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKP 196
            F   V +     DY   +  PMDL TI+ RLEN YY S +    D   + +N   +N+P
Sbjct: 47  YFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEP 106

Query: 197 GEDVVVMAQTLEKLFL 212
             ++   A+ L    L
Sbjct: 107 NSEIAKKAKRLSDWLL 122

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

 Score = 56.1 bits (136), Expect = 8e-10
 Identities = 35/141 (24%), Positives = 55/141 (39%), Gaps = 39/141 (27%)

Query: 80  LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFA 139
           L+FI   ++  +     +WPFH PV+                                  
Sbjct: 1   LSFILDEIVNELKNLPDSWPFHTPVNK--------------------------------- 27

Query: 140 LTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGED 199
             VP      DY+K+IK PMDL TI+K++    Y S +E + D   +  N  +YN P   
Sbjct: 28  KKVP------DYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSV 81

Query: 200 VVVMAQTLEKLFLTKVSARRE 220
               A+ + +L    ++ R E
Sbjct: 82  YTKKAKEMLELAEELLAEREE 102

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|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily

 Score = 55.1 bits (133), Expect = 1e-09
 Identities = 27/92 (29%), Positives = 48/92 (52%), Gaps = 1/92 (1%)

Query: 125 VLSMYIEYPILLAFALTV-PVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDF 183
           +  +Y + P  L F   V P L+ + DY  ++K+PMDL TI+++L+   Y    + + D 
Sbjct: 12  LEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDV 71

Query: 184 NTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
             MF N ++YN+    V      L ++F  ++
Sbjct: 72  WLMFDNAWLYNRKTSRVYKYCTKLAEVFEQEI 103

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 = 54.7 bits (132), Expect = 2e-09
 Identities = 30/122 (24%), Positives = 46/122 (37%), Gaps = 39/122 (31%)

Query: 93  KHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYH 152
            H+ AWPF +PV+                                    VP       Y 
Sbjct: 14  AHEDAWPFLEPVNT---------------------------------KLVP------GYR 34

Query: 153 KVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFL 212
           K+IK PMD  TI+++LE+  Y + +E   D   +F NC  +N+   +V      + K F 
Sbjct: 35  KIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFFE 94

Query: 213 TK 214
            +
Sbjct: 95  KR 96

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|99944 cd05512, Bromo_brd1_like, Bromodomain; brd1_like subfamily

 Score = 54.3 bits (131), Expect = 2e-09
 Identities = 19/45 (42%), Positives = 28/45 (62%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
           DY   IK PMD  T++K+LE+  Y + ++  +DFN +  NC  YN
Sbjct: 33  DYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 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|99951 cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III

 Score = 54.7 bits (132), Expect = 2e-09
 Identities = 22/65 (33%), Positives = 39/65 (60%)

Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY++ IK P+ L  ++ K+   EY++ +E   D+ L+F N  +YN P+  +   A+KLQ 
Sbjct: 38  DYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQK 97

Query: 358 VFETK 362
           + + 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|99945 cd05513, Bromo_brd7_like, Bromodomain, brd7_like subgroup

 Score = 54.0 bits (130), Expect = 3e-09
 Identities = 22/52 (42%), Positives = 29/52 (55%)

Query: 146 IILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPG 197
            I   Y  +IKHPMD  T+K++++N  Y S +E   DF  M  N   YNKP 
Sbjct: 29  FIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPD 80

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

 Score = 52.3 bits (126), Expect = 2e-08
 Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 6/98 (6%)

Query: 266 CNEILKELF---SKKHSSYAWPFYKPVD-AAWLGLNDYHEIIKKPMDLGTVKAKMDAREY 321
              ++  L           A  F  PVD  AW    DY   +  PMDL T++++++ R Y
Sbjct: 26  RERLISGLDKLLLSLQLEIAEYFEYPVDLRAWY--PDYWNRVPVPMDLETIRSRLENRYY 83

Query: 322 KSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVF 359
           +S +    DVRLI +N   +N P+ ++   AK+L D  
Sbjct: 84  RSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWL 121

WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 128

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

 Score = 52.0 bits (125), Expect = 2e-08
 Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY + IK+PM L  VK +++ R Y + + F  D+RLIF N   +   D D   +   L+ 
Sbjct: 32  DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-DFGQVGITLEK 90

Query: 358 VFE 360
            FE
Sbjct: 91  KFE 93

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

 Score = 50.6 bits (121), Expect = 5e-08
 Identities = 27/115 (23%), Positives = 46/115 (40%), Gaps = 39/115 (33%)

Query: 87  VLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLI 146
           +L  ++K++ +WPF +PV A +                                      
Sbjct: 8   ILSKILKYRFSWPFREPVTADEA------------------------------------- 30

Query: 147 ILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVV 201
             +DY KVI +PMDL T++ +     Y S +E + D   +F+N   Y + G  V+
Sbjct: 31  --EDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVL 83

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

 Score = 50.9 bits (122), Expect = 5e-08
 Identities = 18/72 (25%), Positives = 36/72 (50%)

Query: 140 LTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGED 199
           + +P    L +Y+++I+ P+D   IK+R+ N  Y S ++   D   +  N   +N  G  
Sbjct: 29  IQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSL 88

Query: 200 VVVMAQTLEKLF 211
           +   +  L+ +F
Sbjct: 89  IYEDSIVLQSVF 100

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|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup

 Score = 50.1 bits (120), Expect = 8e-08
 Identities = 25/56 (44%), Positives = 29/56 (51%)

Query: 149 QDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMA 204
             YH V+  PMDL TIKK +EN    S  E   D   MF N  +YN    DV +MA
Sbjct: 34  PGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMA 89

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|99940 cd05508, Bromo_RACK7, Bromodomain, RACK7_like subfamily

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 32/106 (30%), Positives = 53/106 (50%), Gaps = 9/106 (8%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           +L++ LK+  E +K+  ++       PF KPVD       DY + + KPMDL T++  + 
Sbjct: 3   QLSKLLKFALERMKQPGAE-------PFLKPVDLEQF--PDYAQYVFKPMDLSTLEKNVR 53

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI 363
            + Y S+  F  D + I  N   YN  DH +   AK +  + E ++
Sbjct: 54  KKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKICEQEM 99

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

 Score = 48.9 bits (117), Expect = 3e-07
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 2/66 (3%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+K+IK+P+ L T+KKRL +  Y + +E ++D   +  N  +YN  G  +   A  LEK
Sbjct: 39  DYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEK 96

Query: 210 LFLTKV 215
                +
Sbjct: 97  YINDVI 102

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 = 48.4 bits (116), Expect = 3e-07
 Identities = 20/62 (32%), Positives = 33/62 (53%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           +Y++ I +P+ L  IKK+++   Y S  + ++D N MF N  +YN+        A  LEK
Sbjct: 39  EYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEK 98

Query: 210 LF 211
             
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 = 48.5 bits (116), Expect = 4e-07
 Identities = 18/63 (28%), Positives = 30/63 (47%)

Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           +Y+E++  P+DL  ++ K+   EY    +   D  L+  N   Y  PD      A KL +
Sbjct: 40  EYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWE 99

Query: 358 VFE 360
           +F 
Sbjct: 100 LFL 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 = 113

>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 = 6e-07
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQ 356
           +Y++ I  P+ L  +K K+  R+YKS  +F +D+ L+F N   YN  D      A  L+
Sbjct: 39  EYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLE 97

Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 104

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

 Score = 47.3 bits (113), Expect = 7e-07
 Identities = 24/66 (36%), Positives = 37/66 (56%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY++ IK+P+ L  I+ +L+N  Y + +E  +D N MF N   YN P   +   A+ L+K
Sbjct: 38  DYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQK 97

Query: 210 LFLTKV 215
           L   K 
Sbjct: 98  LMQAKK 103

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

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

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGT 311
            +    +L+EL   + +  AWPF +PV+    G  DY ++IK+PM  GT
Sbjct: 2   YEALERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGT 50

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

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

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 13/71 (18%)

Query: 272 ELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDV 331
           +LF +K S   +P             DY++II +P+DL T++  +   +Y + +E  DD 
Sbjct: 25  DLFMEKPSKKDYP-------------DYYKIILEPIDLKTIEHNIRNDKYATEEELMDDF 71

Query: 332 RLIFTNCYKYN 342
           +L+F N   YN
Sbjct: 72  KLMFRNARHYN 82

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

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

 Score = 45.5 bits (108), Expect = 4e-06
 Identities = 20/70 (28%), Positives = 38/70 (54%)

Query: 296 LNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKL 355
           L +Y+E+I+KP+D   +K ++   +Y+S ++   DV L+  N   +N     +   +  L
Sbjct: 37  LPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVL 96

Query: 356 QDVFETKIAK 365
           Q VF++   K
Sbjct: 97  QSVFKSARQK 106

SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 107

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

 Score = 44.3 bits (105), Expect = 9e-06
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 149 QDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLE 208
           +DY + IK PM L  +K+RL    Y + +  + D   +F N  ++ K  +D   +  TLE
Sbjct: 31  RDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYK-DDDFGQVGITLE 89

Query: 209 KLF 211
           K F
Sbjct: 90  KKF 92

The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 102

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

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 2/67 (2%)

Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY++IIK P+ L TVK ++    Y +++EF +D+  I  N   YN     +   A  L+ 
Sbjct: 39  DYYKIIKNPLSLNTVKKRL--PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEK 96

Query: 358 VFETKIA 364
                I 
Sbjct: 97  YINDVII 103

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|99948 cd05517, Bromo_polybromo_II, Bromodomain, polybromo repeat II

 Score = 44.0 bits (104), Expect = 1e-05
 Identities = 24/62 (38%), Positives = 38/62 (61%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+ VIK P+DL TI +R+++ YY S ++   D + M  N   +N+PG  V   A  ++K
Sbjct: 38  DYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKK 97

Query: 210 LF 211
           +F
Sbjct: 98  IF 99

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

 Score = 42.7 bits (101), Expect = 4e-05
 Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 138 FALTVPVLII-LQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN-- 194
            A T PV    + DY+++IK PMDL TI ++L+   Y + K+ + D + + TN   YN  
Sbjct: 22  NAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPD 81

Query: 195 --KPGEDVVVMAQTLEKLFLTKVSA 217
                + +   A  L       + A
Sbjct: 82  RDPADKLIRSRACELRDEVHAMIEA 106

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|99955 cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-family

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 17/64 (26%), Positives = 31/64 (48%)

Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY+E I  P+DL T++ ++    YK+ + F  D+  +F N  KY      +     +L+ 
Sbjct: 40  DYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLRK 99

Query: 358 VFET 361
            +  
Sbjct: 100 AYYQ 103

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|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 17/45 (37%), Positives = 22/45 (48%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
           DY  +I  PMDLGT+K+ L    Y    E   D   +F+N   Y 
Sbjct: 37  DYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81

WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 119

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

 Score = 41.3 bits (97), Expect = 1e-04
 Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 13/96 (13%)

Query: 267 NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKE 326
             ++ ELF K  S   +P             DY+ +IK+P+DL T+  ++ +  YKS ++
Sbjct: 20  GRLISELFQKLPSKVLYP-------------DYYAVIKEPIDLKTIAQRIQSGYYKSIED 66

Query: 327 FADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETK 362
              D+ L+  N   +N P   V   A  ++ +F  K
Sbjct: 67  MEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTAK 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|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 42.2 bits (100), Expect = 9e-04
 Identities = 17/86 (19%), Positives = 25/86 (29%), Gaps = 2/86 (2%)

Query: 392 WSPDSSSDSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPASSVKKPAR 451
           + P S++  T + A   A             PA  A        P + P+PA+     A 
Sbjct: 36  YGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAA--AAAAA 93

Query: 452 PPAKTPVKRKAPPMPNKSVSAQHTQP 477
                P    A   P  +       P
Sbjct: 94  AAPAAPPAAAAAAAPAAAAVEDEVTP 119

Length = 1228

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

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           +Y++V+ +P+DL  I+++L+   Y    +  +DF  +  N   Y KP       A  L +
Sbjct: 40  EYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWE 99

Query: 210 LFLTKVSARRE 220
           LFL   SAR E
Sbjct: 100 LFL---SARNE 107

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|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.7 bits (93), Expect = 0.004
 Identities = 19/75 (25%), Positives = 26/75 (34%)

Query: 418 QVTPKPATAAQRKKPPTTPLSAPQPASSVKKPARPPAKTPVKRKAPPMPNKSVSAQHTQP 477
           +       AA   +    P  A  PA++   PA PPA  P    A P      +A    P
Sbjct: 383 RPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAP 442

Query: 478 APVMNDESDEESSKP 492
           A V    +    + P
Sbjct: 443 AAVALAPAPPAQAAP 457

Length = 618

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	566
KOG1474|consensus	640		100.0
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.95
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.94
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.93
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.93
KOG1474|consensus	640		99.93
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.93
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.93
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.93
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.93
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.92
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.92
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.92
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.92
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.92
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.91
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.91
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.91
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.91
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.91
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.91
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.91
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.91
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.9
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.9
COG5076	371	Transcription factor involved in chromatin remodel	99.89
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.89
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.89
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.89
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.89
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.89
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.89
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.89
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.89
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.89
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.89
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.89
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.89
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.88
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.88
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.88
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.88
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.88
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.88
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.88
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.88
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.88
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.88
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.88
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.88
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.88
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.88
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.88
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.88
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.88
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.87
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.87
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.87
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.87
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.86
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.86
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.85
KOG1472|consensus	720		99.85
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.85
smart00297	107	BROMO bromo domain.	99.85
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.84
smart00297	107	BROMO bromo domain.	99.83
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.83
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.81
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.81
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.81
KOG0008|consensus	1563		99.8
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.8
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.78
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.77
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.77
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.74
COG5076	371	Transcription factor involved in chromatin remodel	99.7
KOG1245|consensus	1404		99.64
KOG1245|consensus	1404		99.58
KOG1827|consensus	629		99.42
KOG0008|consensus	1563		99.38
KOG1472|consensus	720		99.37
KOG1828|consensus	418		99.32
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.26
KOG1827|consensus	629		99.16
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.14
KOG0386|consensus	1157		99.09
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	98.94
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	98.92
KOG0955|consensus	1051		98.82
KOG0386|consensus	1157		98.72
KOG0955|consensus	1051		98.72
KOG1828|consensus	418		97.7
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	95.98
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	94.94
KOG0732|consensus	1080		92.07
KOG0644|consensus	1113		89.32
KOG0644|consensus	1113		87.44

>KOG1474|consensus

Probab=100.00  E-value=4.6e-46  Score=417.10  Aligned_cols=416  Identities=39%  Similarity=0.591  Sum_probs=275.0

Q ss_pred             HHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCHHHHHHHh
Q psy245           89 KPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRL  168 (566)
Q Consensus        89 ~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL  168 (566)
                      +.+++|.++|+|..||+.+.+++|                                     +||.+|++|||++||+.++
T Consensus         2 ~~~~~~~~~~~f~~~v~~v~l~~~-------------------------------------~~~~~~~~~~d~~~~~~~~   44 (640)
T KOG1474|consen    2 KEARKHKLAWPFLEPVDAVALNLP-------------------------------------AYYEIIKRPMDIGTIEKRV   44 (640)
T ss_pred             cccccccccccccCccchhhccch-------------------------------------hhhcccCCCCCchhhhhhh
Confidence            346789999999999999999999                                     9999999999999999999


Q ss_pred             hccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcccc-------ccccCC-------------
Q psy245          169 ENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESG-------RQIKKP-------------  228 (566)
Q Consensus       169 ~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~-------~k~~~~-------------  228 (566)
                      .+.+|.+..++.+|+..+|.||+.||.....|+.+++.++..|.+.+..++...       .+....             
T Consensus        45 e~n~~~~~~~~~~~f~~~~sn~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~  124 (640)
T KOG1474|consen   45 ENNYYFSASECIADFKTKFSNCYLFNDSGDDVVRMKQSLEKLFPKKLRSMPSDEEDKSSVGPKASKIPLDKDSSSQVRKL  124 (640)
T ss_pred             ccCccccHhhhhhhccccccchhcccCCccchhhccccchhhcccccccccccccCCcccccccccCcCCCCchhhhhhh
Confidence            999999999999999999999999999999999999999999988877766410       000000             


Q ss_pred             ---C-----------CCCC---C-----C-Cccc-------------cccccc----------CC-------CC------
Q psy245          229 ---N-----------RGSD---E-----G-SFTT-------------QLATSV----------TS-------VG------  249 (566)
Q Consensus       229 ---~-----------~~~~---~-----~-~~~~-------------~~~~~~----------~~-------~~------  249 (566)
                         .           ....   .     + ....             ......          ++       ..      
T Consensus       125 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (640)
T KOG1474|consen  125 SERLKQELQQVRPLTKAVEFSPEPSVVSPVSPASQPFKSKNGVKKVADTCVKSYKSKSEREPSPGQKREGTVAPNSSRES  204 (640)
T ss_pred             hhccccccccCCcccccccccccccccCCCCCcccccccccchhhhhccccccccccCcCCCCccccccccccCcccccc
Confidence               0           0000   0     0 0000             000000          00       00      


Q ss_pred             ------CCCCCCCcchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCC
Q psy245          250 ------DQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKS  323 (566)
Q Consensus       250 ------~~~~~~~~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s  323 (566)
                            .........+..+|++|..||+.|+.|+   ++|||+.|||++.|++||||+||++||||+||+.||.+|.|.+
T Consensus       205 ~~~~~~~~~~~~~~~~~~~lk~C~~iLk~l~~~k---~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~Y~~  281 (640)
T KOG1474|consen  205 GDSAAEEEAKPKSKLTVELLKQCLSILKRLMKHK---HAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGEYKS  281 (640)
T ss_pred             ccccccccccccccccHHHHHHHHHHHHHHHhcc---CCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccccCC
Confidence                  0111234467889999999999999999   5699999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCcCCCCCCCcc--------c---ccCCCCCCC
Q psy245          324 SKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTL--------T---VNKNNIGRW  392 (566)
Q Consensus       324 ~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~~~~~~~~~~~~~--------~---~~~~~~~~s  392 (566)
                      +.+|.+||||||+||++||++|++||.||..|+++|+.+|+.++.............+.        .   ......+..
T Consensus       282 ~~eF~~DVRL~F~Ncm~YNp~g~dV~~Ma~~L~~~Fe~rw~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  361 (640)
T KOG1474|consen  282 AEEFAADVRLTFDNCMTYNPEGSDVYAMAKKLQEVFEERWASMPLEIEESESAVKEEAGMASSDQIPSNSVEGPRSSSFE  361 (640)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccccccCcccccch
Confidence            99999999999999999999999999999999999999999988776544322111100        0   000111101


Q ss_pred             CCCCCC--CCCCchHHHHHHHHHHHhhhcCCCcchhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy245          393 SPDSSS--DSTDSEADERARKLISLQDQVTPKPATAAQRKKPPTTPLSAPQPASSVKKPARPPAKTPVKRKAPPMPNKSV  470 (566)
Q Consensus       393 ~~~~~~--~~~~~~~~e~~~~l~~lq~ql~~~~~k~~~~kk~~~~~~~~~~~~~~k~~~~~~~~s~~~~~~~~~~~~~~~  470 (566)
                      ..+...  ......++++....+.++..+...+............  .++...............+.       .....+
T Consensus       362 ~~~~~~~~~~~~~~~~e~~~~~~~l~~~~~~~~~~l~~~~~~~~~--~~~~~~e~~~~~~~~~~~~~-------~~~~~~  432 (640)
T KOG1474|consen  362 SRESASEPSSELMSEEERKKLLAELKLLLKDVPPQLIALLQRPVS--KPPRKIEEELESDKRPLVTG-------KLIKEK  432 (640)
T ss_pred             hcccccCcccccccHHhhhhhHhhhhcchhhhhHHHHhhhhcccc--Cccccccccccccccccchh-------hhhhhh
Confidence            111111  1234556667777777776665543322221110000  00000000000000000000       000000


Q ss_pred             CCCCCCCCCCCCCCCccccCCCCCHHHHHHHHHhccC-CCCcchHHHHHHH--HhhCCCCCCCCCCcEEEeCCCCC----
Q psy245          471 SAQHTQPAPVMNDESDEESSKPMSYFEKQELSLDINK-LPGKKLGRVVHII--QSREPSLRDSNPDEIEIDFETLK----  543 (566)
Q Consensus       471 ~~~~~~~~~~~~~s~~e~~~~pmT~eEK~~Ls~~I~~-Lp~e~L~~Vv~II--~~~~p~~~~~~~dEiEiDid~L~----  543 (566)
                               ...........+.||..|+..|...+.. +++.+|..+++|+  ..+.+.+. .++++|++|++.++    
T Consensus       433 ---------~~~~~~~~~~~r~~t~~~~~~l~~~~~~~~~p~~l~~~~~~~~~~~~~~~l~-~~~~~~~~~~~~vd~~~~  502 (640)
T KOG1474|consen  433 ---------NKKEKAANENKRDMTAPEKAKLKELLQNLLPPNKLESIVEILKPEKRQLDLS-QNDDEIELDLDSVDGSQS  502 (640)
T ss_pred             ---------hccccccccccccccccccccchhhccCCCCCccccCcccccchhhhccccc-ccccchhhcccccccccc
Confidence                     0001112345678888888888888888 4888888888888  33455553 35678888888877    


Q ss_pred             ---------hHHHH---------HHHHHHHHHhccCCC
Q psy245          544 ---------PSTLR---------ELEKYVATCLRKKPR  563 (566)
Q Consensus       544 ---------~~tLr---------~L~~yV~~cL~kk~~  563 (566)
                               ..|+|         ++..++..|++...+
T Consensus       503 ~~~~~~~~~~e~~~~~~~~~~~~~~~~s~~~~~~~~~~  540 (640)
T KOG1474|consen  503 REPSSNPLEIETIRETLKLSTERELELSKASSSRSLMR  540 (640)
T ss_pred             cCCCcccchhhhhhccccchhhHHHHHHHHhhhhhhcc
Confidence                     55554         555566667666544

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.95  E-value=3.2e-28  Score=213.51  Aligned_cols=107  Identities=73%  Similarity=1.228  Sum_probs=103.2

Q ss_pred             CCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCccccc
Q psy245           75 RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKV  154 (566)
Q Consensus        75 ~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~i  154 (566)
                      |+|+|++++++.|++.|++|+.+|||..|||....++|                                     |||++
T Consensus         1 ~~~~q~~~~~~~il~~l~~~~~s~~F~~PVd~~~~~~p-------------------------------------dY~~i   43 (107)
T cd05497           1 RHTNQLQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLP-------------------------------------DYHKI   43 (107)
T ss_pred             CccHHHHHHHHHHHHHHHhCCcCccccCCCCcccccCC-------------------------------------cHHHH
Confidence            57999999999999999999999999999998877777                                     99999


Q ss_pred             CCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          155 IKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       155 Ik~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      |++||||+||++||++|.|.++.+|..||+|||.||+.||+++|.++.+|..|++.|++.+.++
T Consensus        44 Ik~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~l~~~f~~~l~~~  107 (107)
T cd05497          44 IKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQM  107 (107)
T ss_pred             HcCcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999999999999999999999999999999999999999999999864

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.

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.94  E-value=1e-26  Score=204.07  Aligned_cols=104  Identities=49%  Similarity=0.862  Sum_probs=97.1

Q ss_pred             HHHHHHHH-HHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcc
Q psy245          260 TESLKYCN-EILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNC  338 (566)
Q Consensus       260 ~~~~k~c~-~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  338 (566)
                      +.+++.|. .||..|++++   .+|||.+|||+...++||||++|++||||+||++||++|.|.++.+|.+||+|||.||
T Consensus         3 ~~q~~~~~~~il~~l~~~~---~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na   79 (107)
T cd05497           3 TNQLQYLLKVVLKALWKHK---FAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNC   79 (107)
T ss_pred             cHHHHHHHHHHHHHHHhCC---cCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Confidence            45677774 6799999887   7899999999987789999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          339 YKYNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       339 ~~yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      +.||+++|.|+.+|..|+++|++++++|
T Consensus        80 ~~yN~~~s~i~~~A~~l~~~f~~~l~~~  107 (107)
T cd05497          80 YIYNKPGDDVVLMAQTLEKLFLQKLAQM  107 (107)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999999999875

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

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.93  E-value=3.4e-26  Score=201.17  Aligned_cols=104  Identities=36%  Similarity=0.645  Sum_probs=98.5

Q ss_pred             HHHHHHHHHHHHHHHhc-cCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcc
Q psy245          260 TESLKYCNEILKELFSK-KHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNC  338 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~-~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  338 (566)
                      .++.+.|..+|..|+++ +   .+|||.+|||+...++||||++|++||||+||++||++|.|.++.+|.+||+|||+||
T Consensus         2 ~~l~~~~~~il~~l~~~~~---~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na   78 (108)
T cd05495           2 EELRQALMPTLEKLYKQDP---ESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNA   78 (108)
T ss_pred             HHHHHHHHHHHHHHHHcCc---ccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence            36788999999999988 5   7889999999998889999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          339 YKYNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       339 ~~yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      +.||+++|.+|.+|..|+++|+++++.+
T Consensus        79 ~~yN~~~s~i~~~a~~l~~~F~~~~~~~  106 (108)
T cd05495          79 WLYNRKTSRVYKYCTKLAEVFEQEIDPV  106 (108)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999998764

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

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.93  E-value=2.8e-26  Score=204.47  Aligned_cols=105  Identities=38%  Similarity=0.648  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      .+|.+.|..||..|++++   .+|||.+|||+.  ++||||++|++||||+||++||.+|.|.++.+|.+||+|||.||+
T Consensus         4 ~~w~~~c~~il~~l~~~~---~s~~F~~PVd~~--~~pdY~~iIk~PmDL~tIk~kL~~~~Y~~~~ef~~D~~lif~Na~   78 (119)
T cd05496           4 SDWKKQCKELVNLMWDCE---DSEPFRQPVDLL--KYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSK   78 (119)
T ss_pred             HHHHHHHHHHHHHHHhCC---ccccccCCCChh--hcCcHHHHhCCcccHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH
Confidence            578999999999999987   678999999987  699999999999999999999999999999999999999999999


Q ss_pred             ccCCC-CCHHHHHHHHHHHHHHHHHHcCCCC
Q psy245          340 KYNPP-DHDVVAMAKKLQDVFETKIAKAPDD  369 (566)
Q Consensus       340 ~yN~~-~s~v~~~A~~L~~~fe~~~~~~~~~  369 (566)
                      .||++ +|.||.+|..|+++|++++.++...
T Consensus        79 ~yN~~~~s~i~~~a~~L~~~F~~~~~~l~~~  109 (119)
T cd05496          79 SYTPNKRSRIYSMTLRLSALFEEHIKKIISD  109 (119)
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99985 8999999999999999999988543

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.

>KOG1474|consensus

Probab=99.93  E-value=7e-26  Score=254.55  Aligned_cols=221  Identities=30%  Similarity=0.390  Sum_probs=155.6

Q ss_pred             cHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCC
Q psy245           77 TNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIK  156 (566)
Q Consensus        77 ~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk  156 (566)
                      +..+-+.|..||..||.|+++|||..|||.+.+++|                                     |||+||+
T Consensus       220 ~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLp-------------------------------------DY~~IIK  262 (640)
T KOG1474|consen  220 TVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLP-------------------------------------DYHDIIK  262 (640)
T ss_pred             cHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCc-------------------------------------chhhhcC
Confidence            345555677899999999999999999999999999                                     9999999


Q ss_pred             CCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccccccccCC----CCCC
Q psy245          157 HPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKP----NRGS  232 (566)
Q Consensus       157 ~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~k~~~~----~~~~  232 (566)
                      +||||+||++||.++.|+++.+|..||+|||.||++||.++++||.||..|++.|+.+|..++.........    .+..
T Consensus       263 ~PMDLgTIK~kL~~~~Y~~~~eF~~DVRL~F~Ncm~YNp~g~dV~~Ma~~L~~~Fe~rw~~~~~~~~~~~~~~~~~~~~~  342 (640)
T KOG1474|consen  263 HPMDLGTIKKKLEKGEYKSAEEFAADVRLTFDNCMTYNPEGSDVYAMAKKLQEVFEERWASMPLEIEESESAVKEEAGMA  342 (640)
T ss_pred             CCccHHHHHhhhcccccCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhhccccccccccccccccccc
Confidence            999999999999999999999999999999999999999999999999999999999999987632111110    0000


Q ss_pred             ----CCCCccc---ccccccCCCCCCCCCCCcchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccC
Q psy245          233 ----DEGSFTT---QLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKK  305 (566)
Q Consensus       233 ----~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~  305 (566)
                          ..+....   .+..... .............+....+..++..+....+..+...+..++.........+..+..+
T Consensus       343 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~e~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~e~~~~~~~~  421 (640)
T KOG1474|consen  343 SSDQIPSNSVEGPRSSSFESR-ESASEPSSELMSEEERKKLLAELKLLLKDVPPQLIALLQRPVSKPPRKIEEELESDKR  421 (640)
T ss_pred             cccccccccccCcccccchhc-ccccCcccccccHHhhhhhHhhhhcchhhhhHHHHhhhhccccCcccccccccccccc
Confidence                0000000   0000000 0000002222334455666666666665555556667777887776677788999899


Q ss_pred             CCChHHHHHHhhCCCCCCHHHHHHHHHHHHh
Q psy245          306 PMDLGTVKAKMDAREYKSSKEFADDVRLIFT  336 (566)
Q Consensus       306 PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~  336 (566)
                      ++..+ ...+..............++.....
T Consensus       422 ~~~~~-~~~~~~~~~~~~~~~~~r~~t~~~~  451 (640)
T KOG1474|consen  422 PLVTG-KLIKEKNKKEKAANENKRDMTAPEK  451 (640)
T ss_pred             ccchh-hhhhhhhcccccccccccccccccc
Confidence            98776 4444445555555555555554443

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

Probab=99.93  E-value=4.2e-26  Score=196.55  Aligned_cols=95  Identities=35%  Similarity=0.684  Sum_probs=90.9

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      ++.|.+||+.|++++   .+|||..||+..  ++||||++|++||||+||++||++|.|.|+.+|.+||+|||.||+.||
T Consensus         2 ~~~c~~il~~l~~~~---~s~~F~~pv~~~--~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN   76 (97)
T cd05505           2 LQKCEEILSKILKYR---FSWPFREPVTAD--EAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY   76 (97)
T ss_pred             HHHHHHHHHHHHhCC---CcccccCCCChh--hcccHHHHcCCcCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            578999999999887   678999999987  699999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHH
Q psy245          343 PPDHDVVAMAKKLQDVFETK  362 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~fe~~  362 (566)
                      ++||.|+.+|..|++.|..+
T Consensus        77 ~~~s~i~~~a~~le~~f~~~   96 (97)
T cd05505          77 ENGSYVLSCMRKTEQCCVNL   96 (97)
T ss_pred             CCCCHHHHHHHHHHHHHHHh
Confidence            99999999999999999876

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.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.93  E-value=4.7e-26  Score=198.60  Aligned_cols=101  Identities=53%  Similarity=1.012  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      ++.|.+||..|+++++..++|||..|||+...++|+||++|++||||++|++||++|.|+++.+|.+||+|||.||+.||
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            57899999999998877799999999999877899999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q psy245          343 PPDHDVVAMAKKLQDVFETKI  363 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~fe~~~  363 (566)
                      +++|.++.+|..|++.|+++|
T Consensus        82 ~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          82 PEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999986

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.93  E-value=4.3e-26  Score=198.86  Aligned_cols=102  Identities=71%  Similarity=1.246  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccccc
Q psy245          262 SLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY  341 (566)
Q Consensus       262 ~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~y  341 (566)
                      +++.|.+||+.|+++++..+++||..||++...++|+||++|++||||+||++||++|.|.|+.+|..||+|||+||+.|
T Consensus         1 ~~~~c~~il~~l~~~~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~y   80 (102)
T cd05498           1 QLKFCSGILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKY   80 (102)
T ss_pred             ChhHHHHHHHHHHhCCCccccCcccCcCCccccCCCcHHHHccCCCcHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHH
Confidence            36789999999999987789999999999987789999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHH
Q psy245          342 NPPDHDVVAMAKKLQDVFETKI  363 (566)
Q Consensus       342 N~~~s~v~~~A~~L~~~fe~~~  363 (566)
                      |+++|.++.+|..|++.|+++|
T Consensus        81 n~~~s~i~~~a~~l~~~fe~~~  102 (102)
T cd05498          81 NPPDHPVHAMARKLQDVFEDRW  102 (102)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999987

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.93  E-value=1e-25  Score=200.17  Aligned_cols=109  Identities=38%  Similarity=0.692  Sum_probs=102.2

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHH
Q psy245          254 YAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRL  333 (566)
Q Consensus       254 ~~~~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~L  333 (566)
                      ..+..+..++..|..||..|+.++   .+|+|..||+..  ++||||++|++||||+||++||+.|.|.|+.+|.+||+|
T Consensus         5 ~~~~~~~~~~~~c~~il~~l~~~~---~s~~F~~pvd~~--~~pdY~~vI~~PmDL~tI~~kL~~~~Y~s~~~f~~Dv~L   79 (115)
T cd05504           5 EGRHHGPLNLSALEQLLVEIVKHK---DSWPFLRPVSKI--EVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQL   79 (115)
T ss_pred             ccCCCCHHHHHHHHHHHHHHHhCC---CchhhcCCCCcc--ccccHHHHhcCcccHHHHHHHHccCCCCCHHHHHHHHHH
Confidence            345567789999999999999876   688999999986  689999999999999999999999999999999999999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          334 IFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       334 if~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      ||.||+.||+++|.++.+|..|+++|+++++++.
T Consensus        80 I~~Na~~yN~~~s~i~~~A~~l~~~f~~~~~~~~  113 (115)
T cd05504          80 VFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKLG  113 (115)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999874

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.

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.92  E-value=1.6e-25  Score=196.93  Aligned_cols=104  Identities=30%  Similarity=0.527  Sum_probs=99.3

Q ss_pred             HHHHHHHHHHHHHHHhc-CCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCC
Q psy245           78 NQLAFISKNVLKPVMKH-QHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIK  156 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~-~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk  156 (566)
                      .+|+..|..|++.|+++ +.+|||..||++...++|                                     |||++|+
T Consensus         2 ~~l~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~p-------------------------------------dY~~iIk   44 (108)
T cd05495           2 EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIP-------------------------------------DYFDIVK   44 (108)
T ss_pred             HHHHHHHHHHHHHHHHcCcccchhcCCCCccccCCC-------------------------------------cHHHHhC
Confidence            57888999999999999 999999999998877778                                     9999999


Q ss_pred             CCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          157 HPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       157 ~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      +||||+||++||.+|.|.++.+|..||+|||.||+.||+++|.++.+|..|++.|++.+..+
T Consensus        45 ~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~F~~~~~~~  106 (108)
T cd05495          45 NPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQEIDPV  106 (108)
T ss_pred             CCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999998754

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.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.92  E-value=2.4e-25  Score=192.32  Aligned_cols=96  Identities=40%  Similarity=0.799  Sum_probs=92.2

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      +.+|..||..|+++.   .+++|+.||+..  .+|+||++|++||||+||++||++|.|+|+.+|.+||+|||.||+.||
T Consensus         2 ~~~c~~il~~l~~~~---~~~~F~~pv~~~--~~p~Y~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN   76 (97)
T cd05503           2 LALCETILDEMEAHE---DAWPFLEPVNTK--LVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFN   76 (97)
T ss_pred             HHHHHHHHHHHHcCC---CchhhcCCCCcc--ccCCHHHHhCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            678999999999986   678999999987  689999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q psy245          343 PPDHDVVAMAKKLQDVFETKI  363 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~fe~~~  363 (566)
                      +++|.++.+|..|+++|+++|
T Consensus        77 ~~~s~i~~~a~~l~~~f~~~~   97 (97)
T cd05503          77 EDDSEVGRAGHNMRKFFEKRW   97 (97)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999987

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

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.92  E-value=5e-25  Score=196.44  Aligned_cols=106  Identities=27%  Similarity=0.420  Sum_probs=99.8

Q ss_pred             cHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCC
Q psy245           77 TNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIK  156 (566)
Q Consensus        77 ~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk  156 (566)
                      ...|+..|..|++.|++|+.+|||..|||..  ++|                                     |||++|+
T Consensus         3 ~~~w~~~c~~il~~l~~~~~s~~F~~PVd~~--~~p-------------------------------------dY~~iIk   43 (119)
T cd05496           3 ESDWKKQCKELVNLMWDCEDSEPFRQPVDLL--KYP-------------------------------------DYRDIID   43 (119)
T ss_pred             HHHHHHHHHHHHHHHHhCCccccccCCCChh--hcC-------------------------------------cHHHHhC
Confidence            4689999999999999999999999999964  366                                     9999999


Q ss_pred             CCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCC-CCHHHHHHHHHHHHHHHHhhhhccc
Q psy245          157 HPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKP-GEDVVVMAQTLEKLFLTKVSARRES  221 (566)
Q Consensus       157 ~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~-~s~i~~~A~~L~~~f~~~~~~~~~~  221 (566)
                      +||||+||++||.+|.|.++.+|..||+|||.||++||++ +|.|+.+|..|++.|++.+.++...
T Consensus        44 ~PmDL~tIk~kL~~~~Y~~~~ef~~D~~lif~Na~~yN~~~~s~i~~~a~~L~~~F~~~~~~l~~~  109 (119)
T cd05496          44 TPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNKRSRIYSMTLRLSALFEEHIKKIISD  109 (119)
T ss_pred             CcccHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999985 8999999999999999999998763

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.92  E-value=5.9e-25  Score=190.65  Aligned_cols=98  Identities=54%  Similarity=0.957  Sum_probs=94.2

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      ++.|..||+.|++++   .+|+|..||++...++|+||++|++||||+||++||++|.|.++.+|.+||+|||.||+.||
T Consensus         2 ~~~c~~il~~l~~~~---~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yn   78 (99)
T cd05506           2 MKQCGTLLRKLMKHK---WGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYN   78 (99)
T ss_pred             HHHHHHHHHHHHhCC---CCccccCCCCccccCCCCHHHHHcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            688999999999987   67899999998877899999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q psy245          343 PPDHDVVAMAKKLQDVFETKI  363 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~fe~~~  363 (566)
                      +++|.++.+|..|++.|+++|
T Consensus        79 ~~~s~i~~~a~~l~~~fe~~w   99 (99)
T cd05506          79 PPGNDVHTMAKELLKIFETRW   99 (99)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999987

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.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.92  E-value=1.2e-24  Score=192.12  Aligned_cols=107  Identities=35%  Similarity=0.511  Sum_probs=98.2

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      ...+....|..||..|+++.  ..+|||..||++.  ++||||++|++||||+||++||++|.|+|+.+|.+||+|||.|
T Consensus         4 ~~~~~~~~~~~il~~l~~~~--~~s~~F~~pv~~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~Li~~N   79 (112)
T cd05510           4 GQEEFYESLDKVLNELKTYT--EHSTPFLTKVSKR--EAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKN   79 (112)
T ss_pred             cHHHHHHHHHHHHHHHHhcC--ccccchhcCCChh--hcCCHHHHhcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence            34577889999999999984  2678999999987  6999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCC-HHHHHHHHHHHHHHHHHHcCCC
Q psy245          338 CYKYNPPDH-DVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       338 a~~yN~~~s-~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      |+.||++++ .++.+|..|++.|+.++..+++
T Consensus        80 ~~~yN~~~s~~~~~~A~~l~~~~~~~~~~~~~  111 (112)
T cd05510          80 CLLYNSDPSHPLRRHANFMKKKAEHLLKLIPD  111 (112)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence            999999876 6789999999999999998864

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.

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.91  E-value=1.1e-24  Score=188.19  Aligned_cols=98  Identities=29%  Similarity=0.444  Sum_probs=89.9

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      +.++.|..||.+|+++.+   +++|..++  .  ++||||++|++||||+||++||.+|+|.|+.+|.+||+|||+||+.
T Consensus         2 ~~l~~ce~il~~l~~~~~---s~~f~~~p--~--~~pdY~~iIk~PMDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~N~~~   74 (102)
T cd05501           2 EELLKCEFLLLKVYCMSK---SGFFISKP--Y--YIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKL   74 (102)
T ss_pred             HHHHHHHHHHHHHHhCcc---cccccCCC--C--CCCchHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            467889999999999984   46786533  2  6899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      ||+++ .++.+|..|++.|+++|+++
T Consensus        75 yN~~~-~~~~~a~~L~~~Fek~~~~~   99 (102)
T cd05501          75 FYKDD-DFGQVGITLEKKFEKNFKEV   99 (102)
T ss_pred             HcCCC-HHHHHHHHHHHHHHHHHHHH
Confidence            99999 99999999999999999875

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.91  E-value=1.5e-24  Score=191.34  Aligned_cols=103  Identities=36%  Similarity=0.717  Sum_probs=96.8

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhC---CCCCCHHHHHHHHHHHHh
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA---REYKSSKEFADDVRLIFT  336 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~---~~Y~s~~ef~~Dv~Lif~  336 (566)
                      ..+++.|.+||.+|+++.   .+|||.+||++   .+|+||++|++||||+||++||+.   |.|+++++|.+||+|||+
T Consensus         3 ~~~~~~c~~il~~l~~~~---~s~~F~~pv~~---~~p~Y~~iI~~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~   76 (109)
T cd05502           3 PIDQRKCERLLLELYCHE---LSLPFHEPVSP---SVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFK   76 (109)
T ss_pred             HHHHHHHHHHHHHHHhCC---CChhhcCCCCC---CCCCHHHHCCCCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHH
Confidence            467899999999999985   78999999998   489999999999999999999998   699999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          337 NCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       337 Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      ||+.||+++|.++.+|..|++.|+++|.++.+
T Consensus        77 Na~~yN~~~s~i~~~a~~l~~~f~~~~~~~~p  108 (109)
T cd05502          77 NCYKFNEEDSEVAQAGKELELFFEEQLKEILP  108 (109)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCc
Confidence            99999999999999999999999999998643

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

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.91  E-value=1.6e-24  Score=189.36  Aligned_cols=100  Identities=35%  Similarity=0.526  Sum_probs=95.0

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      .|.+.|..+++.|..++   .++||.+||+..  ++|+||++|++||||+||++||++|.|.++.+|.+||+|||+||+.
T Consensus         3 ~~~~~~~~il~~l~~~~---~a~~F~~pV~~~--~~p~Y~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~   77 (104)
T cd05507           3 AWKKAILLVYRTLASHR---YASVFLKPVTED--IAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIM   77 (104)
T ss_pred             HHHHHHHHHHHHHHcCC---CCHhhcCCCCcc--ccCCHHHHhCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            57889999999999987   678999999986  6899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHc
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAK  365 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~  365 (566)
                      ||+++|.|+.+|..|++.|.+++..
T Consensus        78 yN~~~s~v~~~A~~l~~~~~~~~~~  102 (104)
T cd05507          78 YNSSDHDVYLMAVEMQREVMSQIQQ  102 (104)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999988765

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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.91  E-value=1.4e-24  Score=187.64  Aligned_cols=98  Identities=28%  Similarity=0.426  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           78 NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      ++|+.+|+.+++.++ |+.+|||..||+..  ++|                                     |||.+|++
T Consensus         2 ~~l~~~L~~~~~~~~-~~~s~~F~~PV~~~--~~p-------------------------------------dY~~iIk~   41 (99)
T cd05508           2 DQLSKLLKFALERMK-QPGAEPFLKPVDLE--QFP-------------------------------------DYAQYVFK   41 (99)
T ss_pred             hHHHHHHHHHHHHHh-CcCcchhcCCCChh--hCC-------------------------------------CHHHHcCC
Confidence            689999999999999 99999999999963  456                                     99999999


Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      ||||+||++||++|.|.++++|.+||+|||.||++||+++|.++.+|+.|.+.|...+
T Consensus        42 PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~Na~~YN~~~s~i~~~A~~l~~~~~~e~   99 (99)
T cd05508          42 PMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKICEQEM   99 (99)
T ss_pred             CCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999999999999999999999999999999999999998653

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.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.91  E-value=2.1e-24  Score=188.43  Aligned_cols=100  Identities=40%  Similarity=0.670  Sum_probs=95.3

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      ..+.++|.++|..|+.++   .++||..|||+...++|+||++|++||||+||++||.+|.|.++.+|..||+|||.||+
T Consensus         3 ~~~~~~~~~ii~~l~~~~---~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~   79 (103)
T cd05500           3 KHQHKFLLSSIRSLKRLK---DARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCL   79 (103)
T ss_pred             HHHHHHHHHHHHHHHcCC---CChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence            367899999999999887   67899999999878899999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHH
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETK  362 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~  362 (566)
                      .||+++|.++.+|..|++.|++.
T Consensus        80 ~yN~~~s~~~~~A~~l~~~fe~~  102 (103)
T cd05500          80 TFNGPEHPVSQMGKRLQAAFEKH  102 (103)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHh
Confidence            99999999999999999999975

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

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

Probab=99.91  E-value=1.8e-24  Score=189.95  Aligned_cols=103  Identities=26%  Similarity=0.380  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHHhccCC---CCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcc
Q psy245          262 SLKYCNEILKELFSKKHS---SYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNC  338 (566)
Q Consensus       262 ~~k~c~~iL~~l~~~~~~---~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  338 (566)
                      ..+.|..||+.+..+++.   ..++||.+||+..  ++||||++|++||||+||++||.+|.|.++.+|..||+|||.||
T Consensus         2 l~~~~~~il~~v~~~~d~~g~~~s~~F~~~p~~~--~~pdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na   79 (107)
T cd05516           2 LTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRK--ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNA   79 (107)
T ss_pred             HHHHHHHHHHHHHhhhCcCCCEeeHHhhcCCCcc--cCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHH
Confidence            356788999999888753   4689999999987  78999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          339 YKYNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       339 ~~yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      +.||++||.||.+|..|+++|++.+.++
T Consensus        80 ~~yN~~~s~i~~~a~~l~~~f~~~~~~~  107 (107)
T cd05516          80 QTFNLEGSLIYEDSIVLQSVFKSARQKI  107 (107)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999999999998764

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.

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

Probab=99.91  E-value=2.1e-24  Score=186.07  Aligned_cols=95  Identities=29%  Similarity=0.495  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCH
Q psy245           82 FISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDL  161 (566)
Q Consensus        82 ~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL  161 (566)
                      ..|..|++.|++|+.+|||..||+..  ++|                                     |||++|++||||
T Consensus         3 ~~c~~il~~l~~~~~s~~F~~pv~~~--~~p-------------------------------------dY~~iIk~PmDL   43 (97)
T cd05505           3 QKCEEILSKILKYRFSWPFREPVTAD--EAE-------------------------------------DYKKVITNPMDL   43 (97)
T ss_pred             HHHHHHHHHHHhCCCcccccCCCChh--hcc-------------------------------------cHHHHcCCcCCH
Confidence            35678999999999999999999953  466                                     999999999999


Q ss_pred             HHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          162 GTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       162 ~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      +||++||++|.|.++++|.+||+|||.||++||+++|.|+..|..|++.|.+.+
T Consensus        44 ~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~le~~f~~~~   97 (97)
T cd05505          44 QTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKTEQCCVNLL   97 (97)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999999999999999999999999999999998764

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.

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.91  E-value=3.1e-24  Score=187.62  Aligned_cols=102  Identities=31%  Similarity=0.406  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           78 NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      ..|+..|..|++.|++|+.+|||..||+.  .++|                                     |||++|++
T Consensus         2 ~~~~~~~~~il~~l~~~~~a~~F~~pV~~--~~~p-------------------------------------~Y~~iIk~   42 (104)
T cd05507           2 RAWKKAILLVYRTLASHRYASVFLKPVTE--DIAP-------------------------------------GYHSVVYR   42 (104)
T ss_pred             hHHHHHHHHHHHHHHcCCCCHhhcCCCCc--cccC-------------------------------------CHHHHhCC
Confidence            47889999999999999999999999996  3466                                     99999999


Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      ||||+||++||++|.|.++++|.+||+|||+||.+||+++|.++.+|..|++.|.+.+..+
T Consensus        43 PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~v~~~A~~l~~~~~~~~~~~  103 (104)
T cd05507          43 PMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEMQREVMSQIQQL  103 (104)
T ss_pred             CcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999999999999999999999999999999999999999988653

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.

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.90  E-value=9.2e-24  Score=183.85  Aligned_cols=99  Identities=39%  Similarity=0.699  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      ..+|..||..|..++   .+++|..||++.  .+|+||++|++||||+||++||++|.|.|+.+|.+||+|||+||+.||
T Consensus         3 ~~~~~~il~~l~~~~---~a~~F~~pv~~~--~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN   77 (101)
T cd05509           3 YTQLKKVLDSLKNHK---SAWPFLEPVDKE--EAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYN   77 (101)
T ss_pred             HHHHHHHHHHHHhCC---CchhhcCCCChh--hcCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            568999999999987   678999999998  589999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          343 PPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      +++|.++.+|..|++.|+++++++
T Consensus        78 ~~~s~~~~~a~~l~~~f~~~~~~~  101 (101)
T cd05509          78 GPDTEYYKCANKLEKFFWKKLKEL  101 (101)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhhC
Confidence            999999999999999999998763

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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.90  E-value=1.3e-23  Score=181.63  Aligned_cols=93  Identities=32%  Similarity=0.508  Sum_probs=84.2

Q ss_pred             HHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCC
Q psy245          264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP  343 (566)
Q Consensus       264 k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~  343 (566)
                      ..+..++..|. ++   .+|||.+||++.  ++||||++|++||||+||++||++|.|.++++|.+||+|||.||+.||+
T Consensus         6 ~~L~~~~~~~~-~~---~s~~F~~PV~~~--~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~Na~~YN~   79 (99)
T cd05508           6 KLLKFALERMK-QP---GAEPFLKPVDLE--QFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNG   79 (99)
T ss_pred             HHHHHHHHHHh-Cc---CcchhcCCCChh--hCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            34455666666 44   689999999996  6999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHH
Q psy245          344 PDHDVVAMAKKLQDVFETK  362 (566)
Q Consensus       344 ~~s~v~~~A~~L~~~fe~~  362 (566)
                      ++|.++.+|..|.+.|+..
T Consensus        80 ~~s~i~~~A~~l~~~~~~e   98 (99)
T cd05508          80 GDHKLTQAAKAIVKICEQE   98 (99)
T ss_pred             CCCHHHHHHHHHHHHHHhh
Confidence            9999999999999999864

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.

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

Probab=99.89  E-value=9.5e-24  Score=224.45  Aligned_cols=203  Identities=33%  Similarity=0.488  Sum_probs=171.3

Q ss_pred             hhhhhhhhhccccccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHH
Q psy245          131 EYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKL  210 (566)
Q Consensus       131 ~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~  210 (566)
                      .++.++..|..+|++..+|+||.+|+.||||.+|+++|+++.|.++++|+.|++|||.||.+||++++.++.+|..|++.
T Consensus       161 ~~~~~s~~F~~~p~k~~~PdYy~iIk~Pm~L~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~  240 (371)
T COG5076         161 DGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKY  240 (371)
T ss_pred             cccccccccccCCccccCCChheeecchhhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHHHH
Confidence            67778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhccccccccCCCCCCCCCCcccccccccCCCCCCCCCCCcchHHHHHHHHHHHHHHHhccCCCCCcCcccCCC
Q psy245          211 FLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVD  290 (566)
Q Consensus       211 f~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd  290 (566)
                      |...+..++..............                      ...      +-..++...   .....+|+|..++.
T Consensus       241 ~~~~i~~~~~~~~~~~~~~~~~~----------------------~~~------~~~~~i~~~---~~~~~~~~~~~~~~  289 (371)
T COG5076         241 FLKLIEEIPEEMLELSIKPGREE----------------------REE------RESVLITNS---QAHVGAWPFLRPVS  289 (371)
T ss_pred             HHHHHHhccccchhhccCccccc----------------------ccc------chhhccccc---ccccccccccccCC
Confidence            99999988864432211100000                      000      001112222   23346799999998


Q ss_pred             ccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          291 AAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       291 ~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      ..  ..|+|+++|..+|+++|.+-++..+.|....+|..|..++|+||..||+.....+.-+..+..++...+.-.
T Consensus       290 ~~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  363 (371)
T COG5076         290 DE--EVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKKTRLI  363 (371)
T ss_pred             cc--cccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhccchhhhHhhhhhhh
Confidence            88  689999999999999999999999999999999999999999999999999999999999999988877654

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.89  E-value=1.8e-23  Score=184.75  Aligned_cols=104  Identities=30%  Similarity=0.445  Sum_probs=96.4

Q ss_pred             cHHHHHHHHHHHHHHHhc-CCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           77 TNQLAFISKNVLKPVMKH-QHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        77 ~~~l~~~~~~v~~~l~~~-~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      ..+|...|..|++.|++| +.+|||..||+..  ++|                                     |||++|
T Consensus         5 ~~~~~~~~~~il~~l~~~~~~s~~F~~pv~~~--~~p-------------------------------------dY~~iI   45 (112)
T cd05510           5 QEEFYESLDKVLNELKTYTEHSTPFLTKVSKR--EAP-------------------------------------DYYDII   45 (112)
T ss_pred             HHHHHHHHHHHHHHHHhcCccccchhcCCChh--hcC-------------------------------------CHHHHh
Confidence            357888899999999999 8999999999964  366                                     999999


Q ss_pred             CCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCC-HHHHHHHHHHHHHHHHhhhhc
Q psy245          156 KHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGE-DVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       156 k~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s-~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      ++||||+||++||++|.|.++++|.+||+|||.||+.||++++ .++.+|..|++.|+..+..+|
T Consensus        46 k~PmdL~tI~~kl~~~~Y~s~~ef~~D~~Li~~N~~~yN~~~s~~~~~~A~~l~~~~~~~~~~~~  110 (112)
T cd05510          46 KKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHANFMKKKAEHLLKLIP  110 (112)
T ss_pred             cCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence            9999999999999999999999999999999999999999765 688999999999999999886

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=99.89  E-value=2e-23  Score=182.34  Aligned_cols=100  Identities=35%  Similarity=0.612  Sum_probs=93.1

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      .+...|..|++.|++++.++||..|||+...++|                                     |||++|++|
T Consensus         4 ~~~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p-------------------------------------~Y~~~I~~P   46 (103)
T cd05500           4 HQHKFLLSSIRSLKRLKDARPFLVPVDPVKLNIP-------------------------------------HYPTIIKKP   46 (103)
T ss_pred             HHHHHHHHHHHHHHcCCCChhhcCCCCcccccCC-------------------------------------CHHHHhcCC
Confidence            3445566799999999999999999998777777                                     999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      |||++|++||.+|.|.++.+|..||+|||+||+.||+++|.++.+|..|+..|++.+
T Consensus        47 ~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~l~~~fe~~~  103 (103)
T cd05500          47 MDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAFEKHL  103 (103)
T ss_pred             CCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999999999999999999999999999999999998753

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.89  E-value=1.9e-23  Score=181.19  Aligned_cols=98  Identities=45%  Similarity=0.729  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCC
Q psy245           81 AFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMD  160 (566)
Q Consensus        81 ~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMd  160 (566)
                      ...|..|++.|++++.+|+|..||+....++|                                     +||++|++|||
T Consensus         2 ~~~c~~il~~l~~~~~~~~F~~pv~~~~~~~p-------------------------------------~Y~~~I~~P~d   44 (99)
T cd05506           2 MKQCGTLLRKLMKHKWGWVFNAPVDVVALGLP-------------------------------------DYFDIIKKPMD   44 (99)
T ss_pred             HHHHHHHHHHHHhCCCCccccCCCCccccCCC-------------------------------------CHHHHHcCCCC
Confidence            45788999999999999999999997665666                                     99999999999


Q ss_pred             HHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          161 LGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       161 L~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      |+||++||++|.|.++.+|..|+++||.||+.||+++|.++.+|..|+..|+++|
T Consensus        45 l~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yn~~~s~i~~~a~~l~~~fe~~w   99 (99)
T cd05506          45 LGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETRW   99 (99)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999999999999876

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.

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

Probab=99.89  E-value=4.6e-23  Score=182.23  Aligned_cols=102  Identities=38%  Similarity=0.564  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccccc
Q psy245          262 SLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY  341 (566)
Q Consensus       262 ~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~y  341 (566)
                      ....|..|++.|+.++   .+|||.+|||..  ++||||++|++||||+||++||++|.|.|+.+|.+||+|||+||+.|
T Consensus         4 lr~~L~~il~~l~~~~---~~~~F~~pv~~~--~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~y   78 (112)
T cd05528           4 LRLFLRDVLKRLASDK---RFNAFTKPVDEE--EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEY   78 (112)
T ss_pred             HHHHHHHHHHHHHhCC---CchhhcCCCCcc--ccCcHHHHHcCCCCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHH
Confidence            3456788999999987   678999999998  68999999999999999999999999999999999999999999999


Q ss_pred             CCCC----CHHHHHHHHHHHHHHHHHHcCCC
Q psy245          342 NPPD----HDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       342 N~~~----s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      |+++    +.|+.+|..|++.|.+++.+..+
T Consensus        79 N~~~s~~~s~i~~~A~~L~~~~~~~~~~~~~  109 (112)
T cd05528          79 NPDRDPADKLIRSRACELRDEVHAMIEAELD  109 (112)
T ss_pred             CCCCCccccHHHHHHHHHHHHHHHHHHhcCC
Confidence            9994    79999999999999999998754

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

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.89  E-value=2.7e-23  Score=184.77  Aligned_cols=102  Identities=34%  Similarity=0.649  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      .....|..|++.|++++.+|||..||+..  ++|                                     |||++|++|
T Consensus        12 ~~~~~c~~il~~l~~~~~s~~F~~pvd~~--~~p-------------------------------------dY~~vI~~P   52 (115)
T cd05504          12 LNLSALEQLLVEIVKHKDSWPFLRPVSKI--EVP-------------------------------------DYYDIIKKP   52 (115)
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCCCCcc--ccc-------------------------------------cHHHHhcCc
Confidence            34446678999999999999999999953  466                                     999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      |||+||++||++|.|.++.+|..||+|||.||++||+++|.++.+|..|+..|++.++++.
T Consensus        53 mDL~tI~~kL~~~~Y~s~~~f~~Dv~LI~~Na~~yN~~~s~i~~~A~~l~~~f~~~~~~~~  113 (115)
T cd05504          53 MDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKLG  113 (115)
T ss_pred             ccHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999999999999999998864

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.

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

Probab=99.89  E-value=2.8e-23  Score=181.39  Aligned_cols=99  Identities=27%  Similarity=0.416  Sum_probs=91.8

Q ss_pred             HHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          263 LKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      .+.|.+|++.|+.+++   ...+++|.+||+..  .+|+||++|++||||+||++||+.|.|.|+.+|.+||+|||+||+
T Consensus         2 ~~~~~~i~~~v~~~~~~~~~~~~~~F~~~p~~~--~~pdYy~iIk~Pmdl~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~   79 (103)
T cd05519           2 KAAMLEIYDAVLNCEDETGRKLSELFLEKPSKK--LYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANAR   79 (103)
T ss_pred             HHHHHHHHHHHHHhcCcCCCchhHHhcCCCCCC--CCcCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHH
Confidence            3679999999987773   45789999999987  689999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHH
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKI  363 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~  363 (566)
                      .||+++|.+|.+|..|++.|++++
T Consensus        80 ~yn~~~s~i~~~A~~l~~~f~~~~  103 (103)
T cd05519          80 TYNQEGSIVYEDAVEMEKAFKKKY  103 (103)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999864

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

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.89  E-value=3.6e-23  Score=181.21  Aligned_cols=100  Identities=25%  Similarity=0.433  Sum_probs=91.8

Q ss_pred             HHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          263 LKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      .+.|.+|+..+...++   ...+++|..||+..  ++||||++|++||||+||++||.+|.|.++.+|.+||+|||.||+
T Consensus         2 ~~~~~~~~~~i~~~~d~~~~~~a~~F~~~p~~~--~~pdYy~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~   79 (105)
T cd05515           2 QQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKS--EYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNAC   79 (105)
T ss_pred             hHHHHHHHHHHHHhhCcCCCcccHHhccCCCcc--cCCcHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHH
Confidence            4678888888877764   46899999999887  789999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHH
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKIA  364 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~~  364 (566)
                      .||+++|.+|.+|..|+++|.+...
T Consensus        80 ~yN~~~s~i~~~A~~L~~~~~~~~~  104 (105)
T cd05515          80 KYNEPDSQIYKDALTLQKVLLETKR  104 (105)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999988753

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.

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.89  E-value=3.3e-23  Score=180.34  Aligned_cols=100  Identities=42%  Similarity=0.725  Sum_probs=94.2

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           80 LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      ++..|..|++.|++|+.++||..||+...  +|                                     +||++|++||
T Consensus         2 ~~~~~~~il~~l~~~~~a~~F~~pv~~~~--~p-------------------------------------~Y~~~I~~Pm   42 (101)
T cd05509           2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEE--AP-------------------------------------DYYDVIKKPM   42 (101)
T ss_pred             hHHHHHHHHHHHHhCCCchhhcCCCChhh--cC-------------------------------------CHHHHhcCCC
Confidence            46678899999999999999999999654  56                                     9999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      ||+||++||.+|.|.++++|..||+|||+||+.||+++|.++.+|..|+..|++.++++
T Consensus        43 dL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~a~~l~~~f~~~~~~~  101 (101)
T cd05509          43 DLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL  101 (101)
T ss_pred             CHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999999999999999999999999999999999999999999998764

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.

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.89  E-value=3.5e-23  Score=183.43  Aligned_cols=103  Identities=21%  Similarity=0.376  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHHhccCC---CCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          263 LKYCNEILKELFSKKHS---SYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~---~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      ++.|.+|+..|..+++.   ..+.+|..+|+..  ++|+||++|++||||+||++||.+|.|.|+.+|.+||+|||+||+
T Consensus         4 ~~~c~~il~~l~~~~~~~g~~l~~~F~~~p~~~--~~PdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~   81 (113)
T cd05524           4 IAVCQELYDTIRNYKSEDGRILCESFIRVPKRR--NEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAK   81 (113)
T ss_pred             HHHHHHHHHHHHhhcccCCCchhHHHhcCCCcc--cCCCHHHHhCCccCHHHHHHHhCcCCCCCHHHHHHHHHHHHHHHH
Confidence            57899999999987654   3667899988876  789999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      .||+++|.+|.+|..|+++|++.+.++.
T Consensus        82 ~yN~~~s~~~~~A~~L~~~f~~~~~~~~  109 (113)
T cd05524          82 AYYKPDSPEHKDACKLWELFLSARNEVL  109 (113)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999998874

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.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.89  E-value=2.8e-23  Score=179.42  Aligned_cols=94  Identities=32%  Similarity=0.626  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCHH
Q psy245           83 ISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLG  162 (566)
Q Consensus        83 ~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~  162 (566)
                      .|..|++.|++|+.++||..||+...  +|                                     |||++|++||||+
T Consensus         4 ~c~~il~~l~~~~~~~~F~~pv~~~~--~p-------------------------------------~Y~~iIk~PmdL~   44 (97)
T cd05503           4 LCETILDEMEAHEDAWPFLEPVNTKL--VP-------------------------------------GYRKIIKKPMDFS   44 (97)
T ss_pred             HHHHHHHHHHcCCCchhhcCCCCccc--cC-------------------------------------CHHHHhCCCCCHH
Confidence            57789999999999999999999643  56                                     9999999999999


Q ss_pred             HHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          163 TIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       163 tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      ||++||++|.|.++++|..||+|||.||+.||+++|.++.+|..|++.|++.|
T Consensus        45 tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~f~~~~   97 (97)
T cd05503          45 TIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFFEKRW   97 (97)
T ss_pred             HHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999875

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.89  E-value=6.8e-23  Score=180.81  Aligned_cols=102  Identities=32%  Similarity=0.555  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           78 NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      ...+..|..|+..|++|+.+|||..||+.   ..|                                     +||.+|++
T Consensus         3 ~~~~~~c~~il~~l~~~~~s~~F~~pv~~---~~p-------------------------------------~Y~~iI~~   42 (109)
T cd05502           3 PIDQRKCERLLLELYCHELSLPFHEPVSP---SVP-------------------------------------NYYKIIKT   42 (109)
T ss_pred             HHHHHHHHHHHHHHHhCCCChhhcCCCCC---CCC-------------------------------------CHHHHCCC
Confidence            35566788899999999999999999996   466                                     99999999


Q ss_pred             CCCHHHHHHHhhc---cCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          158 PMDLGTIKKRLEN---FYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       158 PMdL~tI~~kL~~---~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      ||||+||++||++   |.|.++++|.+||+|||+||+.||+++|.++.+|..|++.|++.+.++.
T Consensus        43 PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~f~~~~~~~~  107 (109)
T cd05502          43 PMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKEIL  107 (109)
T ss_pred             CccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence            9999999999998   6999999999999999999999999999999999999999999998864

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

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

Probab=99.89  E-value=4.4e-23  Score=181.22  Aligned_cols=106  Identities=21%  Similarity=0.295  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           80 LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      |+..|+.|++.|+++.+.                                 .++.++.+|..+|.+..+||||.+|++||
T Consensus         2 l~~~~~~il~~v~~~~d~---------------------------------~g~~~s~~F~~~p~~~~~pdYy~iI~~Pm   48 (107)
T cd05516           2 LTKKMNKIVDVVIKYKDS---------------------------------DGRQLAEVFIQLPSRKELPEYYELIRKPV   48 (107)
T ss_pred             HHHHHHHHHHHHHhhhCc---------------------------------CCCEeeHHhhcCCCcccCCCHHHHcCCCC
Confidence            677889999999999872                                 02335555666666667779999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      ||+||++||.+|.|.++++|..||.|||.||+.||+++|.|+.+|..|++.|.+.++++
T Consensus        49 dl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~f~~~~~~~  107 (107)
T cd05516          49 DFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKSARQKI  107 (107)
T ss_pred             CHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999999999999999999988753

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.

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.88  E-value=3.7e-23  Score=183.10  Aligned_cols=102  Identities=33%  Similarity=0.609  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           80 LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      |+++++.|++.|++|+.++||..||+...  .|                                     +||++|++||
T Consensus         1 ~~~~l~~ii~~l~~~~~s~~F~~pv~~~~--~p-------------------------------------~Y~~~I~~Pm   41 (112)
T cd05511           1 LSFILDEIVNELKNLPDSWPFHTPVNKKK--VP-------------------------------------DYYKIIKRPM   41 (112)
T ss_pred             CHHHHHHHHHHHHhCCCchhhcCCCChhh--cc-------------------------------------cHHHHhcCCC
Confidence            46789999999999999999999999643  55                                     9999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ||+||++||.++.|.++++|..||+|||+||+.||+++|.++.+|..|+..|.+.+.+++.
T Consensus        42 dL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~l~~~~~~~~~~~~~  102 (112)
T cd05511          42 DLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELLAEREE  102 (112)
T ss_pred             CHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhHH
Confidence            9999999999999999999999999999999999999999999999999999999998875

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.88  E-value=5e-23  Score=179.57  Aligned_cols=97  Identities=44%  Similarity=0.769  Sum_probs=91.7

Q ss_pred             HHHHHHHHHHHhc---CCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           82 FISKNVLKPVMKH---QHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        82 ~~~~~v~~~l~~~---~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      ..|..|++.|+++   ..++||..||++...++|                                     |||++|++|
T Consensus         3 ~~c~~il~~l~~~~~~~~a~~F~~pv~~~~~~~p-------------------------------------~Y~~~I~~P   45 (102)
T cd05498           3 KFCSGILKELFSKKHKAYAWPFYKPVDPEALGLH-------------------------------------DYHDIIKHP   45 (102)
T ss_pred             hHHHHHHHHHHhCCCccccCcccCcCCccccCCC-------------------------------------cHHHHccCC
Confidence            4677899999999   889999999998766667                                     999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      |||++|++||++|.|.++.+|..||+|||+||+.||+++|.++.+|..|++.|+++|
T Consensus        46 mdl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~yn~~~s~i~~~a~~l~~~fe~~~  102 (102)
T cd05498          46 MDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDRW  102 (102)
T ss_pred             CcHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999999999999999999999999999999999999875

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.

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

Probab=99.88  E-value=6.7e-23  Score=181.18  Aligned_cols=103  Identities=29%  Similarity=0.484  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      +|+.+|..|++.|++|+.+|||..||+...  +|                                     |||++|++|
T Consensus         3 ~lr~~L~~il~~l~~~~~~~~F~~pv~~~~--~p-------------------------------------dY~~vI~~P   43 (112)
T cd05528           3 ELRLFLRDVLKRLASDKRFNAFTKPVDEEE--VP-------------------------------------DYYEIIKQP   43 (112)
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCCCCccc--cC-------------------------------------cHHHHHcCC
Confidence            789999999999999999999999999643  56                                     999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCC----CHHHHHHHHHHHHHHHHhhhhcc
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPG----EDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~----s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      |||+||++||+++.|.++++|..||+|||.||+.||+++    +.|+.+|..|++.|.+++.+..+
T Consensus        44 mdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~~~s~i~~~A~~L~~~~~~~~~~~~~  109 (112)
T cd05528          44 MDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDPADKLIRSRACELRDEVHAMIEAELD  109 (112)
T ss_pred             CCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHCCCCCccccHHHHHHHHHHHHHHHHHHhcCC
Confidence            999999999999999999999999999999999999995    69999999999999999987653

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

>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III

Probab=99.88  E-value=6.7e-23  Score=178.67  Aligned_cols=93  Identities=28%  Similarity=0.504  Sum_probs=84.3

Q ss_pred             HHHHHHHhcc---CCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCC
Q psy245          268 EILKELFSKK---HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPP  344 (566)
Q Consensus       268 ~iL~~l~~~~---~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~  344 (566)
                      .|+..|..++   +...++||.++|+..  .+||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.||++
T Consensus         7 ~l~~~i~~~~~~~g~~~s~pF~~~p~~~--~~PdYy~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~   84 (103)
T cd05520           7 QLYDTIRNARNNQGQLLAEPFLKLPSKR--KYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVP   84 (103)
T ss_pred             HHHHHHHhhcCCCCCCccHhhhcCCCcc--cCCCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            4455555544   456899999999987  68999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHH
Q psy245          345 DHDVVAMAKKLQDVFETK  362 (566)
Q Consensus       345 ~s~v~~~A~~L~~~fe~~  362 (566)
                      +|.+|.+|..|+++|+++
T Consensus        85 ~s~i~~~A~~L~~~f~~~  102 (103)
T cd05520          85 NSRIYKDAEKLQKLMQAK  102 (103)
T ss_pred             CCHHHHHHHHHHHHHHHh
Confidence            999999999999999875

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.

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.88  E-value=6.9e-23  Score=176.75  Aligned_cols=92  Identities=36%  Similarity=0.470  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      .+.|..||+.|..+.   .+++|..||+..  .+||||++|++||||+||++||++|.|.|+.+|.+||+|||.||+.||
T Consensus         3 ~~~l~~il~~l~~~~---~~~~F~~PV~~~--~~pdY~~vIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN   77 (98)
T cd05513           3 QKALEQLIRQLQRKD---PHGFFAFPVTDF--IAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN   77 (98)
T ss_pred             HHHHHHHHHHHHcCC---ccccccCcCCcc--ccccHHHHHcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            467889999999877   567999999976  689999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q psy245          343 PPDHDVVAMAKKLQDVF  359 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~f  359 (566)
                      +++|.+|.+|..|...-
T Consensus        78 ~~~s~~~~~A~~L~~~~   94 (98)
T cd05513          78 KPDTIYYKAAKKLLHSG   94 (98)
T ss_pred             CCCCHHHHHHHHHHHhh
Confidence            99999999999997653

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.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.88  E-value=6.3e-23  Score=178.89  Aligned_cols=97  Identities=46%  Similarity=0.802  Sum_probs=90.0

Q ss_pred             HHHHHHHHHHHhc---CCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           82 FISKNVLKPVMKH---QHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        82 ~~~~~v~~~l~~~---~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      ..|..|++.|+++   ..+|||..|||....++|                                     |||++|++|
T Consensus         3 ~~c~~Il~~l~~~~~~~~s~~F~~pvd~~~~~~p-------------------------------------dY~~~I~~P   45 (102)
T cd05499           3 KFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIP-------------------------------------NYFSIIKKP   45 (102)
T ss_pred             HHHHHHHHHHHcccCCcccchhcCCCCccccCCC-------------------------------------CHHHHhcCC
Confidence            3577899999994   569999999998765666                                     999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      |||++|++||+++.|.++.+|..||+|||.||+.||+++|.++.+|..|++.|+++|
T Consensus        46 ~dL~~I~~kl~~~~Y~s~~ef~~D~~li~~N~~~yn~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          46 MDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             CCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999999999999999999999999999999999999875

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.

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.88  E-value=6.1e-23  Score=177.06  Aligned_cols=95  Identities=29%  Similarity=0.401  Sum_probs=88.3

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           80 LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      |+.+|..|++.|++++.+++|..||+..  .+|                                     |||++|++||
T Consensus         2 l~~~l~~il~~l~~~~~~~~F~~PV~~~--~~p-------------------------------------dY~~vIk~Pm   42 (98)
T cd05513           2 LQKALEQLIRQLQRKDPHGFFAFPVTDF--IAP-------------------------------------GYSSIIKHPM   42 (98)
T ss_pred             HHHHHHHHHHHHHcCCccccccCcCCcc--ccc-------------------------------------cHHHHHcCcc
Confidence            6778899999999999999999999953  366                                     9999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHH
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLT  213 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~  213 (566)
                      ||+||++||+++.|.++.+|+.||+|||.||++||+++|.++++|..|...-.+
T Consensus        43 DL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~~~~   96 (98)
T cd05513          43 DFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKLLHSGMK   96 (98)
T ss_pred             CHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhhh
Confidence            999999999999999999999999999999999999999999999999876443

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.

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.88  E-value=5.8e-23  Score=179.06  Aligned_cols=100  Identities=29%  Similarity=0.480  Sum_probs=93.1

Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCC
Q psy245           81 AFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMD  160 (566)
Q Consensus        81 ~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMd  160 (566)
                      +..|..|++.|+++.+.                                 .+|.++.+|..+|++..+||||++|++|||
T Consensus         2 ~~~~~~l~~~i~~~~d~---------------------------------~gr~~~~~F~~lp~~~~~pdYy~vI~~Pmd   48 (103)
T cd05517           2 KQILEQLLEAVMTATDP---------------------------------SGRLISELFQKLPSKVLYPDYYAVIKEPID   48 (103)
T ss_pred             hHHHHHHHHHHHHhhCc---------------------------------CCCChhHHHhcCCCCCCCCCHHHHcCCCcC
Confidence            56788899999998763                                 156688999999999999999999999999


Q ss_pred             HHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHH
Q psy245          161 LGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLT  213 (566)
Q Consensus       161 L~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~  213 (566)
                      |+||++||.++.|.++.+|..||+|||.||+.||+++|.++.+|..|++.|..
T Consensus        49 L~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          49 LKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             HHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999975

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

>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV

Probab=99.88  E-value=7.6e-23  Score=178.24  Aligned_cols=97  Identities=25%  Similarity=0.397  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHHhcc---CCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          264 KYCNEILKELFSKK---HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       264 k~c~~iL~~l~~~~---~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      +++..|+..|...+   +...+.+|..+|+..  ++||||++|++||||+||++||.+|.|.|+.+|.+||+|||.||+.
T Consensus         3 ~~~~~l~~~v~~~~d~~gr~~~~~F~~~p~~~--~~pdYy~iIk~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~   80 (103)
T cd05518           3 KRMLALFLYVLEYREGSGRRLCDLFMEKPSKK--DYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARH   80 (103)
T ss_pred             HHHHHHHHHHHHhhccCCCcccHHHhcCCCcc--cCccHHHHcCCCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            45667777776654   456788999999987  6899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHH
Q psy245          341 YNPPDHDVVAMAKKLQDVFETK  362 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~  362 (566)
                      ||+++|.||.+|..|+++|+++
T Consensus        81 yN~~~s~i~~~A~~le~~~~~~  102 (103)
T cd05518          81 YNEEGSQVYEDANILEKVLKEK  102 (103)
T ss_pred             HCCCCCHHHHHHHHHHHHHHhc
Confidence            9999999999999999999864

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=99.88  E-value=8.4e-23  Score=178.81  Aligned_cols=103  Identities=22%  Similarity=0.259  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      .|+..|+.|++.|..+.+.                                 .++.++.+|..+|++..+||||++|++|
T Consensus         2 ~l~~~l~~i~~~i~~~kd~---------------------------------~g~~~s~~F~~lp~k~~~pdYy~~I~~P   48 (106)
T cd05525           2 RLAQVLKEICDAIITYKDS---------------------------------NGQSLAIPFINLPSKKKNPDYYERITDP   48 (106)
T ss_pred             hHHHHHHHHHHHHHHhhcc---------------------------------CCCcccHhhccCCCcccCCchhhhCCCC
Confidence            4677788888888888774                                 1455788999999999999999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHH
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTK  214 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~  214 (566)
                      |||++|++||.+|.|.++++|..||.|||.||+.||+++|.++.+|..|++.|++.
T Consensus        49 ~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f~Na~~yn~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          49 VDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             cCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999999999999999999999864

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.

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.88  E-value=8.2e-23  Score=178.14  Aligned_cols=98  Identities=23%  Similarity=0.414  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          263 LKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      .+.|.+|+..|+.+.+   ...+++|..+++..  ++||||++|++||||+||++||++|.|.++.+|..||+|||.||+
T Consensus         2 ~~~~~~l~~~i~~~~d~~gr~~~~~F~~lp~~~--~~pdYy~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~   79 (103)
T cd05517           2 KQILEQLLEAVMTATDPSGRLISELFQKLPSKV--LYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAK   79 (103)
T ss_pred             hHHHHHHHHHHHHhhCcCCCChhHHHhcCCCCC--CCCCHHHHcCCCcCHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHH
Confidence            3578888888887764   35789999999987  689999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHH
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETK  362 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~  362 (566)
                      .||++||.+|.+|..|+++|+..
T Consensus        80 ~yN~~~s~i~~~A~~l~~~f~~~  102 (103)
T cd05517          80 TFNEPGSQVYKDANAIKKIFTAK  102 (103)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHhc
Confidence            99999999999999999999853

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.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.88  E-value=8.9e-23  Score=176.32  Aligned_cols=90  Identities=33%  Similarity=0.569  Sum_probs=84.6

Q ss_pred             HHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCC
Q psy245          264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP  343 (566)
Q Consensus       264 k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~  343 (566)
                      ..+..+|..|..+.   .+|+|.+|||..  .+|+||++|++||||+||++||.+|.|.|+++|..||+|||.||+.||+
T Consensus         4 ~~l~~il~~l~~~~---~~~~F~~pVd~~--~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~   78 (98)
T cd05512           4 VLLRKTLDQLQEKD---TAEIFSEPVDLS--EVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNA   78 (98)
T ss_pred             HHHHHHHHHHHhCC---CchhhcCCCCcc--ccCCHHHHhcCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            45778999999876   788999999987  6899999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q psy245          344 PDHDVVAMAKKLQDV  358 (566)
Q Consensus       344 ~~s~v~~~A~~L~~~  358 (566)
                      ++|.+|.+|..|++.
T Consensus        79 ~~s~~~~~A~~l~~~   93 (98)
T cd05512          79 KDTIFYRAAVRLRDQ   93 (98)
T ss_pred             CCCHHHHHHHHHHHh
Confidence            999999999999875

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.

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.88  E-value=1.4e-22  Score=179.69  Aligned_cols=106  Identities=22%  Similarity=0.256  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCH
Q psy245           82 FISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDL  161 (566)
Q Consensus        82 ~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL  161 (566)
                      ..|..|++.|+++.+.+                                 ++.++.+|..+|++..+||||++|++||||
T Consensus         5 ~~c~~il~~l~~~~~~~---------------------------------g~~l~~~F~~~p~~~~~PdYy~iI~~Pmdl   51 (113)
T cd05524           5 AVCQELYDTIRNYKSED---------------------------------GRILCESFIRVPKRRNEPEYYEVVSNPIDL   51 (113)
T ss_pred             HHHHHHHHHHHhhcccC---------------------------------CCchhHHHhcCCCcccCCCHHHHhCCccCH
Confidence            45677899999887641                                 456788899999999999999999999999


Q ss_pred             HHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          162 GTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       162 ~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      +||++||.++.|.++++|..||+|||.||+.||+++|.++.+|..|++.|++.++++..
T Consensus        52 ~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~  110 (113)
T cd05524          52 LKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLSARNEVLS  110 (113)
T ss_pred             HHHHHHhCcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999999999999999999999999999999999999988764

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=99.88  E-value=1.8e-22  Score=176.78  Aligned_cols=97  Identities=25%  Similarity=0.362  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          264 KYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       264 k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      +.|..||..+...++   ...++||.++++..  .+||||++|++||||+||++||.+|.|.|+.+|..||.|||.||+.
T Consensus         5 ~~l~~i~~~i~~~kd~~g~~~s~~F~~lp~k~--~~pdYy~~I~~P~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f~Na~~   82 (106)
T cd05525           5 QVLKEICDAIITYKDSNGQSLAIPFINLPSKK--KNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEK   82 (106)
T ss_pred             HHHHHHHHHHHHhhccCCCcccHhhccCCCcc--cCCchhhhCCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            456777777766554   36889999999987  7899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHH
Q psy245          341 YNPPDHDVVAMAKKLQDVFETK  362 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~  362 (566)
                      ||++||.+|.+|..|+++|++.
T Consensus        83 yn~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          83 YYGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHc
Confidence            9999999999999999999864

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.

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.88  E-value=2e-22  Score=174.03  Aligned_cols=97  Identities=26%  Similarity=0.283  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      .|++ |+.|+..|+.++++++|..+..    ++|                                     |||++|++|
T Consensus         3 ~l~~-ce~il~~l~~~~~s~~f~~~p~----~~p-------------------------------------dY~~iIk~P   40 (102)
T cd05501           3 ELLK-CEFLLLKVYCMSKSGFFISKPY----YIR-------------------------------------DYCQGIKEP   40 (102)
T ss_pred             HHHH-HHHHHHHHHhCcccccccCCCC----CCC-------------------------------------chHHHcCCC
Confidence            3444 8999999999999999966321    466                                     999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      |||+||++||.+|.|.++.+|++||+|||.||++||+++ .++.+|..|++.|++.|.+.
T Consensus        41 MDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~N~~~yN~~~-~~~~~a~~L~~~Fek~~~~~   99 (102)
T cd05501          41 MWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-DFGQVGITLEKKFEKNFKEV   99 (102)
T ss_pred             CCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999 99999999999999999865

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.

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.88  E-value=1.2e-22  Score=179.91  Aligned_cols=99  Identities=36%  Similarity=0.637  Sum_probs=93.1

Q ss_pred             HHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCC
Q psy245          266 CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPD  345 (566)
Q Consensus       266 c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~  345 (566)
                      ...|+..|+.++   .++||..||++.  .+|+||++|++||||+||++||.+|.|.++.+|.+||+|||.||+.||+++
T Consensus         5 l~~ii~~l~~~~---~s~~F~~pv~~~--~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~   79 (112)
T cd05511           5 LDEIVNELKNLP---DSWPFHTPVNKK--KVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPD   79 (112)
T ss_pred             HHHHHHHHHhCC---CchhhcCCCChh--hcccHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            457888998877   678999999998  589999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHcCCCC
Q psy245          346 HDVVAMAKKLQDVFETKIAKAPDD  369 (566)
Q Consensus       346 s~v~~~A~~L~~~fe~~~~~~~~~  369 (566)
                      |.++.+|..|.+.|+.++..++..
T Consensus        80 s~i~~~A~~l~~~~~~~~~~~~~~  103 (112)
T cd05511          80 SVYTKKAKEMLELAEELLAEREEK  103 (112)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhHHH
Confidence            999999999999999999998654

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=99.88  E-value=1.2e-22  Score=175.48  Aligned_cols=93  Identities=31%  Similarity=0.488  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           80 LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      |..+|+.|++.|+.|+.+|+|..|||..  ++|                                     |||++|++||
T Consensus         2 ~~~~l~~il~~l~~~~~~~~F~~pVd~~--~~p-------------------------------------dY~~iIk~Pm   42 (98)
T cd05512           2 LEVLLRKTLDQLQEKDTAEIFSEPVDLS--EVP-------------------------------------DYLDHIKQPM   42 (98)
T ss_pred             HHHHHHHHHHHHHhCCCchhhcCCCCcc--ccC-------------------------------------CHHHHhcCCc
Confidence            5678889999999999999999999964  366                                     9999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHH
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLF  211 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f  211 (566)
                      ||+||++||.++.|.++++|..||+|||.||+.||+++|.++++|..|++.-
T Consensus        43 DL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~~~~~A~~l~~~~   94 (98)
T cd05512          43 DFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLRDQG   94 (98)
T ss_pred             CHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999998753

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.

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.87  E-value=7e-22  Score=178.95  Aligned_cols=105  Identities=29%  Similarity=0.409  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      ..+...|..+|..|+.......+++|..||+... .+|+||++|++||||+||++||.+|.|.++++|.+||+|||.||+
T Consensus        23 ~~~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~-~~p~Y~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~Na~  101 (128)
T cd05529          23 DEERERLISGLDKLLLSLQLEIAEYFEYPVDLRA-WYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAE  101 (128)
T ss_pred             HHHHHHHHHHHHHHHhcccCcccccccCCCCccc-cCCcHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence            4667788888888885555568999999999875 689999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHc
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKIAK  365 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~~~  365 (566)
                      .||+++|.++.+|..|++.|..++..
T Consensus       102 ~yN~~~s~i~~~A~~l~~~~~~~l~~  127 (128)
T cd05529         102 TFNEPNSEIAKKAKRLSDWLLRILSS  127 (128)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999999999998753

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=99.87  E-value=2.7e-22  Score=174.74  Aligned_cols=83  Identities=34%  Similarity=0.440  Sum_probs=79.6

Q ss_pred             hhhhhhhhccccccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHH
Q psy245          132 YPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLF  211 (566)
Q Consensus       132 ~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f  211 (566)
                      ++.++++|..+|++..+||||++|++||||+||++||.++.|.++++|..||+|||.||+.||+++|.|+.+|..|+++|
T Consensus        20 gr~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le~~~   99 (103)
T cd05518          20 GRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVL   99 (103)
T ss_pred             CCcccHHHhcCCCcccCccHHHHcCCCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            56688899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHH
Q psy245          212 LTK  214 (566)
Q Consensus       212 ~~~  214 (566)
                      .++
T Consensus       100 ~~~  102 (103)
T cd05518         100 KEK  102 (103)
T ss_pred             Hhc
Confidence            764

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=99.87  E-value=2.6e-22  Score=174.96  Aligned_cols=83  Identities=33%  Similarity=0.414  Sum_probs=79.2

Q ss_pred             hhhhhhhhccccccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHH
Q psy245          132 YPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLF  211 (566)
Q Consensus       132 ~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f  211 (566)
                      ++.++.+|..+|++..+||||++|++||||+||++||++|.|.++.+|+.||+|||.||++||+++|.++.+|..|+++|
T Consensus        20 g~~~s~pF~~~p~~~~~PdYy~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~L~~~f   99 (103)
T cd05520          20 GQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKLM   99 (103)
T ss_pred             CCCccHhhhcCCCcccCCCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            55678889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHH
Q psy245          212 LTK  214 (566)
Q Consensus       212 ~~~  214 (566)
                      +++
T Consensus       100 ~~~  102 (103)
T cd05520         100 QAK  102 (103)
T ss_pred             HHh
Confidence            864

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

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

Probab=99.87  E-value=3.8e-22  Score=174.28  Aligned_cols=103  Identities=31%  Similarity=0.401  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           80 LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      |+..|+.|++.|+++++.       +                          ++.++.+|..+|++..+||||.+|++||
T Consensus         1 ~~~~~~~i~~~v~~~~~~-------~--------------------------~~~~~~~F~~~p~~~~~pdYy~iIk~Pm   47 (103)
T cd05519           1 LKAAMLEIYDAVLNCEDE-------T--------------------------GRKLSELFLEKPSKKLYPDYYVIIKRPI   47 (103)
T ss_pred             CHHHHHHHHHHHHHhcCc-------C--------------------------CCchhHHhcCCCCCCCCcCHHHHcCCCc
Confidence            467899999999988753       0                          3446677888888888889999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      ||++|++||++|.|.++.+|..||+|||.||++||+++|.++.+|..|++.|.+++
T Consensus        48 dl~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l~~~f~~~~  103 (103)
T cd05519          48 ALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKKKY  103 (103)
T ss_pred             CHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999998753

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

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.86  E-value=3.7e-22  Score=174.82  Aligned_cols=103  Identities=27%  Similarity=0.355  Sum_probs=91.7

Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCC
Q psy245           81 AFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMD  160 (566)
Q Consensus        81 ~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMd  160 (566)
                      +..|+.|++.|.++.+..                                 ++.++.+|..+|++..+||||.+|++|||
T Consensus         2 ~~~~~~~~~~i~~~~d~~---------------------------------~~~~a~~F~~~p~~~~~pdYy~iIk~Pmd   48 (105)
T cd05515           2 QQKLWELYNAVKNYTDGR---------------------------------GRRLSLIFMRLPSKSEYPDYYDVIKKPID   48 (105)
T ss_pred             hHHHHHHHHHHHHhhCcC---------------------------------CCcccHHhccCCCcccCCcHHHHcCCCcC
Confidence            456788999999987741                                 34466778888888888999999999999


Q ss_pred             HHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhh
Q psy245          161 LGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVS  216 (566)
Q Consensus       161 L~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~  216 (566)
                      |+||++||.++.|.++++|..||.|||.||++||+++|.++.+|..|++.|.+...
T Consensus        49 L~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~~yN~~~s~i~~~A~~L~~~~~~~~~  104 (105)
T cd05515          49 MEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLLETKR  104 (105)
T ss_pred             HHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999999999999999999987653

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.

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

Probab=99.86  E-value=9.9e-22  Score=171.94  Aligned_cols=102  Identities=25%  Similarity=0.310  Sum_probs=93.6

Q ss_pred             HHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           80 LAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      |+..|+.|++.|+++++..                                 ++.++.+|..+|++..+||||++|++||
T Consensus         2 l~~~~~~l~~~i~~~~~~~---------------------------------g~~~~~~F~~lp~~~~~pdYy~iI~~Pm   48 (106)
T cd05521           2 LSKKLKPLYDGIYTLKEEN---------------------------------GIEIHPIFNVLPLRKDYPDYYKIIKNPL   48 (106)
T ss_pred             HHHHHHHHHHHHHhhcCcC---------------------------------CCCchHhhhcCCccccCccHHHHhcCCC
Confidence            5677889999999988741                                 3447788999999999999999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhh
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVS  216 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~  216 (566)
                      ||+||++||++  |.++.+|..|+.|||.||+.||+++|.++.+|..|++.|.+.+.
T Consensus        49 dL~tI~~kl~~--Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le~~~~~~~~  103 (106)
T cd05521          49 SLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKYINDVII  103 (106)
T ss_pred             CHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHhhc
Confidence            99999999998  99999999999999999999999999999999999999998774

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

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

Probab=99.85  E-value=2e-21  Score=169.79  Aligned_cols=98  Identities=27%  Similarity=0.318  Sum_probs=87.5

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      ++.+...|..+.+..+...+++|..+|+..  .+|+||++|++||||++|++||..|.|.++.+|..||+|||.||+.||
T Consensus         6 ~~~i~~~v~~~~d~~g~~l~~~F~~~p~~~--~~pdYy~~I~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn   83 (104)
T cd05522           6 IKNILKGLRKERDENGRLLTLHFEKLPDKA--REPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN   83 (104)
T ss_pred             HHHHHHHHHHHhCcCCCcccHHHhcCCCcc--ccCcHHHHhCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            444555555555555567999999999987  689999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHH
Q psy245          343 PPDHDVVAMAKKLQDVFETK  362 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~fe~~  362 (566)
                      +++|.+|.+|..|++.|+++
T Consensus        84 ~~~s~i~~~A~~l~~~f~~l  103 (104)
T cd05522          84 ENDSQEYKDAVLLEKEARLL  103 (104)
T ss_pred             CCCCHHHHHHHHHHHHHHHh
Confidence            99999999999999999874

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.

>KOG1472|consensus

Probab=99.85  E-value=1.3e-21  Score=215.95  Aligned_cols=98  Identities=34%  Similarity=0.600  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCC
Q psy245          265 YCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPP  344 (566)
Q Consensus       265 ~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~  344 (566)
                      ....+|..|..|.   .+|||.+||+..  ++||||++|++||||.||+.+|..+.|..+..|.+|+.+||+||+.||+.
T Consensus       610 ~~~~il~~l~~h~---~awPf~~Pv~~~--e~pdyy~~I~~pmDl~tM~~~l~~~~y~~~~~f~ad~~~vf~ncr~yn~~  684 (720)
T KOG1472|consen  610 AIQNILDQLQNHG---DAWPFLKPVNKK--EVPDYYDVIKHPMDLRTMQNRLKDNQYTEVELFMADVVRVFANCRMYNGS  684 (720)
T ss_pred             HHHhHHhhhhcCC---ccCCccCccccc--cCCcHHHHhcccccHHHHhhhccccchhhHHHHHHHHHHHHhhhhccCCc
Confidence            4456777777666   789999999998  79999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHcCC
Q psy245          345 DHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       345 ~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      ++..|..|..|..+|..++....
T Consensus       685 ~~~y~k~~~~le~~~~~k~~~~i  707 (720)
T KOG1472|consen  685 DTQYYKCAQALEKFFLFKLNELI  707 (720)
T ss_pred             cchheecccchhhhhcchhhhhh
Confidence            99999999999999999887653

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.85  E-value=4.8e-21  Score=173.51  Aligned_cols=106  Identities=28%  Similarity=0.375  Sum_probs=95.3

Q ss_pred             CCCcHHHHHHHHHHHHHHH---hcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCc
Q psy245           74 GRNTNQLAFISKNVLKPVM---KHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQD  150 (566)
Q Consensus        74 ~~~~~~l~~~~~~v~~~l~---~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pd  150 (566)
                      ......++..+..+++.|+   +++.++||..||+... .+|                                     +
T Consensus        19 ~~~~~~~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~-~~p-------------------------------------~   60 (128)
T cd05529          19 PHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRA-WYP-------------------------------------D   60 (128)
T ss_pred             CCCCHHHHHHHHHHHHHHHhcccCcccccccCCCCccc-cCC-------------------------------------c
Confidence            3445566666667899999   8999999999999652 456                                     9


Q ss_pred             ccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhh
Q psy245          151 YHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSA  217 (566)
Q Consensus       151 Y~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  217 (566)
                      ||++|++||||+||++||.+|.|.++++|..||+|||.||++||+++|.++.+|..|+..|.+.+..
T Consensus        61 Y~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~Na~~yN~~~s~i~~~A~~l~~~~~~~l~~  127 (128)
T cd05529          61 YWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRILSS  127 (128)
T ss_pred             HHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHhcc
Confidence            9999999999999999999999999999999999999999999999999999999999999988764

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

>smart00297 BROMO bromo domain

Probab=99.85  E-value=4.2e-21  Score=168.39  Aligned_cols=101  Identities=44%  Similarity=0.738  Sum_probs=91.7

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      .....|..|++.+.++.   .+++|..||+..  .+|+||++|++||||++|++||++|.|.|+.+|.+||++||.||+.
T Consensus         7 ~~~~~~~~i~~~~~~~~---~~~~F~~~~~~~--~~p~Y~~~i~~P~dl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~   81 (107)
T smart00297        7 KLQSLLKAVLDKLDSHR---LSWPFLKPVDRK--EAPDYYDIIKKPMDLSTIKKKLENGKYSSVEEFVADVQLMFSNAKT   81 (107)
T ss_pred             HHHHHHHHHHHHHHhCc---cchhhccCCChh--hccCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            34566777777776653   789999999988  5899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      ||++++.++.+|..|++.|++.|+++
T Consensus        82 ~n~~~s~~~~~a~~l~~~f~~~~~~~  107 (107)
T smart00297       82 YNGPDSEVYKDAKKLEKFFEKKLREL  107 (107)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999999999999763

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

Probab=99.84  E-value=6.9e-21  Score=166.65  Aligned_cols=97  Identities=25%  Similarity=0.318  Sum_probs=86.8

Q ss_pred             HHHHHHHHHHHhccCC---CCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          264 KYCNEILKELFSKKHS---SYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       264 k~c~~iL~~l~~~~~~---~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      ++|..++..++..++.   ..+.+|..+++..  ++||||++|++||||+||++||.+  |.++.+|.+||+|||+||+.
T Consensus         4 ~~~~~l~~~i~~~~~~~g~~~~~~F~~lp~~~--~~pdYy~iI~~PmdL~tI~~kl~~--Y~s~~ef~~D~~li~~Na~~   79 (106)
T cd05521           4 KKLKPLYDGIYTLKEENGIEIHPIFNVLPLRK--DYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARL   79 (106)
T ss_pred             HHHHHHHHHHHhhcCcCCCCchHhhhcCCccc--cCccHHHHhcCCCCHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHH
Confidence            5677777777766643   4667899888876  689999999999999999999998  99999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHH
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIA  364 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~  364 (566)
                      ||++||.+|.+|..|+++|.+++.
T Consensus        80 yN~~~s~i~~~A~~le~~~~~~~~  103 (106)
T cd05521          80 YNTKGSVIYKYALILEKYINDVII  103 (106)
T ss_pred             HcCCCCHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999998864

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.

>smart00297 BROMO bromo domain

Probab=99.83  E-value=1.3e-20  Score=165.22  Aligned_cols=102  Identities=43%  Similarity=0.675  Sum_probs=96.1

Q ss_pred             cHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCC
Q psy245           77 TNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIK  156 (566)
Q Consensus        77 ~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk  156 (566)
                      ...+..+|..|++.+.+|+.+++|..||+...  .|                                     +||.+|+
T Consensus         5 ~~~~~~~~~~i~~~~~~~~~~~~F~~~~~~~~--~p-------------------------------------~Y~~~i~   45 (107)
T smart00297        5 QKKLQSLLKAVLDKLDSHRLSWPFLKPVDRKE--AP-------------------------------------DYYDIIK   45 (107)
T ss_pred             HHHHHHHHHHHHHHHHhCccchhhccCCChhh--cc-------------------------------------CHHHHhc
Confidence            45788899999999999999999999998643  55                                     9999999


Q ss_pred             CCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhh
Q psy245          157 HPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSA  217 (566)
Q Consensus       157 ~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  217 (566)
                      +||||++|++||++|.|.++.+|..||++||.||..||++++.++.+|..|+..|++.|.+
T Consensus        46 ~P~dl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~~n~~~s~~~~~a~~l~~~f~~~~~~  106 (107)
T smart00297       46 KPMDLSTIKKKLENGKYSSVEEFVADVQLMFSNAKTYNGPDSEVYKDAKKLEKFFEKKLRE  106 (107)
T ss_pred             CCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999999999999999875

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

Probab=99.83  E-value=1.3e-20  Score=164.81  Aligned_cols=100  Identities=27%  Similarity=0.274  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCH
Q psy245           82 FISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDL  161 (566)
Q Consensus        82 ~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL  161 (566)
                      ..++.|++.|.++.++                                 .++.++.+|..+|++..+||||++|++||||
T Consensus         4 ~~~~~i~~~v~~~~d~---------------------------------~g~~l~~~F~~~p~~~~~pdYy~~I~~Pmdl   50 (104)
T cd05522           4 ARIKNILKGLRKERDE---------------------------------NGRLLTLHFEKLPDKAREPEYYQEISNPISL   50 (104)
T ss_pred             HHHHHHHHHHHHHhCc---------------------------------CCCcccHHHhcCCCccccCcHHHHhCCCcCH
Confidence            4567888999888775                                 1344677888999988999999999999999


Q ss_pred             HHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHH
Q psy245          162 GTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTK  214 (566)
Q Consensus       162 ~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~  214 (566)
                      ++|++||.++.|.++.+|..||.|||.||+.||+++|.++.+|..|++.|+..
T Consensus        51 ~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l~~~f~~l  103 (104)
T cd05522          51 DDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKEARLL  103 (104)
T ss_pred             HHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999863

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.

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.81  E-value=6.3e-20  Score=160.74  Aligned_cols=105  Identities=13%  Similarity=0.077  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHHh-cCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           81 AFISKNVLKPVMK-HQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        81 ~~~~~~v~~~l~~-~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      -.+|+.++..+.. .+.++||+.||......                                  +..+|+|+.+|++||
T Consensus         2 ~~~L~f~~~~~k~~lp~~~~~~~~v~~~~~~----------------------------------~~~~pdY~~iIk~Pm   47 (109)
T cd05492           2 NCLLKFIVSRMKSWLPPDTTNRAIVLNKRGK----------------------------------ATKLPKRRRLIHTHL   47 (109)
T ss_pred             chhHHHHHHHHHhcCcccccccccccccCch----------------------------------hccCCCHHHHhCCCC
Confidence            3567778888777 67789999999854322                                  223459999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      ||+||++||++|.|.++++|..||.|||+||..||+++|.++.+|..|.+.+...+.++.
T Consensus        48 DL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~N~~~yNg~~s~~~~~A~~l~~d~~~el~Ei~  107 (109)
T cd05492          48 DVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWLYRDTCHDLRELR  107 (109)
T ss_pred             cHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999888764

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.

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

Probab=99.81  E-value=5.1e-20  Score=154.42  Aligned_cols=84  Identities=51%  Similarity=0.866  Sum_probs=78.0

Q ss_pred             HHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCC
Q psy245          266 CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPD  345 (566)
Q Consensus       266 c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~  345 (566)
                      |..||..|++++   .+++|..||+..  .+|+|+++|++||||++|++||++|.|.++.+|..||++||.||+.||+++
T Consensus         1 C~~il~~l~~~~---~~~~F~~~~~~~--~~p~y~~~i~~P~dL~~I~~kl~~~~Y~s~~~f~~Dv~~i~~Na~~yn~~~   75 (84)
T PF00439_consen    1 CREILEELMKHP---ISSPFSKPVDPK--EYPDYYEIIKNPMDLSTIRKKLENGKYKSIEEFEADVRLIFQNARRYNPPD   75 (84)
T ss_dssp             HHHHHHHHHTST---TGGGGSSSTHTT--TSTTHHHHSSSS--HHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CHHHHHHHHcCC---CchhhcCCCChh--hCCCHHHHHhhccchhhhhHHhhccchhhHHHHHHHHHHHHHHHHHHCCCc
Confidence            899999999988   778999999776  799999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHH
Q psy245          346 HDVVAMAKK  354 (566)
Q Consensus       346 s~v~~~A~~  354 (566)
                      |.+|.+|.+
T Consensus        76 s~~~~~A~~   84 (84)
T PF00439_consen   76 SPIYKAAEK   84 (84)
T ss_dssp             SHHHHHHHH
T ss_pred             CHHHHHhcC
Confidence            999999974

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

>cd04369 Bromodomain Bromodomain

Probab=99.81  E-value=7.1e-20  Score=156.87  Aligned_cols=97  Identities=44%  Similarity=0.673  Sum_probs=89.5

Q ss_pred             HHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCC
Q psy245          264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP  343 (566)
Q Consensus       264 k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~  343 (566)
                      ..|..++..+..+. ...+++|..||+..  .+|+||++|++||||++|++||..|.|.++.+|.+||+|||.||+.||+
T Consensus         3 ~~~~~i~~~l~~~~-~~~~~~F~~~~~~~--~~~~Y~~~i~~P~~l~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~~n~   79 (99)
T cd04369           3 KKLRSLLDALKKLK-RDLSEPFLEPVDPK--EAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNG   79 (99)
T ss_pred             HHHHHHHHHHHhhc-ccccHHHhcCCChh--cCCCHHHHHhCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            56889999998873 22678999999986  5899999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHH
Q psy245          344 PDHDVVAMAKKLQDVFETKI  363 (566)
Q Consensus       344 ~~s~v~~~A~~L~~~fe~~~  363 (566)
                      .++.++.+|..|+..|++.|
T Consensus        80 ~~~~~~~~a~~l~~~~~~~~   99 (99)
T cd04369          80 PGSPIYKDAKKLEKLFEKLL   99 (99)
T ss_pred             CCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999998764

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

>KOG0008|consensus

Probab=99.80  E-value=2.1e-19  Score=204.49  Aligned_cols=217  Identities=27%  Similarity=0.445  Sum_probs=168.4

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      .++-++..++..+....+..||..||+...  ++                                     |||.||+.|
T Consensus      1261 ~~ss~l~~i~n~~~~~~~t~~f~~Pv~~k~--v~-------------------------------------dyy~vi~~P 1301 (1563)
T KOG0008|consen 1261 SLSSILETIINQARSSPNTYPFPTPVNAKE--VK-------------------------------------DYYRVITPP 1301 (1563)
T ss_pred             ecccchHHHHHHHhcCCCCcCCCCccchhh--cc-------------------------------------chhhccCCC
Confidence            567788899999999999999999999754  45                                     999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccccccccCCCCCCCCCCcc
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFT  238 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~k~~~~~~~~~~~~~~  238 (566)
                      |||.++++.+....|.+-++|+.|+.+|+.|..+||++.+.+...++.+...+-..|.+-....-...+....       
T Consensus      1302 ~~lq~~kk~v~kr~y~~r~~fle~~~~~~~ns~~yng~~~~~t~~~q~mls~~~~~~~ekedk~~~lEk~Inp------- 1374 (1563)
T KOG0008|consen 1302 MDLQTQKKLVRKRLYESREHFLEELPLIVSNSTKYNGPLASLTRQQQSMLSLCFEKLKEKEDKLWRLEKAINP------- 1374 (1563)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHhHHHhhchhhhcCchHHHHHHHHHHHHHHHHhhchhHHHHHHHHhhcCc-------
Confidence            9999999999999999999999999999999999999999999999888777766665433322111111000       


Q ss_pred             cccccccCCCCCCCCCCCcchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhC
Q psy245          239 TQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA  318 (566)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~  318 (566)
                                ..+...   .+  ..-....++.++..-   ..+|+|.+||+.+  .+|+||.+|++||||.+|.+++..
T Consensus      1375 ----------lld~~d---~v--~~~~~d~~vs~~~~i---pes~~f~~~v~~k--~~~~yy~kik~pmdl~~i~~n~~~ 1434 (1563)
T KOG0008|consen 1375 ----------LLDDDD---QV--AFFILDNIVSQMKEI---PESWPFHEPVNKK--RVPDYYKKIKNPMDLETILKNIPP 1434 (1563)
T ss_pred             ----------ccCccc---hh--hHhhhhhHHHHHHhc---chhcccccccchh--hchHHHHHhcChhhHHHHhhcCCc
Confidence                      000000   00  011223344443332   3679999999999  589999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHH
Q psy245          319 REYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFET  361 (566)
Q Consensus       319 ~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~  361 (566)
                      +.|.+..+|..||++|+.||..||+..+....-|+.+-.+...
T Consensus      1435 ~~y~s~~e~l~dv~~i~~n~~~~ng~e~~y~~k~~k~~ev~~~ 1477 (1563)
T KOG0008|consen 1435 HKYDSRSEFLDDVNLIYVNSVEYNGAESAYTKKARKIGEVGLA 1477 (1563)
T ss_pred             cccccHHHHhhhhHhhcccceeecCccccccHHHHHHHHHHHH
Confidence            9999999999999999999999999988655555544444333

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.80  E-value=1.8e-19  Score=157.47  Aligned_cols=105  Identities=17%  Similarity=0.172  Sum_probs=96.0

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      .++.++..|+++|++|.+.                                 .||.++++|..||++  +++||.+|+.|
T Consensus         3 ~vq~~l~~l~~~V~~~~D~---------------------------------~Gr~~s~~f~~LP~~--~~~~~~~ik~P   47 (110)
T cd05526           3 LVQELLATLFVSVMNHQDE---------------------------------EGRCYSDSLAELPEL--AVDGVGPKKIP   47 (110)
T ss_pred             HHHHHHHHHHHHHHhccCC---------------------------------CCCCchHHHHHCCCc--ccCchhhhcCC
Confidence            5788899999999999885                                 277899999999994  46888999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      |||.+|++||.+|.|+++++|..||.+||.||++||+++|.||.+|..|..+|...-.++
T Consensus        48 i~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NAr~yN~~~S~iy~dA~eLq~~f~~~rd~~  107 (110)
T cd05526          48 LTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTDSEIYEDAVELQQFFIKIRDEL  107 (110)
T ss_pred             ccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHHHHhCcccCHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999998765543

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.

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.78  E-value=2.8e-19  Score=156.67  Aligned_cols=85  Identities=18%  Similarity=0.202  Sum_probs=78.0

Q ss_pred             CcCcccCCCc---cccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHH
Q psy245          282 AWPFYKPVDA---AWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDV  358 (566)
Q Consensus       282 a~pF~~PVd~---~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~  358 (566)
                      .+||..||.+   ...++|+||++|++||||+||++||++|.|+++++|.+||+|||+||..||+++|.++.+|..|.+.
T Consensus        19 ~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~N~~~yNg~~s~~~~~A~~l~~d   98 (109)
T cd05492          19 DTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWLYRD   98 (109)
T ss_pred             cccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Confidence            4699999974   3335999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHHcC
Q psy245          359 FETKIAKA  366 (566)
Q Consensus       359 fe~~~~~~  366 (566)
                      ....+.++
T Consensus        99 ~~~el~Ei  106 (109)
T cd05492          99 TCHDLREL  106 (109)
T ss_pred             HHHHHHHH
Confidence            88877765

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.

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

Probab=99.77  E-value=5.7e-19  Score=148.04  Aligned_cols=84  Identities=40%  Similarity=0.645  Sum_probs=76.5

Q ss_pred             HHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCHHH
Q psy245           84 SKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGT  163 (566)
Q Consensus        84 ~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~t  163 (566)
                      |..|++.|++|+.+++|..||+..  .+|                                     +|+.+|++||||++
T Consensus         1 C~~il~~l~~~~~~~~F~~~~~~~--~~p-------------------------------------~y~~~i~~P~dL~~   41 (84)
T PF00439_consen    1 CREILEELMKHPISSPFSKPVDPK--EYP-------------------------------------DYYEIIKNPMDLST   41 (84)
T ss_dssp             HHHHHHHHHTSTTGGGGSSSTHTT--TST-------------------------------------THHHHSSSS--HHH
T ss_pred             CHHHHHHHHcCCCchhhcCCCChh--hCC-------------------------------------CHHHHHhhccchhh
Confidence            678999999999999999999643  355                                     99999999999999


Q ss_pred             HHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHH
Q psy245          164 IKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQT  206 (566)
Q Consensus       164 I~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~  206 (566)
                      |++||++|.|.++.+|..||++||.||+.||+++|.++.+|..
T Consensus        42 I~~kl~~~~Y~s~~~f~~Dv~~i~~Na~~yn~~~s~~~~~A~~   84 (84)
T PF00439_consen   42 IRKKLENGKYKSIEEFEADVRLIFQNARRYNPPDSPIYKAAEK   84 (84)
T ss_dssp             HHHHHHTTSSSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHH
T ss_pred             hhHHhhccchhhHHHHHHHHHHHHHHHHHHCCCcCHHHHHhcC
Confidence            9999999999999999999999999999999999999999974

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=99.77  E-value=8.2e-19  Score=150.24  Aligned_cols=95  Identities=41%  Similarity=0.566  Sum_probs=88.3

Q ss_pred             HHHHHHHHHHHhc--CCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCC
Q psy245           82 FISKNVLKPVMKH--QHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPM  159 (566)
Q Consensus        82 ~~~~~v~~~l~~~--~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PM  159 (566)
                      ..|..|++.|+++  +.+++|..||+..  ..|                                     +|+.+|++||
T Consensus         3 ~~~~~i~~~l~~~~~~~~~~F~~~~~~~--~~~-------------------------------------~Y~~~i~~P~   43 (99)
T cd04369           3 KKLRSLLDALKKLKRDLSEPFLEPVDPK--EAP-------------------------------------DYYEVIKNPM   43 (99)
T ss_pred             HHHHHHHHHHHhhcccccHHHhcCCChh--cCC-------------------------------------CHHHHHhCcc
Confidence            4678899999999  9999999999863  355                                     9999999999


Q ss_pred             CHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          160 DLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       160 dL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      ||++|++||.+|.|.++.+|..||++||.||+.||+.++.++.+|..|+..|++.+
T Consensus        44 ~l~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~~n~~~~~~~~~a~~l~~~~~~~~   99 (99)
T cd04369          44 DLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL   99 (99)
T ss_pred             cHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999998753

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

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.74  E-value=6.4e-18  Score=147.68  Aligned_cols=101  Identities=15%  Similarity=0.212  Sum_probs=89.6

Q ss_pred             HHHHHHHHHHHHhcc---CCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          263 LKYCNEILKELFSKK---HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~---~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      ......|+..++.+.   +..++.+|.+.+..    .++||++|++||||++|++||+.|.|+++++|..||.|||.||+
T Consensus         5 q~~l~~l~~~V~~~~D~~Gr~~s~~f~~LP~~----~~~~~~~ik~Pi~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NAr   80 (110)
T cd05526           5 QELLATLFVSVMNHQDEEGRCYSDSLAELPEL----AVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR   80 (110)
T ss_pred             HHHHHHHHHHHHhccCCCCCCchHHHHHCCCc----ccCchhhhcCCccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHHH
Confidence            345667778888877   44688899998873    36889999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      +||.+||.+|.+|..|+.+|....+++.
T Consensus        81 ~yN~~~S~iy~dA~eLq~~f~~~rd~~~  108 (110)
T cd05526          81 RLSRTDSEIYEDAVELQQFFIKIRDELC  108 (110)
T ss_pred             HhCcccCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999998877653

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

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

Probab=99.70  E-value=2e-17  Score=176.05  Aligned_cols=206  Identities=25%  Similarity=0.231  Sum_probs=137.4

Q ss_pred             cccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccccccccCCC
Q psy245          150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPN  229 (566)
Q Consensus       150 dY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~k~~~~~  229 (566)
                      .+.......|....+..... ..... .+...+-.+.+..+.+|+................+...-...+......    
T Consensus        47 ~~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~----  120 (371)
T COG5076          47 NLFQKQLKRMPKEYITSIVD-DREPG-SMANVNDDLENVGGITYSPFEKNRPESLRFDEIVFLAIESVTPESGLGS----  120 (371)
T ss_pred             ccchhhhcccchhhhhhhhc-ccccc-cccccCcchhcccCcccCCccccccccccccceeccccccccccccccc----
Confidence            55556667788888888877 55555 7777777777777777776432222211111111111111011000000    


Q ss_pred             CCCCCCCcccccccccCCCCCCCCCCCcchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCCh
Q psy245          230 RGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDL  309 (566)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL  309 (566)
                       .......++      .............+......+...+..+....+..+.++|..+|+..  .+|+||+||+.||||
T Consensus       121 -~~~~~~~~~------~~k~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~s~~F~~~p~k~--~~PdYy~iIk~Pm~L  191 (371)
T COG5076         121 -LLMAHLKTS------VKKRKTPKIEDELLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKR--EYPDYYEIIKSPMDL  191 (371)
T ss_pred             -cccccchHH------HHhhcCCcccchhHHHHHHHHHHHHHHhhcccccccccccccCCccc--cCCChheeecchhhH
Confidence             000000000      00001111222344455566666666677777777889999999887  699999999999999


Q ss_pred             HHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCC
Q psy245          310 GTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV  370 (566)
Q Consensus       310 ~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~  370 (566)
                      ++|+++|..|.|+++++|..|+.|||+||+.||.+++.||.+|..|++.|..++..++...
T Consensus       192 ~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~~~~~i~~~~~~~  252 (371)
T COG5076         192 LTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEM  252 (371)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHHHHHHHHHHhccccc
Confidence            9999999999999999999999999999999999999999999999999999999887654

>KOG1245|consensus

Probab=99.64  E-value=1.7e-16  Score=189.24  Aligned_cols=96  Identities=41%  Similarity=0.753  Sum_probs=92.4

Q ss_pred             HHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCC
Q psy245          266 CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPD  345 (566)
Q Consensus       266 c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~  345 (566)
                      |..||.+|..|.   .||||++||++.  .+|+||+||++||||+||+.|+..|.|.++.+|..||.|||.||..||.. 
T Consensus      1306 ~e~il~e~~~~~---~awPFlepVn~~--~vp~Y~~IIk~Pmdl~tir~k~~~~~Y~~~eef~~Di~lvf~Nc~~yN~~- 1379 (1404)
T KOG1245|consen 1306 CEDILHELVVHK---AAWPFLEPVNPK--EVPDYYDIIKKPMDLSTIREKLSKGIYPSPEEFATDIELVFDNCETYNED- 1379 (1404)
T ss_pred             HHHHHHHHHHhh---hcchhhccCChh--hcccHHHHhcChhHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHhccc-
Confidence            899999999988   789999999998  69999999999999999999999999999999999999999999999999 


Q ss_pred             CHHHHHHHHHHHHHHHHHHcCC
Q psy245          346 HDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       346 s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      |.|+..+..|.++|++.|....
T Consensus      1380 s~i~~ag~~l~~ff~~~~~~~~ 1401 (1404)
T KOG1245|consen 1380 SEIGRAGTCLRRFFHKRWRKKF 1401 (1404)
T ss_pred             hhhhhhcchHHHHHHHHHHhhc
Confidence            9999999999999999988653

>KOG1245|consensus

Probab=99.58  E-value=1.3e-15  Score=181.82  Aligned_cols=95  Identities=33%  Similarity=0.668  Sum_probs=89.5

Q ss_pred             HHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCHHH
Q psy245           84 SKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGT  163 (566)
Q Consensus        84 ~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~t  163 (566)
                      |..|+..|+.|+.||||++||+...  +|                                     |||+||++||||+|
T Consensus      1306 ~e~il~e~~~~~~awPFlepVn~~~--vp-------------------------------------~Y~~IIk~Pmdl~t 1346 (1404)
T KOG1245|consen 1306 CEDILHELVVHKAAWPFLEPVNPKE--VP-------------------------------------DYYDIIKKPMDLST 1346 (1404)
T ss_pred             HHHHHHHHHHhhhcchhhccCChhh--cc-------------------------------------cHHHHhcChhHHHH
Confidence            7889999999999999999999654  55                                     99999999999999


Q ss_pred             HHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          164 IKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       164 I~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      |+.|+..|.|.+..+|..||.|||.||.+||.+ |.|++....|.++|...|...
T Consensus      1347 ir~k~~~~~Y~~~eef~~Di~lvf~Nc~~yN~~-s~i~~ag~~l~~ff~~~~~~~ 1400 (1404)
T KOG1245|consen 1347 IREKLSKGIYPSPEEFATDIELVFDNCETYNED-SEIGRAGTCLRRFFHKRWRKK 1400 (1404)
T ss_pred             HHHHHhcccCCCHHHHHHHHHHHHHHHHHhccc-hhhhhhcchHHHHHHHHHHhh
Confidence            999999999999999999999999999999999 999999999999999877643

>KOG1827|consensus

Probab=99.42  E-value=2.7e-13  Score=148.39  Aligned_cols=232  Identities=17%  Similarity=0.149  Sum_probs=164.6

Q ss_pred             hhHHHHHHHHHHHHhhhh-hhhhhhhhhccccccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhcc
Q psy245          113 FLIFRFLVFQHWVLSMYI-EYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCY  191 (566)
Q Consensus       113 ~~~~~~~~~~~~~l~~~~-~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~  191 (566)
                      +++.+|...-..+++.-. +++-+++.|.+||.+...|+||.+|..||+|..|++|+..+.|.+++.|..|+.||+.||+
T Consensus        52 ~~~~~f~~il~~~~~~~d~~gk~~~d~feklp~~~~~p~yy~~i~~pisl~~ik~kv~k~~y~~~~~f~~D~~lm~ena~  131 (629)
T KOG1827|consen   52 PLIPKFKTILASLLDLKDDEGKQLFDKFEKLPSRKEFPEYYYVIQQPISLDQIKRKVKKGRYKRLSFFQLDFLLMTENAR  131 (629)
T ss_pred             HHHHHHHHHHHHHHhhccccCcccchhHhhccccccCCCcceeecCcccHHHHHHHHHhcccccHHHHHHHHHHHHHHHH
Confidence            455566555555555444 8899999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHhhhhccccccccCCCCCCCCCCc-cc-ccccccCCCCCCCCCCCcchHHHHHHHHHH
Q psy245          192 VYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSF-TT-QLATSVTSVGDQGSYAKPKLTESLKYCNEI  269 (566)
Q Consensus       192 ~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~k~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~k~c~~i  269 (566)
                      .||..++.++++|..|+..|.....+.......... ......+.. .. ........    .....+        |.-+
T Consensus       132 ~~n~~ds~~~~~s~~l~~~~~~~~~~~~d~e~s~~~-~~~l~~~~l~~~~~~~~~i~~----~~~~~g--------d~vl  198 (629)
T KOG1827|consen  132 LYNRPDSLIYKDSGELEKYFISLEDEKKDGELSMES-NEELKAGGLHYHELGPVEIDG----TKYIVG--------DYVL  198 (629)
T ss_pred             HhcCcchhhhhhhhhhhcchhhhhccccchhhcccc-ccccccCCCCcccCCCccccC----cccccC--------ceee
Confidence            999999999999999999998766431110000000 000000000 00 00000000    000000        0000


Q ss_pred             HHHHHh--ccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCH
Q psy245          270 LKELFS--KKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHD  347 (566)
Q Consensus       270 L~~l~~--~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~  347 (566)
                      +..--.  ..+-.....|+..+|.+  .+++||.+++-+|-+..+.+++..++|-....|..|+..+|.|+..|+.....
T Consensus       199 v~~~~d~~~p~v~~Ier~w~~~dg~--k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~q~l~g~c~v~~~~~y  276 (629)
T KOG1827|consen  199 VQNPADNLKPIVAQIERLWKLPDGE--KWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLVQRLLGKCYVMKPTEY  276 (629)
T ss_pred             ecCcccccCCceeeecccccCcccc--cccceeEeeCCccCccccccchhcccceecccccccHHHHhhcceEEeehhHh
Confidence            000000  00001224566766766  57999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy245          348 VVAMAKKLQDVF  359 (566)
Q Consensus       348 v~~~A~~L~~~f  359 (566)
                      ++..+..|.+.+
T Consensus       277 i~~~p~~ls~~d  288 (629)
T KOG1827|consen  277 ISGDPENLSEED  288 (629)
T ss_pred             hhcCcccccccc
Confidence            999999887654

>KOG0008|consensus

Probab=99.38  E-value=1.7e-13  Score=156.95  Aligned_cols=167  Identities=29%  Similarity=0.439  Sum_probs=139.8

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCH
Q psy245           82 FISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDL  161 (566)
Q Consensus        82 ~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL  161 (566)
                      +++..++..+++...+|||+.||+...  +|                                     +||.+|++||||
T Consensus      1385 ~~~d~~vs~~~~ipes~~f~~~v~~k~--~~-------------------------------------~yy~kik~pmdl 1425 (1563)
T KOG0008|consen 1385 FILDNIVSQMKEIPESWPFHEPVNKKR--VP-------------------------------------DYYKKIKNPMDL 1425 (1563)
T ss_pred             hhhhhHHHHHHhcchhcccccccchhh--ch-------------------------------------HHHHHhcChhhH
Confidence            788888999888999999999999765  55                                     999999999999


Q ss_pred             HHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccccccccCCCCCCCCCCccccc
Q psy245          162 GTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQL  241 (566)
Q Consensus       162 ~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~  241 (566)
                      .+|.+++..+.|.+.++|.+||++|+.||..||+..+.+..-|+.+-.+....+.+.-                      
T Consensus      1426 ~~i~~n~~~~~y~s~~e~l~dv~~i~~n~~~~ng~e~~y~~k~~k~~ev~~~~~~e~~---------------------- 1483 (1563)
T KOG0008|consen 1426 ETILKNIPPHKYDSRSEFLDDVNLIYVNSVEYNGAESAYTKKARKIGEVGLANLLEYI---------------------- 1483 (1563)
T ss_pred             HHHhhcCCccccccHHHHhhhhHhhcccceeecCccccccHHHHHHHHHHHHHHHHHH----------------------
Confidence            9999999999999999999999999999999999999988888888777665543221                      


Q ss_pred             ccccCCCCCCCCCCCcchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCC
Q psy245          242 ATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREY  321 (566)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y  321 (566)
                                            ..|.++=..        .+..|..+|...  +.++|-+++.  ||+.||...+..-+|
T Consensus      1484 ----------------------~~~~~le~~--------is~~~~~a~~~~--ea~~~dd~~~--~d~~t~~d~~~d~e~ 1529 (1563)
T KOG0008|consen 1484 ----------------------EHLLQLEEN--------ISTLFEAAVEKA--EAPDYDDIVP--GDLSTIPDDVRDTEY 1529 (1563)
T ss_pred             ----------------------HHHHHHHHh--------HHHHHHHHHHhh--hcCCccccCC--CCCCCCcchhhcccc
Confidence                                  112111111        223466677665  6899999998  999999999999999


Q ss_pred             CCHHHHHHHHHHHHhcccccCC
Q psy245          322 KSSKEFADDVRLIFTNCYKYNP  343 (566)
Q Consensus       322 ~s~~ef~~Dv~Lif~Na~~yN~  343 (566)
                      .+-.+|.+||..+=.|+-.|-+
T Consensus      1530 ~~~~~~~~~~~q~~~n~~~~~g 1551 (1563)
T KOG0008|consen 1530 SDSMQRDADVWQIKSNAHVYDG 1551 (1563)
T ss_pred             chhhhcccceeeeccccccccC
Confidence            9999999999999999998844

>KOG1472|consensus

Probab=99.37  E-value=3.6e-13  Score=149.66  Aligned_cols=105  Identities=37%  Similarity=0.609  Sum_probs=96.8

Q ss_pred             cHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCC
Q psy245           77 TNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIK  156 (566)
Q Consensus        77 ~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk  156 (566)
                      ...+...+..+++.|.+|.++|||..||+..  ++|                                     |||.+|+
T Consensus       604 ~~~~~s~~~~il~~l~~h~~awPf~~Pv~~~--e~p-------------------------------------dyy~~I~  644 (720)
T KOG1472|consen  604 PGKLFSAIQNILDQLQNHGDAWPFLKPVNKK--EVP-------------------------------------DYYDVIK  644 (720)
T ss_pred             cchhhHHHHhHHhhhhcCCccCCccCccccc--cCC-------------------------------------cHHHHhc
Confidence            3456667778999999999999999999954  366                                     9999999


Q ss_pred             CCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          157 HPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       157 ~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      +||||.||+.+|.++.|..+.+|+.|+.+||.||+.||+.++..++.|..|+..|...+.....
T Consensus       645 ~pmDl~tM~~~l~~~~y~~~~~f~ad~~~vf~ncr~yn~~~~~y~k~~~~le~~~~~k~~~~i~  708 (720)
T KOG1472|consen  645 HPMDLRTMQNRLKDNQYTEVELFMADVVRVFANCRMYNGSDTQYYKCAQALEKFFLFKLNELIL  708 (720)
T ss_pred             ccccHHHHhhhccccchhhHHHHHHHHHHHHhhhhccCCccchheecccchhhhhcchhhhhhh
Confidence            9999999999999999999999999999999999999999999999999999999998887654

>KOG1828|consensus

Probab=99.32  E-value=6.4e-13  Score=136.15  Aligned_cols=203  Identities=18%  Similarity=0.100  Sum_probs=134.9

Q ss_pred             CcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc-----cc-
Q psy245          149 QDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE-----SG-  222 (566)
Q Consensus       149 pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~-----~~-  222 (566)
                      |+|.++|..|||+.|++.+++-++|.++.+|..|.++++.|+..||-.++.++..|++|..+-...+.+--.     .. 
T Consensus        50 p~y~~iis~Pmd~~t~r~kidd~~yl~L~~m~~d~kl~~~na~~yn~~~Tv~~~aaKrL~~v~~~~~qe~~l~f~~~slg  129 (418)
T KOG1828|consen   50 PNYLEIISEPMDRITKRSKIDDTRYLVLSQMEFDRKLPDGNATLYNLHPTVPIVAAKRLCPVRLGMTQERLLSFVNTSLG  129 (418)
T ss_pred             cchHhhhhcccccccccccCCCccceechhhhhhhcccccchhhhhcCCccccccccccchhhcchhhHHHHHhhhcccc
Confidence            399999999999999999999999999999999999999999999999999999999998876655544211     00 


Q ss_pred             --cccc----------------CCC-CC-CCCCCccccccccc----C------CCCCC--CCCC-------CcchHHHH
Q psy245          223 --RQIK----------------KPN-RG-SDEGSFTTQLATSV----T------SVGDQ--GSYA-------KPKLTESL  263 (566)
Q Consensus       223 --~k~~----------------~~~-~~-~~~~~~~~~~~~~~----~------~~~~~--~~~~-------~~~~~~~~  263 (566)
                        ...+                ... .. ...+..........    +      +....  ...+       ...+..-.
T Consensus       130 ~y~~~rn~~~~v~~la~~~~sr~~~~d~~a~~s~ee~~l~v~~~e~~~~~~~~fs~k~~e~~~e~~~~lgds~g~lqtg~  209 (418)
T KOG1828|consen  130 FYEDKRNKVTPVLYLAYGPYSRYHYDDTFANISKEESDLIVSTYEEDSDLPSDFSHKFLETCQERVVTLGDSVGDLQTGG  209 (418)
T ss_pred             hhhhcccccCceeeeccCCccchhhhhhcCCCcccccccccccccccccccccccccccccCccceEehhhhhhhhcccc
Confidence              0000                000 00 00000000000000    0      00000  0000       00010001


Q ss_pred             HHHHHH-HHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          264 KYCNEI-LKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       264 k~c~~i-L~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      .+.... ...+......   ..|..++...  ..|.|--+|++++|++|++.+..++.|.| .+|..|+.||+.||++||
T Consensus       210 ~~l~~~q~~kl~~~~p~---~~lnyg~tas--~aP~YSm~Ik~~~~~~Tygdk~~andy~S-~~f~~D~kl~~l~amT~g  283 (418)
T KOG1828|consen  210 QQLQTLQEDKLNRVDPV---AYLNYGPTAS--FAPGYSMTITEVEPPGTYGDKSSANDYES-LSFTQDRKLIALKAVTNG  283 (418)
T ss_pred             HHHHHHHHHHhcccCch---hhhcccchhh--hcccccccccccCCCcchhhhhhhhhhhh-hhhhcccchhhHHHHhcC
Confidence            111121 1222222211   2355666655  47999999999999999999999999999 999999999999999999


Q ss_pred             CCCCHHHHHHHHHHH
Q psy245          343 PPDHDVVAMAKKLQD  357 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~  357 (566)
                      .+....|.+|..+..
T Consensus       284 ehsk~yyelank~lh  298 (418)
T KOG1828|consen  284 EHSKSYYELANKQLH  298 (418)
T ss_pred             CcchHHHHHHHhhhh
Confidence            999999999988876

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=99.26  E-value=3.5e-12  Score=113.27  Aligned_cols=80  Identities=26%  Similarity=0.363  Sum_probs=61.9

Q ss_pred             HHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCC-------CCCCHHHHHHHHHHHHhcc
Q psy245          266 CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAR-------EYKSSKEFADDVRLIFTNC  338 (566)
Q Consensus       266 c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~-------~Y~s~~ef~~Dv~Lif~Na  338 (566)
                      |..+|..|..+.+...+|||..||++...++||||++|++||||+||+++|..+       .|..-..+.+++..++.||
T Consensus         5 ~~~~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (114)
T cd05494           5 LERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGRR   84 (114)
T ss_pred             HHHHHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHcccccccccccccccccccccccccccc
Confidence            444444444444445889999999997779999999999999999999999987       4555566677777788888


Q ss_pred             cccCCCC
Q psy245          339 YKYNPPD  345 (566)
Q Consensus       339 ~~yN~~~  345 (566)
                      ..+|.-+
T Consensus        85 ~~~~~~~   91 (114)
T cd05494          85 SPSNIYA   91 (114)
T ss_pred             Ccccccc
Confidence            7777643

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

>KOG1827|consensus

Probab=99.16  E-value=5.7e-11  Score=130.40  Aligned_cols=151  Identities=23%  Similarity=0.246  Sum_probs=121.0

Q ss_pred             HHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccccccccCCCCCCCCCCcccccccccCCCCCCCCCCCcch
Q psy245          180 ISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKL  259 (566)
Q Consensus       180 ~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  259 (566)
                      +.|+.||..|+..||.+.+.+++.+..+.+.-......+.          +.                   ....   -.
T Consensus         3 ~~df~l~~e~~~~~~~p~s~p~k~~~~~~~~~~~~k~~~~----------~~-------------------d~p~---i~   50 (629)
T KOG1827|consen    3 VADFPLMTENACSDNEPDSLPGKDAKNLQKTPLHDKTLMG----------RD-------------------DSPV---ID   50 (629)
T ss_pred             hhhhhHHhhccccccCCccccccCcchhhhchhhhhcccC----------CC-------------------Cccc---cC
Confidence            5799999999999999999999999998886544330000          00                   0000   01


Q ss_pred             HHHHHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHh
Q psy245          260 TESLKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFT  336 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~  336 (566)
                      ...+.++..+|..++.+.+   ..+...|.+..+..  ..|+||.+|.+||+|..|++|+..+.|.+.+.|..|+.|||.
T Consensus        51 ~~~~~~f~~il~~~~~~~d~~gk~~~d~feklp~~~--~~p~yy~~i~~pisl~~ik~kv~k~~y~~~~~f~~D~~lm~e  128 (629)
T KOG1827|consen   51 PPLIPKFKTILASLLDLKDDEGKQLFDKFEKLPSRK--EFPEYYYVIQQPISLDQIKRKVKKGRYKRLSFFQLDFLLMTE  128 (629)
T ss_pred             hHHHHHHHHHHHHHHhhccccCcccchhHhhccccc--cCCCcceeecCcccHHHHHHHHHhcccccHHHHHHHHHHHHH
Confidence            2334455666666666554   45777899988887  689999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHH
Q psy245          337 NCYKYNPPDHDVVAMAKKLQDVFETKIA  364 (566)
Q Consensus       337 Na~~yN~~~s~v~~~A~~L~~~fe~~~~  364 (566)
                      ||+.||..++.+|.++..|+..|..+..
T Consensus       129 na~~~n~~ds~~~~~s~~l~~~~~~~~~  156 (629)
T KOG1827|consen  129 NARLYNRPDSLIYKDSGELEKYFISLED  156 (629)
T ss_pred             HHHHhcCcchhhhhhhhhhhcchhhhhc
Confidence            9999999999999999999999998664

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=99.14  E-value=3.9e-11  Score=106.54  Aligned_cols=79  Identities=25%  Similarity=0.319  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      .+..++ .+++.++.|+.+|||..||+....++|                                     |||++|++|
T Consensus         4 ~~~~~l-~~l~~~~~~~~~~pF~~PVd~~~~~~p-------------------------------------dY~~iIK~P   45 (114)
T cd05494           4 ALERVL-RELKRHRRNEDAWPFLEPVNPPRRGAP-------------------------------------DYRDVIKRP   45 (114)
T ss_pred             HHHHHH-HHHHHhhhCCCCCCcCCCCCchhcCCC-------------------------------------ChhhhcCCC
Confidence            344444 477888888899999999998777788                                     999999999


Q ss_pred             CCHHHHHHHhhccCC-------CCHHHHHHHHHHhhhhccccCC
Q psy245          159 MDLGTIKKRLENFYY-------WSGKEAISDFNTMFTNCYVYNK  195 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y-------~s~~ef~~Dv~lif~N~~~yN~  195 (566)
                      |||+||+++|.++.+       ..-....+++..++.||..+|.
T Consensus        46 MDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (114)
T cd05494          46 MSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGRRSPSNI   89 (114)
T ss_pred             CChHHHHHHHHccccccccccccccccccccccccccccCcccc
Confidence            999999999999744       3333445556666666666654

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

>KOG0386|consensus

Probab=99.09  E-value=1.9e-10  Score=129.83  Aligned_cols=106  Identities=28%  Similarity=0.348  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCH
Q psy245           82 FISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDL  161 (566)
Q Consensus        82 ~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL  161 (566)
                      ..+..|+....+|.++                                 .+|.+++.|.++|++..|||||.+|+.||++
T Consensus      1027 ~~~~~i~~~~~~~~~~---------------------------------~~r~~~~~~~~~~s~k~~~d~~~~i~~~~~~ 1073 (1157)
T KOG0386|consen 1027 KQALKIASTSIKYKDS---------------------------------AGRELSEVFLKLPSRKEYPDYYEIIKKPVAI 1073 (1157)
T ss_pred             HHHHHHHHHHHhcccc---------------------------------cccccchhcccCcccccccchHHHhcchhhH
Confidence            4566788888888775                                 1567889999999999999999999999999


Q ss_pred             HHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          162 GTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       162 ~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ..|.++|.++.|.+..+...||.++|.|+++||..+|.+|.+|..|..+|......+..
T Consensus      1074 ~~~~~~i~~~~~~~~~~~~~~~~~~~~na~~~~~egs~~y~d~~~l~~~~~~~~~~~~~ 1132 (1157)
T KOG0386|consen 1074 DKIKKRIENHKYNSLKELEKDFMLLFNNARTYNEEGSRVYEDAIVLQSVFKSARQEISK 1132 (1157)
T ss_pred             HHHhhhccccccchHHHHHHHHHhhcchhhhhccCCceechhHHHHHHHHhhhHHHHhc
Confidence            99999999999999999999999999999999999999999999999999988888765

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=98.94  E-value=4.4e-10  Score=98.84  Aligned_cols=41  Identities=22%  Similarity=0.395  Sum_probs=39.4

Q ss_pred             CCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCC
Q psy245          305 KPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPD  345 (566)
Q Consensus       305 ~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~  345 (566)
                      .||||+||++||.+|.|.++.+|.+||+|||+||+.||.++
T Consensus        63 y~MDL~tIe~RL~ng~Y~tp~~F~~DiklI~~Nc~~ynd~d  103 (119)
T cd05491          63 YNMDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKTIGDRE  103 (119)
T ss_pred             eccCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCHH
Confidence            68999999999999999999999999999999999999864

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.

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=98.92  E-value=1.1e-09  Score=96.31  Aligned_cols=40  Identities=30%  Similarity=0.409  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCC
Q psy245          157 HPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKP  196 (566)
Q Consensus       157 ~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~  196 (566)
                      .||||+||++||.+|+|.++.+|++||+|||.||+.||.+
T Consensus        63 y~MDL~tIe~RL~ng~Y~tp~~F~~DiklI~~Nc~~ynd~  102 (119)
T cd05491          63 YNMDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKTIGDR  102 (119)
T ss_pred             eccCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCH
Confidence            5899999999999999999999999999999999999975

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

Probab=98.82  E-value=4.7e-09  Score=121.86  Aligned_cols=105  Identities=31%  Similarity=0.492  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      ...+.++.++..+....-.   ..|..|||..  ++|||+++|++||||.|++.++.+|.|.++++|.+|+.||..||+.
T Consensus       565 p~~kLl~~~l~~lq~kD~~---gif~~pvd~~--e~pdy~~iik~pmd~~t~~~kl~s~~y~tle~ieed~~l~~~nc~~  639 (1051)
T KOG0955|consen  565 PFKKLLQKSLDKLQKKDSY---GIFAEPVDPS--ELPDYIDIIKKPMDFFTMRLKLESGAYSTLEPIEEDVNLIVSNCME  639 (1051)
T ss_pred             hHHHHHHHHHHHhhccccc---CceeeccChh--hcccHHHHhcCccchhhhhhhccccchhhhhHHHHhHhHhHhHHHH
Confidence            3455666777777665532   3799999998  6899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHcCCCCC
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAKAPDDV  370 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~  370 (566)
                      ||..+..+|..|..+++.-...+.+++.+.
T Consensus       640 yn~~dtv~~r~av~~~e~~~~~~~~arke~  669 (1051)
T KOG0955|consen  640 YNAKDTVYYRAAVRLRELIKKDFRNARKEP  669 (1051)
T ss_pred             hhccCeehHhhhHHHHhhhhhHHHhcccch
Confidence            999999999999999999999998876654

>KOG0386|consensus

Probab=98.72  E-value=1.6e-08  Score=114.77  Aligned_cols=102  Identities=30%  Similarity=0.408  Sum_probs=91.9

Q ss_pred             HHHHHHHHHHHhccCC---CCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          264 KYCNEILKELFSKKHS---SYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       264 k~c~~iL~~l~~~~~~---~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      +.|..|+.....+.+.   ..+..|...+...  .+||||+||+.||++..|.+++..+.|.+..+...||.++|.||+.
T Consensus      1027 ~~~~~i~~~~~~~~~~~~r~~~~~~~~~~s~k--~~~d~~~~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~na~~ 1104 (1157)
T KOG0386|consen 1027 KQALKIASTSIKYKDSAGRELSEVFLKLPSRK--EYPDYYEIIKKPVAIDKIKKRIENHKYNSLKELEKDFMLLFNNART 1104 (1157)
T ss_pred             HHHHHHHHHHHhcccccccccchhcccCcccc--cccchHHHhcchhhHHHHhhhccccccchHHHHHHHHHhhcchhhh
Confidence            5588888877766653   4567899888887  5899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      ||..||.||.+|..|+.+|......+.
T Consensus      1105 ~~~egs~~y~d~~~l~~~~~~~~~~~~ 1131 (1157)
T KOG0386|consen 1105 YNEEGSRVYEDAIVLQSVFKSARQEIS 1131 (1157)
T ss_pred             hccCCceechhHHHHHHHHhhhHHHHh
Confidence            999999999999999999999887764

>KOG0955|consensus

Probab=98.72  E-value=1.3e-08  Score=118.34  Aligned_cols=106  Identities=28%  Similarity=0.395  Sum_probs=95.6

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           76 NTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        76 ~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      +.+..+.++..+++.|.+.+....|..|||...  +|                                     ||.++|
T Consensus       562 ~l~p~~kLl~~~l~~lq~kD~~gif~~pvd~~e--~p-------------------------------------dy~~ii  602 (1051)
T KOG0955|consen  562 GLNPFKKLLQKSLDKLQKKDSYGIFAEPVDPSE--LP-------------------------------------DYIDII  602 (1051)
T ss_pred             cCchHHHHHHHHHHHhhcccccCceeeccChhh--cc-------------------------------------cHHHHh
Confidence            455677788888899999998889999999644  45                                     999999


Q ss_pred             CCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          156 KHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       156 k~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ++||||.||..++.+|.|.++++|..|+.+|+.||+.||..+..+|+.|..+++.....+...+.
T Consensus       603 k~pmd~~t~~~kl~s~~y~tle~ieed~~l~~~nc~~yn~~dtv~~r~av~~~e~~~~~~~~ark  667 (1051)
T KOG0955|consen  603 KKPMDFFTMRLKLESGAYSTLEPIEEDVNLIVSNCMEYNAKDTVYYRAAVRLRELIKKDFRNARK  667 (1051)
T ss_pred             cCccchhhhhhhccccchhhhhHHHHhHhHhHhHHHHhhccCeehHhhhHHHHhhhhhHHHhccc
Confidence            99999999999999999999999999999999999999999999999999999998888877654

>KOG1828|consensus

Probab=97.70  E-value=1.5e-05  Score=82.62  Aligned_cols=73  Identities=14%  Similarity=0.053  Sum_probs=65.8

Q ss_pred             hhhhccccccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHH
Q psy245          136 LAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK  209 (566)
Q Consensus       136 ~~~f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~  209 (566)
                      .+||.-.|.....|.|..+|++|++..|++.+..++.|.| -+|..|+.+|+.||++||+++..+|..|+.+..
T Consensus       226 ~~~lnyg~tas~aP~YSm~Ik~~~~~~Tygdk~~andy~S-~~f~~D~kl~~l~amT~gehsk~yyelank~lh  298 (418)
T KOG1828|consen  226 VAYLNYGPTASFAPGYSMTITEVEPPGTYGDKSSANDYES-LSFTQDRKLIALKAVTNGEHSKSYYELANKQLH  298 (418)
T ss_pred             hhhhcccchhhhcccccccccccCCCcchhhhhhhhhhhh-hhhhcccchhhHHHHhcCCcchHHHHHHHhhhh
Confidence            3455556666777899999999999999999999999999 899999999999999999999999999988876

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

Probab=95.98  E-value=0.009  Score=54.09  Aligned_cols=66  Identities=20%  Similarity=0.262  Sum_probs=57.8

Q ss_pred             CCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCCC
Q psy245          306 PMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVP  371 (566)
Q Consensus       306 PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~~  371 (566)
                      |.||..|++||+.|.|.++.+|..||-.|+.-++.-.+...++-+....+.-+|-+++.++..+..
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~vf~Wf~  124 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFN  124 (131)
T ss_pred             cccHHHHHHHHhccceehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHhccccc
Confidence            889999999999999999999999999999988887776666666677788889999988887764

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.

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

Probab=94.94  E-value=0.028  Score=50.95  Aligned_cols=61  Identities=16%  Similarity=0.252  Sum_probs=45.9

Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhh
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSAR  218 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~  218 (566)
                      |-||..|++|+..|.|.++.+|.+||-.|++-++.=.+....+-+.-..+..+|.+.+..+
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~v  119 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESV  119 (131)
T ss_pred             cccHHHHHHHHhccceehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHh
Confidence            7899999999999999999999999999998777554433334443444555666666554

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.

>KOG0732|consensus

Probab=92.07  E-value=0.19  Score=59.66  Aligned_cols=50  Identities=16%  Similarity=0.106  Sum_probs=47.7

Q ss_pred             CCcccccCCCCCCHHHHHHHhhccCCCCHHHHHH--HHHHhhhhccccCCCC
Q psy245          148 LQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAIS--DFNTMFTNCYVYNKPG  197 (566)
Q Consensus       148 ~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~--Dv~lif~N~~~yN~~~  197 (566)
                      +++|..+|+++||+...-.++..+.|.++.+|..  ++.|||.|++.||+..
T Consensus       550 ~~~~~~~iq~~~~va~~~~k~~e~~~~~v~~~e~~~~i~lic~~~lli~~~~  601 (1080)
T KOG0732|consen  550 FQDALEDIQGLMDVASSMAKIEEHLKLLVRSFESNFAIRLICRPRLLINGGK  601 (1080)
T ss_pred             hHHHHHHhhcchhHHhhhhhHHHHhHHHHHhhhcccchhhhcCcHHhcCCCc
Confidence            5599999999999999999999999999999999  9999999999999865

>KOG0644|consensus

Probab=89.32  E-value=0.31  Score=55.80  Aligned_cols=61  Identities=26%  Similarity=0.404  Sum_probs=52.8

Q ss_pred             CCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHh
Q psy245          155 IKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       155 Ik~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~  215 (566)
                      ..-|..+..|..||++.+|++.+.|..|+-.|..||.+|.+.+..+...+..|...|...+
T Consensus      1050 fpvpls~evi~~rlEn~yYrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~Tl 1110 (1113)
T KOG0644|consen 1050 FPVPLSLEVIRSRLENNYYRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRTL 1110 (1113)
T ss_pred             CCCcccHHHHHHHHHhhhhhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhhhc
Confidence            4568899999999999999999999999999999999999988777766777777666544

>KOG0644|consensus

Probab=87.44  E-value=0.42  Score=54.85  Aligned_cols=61  Identities=16%  Similarity=0.403  Sum_probs=52.9

Q ss_pred             ccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHH
Q psy245          303 IKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI  363 (566)
Q Consensus       303 Ik~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~  363 (566)
                      -.-|..|..|+.+|++..|++.+.|..||..|.+||.+|.+-+..+-..+..|..+|..-+
T Consensus      1050 fpvpls~evi~~rlEn~yYrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~Tl 1110 (1113)
T KOG0644|consen 1050 FPVPLSLEVIRSRLENNYYRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRTL 1110 (1113)
T ss_pred             CCCcccHHHHHHHHHhhhhhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhhhc
Confidence            3568999999999999999999999999999999999999988877777777777776543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	566
3oni_A	114	Crystal Structure Of The Second Bromodomain Of Huma		4e-46
2dvv_A	112	Crystal Structure Of The Second Bromodomain Of The		6e-45
2g4a_A	116	Solution Structure Of A Bromodomain From Ring3 Prot		8e-45
2oo1_A	113	Crystal Structure Of The Bromo Domain 2 Of Human Br		2e-43
2ouo_A	130	Crystal Structure Of The Bromo Domain 2 In Human Br		4e-43
2lsp_B	128	Solution Structures Of Brd4 Second Bromodomain With		5e-43
3jvl_A	120	Crystal Structure Of Bromodomain 2 Of Mouse Brd4 Le		6e-43
2e7n_A	117	Solution Structure Of The Second Bromodomain From H		1e-42
2wp1_A	126	Structure Of Brdt Bromodomain 2 Bound To An Acetyla		2e-42
2i8n_A	114	Solution Structure Of The Second Bromodomain Of Brd		2e-40
2dww_A	114	Crystal Structure Of Bromodomain-Containing Protein		1e-39
2nxb_A	123	Crystal Structure Of Human Bromodomain Containing P		4e-37
2nxb_A	123	Crystal Structure Of Human Bromodomain Containing P		9e-23
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		5e-37
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		9e-23
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		6e-37
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		1e-22
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		3e-36
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		9e-23
2ydw_A	153	Crystal Structure Of The First Bromodomain Of Human		3e-36
2ydw_A	153	Crystal Structure Of The First Bromodomain Of Human		9e-23
2oss_A	127	Crystal Structure Of The Bromo Domain 1 In Human Br		5e-36
2oss_A	127	Crystal Structure Of The Bromo Domain 1 In Human Br		1e-19
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		5e-36
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		1e-19
3jvj_A	131	Crystal Structure Of The Bromodomain 1 In Mouse Brd		5e-36
3jvj_A	131	Crystal Structure Of The Bromodomain 1 In Mouse Brd		1e-19
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		6e-36
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		2e-19
3aqa_A	128	Crystal Structure Of The Human Brd2 Bd1 Bromodomain		4e-33
3aqa_A	128	Crystal Structure Of The Human Brd2 Bd1 Bromodomain		9e-21
1x0j_A	122	Crystal Structure Analysis Of The N-Terminal Bromod		5e-33
1x0j_A	122	Crystal Structure Analysis Of The N-Terminal Bromod		2e-20
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		5e-32
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		1e-20
2wp2_A	120	Structure Of Brdt Bromodomain Bd1 Bound To A Diacet		7e-32
2wp2_A	120	Structure Of Brdt Bromodomain Bd1 Bound To A Diacet		1e-18
2jns_A	90	Solution Structure Of The Bromodomain-Containing Pr		5e-31
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		6e-16
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		2e-09
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		7e-16
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		3e-09
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		8e-16
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		3e-09
3dwy_A	119	Crystal Structure Of The Bromodomain Of Human Crebb		9e-14
1jsp_B	121	Nmr Structure Of Cbp Bromodomain In Complex With P5		1e-13
3i3j_A	124	Crystal Structure Of The Bromodomain Of Human Ep300		1e-13
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		2e-12
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		6e-12
1e6i_A	121	Bromodomain From Gcn5 Complexed With Acetylated H4		2e-12
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		2e-12
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		3e-12
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		6e-12
3g0l_A	117	Crystal Structure Of Human Bromodomain Adjacent To		5e-12
2e7o_A	112	Solution Structure Of The Bromodomain From Human Br		3e-11
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		4e-11
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		6e-11
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		7e-11
1f68_A	103	Nmr Solution Structure Of The Bromodomain From Huma		8e-11
3d7c_A	112	Crystal Structure Of The Bromodomain Of Human Gcn5,		9e-11
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		2e-10
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		2e-10
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		3e-10
3nxb_A	116	Crystal Structure Of The Bromodomain Of Human Cecr2		3e-10
2yyn_A	135	Crystal Sturcture Of Human Bromodomain Protein Leng		6e-10
3o33_A	184	Crystal Structure Of Trim24 Phd-Bromo In The Free S		1e-09
2f6j_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		1e-09
3uv4_A	158	Crystal Structure Of The Second Bromodomain Of Huma		2e-09
3hmh_A	155	Crystal Structure Of The Second Bromodomain Of Huma		9e-09
3lxj_A	136	Crystal Structure Of The Bromodomain Of Human Aaa D		3e-08
3hme_A	123	Crystal Structure Of Human Bromodomain Containing 9		6e-08
3fkm_X	166	Plasmodium Falciparum Bromodomain-Containing Protei		2e-07
2dkw_A	131	Solution Structure Of The Bromodomain Of Human Prot		4e-07
3u5m_A	207	Crystal Structure Of Trim33 Phd-Bromo In The Free S		9e-07
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		1e-06
2ktb_B	121	Solution Structure Of The Second Bromodomain Of Hum		2e-06
2ktb_B	121	Solution Structure Of The Second Bromodomain Of Hum		2e-05
3hmf_A	116	Crystal Structure Of The Second Bromodomain Of Huma		2e-06
3hmf_A	116	Crystal Structure Of The Second Bromodomain Of Huma		2e-05
3ljw_A	120	Crystal Structure Of The Second Bromodomain Of Huma		2e-06
3ljw_A	120	Crystal Structure Of The Second Bromodomain Of Huma		2e-05
2d9e_A	121	Solution Structure Of The Bromodomain Of Peregrin L		4e-06
3dai_A	130	Crystal Structure Of The Bromodomain Of The Human A		6e-06
3tlp_A	150	Crystal Structure Of The Fourth Bromodomain Of Huma		8e-06
2i7k_A	117	Solution Structure Of The Bromodomain Of Human Brd7		1e-05
2i7k_A	117	Solution Structure Of The Bromodomain Of Human Brd7		3e-05
3k2j_A	130	Crystal Structure Of The 3rd Bromodomain Of Human P		7e-05
2r0v_A	346	Structure Of The Rsc4 Tandem Bromodomain Acetylated		3e-04
2r10_A	361	Structure Of An Acetylated Rsc4 Tandem Bromodomain		4e-04

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

Iteration: 1
 Score =  182 bits (462), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 82/111 (73%), Positives = 98/111 (88%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           KL+E LK+CN ILKEL SKKH++YAWPFYKPVDA+ LGL+DYH+IIK PMDL TVK KM+
Sbjct: 4   KLSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKME 63
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
            R+Y+ ++EFA DVRL+F+NCYKYNPPDHDVVAMA+KLQDVFE + AK PD
Sbjct: 64  NRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 114

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

Iteration: 1
 Score =  178 bits (452), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 80/108 (74%), Positives = 95/108 (87%)
Query: 261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDARE 320
           E LK+CN ILKEL SKKH++YAWPFYKPVDA+ LGL+DYH+IIK PMDL TVK KM+ R+
Sbjct: 5   EQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD 64
Query: 321 YKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
           Y+ ++EFA DVRL+F+NCYKYNPPDHDVVAMA+KLQDVFE + AK PD
Sbjct: 65  YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 112

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

Iteration: 1
 Score =  178 bits (451), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 80/108 (74%), Positives = 95/108 (87%)
Query: 261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDARE 320
           E LK+CN ILKEL SKKH++YAWPFYKPVDA+ LGL+DYH+IIK PMDL TVK KM+ R+
Sbjct: 1   EQLKHCNVILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRD 60
Query: 321 YKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
           Y+ ++EFA DVRL+F+NCYKYNPPDHDVVAMA+KLQDVFE + AK PD
Sbjct: 61  YRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 108

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

Iteration: 1
 Score =  173 bits (439), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 77/110 (70%), Positives = 93/110 (84%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           KL+E L+YC+ IL+E+ SKKH++YAWPFYKPVDA  L L+DYH+IIK PMDL TVK KMD
Sbjct: 4   KLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMD 63
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP 367
            REY  ++ FA DVRL+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK P
Sbjct: 64  GREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMP 113

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

Iteration: 1
 Score =  172 bits (437), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 78/130 (60%), Positives = 103/130 (79%), Gaps = 4/130 (3%)
Query: 244 SVTSVGDQGSYAKP----KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDY 299
           S+  V D   +  P    K++E LK C+ ILKE+F+KKH++YAWPFYKPVD   LGL+DY
Sbjct: 1   SMKDVPDSQQHPAPEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDY 60
Query: 300 HEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVF 359
            +IIK PMD+ T+K+K++AREY+ ++EF  DVRL+F+NCYKYNPPDH+VVAMA+KLQDVF
Sbjct: 61  CDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 120
Query: 360 ETKIAKAPDD 369
           E + AK PD+
Sbjct: 121 EMRFAKMPDE 130

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

Iteration: 1
 Score =  172 bits (436), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 74/112 (66%), Positives = 97/112 (86%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           K++E LK C+ ILKE+F+KKH++YAWPFYKPVD   LGL+DY +IIK PMD+ T+K+K++
Sbjct: 17  KVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLE 76
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           AREY+ ++EF  DVRL+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK PD+
Sbjct: 77  AREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE 128

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

Iteration: 1
 Score =  172 bits (435), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 76/121 (62%), Positives = 100/121 (82%), Gaps = 4/121 (3%)
Query: 249 GDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMD 308
           G  GS    K++E LK C+ ILKE+F+KKH++YAWPFYKPVD   LGL+DY +IIK PMD
Sbjct: 1   GAMGS----KISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMD 56
Query: 309 LGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
           + T+K+K+++REY+ ++EF  DVRL+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK PD
Sbjct: 57  MSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD 116
Query: 369 D 369
           +
Sbjct: 117 E 117

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

Iteration: 1
 Score =  171 bits (433), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 76/108 (70%), Positives = 92/108 (85%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           KL+E L+YC+ IL+E+ SKKH++YAWPFYKPVDA  L L+DYH+IIK PMDL TVK KMD
Sbjct: 9   KLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMD 68
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
            REY  ++ FA DVRL+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK
Sbjct: 69  GREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAK 116

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

Iteration: 1
 Score =  170 bits (431), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 78/117 (66%), Positives = 96/117 (82%), Gaps = 1/117 (0%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           K+TE LK+C+EILKE+ +KKH  YAWPFY PVDA  LGL++Y++++K PMDLGT+K KMD
Sbjct: 11  KVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMD 70
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVS 374
            +EYK + EFA DVRL+F NCYKYNPPDH+VVAMA+ LQDVFE   AK PD+ PI S
Sbjct: 71  NQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVFELHFAKIPDE-PIES 126

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

Iteration: 1
 Score =  163 bits (413), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 71/105 (67%), Positives = 91/105 (86%)
Query: 261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDARE 320
           E LK C+ ILKE+F+KKH++YAWPFYKPVD   LGL+DY +IIK PMD+ T+K+K++ARE
Sbjct: 1   EQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE 60
Query: 321 YKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
           Y+ ++EF  DVRL+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK
Sbjct: 61  YRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAK 105

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

Iteration: 1
 Score =  161 bits (407), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 71/111 (63%), Positives = 91/111 (81%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           K++E LK C+ ILKE F+KKH++YAWPFYKPVD   LGL+DY +IIK P D  T+K+K++
Sbjct: 4   KISEQLKCCSGILKEXFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPXDXSTIKSKLE 63
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
           +REY+ ++EF  DVRL F+NCYKYNPPDH+VVA A+KLQDVFE + AK PD
Sbjct: 64  SREYRDAQEFGADVRLXFSNCYKYNPPDHEVVAXARKLQDVFEXRFAKXPD 114

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

Iteration: 1
 Score =  152 bits (385), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 74/143 (51%), Positives = 89/143 (62%), Gaps = 37/143 (25%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL ++   V+K + KHQ AWPF+QPVDAI LNLP                     
Sbjct: 12  GRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLP--------------------- 50
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DYHK+IK+PMD+GTIKKRLEN YYWS  E + DFNTMFTNCY+Y
Sbjct: 51  ----------------DYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIY 94
Query: 194 NKPGEDVVVMAQTLEKLFLTKVS 216
           NKP +D+V+MAQ LEK+FL KV+
Sbjct: 95  NKPTDDIVLMAQALEKIFLQKVA 117

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

Iteration: 1
 Score =  105 bits (261), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/111 (46%), Positives = 73/111 (65%), Gaps = 4/111 (3%)
Query: 260 TESLKYC-NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA 318
           T  L+Y  N ++K L+  KH  +AWPFY+PVDA  L L DYH+IIK PMD+GT+K +++ 
Sbjct: 15  TNQLQYMQNVVVKTLW--KHQ-FAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLEN 71
Query: 319 REYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
             Y S+ E   D   +FTNCY YN P  D+V MA+ L+ +F  K+A+ P +
Sbjct: 72  NYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQE 122

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

Iteration: 1
 Score =  152 bits (384), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 74/143 (51%), Positives = 89/143 (62%), Gaps = 37/143 (25%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL ++   V+K + KHQ AWPF+QPVDAI LNLP                     
Sbjct: 14  GRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLP--------------------- 52
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DYHK+IK+PMD+GTIKKRLEN YYWS  E + DFNTMFTNCY+Y
Sbjct: 53  ----------------DYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIY 96
Query: 194 NKPGEDVVVMAQTLEKLFLTKVS 216
           NKP +D+V+MAQ LEK+FL KV+
Sbjct: 97  NKPTDDIVLMAQALEKIFLQKVA 119

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

Iteration: 1
 Score =  105 bits (261), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/111 (46%), Positives = 73/111 (65%), Gaps = 4/111 (3%)
Query: 260 TESLKYC-NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA 318
           T  L+Y  N ++K L+  KH  +AWPFY+PVDA  L L DYH+IIK PMD+GT+K +++ 
Sbjct: 17  TNQLQYMQNVVVKTLW--KHQ-FAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLEN 73
Query: 319 REYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
             Y S+ E   D   +FTNCY YN P  D+V MA+ L+ +F  K+A+ P +
Sbjct: 74  NYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQE 124

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

Iteration: 1
 Score =  152 bits (383), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 74/143 (51%), Positives = 89/143 (62%), Gaps = 37/143 (25%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL ++   V+K + KHQ AWPF+QPVDAI LNLP                     
Sbjct: 16  GRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLP--------------------- 54
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DYHK+IK+PMD+GTIKKRLEN YYWS  E + DFNTMFTNCY+Y
Sbjct: 55  ----------------DYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIY 98
Query: 194 NKPGEDVVVMAQTLEKLFLTKVS 216
           NKP +D+V+MAQ LEK+FL KV+
Sbjct: 99  NKPTDDIVLMAQALEKIFLQKVA 121

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

Iteration: 1
 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 52/111 (46%), Positives = 73/111 (65%), Gaps = 4/111 (3%)
Query: 260 TESLKYC-NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA 318
           T  L+Y  N ++K L+  KH  +AWPFY+PVDA  L L DYH+IIK PMD+GT+K +++ 
Sbjct: 19  TNQLQYMQNVVVKTLW--KHQ-FAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLEN 75
Query: 319 REYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
             Y S+ E   D   +FTNCY YN P  D+V MA+ L+ +F  K+A+ P +
Sbjct: 76  NYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQE 126

>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 =  150 bits (378), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/144 (50%), Positives = 89/144 (61%), Gaps = 37/144 (25%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL ++ K V+K + KHQ AWPF QPVDA+ L LP                     
Sbjct: 27  GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLP--------------------- 65
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DYHK+IK PMD+GTIK+RLEN YYW+  E + DFNTMFTNCY+Y
Sbjct: 66  ----------------DYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIY 109
Query: 194 NKPGEDVVVMAQTLEKLFLTKVSA 217
           NKP +D+V+MAQTLEK+FL KV++
Sbjct: 110 NKPTDDIVLMAQTLEKIFLQKVAS 133

>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 =  105 bits (261), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 47/112 (41%), Positives = 73/112 (65%), Gaps = 2/112 (1%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           ++T  L+Y ++++ +   K    +AWPF +PVDA  LGL DYH+IIK+PMD+GT+K +++
Sbjct: 28  RVTNQLQYLHKVVMKALWK--HQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLE 85
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
              Y ++ E   D   +FTNCY YN P  D+V MA+ L+ +F  K+A  P +
Sbjct: 86  NNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQE 137

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

Iteration: 1
 Score =  149 bits (377), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/144 (50%), Positives = 89/144 (61%), Gaps = 37/144 (25%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL ++ K V+K + KHQ AWPF QPVDA+ L LP                     
Sbjct: 27  GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLP--------------------- 65
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DYHK+IK PMD+GTIK+RLEN YYW+  E + DFNTMFTNCY+Y
Sbjct: 66  ----------------DYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIY 109
Query: 194 NKPGEDVVVMAQTLEKLFLTKVSA 217
           NKP +D+V+MAQTLEK+FL KV++
Sbjct: 110 NKPTDDIVLMAQTLEKIFLQKVAS 133

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

Iteration: 1
 Score =  105 bits (261), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 47/112 (41%), Positives = 73/112 (65%), Gaps = 2/112 (1%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           ++T  L+Y ++++ +   K    +AWPF +PVDA  LGL DYH+IIK+PMD+GT+K +++
Sbjct: 28  RVTNQLQYLHKVVMKALWK--HQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLE 85
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
              Y ++ E   D   +FTNCY YN P  D+V MA+ L+ +F  K+A  P +
Sbjct: 86  NNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQE 137

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

Iteration: 1
 Score =  149 bits (375), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 72/142 (50%), Positives = 89/142 (62%), Gaps = 37/142 (26%)
Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
           R TNQL ++ + VLK + KHQ AWPF QPVDA+ LNLP                      
Sbjct: 17  RQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLP---------------------- 54
Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                          DY+K+IK PMD+GTIKKRLEN YYW+ +E I DFNTMFTNCY+YN
Sbjct: 55  ---------------DYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYN 99
Query: 195 KPGEDVVVMAQTLEKLFLTKVS 216
           KPG+D+V+MA+ LEKLFL K++
Sbjct: 100 KPGDDIVLMAEALEKLFLQKIN 121

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/101 (45%), Positives = 67/101 (66%), Gaps = 3/101 (2%)
Query: 269 ILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFA 328
           +LK L+  KH  +AWPF +PVDA  L L DY++IIK PMD+GT+K +++   Y +++E  
Sbjct: 29  VLKTLW--KHQ-FAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECI 85
Query: 329 DDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
            D   +FTNCY YN P  D+V MA+ L+ +F  KI + P +
Sbjct: 86  QDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTE 126

>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 =  149 bits (375), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 72/142 (50%), Positives = 89/142 (62%), Gaps = 37/142 (26%)
Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
           R TNQL ++ + VLK + KHQ AWPF QPVDA+ LNLP                      
Sbjct: 37  RQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLP---------------------- 74
Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                          DY+K+IK PMD+GTIKKRLEN YYW+ +E I DFNTMFTNCY+YN
Sbjct: 75  ---------------DYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYN 119
Query: 195 KPGEDVVVMAQTLEKLFLTKVS 216
           KPG+D+V+MA+ LEKLFL K++
Sbjct: 120 KPGDDIVLMAEALEKLFLQKIN 141

>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 = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 52/114 (45%), Positives = 73/114 (64%), Gaps = 5/114 (4%)
Query: 256 KPK-LTESLKYC-NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVK 313
           KPK  T  L+Y    +LK L+  KH  +AWPF +PVDA  L L DY++IIK PMD+GT+K
Sbjct: 34  KPKRQTNQLQYLLRVVLKTLW--KHQ-FAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIK 90
Query: 314 AKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP 367
            +++   Y +++E   D   +FTNCY YN P  D+V MA+ L+ +F  KI + P
Sbjct: 91  KRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELP 144

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

Iteration: 1
 Score =  149 bits (375), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 72/142 (50%), Positives = 89/142 (62%), Gaps = 37/142 (26%)
Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
           R TNQL ++ + VLK + KHQ AWPF QPVDA+ LNLP                      
Sbjct: 21  RQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLP---------------------- 58
Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                          DY+K+IK PMD+GTIKKRLEN YYW+ +E I DFNTMFTNCY+YN
Sbjct: 59  ---------------DYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYN 103
Query: 195 KPGEDVVVMAQTLEKLFLTKVS 216
           KPG+D+V+MA+ LEKLFL K++
Sbjct: 104 KPGDDIVLMAEALEKLFLQKIN 125

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 52/116 (44%), Positives = 74/116 (63%), Gaps = 5/116 (4%)
Query: 256 KPK-LTESLKYC-NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVK 313
           KPK  T  L+Y    +LK L+  KH  +AWPF +PVDA  L L DY++IIK PMD+GT+K
Sbjct: 18  KPKRQTNQLQYLLRVVLKTLW--KHQ-FAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIK 74
Query: 314 AKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
            +++   Y +++E   D   +FTNCY YN P  D+V MA+ L+ +F  KI + P +
Sbjct: 75  KRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTE 130

>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 =  149 bits (375), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 72/142 (50%), Positives = 89/142 (62%), Gaps = 37/142 (26%)
Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
           R TNQL ++ + VLK + KHQ AWPF QPVDA+ LNLP                      
Sbjct: 17  RETNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLP---------------------- 54
Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                          DY+K+IK PMD+GTIKKRLEN YYW+ +E I DFNTMFTNCY+YN
Sbjct: 55  ---------------DYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYN 99
Query: 195 KPGEDVVVMAQTLEKLFLTKVS 216
           KPG+D+V+MA+ LEKLFL K++
Sbjct: 100 KPGDDIVLMAEALEKLFLQKIN 121

>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 = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/101 (45%), Positives = 67/101 (66%), Gaps = 3/101 (2%)
Query: 269 ILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFA 328
           +LK L+  KH  +AWPF +PVDA  L L DY++IIK PMD+GT+K +++   Y +++E  
Sbjct: 29  VLKTLW--KHQ-FAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECI 85
Query: 329 DDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
            D   +FTNCY YN P  D+V MA+ L+ +F  KI + P +
Sbjct: 86  QDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTE 126

>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 =  139 bits (350), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 69/144 (47%), Positives = 83/144 (57%), Gaps = 37/144 (25%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL ++ K V K + KHQ AWPF QPVDA+ L LP                     
Sbjct: 7   GRVTNQLQYLHKVVXKALWKHQFAWPFRQPVDAVKLGLP--------------------- 45
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DYHK+IK P D GTIK+RLEN YYW+  E   DFNT FTNCY+Y
Sbjct: 46  ----------------DYHKIIKQPXDXGTIKRRLENNYYWAASECXQDFNTXFTNCYIY 89
Query: 194 NKPGEDVVVMAQTLEKLFLTKVSA 217
           NKP +D+V+ AQTLEK+FL KV++
Sbjct: 90  NKPTDDIVLXAQTLEKIFLQKVAS 113

>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 = 98.6 bits (244), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 48/121 (39%), Positives = 72/121 (59%), Gaps = 4/121 (3%)
Query: 249 GDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMD 308
           G  GS  +  +T  L+Y ++++ +   K    +AWPF +PVDA  LGL DYH+IIK+P D
Sbjct: 1   GSSGSSGR--VTNQLQYLHKVVXKALWKHQ--FAWPFRQPVDAVKLGLPDYHKIIKQPXD 56
Query: 309 LGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
            GT+K +++   Y ++ E   D    FTNCY YN P  D+V  A+ L+ +F  K+A  P 
Sbjct: 57  XGTIKRRLENNYYWAASECXQDFNTXFTNCYIYNKPTDDIVLXAQTLEKIFLQKVASXPQ 116
Query: 369 D 369
           +
Sbjct: 117 E 117

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

Iteration: 1
 Score =  139 bits (349), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 69/152 (45%), Positives = 87/152 (57%), Gaps = 37/152 (24%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL ++ K V K + KHQ AWPF QPVDA+ L LP                     
Sbjct: 1   GRVTNQLQYLHKVVXKALWKHQFAWPFRQPVDAVKLGLP--------------------- 39
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DYHK+IK P D GTIK+RLEN YYW+  E   DFNT FTNCY+Y
Sbjct: 40  ----------------DYHKIIKQPXDXGTIKRRLENNYYWAASECXQDFNTXFTNCYIY 83
Query: 194 NKPGEDVVVMAQTLEKLFLTKVSARRESGRQI 225
           NKP +D+V+ AQTLEK+FL KV++  +  +++
Sbjct: 84  NKPTDDIVLXAQTLEKIFLQKVASXPQEEQEL 115

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

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/112 (40%), Positives = 69/112 (61%), Gaps = 2/112 (1%)
Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           ++T  L+Y ++++ +   K    +AWPF +PVDA  LGL DYH+IIK+P D GT+K +++
Sbjct: 2   RVTNQLQYLHKVVXKALWK--HQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRLE 59
Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
              Y ++ E   D    FTNCY YN P  D+V  A+ L+ +F  K+A  P +
Sbjct: 60  NNYYWAASECXQDFNTXFTNCYIYNKPTDDIVLXAQTLEKIFLQKVASXPQE 111

>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 =  135 bits (341), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 68/143 (47%), Positives = 84/143 (58%), Gaps = 37/143 (25%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL ++ K VLK + KH  +WPF +PVDA+ L LP                     
Sbjct: 8   GRLTNQLQYLQKVVLKDLWKHSFSWPFQRPVDAVKLQLP--------------------- 46
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DY+ +IK+PMDL TIKKRLEN YY    E I DFNTMF+NCY+Y
Sbjct: 47  ----------------DYYTIIKNPMDLNTIKKRLENKYYAKASECIEDFNTMFSNCYLY 90
Query: 194 NKPGEDVVVMAQTLEKLFLTKVS 216
           NKPG+D+V+MAQ LEKLF+ K+S
Sbjct: 91  NKPGDDIVLMAQALEKLFMQKLS 113

>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 = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 48/113 (42%), Positives = 75/113 (66%), Gaps = 4/113 (3%)
Query: 258 KLTESLKYCNEI-LKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKM 316
           +LT  L+Y  ++ LK+L+  KHS ++WPF +PVDA  L L DY+ IIK PMDL T+K ++
Sbjct: 9   RLTNQLQYLQKVVLKDLW--KHS-FSWPFQRPVDAVKLQLPDYYTIIKNPMDLNTIKKRL 65
Query: 317 DAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           + + Y  + E  +D   +F+NCY YN P  D+V MA+ L+ +F  K+++ P +
Sbjct: 66  ENKYYAKASECIEDFNTMFSNCYLYNKPGDDIVLMAQALEKLFMQKLSQMPQE 118

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

Iteration: 1
 Score =  135 bits (339), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 69/143 (48%), Positives = 82/143 (57%), Gaps = 37/143 (25%)
Query: 74  GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
           GR TNQL F+ + VLK + KH  +WPF QPVDA+ L LP                     
Sbjct: 9   GRLTNQLQFLQRVVLKALWKHGFSWPFQQPVDAVKLKLP--------------------- 47
Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                           DY+ +IK PMDL TIKKRLEN YY    E I DFNTMF+NCY+Y
Sbjct: 48  ----------------DYYTIIKTPMDLNTIKKRLENKYYEKASECIEDFNTMFSNCYLY 91
Query: 194 NKPGEDVVVMAQTLEKLFLTKVS 216
           NK G+D+VVMAQ LEKLF+ K+S
Sbjct: 92  NKTGDDIVVMAQALEKLFMQKLS 114

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

Iteration: 1
 Score = 91.3 bits (225), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/113 (39%), Positives = 72/113 (63%), Gaps = 4/113 (3%)
Query: 258 KLTESLKYCNEI-LKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKM 316
           +LT  L++   + LK L+  KH  ++WPF +PVDA  L L DY+ IIK PMDL T+K ++
Sbjct: 10  RLTNQLQFLQRVVLKALW--KHG-FSWPFQQPVDAVKLKLPDYYTIIKTPMDLNTIKKRL 66
Query: 317 DAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           + + Y+ + E  +D   +F+NCY YN    D+V MA+ L+ +F  K+++ P +
Sbjct: 67  ENKYYEKASECIEDFNTMFSNCYLYNKTGDDIVVMAQALEKLFMQKLSQMPQE 119

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

Iteration: 1
 Score =  132 bits (332), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 65/78 (83%), Positives = 73/78 (93%), Gaps = 1/78 (1%)
Query: 488 ESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTL 547
           +  KPMSY EK++LSLDINKLPG+KLGRVVHIIQSREPSL++SNPDEIEIDFETLKPSTL
Sbjct: 13  DKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTL 72
Query: 548 RELEKYVATCLRKKPRKP 565
           RELE+YV +CLRKK RKP
Sbjct: 73  RELERYVTSCLRKK-RKP 89

>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 = 82.4 bits (202), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 100/216 (46%), Gaps = 33/216 (15%)
Query: 147 ILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQT 206
           +++DY+K+I  PMDL T+++ +    Y S +E       +  N   YN P   +  ++Q+
Sbjct: 76  VVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQS 135
Query: 207 LEKLFLTKVSARRESGRQIKKPNR----GSDEGSFTTQLATSVTSVGDQGSYAKPKLTES 262
           +  L   K+  + +   +++K         D+ +F+  L   VT    Q   A P     
Sbjct: 136 MLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVT----QKMMAVPD---- 187
Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
                              +WPF+ PV+  ++   DY+++I  PMDL T++  +   +Y+
Sbjct: 188 -------------------SWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQ 226
Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDV 358
           S + F DDV LI  N  KYN P+      A+++ +V
Sbjct: 227 SRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNV 262

>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 = 60.5 bits (145), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 51/87 (58%), Gaps = 2/87 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
            +PF+ PV+A  +   DY++II +PMDL T++  +  R Y S +EF + + LI  N   Y
Sbjct: 65  TYPFHTPVNAKVVK--DYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATY 122
Query: 342 NPPDHDVVAMAKKLQDVFETKIAKAPD 368
           N P H +  +++ + D+ + K+ +  D
Sbjct: 123 NGPKHSLTQISQSMLDLCDEKLKEKED 149

>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 = 82.0 bits (201), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 100/216 (46%), Gaps = 33/216 (15%)
Query: 147 ILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQT 206
           +++DY+K+I  PMDL T+++ +    Y S +E       +  N   YN P   +  ++Q+
Sbjct: 43  VVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQS 102
Query: 207 LEKLFLTKVSARRESGRQIKKPNR----GSDEGSFTTQLATSVTSVGDQGSYAKPKLTES 262
           +  L   K+  + +   +++K         D+ +F+  L   VT    Q   A P     
Sbjct: 103 MLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVT----QKMMAVPD---- 154
Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
                              +WPF+ PV+  ++   DY+++I  PMDL T++  +   +Y+
Sbjct: 155 -------------------SWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQ 193
Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDV 358
           S + F DDV LI  N  KYN P+      A+++ +V
Sbjct: 194 SRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNV 229

>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 = 60.1 bits (144), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 51/87 (58%), Gaps = 2/87 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
            +PF+ PV+A  +   DY++II +PMDL T++  +  R Y S +EF + + LI  N   Y
Sbjct: 32  TYPFHTPVNAKVVK--DYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATY 89
Query: 342 NPPDHDVVAMAKKLQDVFETKIAKAPD 368
           N P H +  +++ + D+ + K+ +  D
Sbjct: 90  NGPKHSLTQISQSMLDLCDEKLKEKED 116

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 100/216 (46%), Gaps = 33/216 (15%)
Query: 147 ILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQT 206
           +++DY+K+I  PMDL T+++ +    Y S +E       +  N   YN P   +  ++Q+
Sbjct: 55  VVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQS 114
Query: 207 LEKLFLTKVSARRESGRQIKKPNR----GSDEGSFTTQLATSVTSVGDQGSYAKPKLTES 262
           +  L   K+  + +   +++K         D+ +F+  L   VT    Q   A P     
Sbjct: 115 MLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVT----QKMMAVPD---- 166
Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
                              +WPF+ PV+  ++   DY+++I  PMDL T++  +   +Y+
Sbjct: 167 -------------------SWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQ 205
Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDV 358
           S + F DDV LI  N  KYN P+      A+++ +V
Sbjct: 206 SRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNV 241

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 51/87 (58%), Gaps = 2/87 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
            +PF+ PV+A  +   DY++II +PMDL T++  +  R Y S +EF + + LI  N   Y
Sbjct: 44  TYPFHTPVNAKVVK--DYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATY 101
Query: 342 NPPDHDVVAMAKKLQDVFETKIAKAPD 368
           N P H +  +++ + D+ + K+ +  D
Sbjct: 102 NGPKHSLTQISQSMLDLCDEKLKEKED 128

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 49/80 (61%)
Query: 284 PFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP 343
           PF +PVD   LG+ DY +I+K PMDL T+K K+D  +Y+   ++ DDV L+F N + YN 
Sbjct: 32  PFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNR 91
Query: 344 PDHDVVAMAKKLQDVFETKI 363
               V     KL +VFE +I
Sbjct: 92  KTSRVYKFCSKLAEVFEQEI 111

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 49/80 (61%)
Query: 284 PFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP 343
           PF +PVD   LG+ DY +I+K PMDL T+K K+D  +Y+   ++ DDV L+F N + YN 
Sbjct: 34  PFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNR 93
Query: 344 PDHDVVAMAKKLQDVFETKI 363
               V     KL +VFE +I
Sbjct: 94  KTSRVYKFCSKLAEVFEQEI 113

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

Iteration: 1
 Score = 74.7 bits (182), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/80 (42%), Positives = 49/80 (61%)
Query: 284 PFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP 343
           PF +PVD   LG+ DY +I+K PMDL T+K K+D  +Y+   ++ DD+ L+F N + YN 
Sbjct: 37  PFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNR 96
Query: 344 PDHDVVAMAKKLQDVFETKI 363
               V     KL +VFE +I
Sbjct: 97  KTSRVYKYCSKLSEVFEQEI 116

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 46/148 (31%), Positives = 67/148 (45%), Gaps = 42/148 (28%)
Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
           R+ +QL    K++L+ V  HQ AWPF +PV   +                          
Sbjct: 11  RDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTE-------------------------- 44
Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                   P       Y++VI+ PMDL T+ +RL+N YY S K  ++D   +FTNC  YN
Sbjct: 45  -------AP------GYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYN 91
Query: 195 KPGEDVVVMAQTLEKLFLTKVSARRESG 222
            P  +    A  LEK F +K+   +E+G
Sbjct: 92  PPESEYYKCANILEKFFFSKI---KEAG 116

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 37/91 (40%), Positives = 53/91 (58%), Gaps = 3/91 (3%)
Query: 276 KKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIF 335
           K H S AWPF +PV         Y+E+I+ PMDL T+  ++  R Y S K F  D++ +F
Sbjct: 28  KSHQS-AWPFMEPVKRT--EAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVF 84
Query: 336 TNCYKYNPPDHDVVAMAKKLQDVFETKIAKA 366
           TNC +YNPP+ +    A  L+  F +KI +A
Sbjct: 85  TNCKEYNPPESEYYKCANILEKFFFSKIKEA 115

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/100 (36%), Positives = 61/100 (61%), Gaps = 5/100 (5%)
Query: 269 ILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFA 328
           IL EL  + H++ AWPF +PV+   +   DY++ IK+PMDL T++ K+++ +Y+  ++F 
Sbjct: 21  ILTEL--QNHAA-AWPFLQPVNKEEVP--DYYDFIKEPMDLSTMEIKLESNKYQKMEDFI 75
Query: 329 DDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
            D RL+F NC  YN  +      A +L+  F  K+ + P+
Sbjct: 76  YDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPE 115

>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 = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 42/110 (38%), Positives = 58/110 (52%), Gaps = 6/110 (5%)
Query: 264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKS 323
           K C E++  +F  + S    PF +PVD   +   DY +II  PMD GTV+  +DA  Y S
Sbjct: 13  KQCKELVNLIFQCEDSE---PFRQPVDL--VEYPDYRDIIDTPMDFGTVRETLDAGNYDS 67
Query: 324 SKEFADDVRLIFTNCYKYNPPDHD-VVAMAKKLQDVFETKIAKAPDDVPI 372
             EF  D+RLIF+N   Y P     + +M  +L  +FE K+ K   D  I
Sbjct: 68  PLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKISSDFKI 117

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 45/148 (30%), Positives = 66/148 (44%), Gaps = 42/148 (28%)
Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
           R+ +QL    K++L+ V  HQ AWPF +PV   +                          
Sbjct: 9   RDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEA------------------------- 43
Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                           Y++VI+ PMDL T+ +RL+N YY S K  ++D   +FTNC  YN
Sbjct: 44  --------------PGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYN 89
Query: 195 KPGEDVVVMAQTLEKLFLTKVSARRESG 222
            P  +    A  LEK F +K+   +E+G
Sbjct: 90  PPESEYYKCANILEKFFFSKI---KEAG 114

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 37/91 (40%), Positives = 53/91 (58%), Gaps = 3/91 (3%)
Query: 276 KKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIF 335
           K H S AWPF +PV         Y+E+I+ PMDL T+  ++  R Y S K F  D++ +F
Sbjct: 26  KSHQS-AWPFMEPVKRT--EAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVF 82
Query: 336 TNCYKYNPPDHDVVAMAKKLQDVFETKIAKA 366
           TNC +YNPP+ +    A  L+  F +KI +A
Sbjct: 83  TNCKEYNPPESEYYKCANILEKFFFSKIKEA 113

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 42/112 (37%), Positives = 62/112 (55%), Gaps = 7/112 (6%)
Query: 253 SYAKPKLTES--LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLG 310
           S  KPK  +S  L  C+ IL E+  + H   AWPF  PV+   +    Y ++IKKPMD  
Sbjct: 3   SVKKPKRDDSKDLALCSMILTEM--ETHED-AWPFLLPVNLKLVP--GYKKVIKKPMDFS 57
Query: 311 TVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETK 362
           T++ K+ + +Y + + FA DVRL+F NC  +N  D D+      ++  FE K
Sbjct: 58  TIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKK 109

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/100 (37%), Positives = 56/100 (56%), Gaps = 5/100 (5%)
Query: 263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYK 322
           L  C+ IL E+  + H   AWPF  PV+   +    Y ++IKKPMD  T++ K+ + +Y 
Sbjct: 12  LALCSMILTEM--ETHED-AWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREKLSSGQYP 66
Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETK 362
           + + FA DVRL+F NC  +N  D D+      ++  FE K
Sbjct: 67  NLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKK 106

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 40/115 (34%), Positives = 58/115 (50%), Gaps = 5/115 (4%)
Query: 249 GDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMD 308
           G  GS   P   +  +    +L+ L + K    AWPF +PVD       DY+ +IK+PMD
Sbjct: 1   GPLGSVLTPLTEKDYEGLKRVLRSLQAHKM---AWPFLEPVDPN--DAPDYYGVIKEPMD 55
Query: 309 LGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI 363
           L T++ ++  R Y+   EF  D+  IF NC  YNP D      A+ L+  F  K+
Sbjct: 56  LATMEERVQRRYYEKLTEFVADMTAIFDNCRYYNPSDSPFYQCAEVLESFFVQKL 110

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 40/107 (37%), Positives = 55/107 (51%), Gaps = 6/107 (5%)
Query: 264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKS 323
           K C E+L  +F  + S    PF +PVD   L   DY +II  PMD  TV+  ++A  Y+S
Sbjct: 24  KQCEELLNLIFQCEDSE---PFRQPVD--LLEYPDYRDIIDTPMDFATVRETLEAGNYES 78
Query: 324 SKEFADDVRLIFTNCYKYNPPDHD-VVAMAKKLQDVFETKIAKAPDD 369
             E   DVRLIF+N   Y P     + +M+ +L   FE  I+    D
Sbjct: 79  PMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSD 125

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 40/115 (34%), Positives = 58/115 (50%), Gaps = 5/115 (4%)
Query: 249 GDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMD 308
           G  GS   P   +  +    +L+ L + K    AWPF +PVD       DY+ +IK+PMD
Sbjct: 1   GPLGSVLTPLTEKDYEGLKRVLRSLQAHKM---AWPFLEPVDPN--DAPDYYGVIKEPMD 55
Query: 309 LGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI 363
           L T++ ++  R Y+   EF  D+  IF NC  YNP D      A+ L+  F  K+
Sbjct: 56  LATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKL 110

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 55/96 (57%), Gaps = 5/96 (5%)
Query: 270 LKELFS--KKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEF 327
           LK L +  K H S AWPF +PV  +     DY+E+I+ P+DL T+  ++ +R Y + K F
Sbjct: 8   LKNLLAQIKSHPS-AWPFMEPVKKS--EAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLF 64
Query: 328 ADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI 363
             D++ +  NC +YNPPD +    A  L+  F  K+
Sbjct: 65  VADLQRVIANCREYNPPDSEYCRCASALEKFFYFKL 100

>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 = 65.1 bits (157), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 36/99 (36%), Positives = 56/99 (56%), Gaps = 5/99 (5%)
Query: 270 LKELFS--KKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEF 327
           LK L +  K H S AWPF +PV  +     DY+E+I+ P+DL T+  ++ +R Y + K F
Sbjct: 12  LKNLLAQIKSHPS-AWPFMEPVKKS--EAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLF 68
Query: 328 ADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKA 366
             D++ +  NC +YNPPD +    A  L+  F  K+ + 
Sbjct: 69  VADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEG 107

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
           AWPF +PVD       DY+ +IK+PMDL T++ ++  R Y+   EF  D+  IF NC  Y
Sbjct: 38  AWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYY 95
Query: 342 NPPDHDVVAMAKKLQDVFETKI 363
           NP D      A+ L+  F  K+
Sbjct: 96  NPSDSPFYQCAEVLESFFVQKL 117

>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 = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
           AWPF +PVD       DY+ +IK+PMDL T++ ++  R Y+   EF  D+  IF NC  Y
Sbjct: 90  AWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYY 147
Query: 342 NPPDHDVVAMAKKLQDVFETKI 363
           NP D      A+ L+  F  K+
Sbjct: 148 NPSDSPFYQCAEVLESFFVQKL 169

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
           AWPF +PVD       DY+ +IK+PMDL T++ ++  R Y+   EF  D+  IF NC  Y
Sbjct: 90  AWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYY 147
Query: 342 NPPDHDVVAMAKKLQDVFETKI 363
           NP D      A+ L+  F  K+
Sbjct: 148 NPSDSPFYQCAEVLESFFVQKL 169

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 51/84 (60%), Gaps = 2/84 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
           +WPF +PVD ++    +Y++IIK PMD+ +++ K++   Y + +EF +D++ +F NC KY
Sbjct: 34  SWPFLEPVDESYAP--NYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKY 91
Query: 342 NPPDHDVVAMAKKLQDVFETKIAK 365
           N    +   M+  L+  F   + K
Sbjct: 92  NGESSEYTKMSDNLERCFHRAMMK 115

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 44/73 (60%), Gaps = 2/73 (2%)
Query: 290 DAAWLGLNDYHEIIKKPMDLGTVKAKM--DAREYKSSKEFADDVRLIFTNCYKYNPPDHD 347
           D   L + DY++IIK PMDL T+K ++  D   Y   ++F  D RLIF NC ++N PD +
Sbjct: 43  DPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSE 102
Query: 348 VVAMAKKLQDVFE 360
           V     KL++ FE
Sbjct: 103 VANAGIKLENYFE 115

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 43/69 (62%), Gaps = 2/69 (2%)
Query: 294 LGLNDYHEIIKKPMDLGTVKAKM--DAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAM 351
           L + DY++IIK PMDL T+K ++  D   Y   ++F  D RLIF NC ++N PD +V   
Sbjct: 108 LTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANA 167
Query: 352 AKKLQDVFE 360
             KL++ FE
Sbjct: 168 GIKLENYFE 176

>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 = 61.6 bits (148), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/117 (32%), Positives = 55/117 (47%), Gaps = 5/117 (4%)
Query: 247 SVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKP 306
           S  D  +   P   +  +    +L+ L + K    AWPF +PVD       DY+ +IK+P
Sbjct: 58  STEDAXTVLTPLTEKDYEGLKRVLRSLQAHK---XAWPFLEPVDPN--DAPDYYGVIKEP 112
Query: 307 MDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI 363
            DL T + ++  R Y+   EF  D   IF NC  YNP D      A+ L+  F  K+
Sbjct: 113 XDLATXEERVQRRYYEKLTEFVADXTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKL 169

>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 = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
           +WPF+ PV+  ++   DY+++I  PMDL T++  +   +Y+S + F DDV LI  N  KY
Sbjct: 48  SWPFHHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKY 105
Query: 342 NPPDHDVVAMAKKLQDV 358
           N P+      A+++ +V
Sbjct: 106 NGPESQYTKTAQEIVNV 122

>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 = 58.5 bits (140), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 282 AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY 341
           +WPF+ PV+  ++   DY+++I  P+DL T++  +   +Y+S + F DDV LI  N  KY
Sbjct: 45  SWPFHHPVNKKFVP--DYYKMIVNPVDLETIRKNISKHKYQSRESFLDDVNLILANSVKY 102
Query: 342 NPPDHDVVAMAKKLQDV 358
           N P+      A+++ ++
Sbjct: 103 NGPESQYTKTAQEIVNI 119

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/59 (47%), Positives = 38/59 (64%), Gaps = 2/59 (3%)
Query: 285 FYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP 343
           F KPVD   +   DY E+IK+PMDL TV  K+D   Y ++K+F  D+ LI +N  +YNP
Sbjct: 33  FSKPVDIEEVS--DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 89

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 34/78 (43%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 278 HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN 337
           H  +A+P     DA   G   Y  IIK PMD GT+K K+ A EYKS  EF  D +L+  N
Sbjct: 31  HGFFAFPV---TDAIAPG---YSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDN 84
Query: 338 CYKYNPPDHDVVAMAKKL 355
              YN PD     +AKK+
Sbjct: 85  AMTYNRPDTVYYKLAKKI 102

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 39/79 (49%)
Query: 285 FYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPP 344
           F K VDA      DY+++IK P     +K K+   +Y    EF  DV+LIF NC  YN  
Sbjct: 42  FEKLVDAKKQNCPDYYDVIKNPXSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLYNTS 101
Query: 345 DHDVVAMAKKLQDVFETKI 363
           +  V    K ++  F  ++
Sbjct: 102 NSVVAITGKNIETYFNNQL 120

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 27/59 (45%), Positives = 37/59 (62%), Gaps = 7/59 (11%)
Query: 285 FYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP 343
           F KPV       +DY E+IK+PMDL TV  K+D   Y ++K+F  D+ LI +N  +YNP
Sbjct: 33  FSKPV-------SDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 84

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 32/80 (40%), Positives = 48/80 (60%), Gaps = 9/80 (11%)
Query: 266 CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD---AREYK 322
           C  +L  L+  + S     F +PV A+   + +Y++IIKKPMDL TVK K+    ++ Y+
Sbjct: 86  CERLLLYLYCHELS---IEFQEPVPAS---IPNYYKIIKKPMDLSTVKKKLQKKHSQHYQ 139
Query: 323 SSKEFADDVRLIFTNCYKYN 342
              +F  DVRLIF NC ++N
Sbjct: 140 IPDDFVADVRLIFKNCERFN 159

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/60 (41%), Positives = 36/60 (60%)
Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY + IK PMD  T++ +++A+ YK+  EF +D  LI  NC KYN  D      A +L+D
Sbjct: 45  DYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRD 104

>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 = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 37/65 (56%)
Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+ +IK P+DL TI +R++N  Y S      D + +  N   YN+PG  V   A +++K
Sbjct: 47  DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKK 106
Query: 210 LFLTK 214
           +F  K
Sbjct: 107 IFYMK 111

>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 = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 45/97 (46%), Gaps = 13/97 (13%)
Query: 269 ILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFA 328
           ++ ELF K  S   +P             DY+ IIK+P+DL T+  ++    YKS    A
Sbjct: 31  LISELFQKLPSKVQYP-------------DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMA 77
Query: 329 DDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
            D+ L+  N   YN P   V   A  ++ +F  K A+
Sbjct: 78  KDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAE 114

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 37/65 (56%)
Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+ +IK P+DL TI +R++N  Y S      D + +  N   YN+PG  V   A +++K
Sbjct: 44  DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKK 103
Query: 210 LFLTK 214
           +F  K
Sbjct: 104 IFYMK 108

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 45/97 (46%), Gaps = 13/97 (13%)
Query: 269 ILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFA 328
           ++ ELF K  S   +P             DY+ IIK+P+DL T+  ++    YKS    A
Sbjct: 28  LISELFQKLPSKVQYP-------------DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMA 74
Query: 329 DDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
            D+ L+  N   YN P   V   A  ++ +F  K A+
Sbjct: 75  KDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAE 111

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 37/65 (56%)
Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+ +IK P+DL TI +R++N  Y S      D + +  N   YN+PG  V   A +++K
Sbjct: 46  DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKK 105
Query: 210 LFLTK 214
           +F  K
Sbjct: 106 IFYMK 110

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 45/97 (46%), Gaps = 13/97 (13%)
Query: 269 ILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFA 328
           ++ ELF K  S   +P             DY+ IIK+P+DL T+  ++    YKS    A
Sbjct: 30  LISELFQKLPSKVQYP-------------DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMA 76
Query: 329 DDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
            D+ L+  N   YN P   V   A  ++ +F  K A+
Sbjct: 77  KDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAE 113

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 35/60 (58%)
Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY + IKKPMD  T+K  ++A  Y +  +F +D  LI +NC KYN  D      A +L++
Sbjct: 39  DYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLRE 98

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 38/59 (64%), Gaps = 2/59 (3%)
Query: 285 FYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNP 343
           F KPVD     + DY  +IK+PMDL +V +K+D  +Y + K++  D+ LI +N  +YNP
Sbjct: 31  FTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 87

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           DY+K+I  PMDL  I+  + N  Y   +  I D   MF N   YN+ G  V   A  LEK
Sbjct: 63  DYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEK 122
Query: 210 LFLTKVSARRESG 222
           L   K   R+E G
Sbjct: 123 LLKEK---RKELG 132

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 30/46 (65%)
Query: 151 YHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKP 196
           Y  +IKHPMD  T+K++++N  Y S +E   +F  M TN  +YNKP
Sbjct: 41  YSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKP 86

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 33/57 (57%)
Query: 299 YHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKL 355
           Y  IIK PMD  T+K K+   +Y+S +E  D+ +L+ TN   YN P+      AKKL
Sbjct: 41  YSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKL 97

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 36/65 (55%)
Query: 298 DYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQD 357
           DY++ IK P+ L  ++ K+  +EY++      D+ L+F N  +YN P+  +     KLQ 
Sbjct: 55  DYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQ 114
Query: 358 VFETK 362
           V + K
Sbjct: 115 VMQAK 119

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 49/224 (21%), Positives = 92/224 (41%), Gaps = 33/224 (14%)
Query: 151 YHKVIKHPMDLGTIKKRLENFYYWSG-KEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           Y+  I+ PM +  IK R  ++ Y  G    + D   +  NC  YN+   D +++  +++ 
Sbjct: 98  YYYKIQQPMSINEIKSR--DYEYEDGPSNFLLDVELLTKNCQAYNE--YDSLIVKNSMQV 153
Query: 210 LFLTKVSARRESGRQIKKPNRGSDEG-----SFTTQLATSVTSVGDQ---GSYAKPKLTE 261
           + L +    +   + +K+    + E       +  +L  +     +Q   G+ +   L +
Sbjct: 154 VMLIEFEVLK--AKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDD 211
Query: 262 SLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREY 321
            +K                   PF + VD   L   +Y+EI+  PM L  VK  ++  +Y
Sbjct: 212 KVKLSE----------------PFMELVDKDELP--EYYEIVHSPMALSIVKQNLEIGQY 253
Query: 322 KSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
               +F  D+ L+F N + +N P   +   A  L + F   I K
Sbjct: 254 SKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQK 297

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 52/216 (24%), Positives = 95/216 (43%), Gaps = 17/216 (7%)
Query: 151 YHKVIKHPMDLGTIKKRLENFYYWSG-KEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           Y+  I+ PM +  IK R  ++ Y  G    + D   +  NC  YN+   D +++  +++ 
Sbjct: 113 YYYKIQQPMSINEIKSR--DYEYEDGPSNFLLDVELLTKNCQAYNE--YDSLIVKNSMQV 168
Query: 210 LFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEI 269
           + L +    +   + +K+    + E     +L   +  + D     + K+ ++L   +  
Sbjct: 169 VMLIEFEVLK--AKNLKRNYLINSE--VKAKLLHYLNKLVDA---TEKKINQALLGASSP 221
Query: 270 LKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFAD 329
            K L  K   S   PF + VD   L   +Y+EI+  PM L  VK  ++  +Y    +F  
Sbjct: 222 -KNLDDKVKLS--EPFMELVDKDELP--EYYEIVHSPMALSIVKQNLEIGQYSKIYDFII 276
Query: 330 DVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
           D+ L+F N + +N P   +   A  L + F   I K
Sbjct: 277 DMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQK 312

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	566
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	7e-66
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	3e-31
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	2e-29
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	7e-65
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	2e-29
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	8e-28
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	4e-61
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	2e-37
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	5e-58
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	1e-37
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	9e-55
3p1f_A	119	CREB-binding protein; structural genomics consorti	5e-51
3p1f_A	119	CREB-binding protein; structural genomics consorti	2e-33
2r10_A	361	Chromatin structure-remodeling complex protein RSC	3e-50
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	6e-49
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	1e-35
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	7e-48
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	3e-30
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	4e-47
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	2e-46
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	8e-47
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	3e-41
4alg_A	154	Bromodomain-containing protein 2; signaling protei	5e-46
4alg_A	154	Bromodomain-containing protein 2; signaling protei	2e-45
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	5e-46
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	8e-30
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	3e-45
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	2e-39
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	1e-44
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	1e-34
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	6e-43
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	3e-36
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	1e-41
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	4e-32
3d7c_A	112	General control of amino acid synthesis protein 5;	4e-41
3d7c_A	112	General control of amino acid synthesis protein 5;	7e-40
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	3e-40
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	2e-38
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	9e-40
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	1e-28
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	2e-39
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	3e-32
3uv4_A	158	Second bromodomain of human transcription initiat	4e-39
3uv4_A	158	Second bromodomain of human transcription initiat	1e-34
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	3e-38
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	3e-30
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	3e-38
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	5e-33
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	5e-38
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	8e-31
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	6e-38
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	5e-26
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	8e-37
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-27
2dat_A	123	Possible global transcription activator SNF2L2; br	2e-35
2dat_A	123	Possible global transcription activator SNF2L2; br	2e-27
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	3e-35
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	6e-30
2grc_A	129	Probable global transcription activator SNF2L4; br	4e-35
2grc_A	129	Probable global transcription activator SNF2L4; br	1e-26
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	7e-35
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-24
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-34
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-29
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-32
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-29
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	3e-32
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	1e-26
2jns_A	90	Bromodomain-containing protein 4; ET-domain, struc	4e-29
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	7e-27
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	3e-19
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-23
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-16
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	6e-22
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	1e-12
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	3e-16
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	4e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07

>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 =  214 bits (546), Expect = 7e-66
 Identities = 60/299 (20%), Positives = 117/299 (39%), Gaps = 64/299 (21%)

Query: 72  RPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIE 131
           R       L+ I ++++  +    + +PFH PV+A                         
Sbjct: 7   RRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAK-----------------------V 43

Query: 132 YPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCY 191
                             DY+K+I  PMDL T+++ +    Y S +E       +  N  
Sbjct: 44  VK----------------DYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSA 87

Query: 192 VYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQ 251
            YN P   +  ++Q++  L   K+  + +   +++K                        
Sbjct: 88  TYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAIN--------------------P 127

Query: 252 GSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGT 311
                 ++  S    N + +++ +   S   WPF+ PV+  ++   DY+++I  PMDL T
Sbjct: 128 LLDDDDQVAFSFILDNIVTQKMMAVPDS---WPFHHPVNKKFVP--DYYKVIVNPMDLET 182

Query: 312 VKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV 370
           ++  +   +Y+S + F DDV LI  N  KYN P+      A+++ +V    + +  + +
Sbjct: 183 IRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHL 241

>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 =  121 bits (304), Expect = 3e-31
 Identities = 38/194 (19%), Positives = 62/194 (31%), Gaps = 39/194 (20%)

Query: 41  LSNGGEPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPF 100
           +S        E+ + +          + P             +   V + +M    +WPF
Sbjct: 99  ISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPF 158

Query: 101 HQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMD 160
           H PV+                           P                DY+KVI +PMD
Sbjct: 159 HHPVNKK-----------------------FVP----------------DYYKVIVNPMD 179

Query: 161 LGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE 220
           L TI+K +    Y S +  + D N +  N   YN P       AQ +  +    ++   E
Sbjct: 180 LETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDE 239

Query: 221 SGRQIKKPNRGSDE 234
              Q++K    + E
Sbjct: 240 HLTQLEKDICTAKE 253

>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 =  116 bits (292), Expect = 2e-29
 Identities = 31/110 (28%), Positives = 60/110 (54%), Gaps = 3/110 (2%)

Query: 255 AKPKLTESLKYCNEILKELFSK-KHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVK 313
              + T+ +   + IL+ + +  +     +PF+ PV+A    + DY++II +PMDL T++
Sbjct: 4   IHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAK--VVKDYYKIITRPMDLQTLR 61

Query: 314 AKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI 363
             +  R Y S +EF + + LI  N   YN P H +  +++ + D+ + K+
Sbjct: 62  ENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKL 111

>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 =  212 bits (542), Expect = 7e-65
 Identities = 62/325 (19%), Positives = 121/325 (37%), Gaps = 64/325 (19%)

Query: 46  EPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVD 105
            P  +           +  P      R       L+ I ++++  +    + +PFH PV+
Sbjct: 14  PPKKKRRVGTTVHCDYLNRPHKSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVN 73

Query: 106 AIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIK 165
           A                                           DY+K+I  PMDL T++
Sbjct: 74  AK-----------------------VVK----------------DYYKIITRPMDLQTLR 94

Query: 166 KRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQI 225
           + +    Y S +E       +  N   YN P   +  ++Q++  L   K+  + +   ++
Sbjct: 95  ENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARL 154

Query: 226 KKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPF 285
           +K                              ++  S    N + +++ +   S   WPF
Sbjct: 155 EKAIN--------------------PLLDDDDQVAFSFILDNIVTQKMMAVPDS---WPF 191

Query: 286 YKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPD 345
           + PV+  ++   DY+++I  PMDL T++  +   +Y+S + F DDV LI  N  KYN P+
Sbjct: 192 HHPVNKKFVP--DYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPE 249

Query: 346 HDVVAMAKKLQDVFETKIAKAPDDV 370
                 A+++ +V    + +  + +
Sbjct: 250 SQYTKTAQEIVNVCYQTLTEYDEHL 274

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

 Score =  117 bits (293), Expect = 2e-29
 Identities = 37/187 (19%), Positives = 59/187 (31%), Gaps = 39/187 (20%)

Query: 42  SNGGEPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFH 101
           S        E+ + +          + P             +   V + +M    +WPFH
Sbjct: 133 SQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFH 192

Query: 102 QPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDL 161
            PV+                           P                DY+KVI +PMDL
Sbjct: 193 HPVNKK-----------------------FVP----------------DYYKVIVNPMDL 213

Query: 162 GTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRES 221
            TI+K +    Y S +  + D N +  N   YN P       AQ +  +    ++   E 
Sbjct: 214 ETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEH 273

Query: 222 GRQIKKP 228
             Q++K 
Sbjct: 274 LTQLEKD 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 =  112 bits (281), Expect = 8e-28
 Identities = 34/144 (23%), Positives = 66/144 (45%), Gaps = 4/144 (2%)

Query: 221 SGRQIKKPNRGSD-EGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSK-KH 278
           S   +K P +    +             +         + T+ +   + IL+ + +  + 
Sbjct: 2   SHMVLKFPKQQLPPKKKRRVGTTVHCDYLNRPHKSIHRRRTDPMVTLSSILESIINDMRD 61

Query: 279 SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNC 338
               +PF+ PV+A    + DY++II +PMDL T++  +  R Y S +EF + + LI  N 
Sbjct: 62  LPNTYPFHTPVNAK--VVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNS 119

Query: 339 YKYNPPDHDVVAMAKKLQDVFETK 362
             YN P H +  +++ + D+ + K
Sbjct: 120 ATYNGPKHSLTQISQSMLDLCDEK 143

>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 =  196 bits (501), Expect = 4e-61
 Identities = 73/115 (63%), Positives = 97/115 (84%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
             K++E LK C+ ILKE+F+KKH++YAWPFYKPVD   LGL+DY +IIK PMD+ T+K+K
Sbjct: 4   GSKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSK 63

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV 370
           +++REY+ ++EF  DVRL+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK PD+ 
Sbjct: 64  LESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEP 118

>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 =  133 bits (337), Expect = 2e-37
 Identities = 44/152 (28%), Positives = 65/152 (42%), Gaps = 41/152 (26%)

Query: 72  RPGRNTNQLAFISKNVLKPVMKHQH---AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSM 128
              + + QL      +LK +   +H   AWPF++PVD   L L                 
Sbjct: 3   MGSKISEQLKCC-SGILKEMFAKKHAAYAWPFYKPVDVEALGLH---------------- 45

Query: 129 YIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFT 188
                                DY  +IKHPMD+ TIK +LE+  Y   +E  +D   MF+
Sbjct: 46  ---------------------DYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFS 84

Query: 189 NCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE 220
           NCY YN P  +VV MA+ L+ +F  + +   +
Sbjct: 85  NCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD 116

>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 =  189 bits (481), Expect = 5e-58
 Identities = 74/114 (64%), Positives = 97/114 (85%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
             K++E LK C+ ILKE+F+KKH++YAWPFYKPVD   LGL+DY +IIK PMD+ T+K+K
Sbjct: 17  SSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSK 76

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           ++AREY+ ++EF  DVRL+F+NCYKYNPPDH+VVAMA+KLQDVFE + AK PD+
Sbjct: 77  LEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE 130

>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 =  134 bits (339), Expect = 1e-37
 Identities = 46/162 (28%), Positives = 68/162 (41%), Gaps = 41/162 (25%)

Query: 58  VNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQH---AWPFHQPVDAIDLNLPFL 114
           +  +      P P +  + + QL      +LK +   +H   AWPF++PVD   L L   
Sbjct: 2   MKDVPDSQQHPAPEKSSKVSEQLKCC-SGILKEMFAKKHAAYAWPFYKPVDVEALGLH-- 58

Query: 115 IFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYW 174
                                              DY  +IKHPMD+ TIK +LE   Y 
Sbjct: 59  -----------------------------------DYCDIIKHPMDMSTIKSKLEAREYR 83

Query: 175 SGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVS 216
             +E  +D   MF+NCY YN P  +VV MA+ L+ +F  + +
Sbjct: 84  DAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFA 125

>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 =  186 bits (474), Expect = 9e-55
 Identities = 55/363 (15%), Positives = 100/363 (27%), Gaps = 62/363 (17%)

Query: 44  GGEPPAREEPR-LEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQ 102
           G +P   +    L P + +       P     +    ++F    ++           F +
Sbjct: 1   GIDPFTVDYNAPLNPKSELFLDDWHIP-----KFNRFISFTLDVLID--KYKDIFKDFIK 53

Query: 103 PVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLG 162
                                        +P                 Y+  I+ PM + 
Sbjct: 54  LPSRK-----------------------FHP----------------QYYYKIQQPMSIN 74

Query: 163 TIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESG 222
            IK R    Y       + D   +  NC  YN+    +V  +  +  L   +V   +   
Sbjct: 75  EIKSRDYE-YEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLK 133

Query: 223 RQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYA 282
           R     +    +           T              +  +                 +
Sbjct: 134 RNYLINSEVKAKLLHYLNKLVDAT------------EKKINQALLGASSPKNLDDKVKLS 181

Query: 283 WPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN 342
            PF + VD   L   +Y+EI+  PM L  VK  ++  +Y    +F  D+ L+F N + +N
Sbjct: 182 EPFMELVDKDELP--EYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFN 239

Query: 343 PPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRWSPDSSSDSTD 402
            P   +   A  L + F   I K         +      L  +K     +          
Sbjct: 240 DPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKFEFENYLAIGGGGPAA 299

Query: 403 SEA 405
           + A
Sbjct: 300 AGA 302

>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 =  170 bits (432), Expect = 5e-51
 Identities = 39/113 (34%), Positives = 59/113 (52%), Gaps = 2/113 (1%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           K  E  +     L+ L+  +    + PF +PVD   LG+ DY +I+K PMDL T+K K+D
Sbjct: 8   KPEELRQALMPTLEALY--RQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLD 65

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV 370
             +Y+   ++ DDV L+F N + YN     V     KL +VFE +I      +
Sbjct: 66  TGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 118

>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 =  122 bits (309), Expect = 2e-33
 Identities = 31/138 (22%), Positives = 52/138 (37%), Gaps = 38/138 (27%)

Query: 85  KNVLKPVMK-HQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVP 143
              L+ + +    + PF QPVD   L +P                               
Sbjct: 17  MPTLEALYRQDPESLPFRQPVDPQLLGIP------------------------------- 45

Query: 144 VLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVM 203
                 DY  ++K+PMDL TIK++L+   Y    + + D   MF N ++YN+    V   
Sbjct: 46  ------DYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKF 99

Query: 204 AQTLEKLFLTKVSARRES 221
              L ++F  ++    +S
Sbjct: 100 CSKLAEVFEQEIDPVMQS 117

>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 =  176 bits (446), Expect = 3e-50
 Identities = 51/355 (14%), Positives = 95/355 (26%), Gaps = 60/355 (16%)

Query: 20  KVAKAGTRSIDPKSMDEKDFALSNGGEPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQ 79
           K  + G   +  + +  +        +    + P+ +     V       P       + 
Sbjct: 15  KAPRKGGMVVKKRKLATEAGGSDERPKYLPGKHPKNQEKTPHVDYNAPLNPKSELFLDDW 74

Query: 80  LAFISKNVLKPVMK------HQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYP 133
                   +   +             F +                             +P
Sbjct: 75  HIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRK-----------------------FHP 111

Query: 134 ILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVY 193
                            Y+  I+ PM +  IK R    Y       + D   +  NC  Y
Sbjct: 112 ----------------QYYYKIQQPMSINEIKSRDYE-YEDGPSNFLLDVELLTKNCQAY 154

Query: 194 NKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGS 253
           N+    +V  +  +  L   +V   +   R     +    +           T       
Sbjct: 155 NEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDAT------- 207

Query: 254 YAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVK 313
                  +  +                 + PF + VD   L   +Y+EI+  PM L  VK
Sbjct: 208 -----EKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELP--EYYEIVHSPMALSIVK 260

Query: 314 AKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
             ++  +Y    +F  D+ L+F N + +N P   +   A  L + F   I K   
Sbjct: 261 QNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFF 315

>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 =  164 bits (417), Expect = 6e-49
 Identities = 37/112 (33%), Positives = 59/112 (52%), Gaps = 5/112 (4%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
           K   ++ L  C+ IL E+ + +    AWPF  PV+   +    Y ++IKKPMD  T++ K
Sbjct: 8   KRDDSKDLALCSMILTEMETHED---AWPFLLPVNLKLVP--GYKKVIKKPMDFSTIREK 62

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP 367
           + + +Y + + FA DVRL+F NC  +N  D D+      ++  FE K     
Sbjct: 63  LSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTF 114

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

 Score =  128 bits (325), Expect = 1e-35
 Identities = 33/145 (22%), Positives = 53/145 (36%), Gaps = 39/145 (26%)

Query: 70  PHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMY 129
             +P R+ ++   +   +L  +  H+ AWPF  PV+                        
Sbjct: 4   VKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKL--------------------- 42

Query: 130 IEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTN 189
                       VP       Y KVIK PMD  TI+++L +  Y + +    D   +F N
Sbjct: 43  ------------VP------GYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDN 84

Query: 190 CYVYNKPGEDVVVMAQTLEKLFLTK 214
           C  +N+   D+      + K F  K
Sbjct: 85  CETFNEDDSDIGRAGHNMRKYFEKK 109

>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 =  161 bits (410), Expect = 7e-48
 Identities = 41/119 (34%), Positives = 59/119 (49%), Gaps = 6/119 (5%)

Query: 255 AKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA 314
                +   K C E++  +F  +    + PF +PVD   +   DY +II  PMD GTV+ 
Sbjct: 4   TNYVESNWKKQCKELVNLIFQCED---SEPFRQPVD--LVEYPDYRDIIDTPMDFGTVRE 58

Query: 315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDH-DVVAMAKKLQDVFETKIAKAPDDVPI 372
            +DA  Y S  EF  D+RLIF+N   Y P     + +M  +L  +FE K+ K   D  I
Sbjct: 59  TLDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKISSDFKI 117

>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 =  113 bits (286), Expect = 3e-30
 Identities = 31/146 (21%), Positives = 49/146 (33%), Gaps = 40/146 (27%)

Query: 85  KNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPV 144
           K ++  + + + + PF QPVD   +  P                                
Sbjct: 16  KELVNLIFQCEDSEPFRQPVDL--VEYP-------------------------------- 41

Query: 145 LIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN-KPGEDVVVM 203
                DY  +I  PMD GT+++ L+   Y S  E   D   +F+N   Y       +  M
Sbjct: 42  -----DYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSM 96

Query: 204 AQTLEKLFLTKVSARRESGRQIKKPN 229
              L  LF  K+       +  +K N
Sbjct: 97  TLRLSALFEEKMKKISSDFKIGQKFN 122

>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 =  159 bits (405), Expect = 4e-47
 Identities = 76/153 (49%), Positives = 95/153 (62%), Gaps = 37/153 (24%)

Query: 64  PPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQH 123
           PP    P++P R TNQL ++ + VLK + KHQ AWPF QPVDA+ LNLP           
Sbjct: 6   PPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLP----------- 54

Query: 124 WVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDF 183
                                     DY+K+IK PMD+GTIKKRLEN YYW+ +E I DF
Sbjct: 55  --------------------------DYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDF 88

Query: 184 NTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVS 216
           NTMFTNCY+YNKPG+D+V+MA+ LEKLFL K++
Sbjct: 89  NTMFTNCYIYNKPGDDIVLMAEALEKLFLQKIN 121

>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 =  158 bits (401), Expect = 2e-46
 Identities = 47/115 (40%), Positives = 71/115 (61%), Gaps = 4/115 (3%)

Query: 256 KPKLTESLKY-CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA 314
             + T  L+Y    +LK L+  +   +AWPF +PVDA  L L DY++IIK PMD+GT+K 
Sbjct: 15  PKRQTNQLQYLLRVVLKTLWKHQ---FAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKK 71

Query: 315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           +++   Y +++E   D   +FTNCY YN P  D+V MA+ L+ +F  KI + P +
Sbjct: 72  RLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTE 126

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

 Score =  160 bits (407), Expect = 8e-47
 Identities = 35/153 (22%), Positives = 62/153 (40%), Gaps = 4/153 (2%)

Query: 256 KPKLTESL-KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA 314
             +  +      N+++  L   +       F K VDA      DY+++IK PM    +K 
Sbjct: 15  YFQGNKQWYLLANQLILSLSKYEG---GHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKT 71

Query: 315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVS 374
           K+   +Y    EF  DV+LIF NC  YN  +  V    K ++  F  ++     +  I+ 
Sbjct: 72  KLKKGQYAYPSEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFNNQLIVMGYNNFILK 131

Query: 375 SSSMVPTLTVNKNNIGRWSPDSSSDSTDSEADE 407
              +   L + +    +WS +      + +  E
Sbjct: 132 EKKINDMLKLVEEENIKWSKEKEDQIEEIDELE 164

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

 Score =  145 bits (367), Expect = 3e-41
 Identities = 33/200 (16%), Positives = 64/200 (32%), Gaps = 38/200 (19%)

Query: 63  QPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQ 122
              +    +   +   Q   ++  ++  + K++    F + VDA   N P          
Sbjct: 5   HHHSSGRENLYFQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCP---------- 54

Query: 123 HWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISD 182
                                      DY+ VIK+PM    IK +L+   Y    E + D
Sbjct: 55  ---------------------------DYYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKD 87

Query: 183 FNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGSFTTQLA 242
              +F NC +YN     V +  + +E  F  ++     +   I K  + +D      +  
Sbjct: 88  VQLIFDNCSLYNTSNSVVAITGKNIETYFNNQLIVMGYN-NFILKEKKINDMLKLVEEEN 146

Query: 243 TSVTSVGDQGSYAKPKLTES 262
              +   +       +L  +
Sbjct: 147 IKWSKEKEDQIEEIDELENN 166

>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 =  157 bits (400), Expect = 5e-46
 Identities = 74/166 (44%), Positives = 98/166 (59%), Gaps = 37/166 (22%)

Query: 63  QPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQ 122
           +   +  P +PGR TNQL ++ K V+K + KHQ AWPF QPVDA+ L LP          
Sbjct: 16  RGSHMSNPKKPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLP---------- 65

Query: 123 HWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISD 182
                                      DYHK+IK PMD+GTIK+RLEN YYW+  E + D
Sbjct: 66  ---------------------------DYHKIIKQPMDMGTIKRRLENNYYWAASECMQD 98

Query: 183 FNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKP 228
           FNTMFTNCY+YNKP +D+V+MAQTLEK+FL KV++  +  +++   
Sbjct: 99  FNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQELVVT 144

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

 Score =  156 bits (395), Expect = 2e-45
 Identities = 48/114 (42%), Positives = 74/114 (64%), Gaps = 4/114 (3%)

Query: 256 KPKLTESLKYCNE-ILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA 314
             ++T  L+Y ++ ++K L+  +   +AWPF +PVDA  LGL DYH+IIK+PMD+GT+K 
Sbjct: 26  PGRVTNQLQYLHKVVMKALWKHQ---FAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKR 82

Query: 315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD 368
           +++   Y ++ E   D   +FTNCY YN P  D+V MA+ L+ +F  K+A  P 
Sbjct: 83  RLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQ 136

>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 =  157 bits (398), Expect = 5e-46
 Identities = 40/115 (34%), Positives = 56/115 (48%), Gaps = 6/115 (5%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
              +    K C E+L  +F  + S    PF +PVD   L   DY +II  PMD  TV+  
Sbjct: 16  SYDIQAWKKQCEELLNLIFQCEDS---EPFRQPVD--LLEYPDYRDIIDTPMDFATVRET 70

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDH-DVVAMAKKLQDVFETKIAKAPDD 369
           ++A  Y+S  E   DVRLIF+N   Y P     + +M+ +L   FE  I+    D
Sbjct: 71  LEAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSD 125

>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 =  113 bits (284), Expect = 8e-30
 Identities = 31/156 (19%), Positives = 48/156 (30%), Gaps = 41/156 (26%)

Query: 63  QPPTVPPPHRP-GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVF 121
             P     +R    +        + +L  + + + + PF QPVD   L  P         
Sbjct: 4   HQPRRRLRNRAQSYDIQAWKKQCEELLNLIFQCEDSEPFRQPVDL--LEYP--------- 52

Query: 122 QHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAIS 181
                                       DY  +I  PMD  T+++ LE   Y S  E   
Sbjct: 53  ----------------------------DYRDIIDTPMDFATVRETLEAGNYESPMELCK 84

Query: 182 DFNTMFTNCYVYNKP-GEDVVVMAQTLEKLFLTKVS 216
           D   +F+N   Y       +  M+  L   F   +S
Sbjct: 85  DVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHIS 120

>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 =  154 bits (391), Expect = 3e-45
 Identities = 38/118 (32%), Positives = 65/118 (55%), Gaps = 5/118 (4%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
           +PK          IL EL  + H+  AWPF +PV+     + DY++ IK+PMDL T++ K
Sbjct: 8   RPKRGPHDAAIQNILTEL--QNHA-AAWPFLQPVNK--EEVPDYYDFIKEPMDLSTMEIK 62

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIV 373
           +++ +Y+  ++F  D RL+F NC  YN  +      A +L+  F  K+ + P+   ++
Sbjct: 63  LESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPEYSHLI 120

>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 =  138 bits (351), Expect = 2e-39
 Identities = 43/151 (28%), Positives = 58/151 (38%), Gaps = 41/151 (27%)

Query: 70  PHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMY 129
             RP R  +  A   +N+L  +  H  AWPF QPV+  +                     
Sbjct: 6   AQRPKRGPHDAAI--QNILTELQNHAAAWPFLQPVNKEE--------------------- 42

Query: 130 IEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTN 189
                       VP      DY+  IK PMDL T++ +LE+  Y   ++ I D   +F N
Sbjct: 43  ------------VP------DYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNN 84

Query: 190 CYVYNKPGEDVVVMAQTLEKLFLTKVSARRE 220
           C +YN         A  LEK F  KV    E
Sbjct: 85  CRMYNGENTSYYKYANRLEKFFNNKVKEIPE 115

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

 Score =  153 bits (389), Expect = 1e-44
 Identities = 39/129 (30%), Positives = 61/129 (47%), Gaps = 8/129 (6%)

Query: 243 TSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEI 302
           +S +S   +            + C  +L  L+  + S     F  PV    L + DY++I
Sbjct: 2   SSGSSGKKKTEGLVKLTPIDKRKCERLLLFLYCHEMS---LAFQDPVP---LTVPDYYKI 55

Query: 303 IKKPMDLGTVKAKM--DAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFE 360
           IK PMDL T+K ++  D   Y   ++F  D RLIF NC ++N PD +V     KL++ FE
Sbjct: 56  IKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFE 115

Query: 361 TKIAKAPDD 369
             +     +
Sbjct: 116 ELLKNLYPE 124

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

 Score =  126 bits (319), Expect = 1e-34
 Identities = 36/149 (24%), Positives = 56/149 (37%), Gaps = 42/149 (28%)

Query: 69  PPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSM 128
                 + T       + +L  +  H+ +  F  PV    L +P                
Sbjct: 10  KTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVP---LTVP---------------- 50

Query: 129 YIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFY--YWSGKEAISDFNTM 186
                                DY+K+IK+PMDL TIKKRL+  Y  Y   ++ ++DF  +
Sbjct: 51  ---------------------DYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLI 89

Query: 187 FTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
           F NC  +N+P  +V      LE  F   +
Sbjct: 90  FQNCAEFNEPDSEVANAGIKLENYFEELL 118

>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 =  148 bits (375), Expect = 6e-43
 Identities = 31/108 (28%), Positives = 58/108 (53%), Gaps = 5/108 (4%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           +L +      ++L  + + K    +WPF +PVD       +Y++IIK PMD+ +++ K++
Sbjct: 13  ELDDDFTAMYKVLDVVKAHKD---SWPFLEPVDE--SYAPNYYQIIKAPMDISSMEKKLN 67

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
              Y + +EF +D++ +F NC KYN    +   M+  L+  F   + K
Sbjct: 68  GGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 115

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

 Score =  130 bits (328), Expect = 3e-36
 Identities = 33/131 (25%), Positives = 53/131 (40%), Gaps = 39/131 (29%)

Query: 85  KNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPV 144
             VL  V  H+ +WPF +PVD                                     P 
Sbjct: 22  YKVLDVVKAHKDSWPFLEPVDESY---------------------------------AP- 47

Query: 145 LIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMA 204
                +Y+++IK PMD+ +++K+L    Y + +E ++D  TMF NC  YN    +   M+
Sbjct: 48  -----NYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMS 102

Query: 205 QTLEKLFLTKV 215
             LE+ F   +
Sbjct: 103 DNLERCFHRAM 113

>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 =  145 bits (367), Expect = 1e-41
 Identities = 38/112 (33%), Positives = 51/112 (45%), Gaps = 5/112 (4%)

Query: 255 AKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA 314
           A+ + T   +     L++L  K        F  PV  A      Y  IIK PMD GT+K 
Sbjct: 7   AENESTPIQQLLEHFLRQLQRKDP---HGFFAFPVTDA--IAPGYSMIIKHPMDFGTMKD 61

Query: 315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKA 366
           K+ A EYKS  EF  D +L+  N   YN PD     +AKK+       ++K 
Sbjct: 62  KIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKE 113

>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 =  118 bits (299), Expect = 4e-32
 Identities = 28/143 (19%), Positives = 46/143 (32%), Gaps = 39/143 (27%)

Query: 77  TNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILL 136
           +  +  + ++ L+ + +      F  PV                                
Sbjct: 11  STPIQQLLEHFLRQLQRKDPHGFFAFPVTDAI---------------------------- 42

Query: 137 AFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKP 196
                 P       Y  +IKHPMD GT+K ++    Y S  E  +DF  M  N   YN+P
Sbjct: 43  -----AP------GYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRP 91

Query: 197 GEDVVVMAQTLEKLFLTKVSARR 219
                 +A+ +       +S  R
Sbjct: 92  DTVYYKLAKKILHAGFKMMSKER 114

>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 =  143 bits (362), Expect = 4e-41
 Identities = 33/111 (29%), Positives = 56/111 (50%), Gaps = 6/111 (5%)

Query: 258 KLTESLKY-CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKM 316
           +  + L      +L ++ S      AWPF +PV        DY+E+I+ P+DL T+  ++
Sbjct: 3   EDPDQLYTTLKNLLAQIKSHPS---AWPFMEPVKK--SEAPDYYEVIRFPIDLKTMTERL 57

Query: 317 DAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP 367
            +R Y + K F  D++ +  NC +YNPPD +    A  L+  F  K+ +  
Sbjct: 58  RSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEGG 108

>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 =  140 bits (354), Expect = 7e-40
 Identities = 38/141 (26%), Positives = 57/141 (40%), Gaps = 39/141 (27%)

Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
            + +QL    KN+L  +  H  AWPF +PV   +                          
Sbjct: 3   EDPDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSE-------------------------- 36

Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                   P      DY++VI+ P+DL T+ +RL + YY + K  ++D   +  NC  YN
Sbjct: 37  -------AP------DYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYN 83

Query: 195 KPGEDVVVMAQTLEKLFLTKV 215
            P  +    A  LEK F  K+
Sbjct: 84  PPDSEYCRCASALEKFFYFKL 104

>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 =  143 bits (361), Expect = 3e-40
 Identities = 37/112 (33%), Positives = 55/112 (49%), Gaps = 5/112 (4%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
            P   +  +    +L+ L + K    AWPF +PVD       DY+ +IK+PMDL T++ +
Sbjct: 67  TPLTEKDYEGLKRVLRSLQAHKM---AWPFLEPVDPN--DAPDYYGVIKEPMDLATMEER 121

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP 367
           +  R Y+   EF  D+  IF NC  YNP D      A+ L+  F  K+    
Sbjct: 122 VQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 173

>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 =  138 bits (348), Expect = 2e-38
 Identities = 41/169 (24%), Positives = 60/169 (35%), Gaps = 39/169 (23%)

Query: 47  PPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDA 106
               E   ++         T          T +     K VL+ +  H+ AWPF +PVD 
Sbjct: 40  ILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDP 99

Query: 107 IDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKK 166
            D                                  P      DY+ VIK PMDL T+++
Sbjct: 100 ND---------------------------------AP------DYYGVIKEPMDLATMEE 120

Query: 167 RLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
           R++  YY    E ++D   +F NC  YN         A+ LE  F+ K+
Sbjct: 121 RVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKL 169

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

 Score =  140 bits (354), Expect = 9e-40
 Identities = 41/123 (33%), Positives = 56/123 (45%), Gaps = 16/123 (13%)

Query: 252 GSYAKP--KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDL 309
           GS       L E   +  ++ K L + K       F KPV        DY E+IK+PMDL
Sbjct: 1   GSSGSSGNTLRELRLFLRDVTKRLATDKR---FNIFSKPVS-------DYLEVIKEPMDL 50

Query: 310 GTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPP----DHDVVAMAKKLQDVFETKIAK 365
            TV  K+D   Y ++K+F  D+ LI +N  +YNP     D  +   A  L+D     IA 
Sbjct: 51  STVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAA 110

Query: 366 APD 368
             D
Sbjct: 111 ELD 113

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

 Score =  109 bits (274), Expect = 1e-28
 Identities = 24/152 (15%), Positives = 45/152 (29%), Gaps = 44/152 (28%)

Query: 70  PHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMY 129
               G    +L    ++V K +   +    F +PV                         
Sbjct: 3   SGSSGNTLRELRLFLRDVTKRLATDKRFNIFSKPVS------------------------ 38

Query: 130 IEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTN 189
                               DY +VIK PMDL T+  +++   Y + K+ + D + + +N
Sbjct: 39  --------------------DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSN 78

Query: 190 CYVYNKPGEDVVVMAQTLEKLFLTKVSARRES 221
              YN   +    + +           A   +
Sbjct: 79  ALEYNPDKDPGDKIIRHRACTLKDTAHAIIAA 110

>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 =  139 bits (351), Expect = 2e-39
 Identities = 32/116 (27%), Positives = 52/116 (44%), Gaps = 5/116 (4%)

Query: 255 AKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA 314
                +  L    + L++L  K        F +PV  +   + DY + IKKPMD  T+K 
Sbjct: 1   GSSGSSGFLILLRKTLEQLQEKDT---GNIFSEPVPLS--EVPDYLDHIKKPMDFFTMKQ 55

Query: 315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV 370
            ++A  Y +  +F +D  LI +NC KYN  D      A +L++     + +A    
Sbjct: 56  NLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQA 111

>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 =  119 bits (300), Expect = 3e-32
 Identities = 28/151 (18%), Positives = 48/151 (31%), Gaps = 39/151 (25%)

Query: 75  RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPI 134
             ++    + +  L+ + +      F +PV   +                          
Sbjct: 3   SGSSGFLILLRKTLEQLQEKDTGNIFSEPVPLSE-------------------------- 36

Query: 135 LLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYN 194
                  VP      DY   IK PMD  T+K+ LE + Y +  +   DFN + +NC  YN
Sbjct: 37  -------VP------DYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYN 83

Query: 195 KPGEDVVVMAQTLEKLFLTKVSARRESGRQI 225
                    A  L +     +   R    ++
Sbjct: 84  AKDTIFYRAAVRLREQGGAVLRQARRQAEKM 114

>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 =  139 bits (352), Expect = 4e-39
 Identities = 31/119 (26%), Positives = 60/119 (50%), Gaps = 4/119 (3%)

Query: 255 AKPKLTESLKYCNEILKELFSKKHSS--YAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTV 312
               + +     + IL  + ++K  +   +WPF+ PV+     + DY+++I  PMDL T+
Sbjct: 19  YFQSMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNK--KFVPDYYKVIVNPMDLETI 76

Query: 313 KAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVP 371
           +  +   +Y+S + F DDV LI  N  KYN P+      A+++ +V    + +  + + 
Sbjct: 77  RKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLT 135

>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 =  126 bits (319), Expect = 1e-34
 Identities = 36/150 (24%), Positives = 54/150 (36%), Gaps = 39/150 (26%)

Query: 85  KNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPV 144
             V + +M    +WPFH PV+                                    VP 
Sbjct: 36  NIVTQKMMAVPDSWPFHHPVNKKF---------------------------------VP- 61

Query: 145 LIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMA 204
                DY+KVI +PMDL TI+K +    Y S +  + D N +  N   YN P       A
Sbjct: 62  -----DYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTA 116

Query: 205 QTLEKLFLTKVSARRESGRQIKKPNRGSDE 234
           Q +  +    ++   E   Q++K    + E
Sbjct: 117 QEIVNVCYQTLTEYDEHLTQLEKDICTAKE 146

>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 =  138 bits (348), Expect = 3e-38
 Identities = 37/106 (34%), Positives = 55/106 (51%), Gaps = 8/106 (7%)

Query: 264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKM--DAREY 321
           + C  +L  L+  + S     F  PV    L + DY++IIK PMDL T+K ++  D   Y
Sbjct: 84  RKCERLLLFLYCHEMS---LAFQDPVP---LTVPDYYKIIKNPMDLSTIKKRLQEDYSMY 137

Query: 322 KSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP 367
              ++F  D RLIF NC ++N PD +V     KL++ FE  +    
Sbjct: 138 SKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLY 183

>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 =  116 bits (291), Expect = 3e-30
 Identities = 36/161 (22%), Positives = 57/161 (35%), Gaps = 42/161 (26%)

Query: 57  PVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIF 116
             +               + T       + +L  +  H+ +  F  PV    L +P    
Sbjct: 59  DCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVP---LTVP---- 111

Query: 117 RFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFY--YW 174
                                            DY+K+IK+PMDL TIKKRL+  Y  Y 
Sbjct: 112 ---------------------------------DYYKIIKNPMDLSTIKKRLQEDYSMYS 138

Query: 175 SGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
             ++ ++DF  +F NC  +N+P  +V      LE  F   +
Sbjct: 139 KPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELL 179

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

 Score =  135 bits (342), Expect = 3e-38
 Identities = 31/114 (27%), Positives = 53/114 (46%), Gaps = 5/114 (4%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
           + + T   +  N+++++L  K     +  F  PV         Y  IIK PMD  T+K K
Sbjct: 3   EVEQTPLQEALNQLMRQLQRKDP---SAFFSFPVTD--FIAPGYSMIIKHPMDFSTMKEK 57

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           +   +Y+S +E  D+ +L+ TN   YN P+      AKKL       +++   +
Sbjct: 58  IKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERLE 111

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

 Score =  121 bits (305), Expect = 5e-33
 Identities = 29/135 (21%), Positives = 47/135 (34%), Gaps = 39/135 (28%)

Query: 85  KNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPV 144
             +++ + +   +  F  PV                                      P 
Sbjct: 14  NQLMRQLQRKDPSAFFSFPVTDFI---------------------------------AP- 39

Query: 145 LIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMA 204
                 Y  +IKHPMD  T+K++++N  Y S +E   +F  M TN  +YNKP       A
Sbjct: 40  -----GYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAA 94

Query: 205 QTLEKLFLTKVSARR 219
           + L    +  +S  R
Sbjct: 95  KKLLHSGMKILSQER 109

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

 Score =  135 bits (342), Expect = 5e-38
 Identities = 36/115 (31%), Positives = 56/115 (48%), Gaps = 5/115 (4%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
           + +LT        +L +L  K     A  F +PV      + DY + IK PMD  T++ +
Sbjct: 8   ELRLTPLTVLLRSVLDQLQDKDP---ARIFAQPVSLK--EVPDYLDHIKHPMDFATMRKR 62

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV 370
           ++A+ YK+  EF +D  LI  NC KYN  D      A +L+D     + +A  +V
Sbjct: 63  LEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREV 117

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

 Score =  115 bits (291), Expect = 8e-31
 Identities = 38/156 (24%), Positives = 50/156 (32%), Gaps = 40/156 (25%)

Query: 77  TNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILL 136
              L  + ++VL  +     A  F QPV   +                            
Sbjct: 11  LTPLTVLLRSVLDQLQDKDPARIFAQPVSLKE---------------------------- 42

Query: 137 AFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKP 196
                VP      DY   IKHPMD  T++KRLE   Y +  E   DF+ +  NC  YN  
Sbjct: 43  -----VP------DYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNAR 91

Query: 197 GEDVVVMAQTLEKLFLTKVS-ARRESGRQIKKPNRG 231
                  A  L       +  ARRE      +   G
Sbjct: 92  DTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASG 127

>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 =  135 bits (341), Expect = 6e-38
 Identities = 34/117 (29%), Positives = 53/117 (45%), Gaps = 9/117 (7%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
           +    E   +   +   L   K       F KPVD     + DY  +IK+PMDL +V +K
Sbjct: 5   EDTFRELRIFLRNVTHRLAIDKR---FRVFTKPVDPD--EVPDYVTVIKQPMDLSSVISK 59

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPP----DHDVVAMAKKLQDVFETKIAKAPD 368
           +D  +Y + K++  D+ LI +N  +YNP     D  +   A  L+D     I +  D
Sbjct: 60  IDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELD 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 =  102 bits (255), Expect = 5e-26
 Identities = 26/142 (18%), Positives = 46/142 (32%), Gaps = 43/142 (30%)

Query: 78  NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLA 137
            +L    +NV   +   +    F +PVD  +                             
Sbjct: 9   RELRIFLRNVTHRLAIDKRFRVFTKPVDPDE----------------------------- 39

Query: 138 FALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPG 197
               VP      DY  VIK PMDL ++  +++   Y + K+ + D + + +N   YN   
Sbjct: 40  ----VP------DYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDR 89

Query: 198 ED----VVVMAQTLEKLFLTKV 215
           +     +   A  L       +
Sbjct: 90  DPGDRLIRHRACALRDTAYAII 111

>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 =  132 bits (333), Expect = 8e-37
 Identities = 26/112 (23%), Positives = 47/112 (41%), Gaps = 2/112 (1%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
            L        + ++   + +    A PFY           DY++ IK P+ L  ++ K+ 
Sbjct: 17  NLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYP--DYYQQIKMPISLQQIRTKLK 74

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
            +EY++      D+ L+F N  +YN P+  +     KLQ V + K  +    
Sbjct: 75  NQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARR 126

>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 =  106 bits (266), Expect = 2e-27
 Identities = 30/150 (20%), Positives = 44/150 (29%), Gaps = 45/150 (30%)

Query: 72  RPGRNTNQLAFISKNVLKPVMK------HQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWV 125
                T  L F S  +   V           A PF+                        
Sbjct: 10  GVDLGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKK------------------ 51

Query: 126 LSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNT 185
                +YP                DY++ IK P+ L  I+ +L+N  Y +      D N 
Sbjct: 52  -----KYP----------------DYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNL 90

Query: 186 MFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
           MF N   YN P   +      L+++   K 
Sbjct: 91  MFENAKRYNVPNSAIYKRVLKLQQVMQAKK 120

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

 Score =  128 bits (323), Expect = 2e-35
 Identities = 25/113 (22%), Positives = 48/113 (42%), Gaps = 2/113 (1%)

Query: 257 PKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKM 316
           PKLT+ +    + +           +  F +      L   +Y+E+I+KP+D   +K ++
Sbjct: 12  PKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELP--EYYELIRKPVDFKKIKERI 69

Query: 317 DAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
              +Y+S  +   DV L+  N   +N     +   +  LQ VF++     P  
Sbjct: 70  RNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQSGPSS 122

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

 Score =  105 bits (265), Expect = 2e-27
 Identities = 29/157 (18%), Positives = 49/157 (31%), Gaps = 41/157 (26%)

Query: 68  PPPHRPGRNTNQLAFISKNV--LKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWV 125
                P + T Q+  I   V   K     Q +  F Q                       
Sbjct: 6   SGSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRK------------------ 47

Query: 126 LSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNT 185
                E P                +Y+++I+ P+D   IK+R+ N  Y S  +   D   
Sbjct: 48  -----ELP----------------EYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVML 86

Query: 186 MFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESG 222
           +  N   +N  G  +   +  L+ +F +   +   SG
Sbjct: 87  LCHNAQTFNLEGSQIYEDSIVLQSVFKSARQSGPSSG 123

>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 =  127 bits (321), Expect = 3e-35
 Identities = 30/113 (26%), Positives = 47/113 (41%), Gaps = 2/113 (1%)

Query: 257 PKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKM 316
             L E L+   E +    +      +  F K      +   DY+ IIK+P+DL T+  ++
Sbjct: 7   AYLKEILEQLLEAIVVATNPSGRLISELFQKLPSK--VQYPDYYAIIKEPIDLKTIAQRI 64

Query: 317 DAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
               YKS    A D+ L+  N   YN P   V   A  ++ +F  K A+    
Sbjct: 65  QNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEHH 117

>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 =  112 bits (283), Expect = 6e-30
 Identities = 29/149 (19%), Positives = 51/149 (34%), Gaps = 41/149 (27%)

Query: 70  PHRPGRNTNQLAFISKNVLKPVMK--HQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLS 127
              P      L  + + ++          +  F +    +                    
Sbjct: 3   GSSPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKV-------------------- 42

Query: 128 MYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMF 187
              +YP                DY+ +IK P+DL TI +R++N  Y S      D + + 
Sbjct: 43  ---QYP----------------DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLA 83

Query: 188 TNCYVYNKPGEDVVVMAQTLEKLFLTKVS 216
            N   YN+PG  V   A +++K+F  K +
Sbjct: 84  KNAKTYNEPGSQVFKDANSIKKIFYMKKA 112

>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 =  127 bits (322), Expect = 4e-35
 Identities = 27/114 (23%), Positives = 51/114 (44%), Gaps = 3/114 (2%)

Query: 257 PKLTESLKY-CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
           P LT+ +K   + ++K   S      +  F +        L +Y+E+I+KP+D   +K +
Sbjct: 10  PNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSR--KELPEYYELIRKPVDFKKIKER 67

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           +   +Y+S  +   DV L+  N   +N     +   +  LQ VF +   K   +
Sbjct: 68  IRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKE 121

>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 =  104 bits (260), Expect = 1e-26
 Identities = 26/150 (17%), Positives = 46/150 (30%), Gaps = 42/150 (28%)

Query: 69  PPHRPGRNTNQLAFISKNVLK---PVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWV 125
               P   T ++  I   V+K        Q +  F Q                       
Sbjct: 5   LSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRK------------------ 46

Query: 126 LSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNT 185
                E P                +Y+++I+ P+D   IK+R+ N  Y S  +   D   
Sbjct: 47  -----ELP----------------EYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVML 85

Query: 186 MFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
           +  N   +N  G  +   +  L+ +F +  
Sbjct: 86  LCQNAQTFNLEGSLIYEDSIVLQSVFTSVR 115

>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 =  126 bits (319), Expect = 7e-35
 Identities = 24/110 (21%), Positives = 42/110 (38%), Gaps = 5/110 (4%)

Query: 263 LKYCNEILKELFSKKHSS---YAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAR 319
           +  C+E+   +   K          F +          DY+E++ +P+DL  ++ K+   
Sbjct: 7   IAVCHELYNTIRDYKDEQGRLLCELFIRAPKRR--NQPDYYEVVSQPIDLMKIQQKLKME 64

Query: 320 EYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           EY        D +L+F N   Y  PD      A KL D++     +    
Sbjct: 65  EYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQK 114

>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 = 97.8 bits (244), Expect = 1e-24
 Identities = 24/151 (15%), Positives = 44/151 (29%), Gaps = 46/151 (30%)

Query: 78  NQLAFISKNVLKPVMKHQH------AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIE 131
           + +A     +   +  ++          F +                             
Sbjct: 5   DPIAVC-HELYNTIRDYKDEQGRLLCELFIRAPKRR-----------------------N 40

Query: 132 YPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCY 191
            P                DY++V+  P+DL  I+++L+   Y       +DF  +F N  
Sbjct: 41  QP----------------DYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAK 84

Query: 192 VYNKPGEDVVVMAQTLEKLFLTKVSARRESG 222
            Y KP       A  L  L+L   +   + G
Sbjct: 85  SYYKPDSPEYKAACKLWDLYLRTRNEFVQKG 115

>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 =  125 bits (315), Expect = 5e-34
 Identities = 27/125 (21%), Positives = 49/125 (39%), Gaps = 6/125 (4%)

Query: 256 KPKLTESLKYCNEILKELFSKKHS-SYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA 314
           K    + +K    ++ E             F            DY++II +PMDL  ++ 
Sbjct: 22  KNIRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSK--KDYPDYYKIILEPMDLKIIEH 79

Query: 315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK---APDDVP 371
            +   +Y   +   +D++L+F N   YN     V   A  L+ + + K  +    PDD  
Sbjct: 80  NIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKELGPLPDDDD 139

Query: 372 IVSSS 376
           + S +
Sbjct: 140 MASPA 144

>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 =  112 bits (281), Expect = 3e-29
 Identities = 30/156 (19%), Positives = 44/156 (28%), Gaps = 42/156 (26%)

Query: 63  QPPTVPPPHRPGRNTNQLAFISK---NVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFL 119
              +     +      ++  +        +P    +    F                   
Sbjct: 12  DTGSAKRKSKKNIRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKK------------ 59

Query: 120 VFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEA 179
                      +YP                DY+K+I  PMDL  I+  + N  Y   +  
Sbjct: 60  -----------DYP----------------DYYKIILEPMDLKIIEHNIRNDKYAGEEGM 92

Query: 180 ISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
           I D   MF N   YN+ G  V   A  LEKL   K 
Sbjct: 93  IEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKR 128

>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 =  120 bits (303), Expect = 1e-32
 Identities = 29/126 (23%), Positives = 52/126 (41%), Gaps = 2/126 (1%)

Query: 244 SVTSVGDQGSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEII 303
           S++ +  + S     + + L    E +K    K+    +  F +    + L   DY+  I
Sbjct: 1   SMSGISPKKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELP--DYYLTI 58

Query: 304 KKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKI 363
           KKPMD+  +++ M A +Y+      +D  ++F N   YN P+  +   A  L  V     
Sbjct: 59  KKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETR 118

Query: 364 AKAPDD 369
                D
Sbjct: 119 RDLEGD 124

>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 =  111 bits (279), Expect = 2e-29
 Identities = 27/157 (17%), Positives = 43/157 (27%), Gaps = 47/157 (29%)

Query: 65  PTVPPPHRPGRNTNQLAFISKNVLKPVMK------HQHAWPFHQPVDAIDLNLPFLIFRF 118
             + P  +  +    +      V + V         + +  F +                
Sbjct: 3   SGISP--KKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRS----------- 49

Query: 119 LVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKE 178
                       E P                DY+  IK PMD+  I+  +    Y     
Sbjct: 50  ------------ELP----------------DYYLTIKKPMDMEKIRSHMMANKYQDIDS 81

Query: 179 AISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKV 215
            + DF  MF N   YN+P   +   A  L K+ L   
Sbjct: 82  MVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETR 118

>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 =  119 bits (300), Expect = 3e-32
 Identities = 23/122 (18%), Positives = 45/122 (36%), Gaps = 2/122 (1%)

Query: 256 KPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAK 315
             +L +  K   + +         + A P             DY+E I  P+DL T++ +
Sbjct: 7   AARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKK--KNADYYEKISDPLDLITIEKQ 64

Query: 316 MDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSS 375
           +    YK+ + F  D+  +F N  KY      V     +L+  +     +A   +  +  
Sbjct: 65  ILTGYYKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQIDEIVG 124

Query: 376 SS 377
            +
Sbjct: 125 ET 126

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

 Score =  103 bits (259), Expect = 1e-26
 Identities = 24/149 (16%), Positives = 38/149 (25%), Gaps = 41/149 (27%)

Query: 70  PHRPGRNTNQLAFISKNV--LKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLS 127
             R  R       I   +   K   +   A P                            
Sbjct: 4   VARAARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKK-------------------- 43

Query: 128 MYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMF 187
              +                  DY++ I  P+DL TI+K++   YY + +   +D   +F
Sbjct: 44  ---KNA----------------DYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVF 84

Query: 188 TNCYVYNKPGEDVVVMAQTLEKLFLTKVS 216
            N   Y      V      L K +     
Sbjct: 85  RNAEKYYGRKSPVGRDVCRLRKAYYNARH 113

>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 =  109 bits (274), Expect = 4e-29
 Identities = 63/88 (71%), Positives = 75/88 (85%)

Query: 477 PAPVMNDESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIE 536
            +    +  +E+  KPMSY EK++LSLDINKLPG+KLGRVVHIIQSREPSL++SNPDEIE
Sbjct: 2   SSGSSGESEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIE 61

Query: 537 IDFETLKPSTLRELEKYVATCLRKKPRK 564
           IDFETLKPSTLRELE+YV +CLRKK + 
Sbjct: 62  IDFETLKPSTLRELERYVTSCLRKKRKP 89

>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 =  107 bits (267), Expect = 7e-27
 Identities = 37/136 (27%), Positives = 54/136 (39%), Gaps = 23/136 (16%)

Query: 254 YAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVK 313
             K     S     +  + L        +  F +PV      + +Y++IIKKPMDL TVK
Sbjct: 71  KGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVP---ASIPNYYKIIKKPMDLSTVK 127

Query: 314 AKMDAR---EYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMA-----------------K 353
            K+  +    Y+   +F  DVRLIF NC ++N     V   A                 K
Sbjct: 128 KKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGK 187

Query: 354 KLQDVFETKIAKAPDD 369
            +   FE K+ +   D
Sbjct: 188 AVALYFEDKLTEIYSD 203

>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 = 85.3 bits (210), Expect = 3e-19
 Identities = 32/184 (17%), Positives = 58/184 (31%), Gaps = 43/184 (23%)

Query: 34  MDEKDFALSNGGEPPAREEPRLEPVNGIVQPPTVPPPHRPGRNTNQLAFISKNVLKPVMK 93
                F   +      R+  + E                    +       + +L  +  
Sbjct: 36  PTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYC 95

Query: 94  HQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHK 153
           H+ +  F +PV A                                         + +Y+K
Sbjct: 96  HELSIEFQEPVPAS----------------------------------------IPNYYK 115

Query: 154 VIKHPMDLGTIKKRLE---NFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKL 210
           +IK PMDL T+KK+L+   + +Y    + ++D   +F NC  +N+  + V V A T E  
Sbjct: 116 IIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEIN 175

Query: 211 FLTK 214
               
Sbjct: 176 LKAD 179

>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 = 96.1 bits (239), Expect = 1e-23
 Identities = 17/144 (11%), Positives = 49/144 (34%), Gaps = 9/144 (6%)

Query: 264 KYCNEILKELFSKKHSS---YAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDARE 320
           +  + +   + S +      Y+    +          D +   K P+    ++  ++   
Sbjct: 10  ELIHNLFVSVMSHQDDEGRCYSDSLAEIPA------VDPNFPNKPPLTFDIIRKNVENNR 63

Query: 321 YKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVP 380
           Y+    F + +  +     + N  D ++   A +LQ  F     +   +  I+ S ++  
Sbjct: 64  YRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCKNGEILLSPALSY 123

Query: 381 TLTVNKNNIGRWSPDSSSDSTDSE 404
           T     N++ +   +      + +
Sbjct: 124 TTKHLHNDVEKERKEKLPKEIEED 147

>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 = 76.1 bits (187), Expect = 1e-16
 Identities = 14/92 (15%), Positives = 29/92 (31%)

Query: 150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK 209
           D +   K P+    I+K +EN  Y            +       N+   ++   A  L++
Sbjct: 41  DPNFPNKPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQ 100

Query: 210 LFLTKVSARRESGRQIKKPNRGSDEGSFTTQL 241
            F+       ++G  +  P            +
Sbjct: 101 FFIKIRDELCKNGEILLSPALSYTTKHLHNDV 132

>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 = 92.6 bits (229), Expect = 6e-22
 Identities = 25/107 (23%), Positives = 42/107 (39%), Gaps = 11/107 (10%)

Query: 266 CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAR---EYK 322
           C  +L  LF  +      P ++    +        +     +DL  ++A++  +    Y 
Sbjct: 81  CERVLLALFCHEPC---RPLHQLATDST----FSLDQPGGTLDLTLIRARLQEKLSPPYS 133

Query: 323 SSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
           S +EFA DV  +F    K        V     LQ  FET++ +A  D
Sbjct: 134 SPQEFAQDVGRMFKQFNKLTEDK-ADVQSIIGLQRFFETRMNEAFGD 179

>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 = 65.7 bits (159), Expect = 1e-12
 Identities = 18/129 (13%), Positives = 32/129 (24%), Gaps = 7/129 (5%)

Query: 90  PVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQ 149
                +               +  L          VL     +                 
Sbjct: 49  LPDLKEEDGSLSLDGADSTGVVAKLSPANQRKCERVLLALFCHEPCRPLHQLATDS---T 105

Query: 150 DYHKVIKHPMDLGTIKKRLE---NFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQT 206
                    +DL  I+ RL+   +  Y S +E   D   MF       +  +  V     
Sbjct: 106 FSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLTED-KADVQSIIG 164

Query: 207 LEKLFLTKV 215
           L++ F T++
Sbjct: 165 LQRFFETRM 173

>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 = 76.2 bits (186), Expect = 3e-16
 Identities = 16/67 (23%), Positives = 29/67 (43%)

Query: 299 YHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDV 358
                ++P+DL  VK KMD   Y S  EF+DD+  I       +    ++      ++  
Sbjct: 97  LRYRQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSF 156

Query: 359 FETKIAK 365
           F  ++ +
Sbjct: 157 FIRQMER 163

>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 = 61.1 bits (147), Expect = 4e-11
 Identities = 9/65 (13%), Positives = 25/65 (38%)

Query: 151 YHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKL 210
                + P+DL  +K++++   Y S  E   D   +       +    ++      ++  
Sbjct: 97  LRYRQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSF 156

Query: 211 FLTKV 215
           F+ ++
Sbjct: 157 FIRQM 161

>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 = 54.1 bits (129), Expect = 1e-07
 Identities = 57/452 (12%), Positives = 114/452 (25%), Gaps = 164/452 (36%)

Query: 19  WKVAKAGTRSIDPKSMDEKDFA-----LSNGGEP-PAREEPRLEPVNGIVQPPTVPPPH- 71
           + ++   T    P SM  + +      L N  +        RL+P   + Q         
Sbjct: 93  FLMSPIKTEQRQP-SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ-------AL 144

Query: 72  ---RPGRNTNQLAFIS--------KNVL-KPVMKHQHAWPFHQPVDAIDLNLPFLIFRFL 119
              RP +N      +         K  +   V               +   + F IF   
Sbjct: 145 LELRPAKN------VLIDGVLGSGKTWVALDVCLS----------YKVQCKMDFKIF--- 185

Query: 120 VFQHWVLSMYIEYPILLAFALTVPVLIILQD-YHKVIKHPMDLG----TIKKRLENFYYW 174
               W+       P  +        L +LQ   +++  +          IK R+      
Sbjct: 186 ----WLNLKNCNSPETV--------LEMLQKLLYQIDPNWTSRSDHSSNIKLRIH----- 228

Query: 175 SGKEAISDF--NTMFTNCY-----VYNKPGEDVV----VMAQTLEKLFLTKVSARRESGR 223
           S +  +     +  + NC      V N           +  + L                
Sbjct: 229 SIQAELRRLLKSKPYENCLLVLLNVQNA---KAWNAFNLSCKIL---------------- 269

Query: 224 QIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLK-YCNEILKELFSKKHSSYA 282
                         TT+    VT      +     L         + +K L  K      
Sbjct: 270 -------------LTTRFK-QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK------ 309

Query: 283 WPFYKPVDAAWLGLNDY---HEIIK-KPMDLGTVKAKMDAREYKSSKEF-----ADDVRL 333
                     +L         E++   P  L  +   +  R+  ++ +       D +  
Sbjct: 310 ----------YLDCRPQDLPREVLTTNPRRLSIIAESI--RDGLATWDNWKHVNCDKLTT 357

Query: 334 IFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPIVSSSSMVPTLTVNKNNIGRWS 393
           I  +      P         + + +F+ +++  P    I         L++       W 
Sbjct: 358 IIESSLNVLEPA--------EYRKMFD-RLSVFPPSAHI-----PTILLSL------IWF 397

Query: 394 PDSSSDSTDSEADERARKLISLQDQVTPKPAT 425
            D          ++  +  +  +    PK +T
Sbjct: 398 -DVIKSDVMVVVNKLHKYSLVEKQ---PKEST 425

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	566
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	100.0
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	100.0
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	100.0
2r10_A	361	Chromatin structure-remodeling complex protein RSC	100.0
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.96
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.96
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.95
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.95
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.94
2dat_A	123	Possible global transcription activator SNF2L2; br	99.94
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.94
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.94
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.93
3d7c_A	112	General control of amino acid synthesis protein 5;	99.93
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.93
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.93
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.93
2grc_A	129	Probable global transcription activator SNF2L4; br	99.93
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.93
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.93
3d7c_A	112	General control of amino acid synthesis protein 5;	99.93
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.92
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.92
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.92
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.92
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.92
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.92
2dat_A	123	Possible global transcription activator SNF2L2; br	99.92
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.92
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.92
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.92
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.92
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.92
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.91
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.91
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.91
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.91
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.91
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.91
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.91
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.91
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.91
2grc_A	129	Probable global transcription activator SNF2L4; br	99.91
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.9
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.9
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.9
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.9
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.9
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.9
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.9
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.9
3uv4_A	158	Second bromodomain of human transcription initiat	99.9
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.9
2jns_A	90	Bromodomain-containing protein 4; ET-domain, struc	99.89
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.89
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.89
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.88
3uv4_A	158	Second bromodomain of human transcription initiat	99.88
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.88
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.88
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.87
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.87
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.87
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.86
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.86
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.86
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.86
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.86
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.84
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.83
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.83
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.79
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.77
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.76
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.72
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.44
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.4
2lm0_A	125	AF4/FMR2 family member 1/protein AF-9 chimera; int	95.53

>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=100.00  E-value=1.7e-46  Score=379.70  Aligned_cols=227  Identities=26%  Similarity=0.474  Sum_probs=192.1

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           76 NTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        76 ~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      ....|..+|..||+.|++|+.+|||..||+...  +|                                     |||.+|
T Consensus        11 ~~~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~--~p-------------------------------------dY~~iI   51 (265)
T 3uv5_A           11 PMVTLSSILESIINDMRDLPNTYPFHTPVNAKV--VK-------------------------------------DYYKII   51 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHTSTTCGGGTSCCCTTT--ST-------------------------------------THHHHC
T ss_pred             cHHHHHHHHHHHHHHHHcCCCchhhhCCCChhh--cC-------------------------------------CHHHHh
Confidence            356899999999999999999999999999643  56                                     999999


Q ss_pred             CCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccccccccCCCCCCCCC
Q psy245          156 KHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEG  235 (566)
Q Consensus       156 k~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~k~~~~~~~~~~~  235 (566)
                      ++||||+||++||++|.|.++.+|+.||+|||+||++||+++|.|+.+|..|...|++.|.++...-....+...     
T Consensus        52 ~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~l~~~~~~~~~~~~~~~~~~ek~i~-----  126 (265)
T 3uv5_A           52 TRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAIN-----  126 (265)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHS-----
T ss_pred             CCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhhhcCCCCChHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhh-----
Confidence            999999999999999999999999999999999999999999999999999999999999987642111100000     


Q ss_pred             CcccccccccCCCCCCCCCCCcchHHHHHHHHHHHHHHHhcc--CCCCCcCcccCCCccccCCCchhhhccCCCChHHHH
Q psy245          236 SFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSKK--HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVK  313 (566)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~~l~~~~--~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk  313 (566)
                              +.        ...    .....|..+|..+..++  ....+|||..||+..  .+||||++|++||||+||+
T Consensus       127 --------p~--------~dd----~~~~~~~~il~~i~~~~l~~~~~~~~F~~pv~~~--~~pdY~~iIk~Pmdl~tI~  184 (265)
T 3uv5_A          127 --------PL--------LDD----DDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKK--FVPDYYKVIVNPMDLETIR  184 (265)
T ss_dssp             --------TT--------TTC----HHHHHHHHHHHHHHHHTTTTSTTCGGGTSCCCTT--TSTTHHHHCSSCCCHHHHH
T ss_pred             --------hc--------ccc----chhhHHHHHHHHHHHHHHHhhhhhHHHhCCCChh--HhCcHHHHhCCcccHHHHH
Confidence                    00        000    11233444555544322  234789999999988  6999999999999999999


Q ss_pred             HHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          314 AKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       314 ~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      +||++|.|.++.+|..||+|||+||+.||+++|.||.+|..|+++|++.|.++..
T Consensus       185 ~kl~~~~Y~~~~~f~~D~~lif~Na~~yN~~~s~~~~~A~~l~~~~~~~~~~~~~  239 (265)
T 3uv5_A          185 KNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDE  239 (265)
T ss_dssp             HHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999998853

>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=100.00  E-value=3.2e-45  Score=374.92  Aligned_cols=225  Identities=26%  Similarity=0.469  Sum_probs=189.0

Q ss_pred             cHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCC
Q psy245           77 TNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIK  156 (566)
Q Consensus        77 ~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk  156 (566)
                      ...+..+|..||+.|++|+.+|||.+||+..  .+|                                     |||++|+
T Consensus        45 ~~~l~~~~~~il~~l~~~~~a~~F~~pV~~~--~~p-------------------------------------dY~~iIk   85 (292)
T 3aad_A           45 MVTLSSILESIINDMRDLPNTYPFHTPVNAK--VVK-------------------------------------DYYKIIT   85 (292)
T ss_dssp             HHHHHHHHHHHHHHHSSSTTCGGGSSSCCTT--TST-------------------------------------THHHHCS
T ss_pred             HHHHHHHHHHHHHHHHhCCcchhhcCCCCch--hcc-------------------------------------cHHHHcC
Confidence            3678899999999999999999999999964  356                                     9999999


Q ss_pred             CCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccccccccCCCCCCCCCC
Q psy245          157 HPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKKPNRGSDEGS  236 (566)
Q Consensus       157 ~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~k~~~~~~~~~~~~  236 (566)
                      +||||+||++||++|.|.++.+|..||+|||+||++||+++|.++.+|..|++.|++.|.++...-....+...      
T Consensus        86 ~PmDL~tIk~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~~~~~~~~~~~~~~~~e~~i~------  159 (292)
T 3aad_A           86 RPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAIN------  159 (292)
T ss_dssp             SCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCSSSHHHHHHTHHHHTTTTTGGGSHHHHHHHHHTTS------
T ss_pred             CcCCHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHhhhhcchhhhhhhhhccc------
Confidence            99999999999999999999999999999999999999999999999999999999999887542111100000      


Q ss_pred             cccccccccCCCCCCCCCCCcchHHHHHHHHHHHHHHHhc--cCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHH
Q psy245          237 FTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKELFSK--KHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA  314 (566)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~~l~~~--~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~  314 (566)
                             +.        ...    .....|..+|+.+...  .....+|||..|||..  .+||||++|++||||+||++
T Consensus       160 -------Pl--------~dd----~~~~~~~~~l~~i~~~~l~~~~~s~~F~~pvd~~--~~pdY~~iIk~PmdL~tI~~  218 (292)
T 3aad_A          160 -------PL--------LDD----DDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKK--FVPDYYKVIVNPMDLETIRK  218 (292)
T ss_dssp             -------SS--------TTC----HHHHHHHHHHHHHHHHTGGGSTTCGGGTSCCCTT--TSTTHHHHCSSCCCHHHHHH
T ss_pred             -------cc--------ccc----chhHHHHHHHHHHhhhhhhcCcchhHHHhccccc--ccccHHHHcCCcCCHHHHHH
Confidence                   00        000    0011244445544322  1234789999999987  69999999999999999999


Q ss_pred             HhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       315 kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      ||++|.|.++.+|.+||+|||+||+.||+++|.||.+|..|+++|++.|..+.
T Consensus       219 kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s~i~~~A~~L~~~~~~~~~~~~  271 (292)
T 3aad_A          219 NISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYD  271 (292)
T ss_dssp             HHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999998864

>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=100.00  E-value=5.2e-42  Score=353.24  Aligned_cols=205  Identities=24%  Similarity=0.346  Sum_probs=167.3

Q ss_pred             hhhhhhhhhccccccccCCcccccCCCCCCHHHHHHHhhccCCC-CHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHH
Q psy245          131 EYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYW-SGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEK  209 (566)
Q Consensus       131 ~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~-s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~  209 (566)
                      .+|.++.+|..+|++..+||||++|++||||+||++||  +.|. ++++|+.||+|||.||++||+++|.|+.+|..|++
T Consensus        43 ~~r~~~~~F~~p~~~~~~PdY~~iIk~PmDL~tI~~kl--~~y~~s~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~l~~  120 (311)
T 2r0y_A           43 KYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVM  120 (311)
T ss_dssp             HSHHHHGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHSC--CCSTTHHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHH
T ss_pred             cCCchhHHhcCCCCcccCCChHHHcCCCCCHHHHHHHH--hcccCCHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHH
Confidence            56777788888888888889999999999999999999  5555 89999999999999999999999999999999999


Q ss_pred             HHHHHhhhhccccccccCCCCCCCCCCcccccccccCCCCCCCCCCCcchHHHHHHHHHHHH-------HHH----hc--
Q psy245          210 LFLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILK-------ELF----SK--  276 (566)
Q Consensus       210 ~f~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~-------~l~----~~--  276 (566)
                      .|++.|.+......    +...     .      +            .......+.|..++.       .++    ..  
T Consensus       121 ~~~~~~~k~k~~~~----~~~i-----~------~------------~~k~~l~~~~~~l~~~~~~~i~~~l~~~r~~k~  173 (311)
T 2r0y_A          121 LIEFEVLKAKNLKR----NYLI-----N------S------------EVKAKLLHYLNKLVDATEKKINQALLGASSPKN  173 (311)
T ss_dssp             HHHHHHHHHHTGGG----CCBC-----C------H------------HHHHHHHHHHHHHHHCCHHHHHHHHHGGGSCSS
T ss_pred             HHHHHHhhcccCCC----CCCC-----C------h------------HHHHHHHHHHHHHHhhhHHHHHHHHhccccccc
Confidence            99999987532110    0000     0      0            000112223333321       111    10  


Q ss_pred             --cCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHH
Q psy245          277 --KHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKK  354 (566)
Q Consensus       277 --~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~  354 (566)
                        ....++|||++|||..  ++||||+||++||||+||++||++|.|.++.+|.+||+|||+||+.||+++|.||.+|..
T Consensus       174 ~~~~~~~s~~F~~pvd~~--~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~  251 (311)
T 2r0y_A          174 LDDKVKLSEPFMELVDKD--ELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATT  251 (311)
T ss_dssp             CCCSSCTTGGGSSCCCTT--TCHHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHH
T ss_pred             cccCCccHHHHhCCCChh--hcccHHHHhCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence              1235899999999987  689999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcC
Q psy245          355 LQDVFETKIAKA  366 (566)
Q Consensus       355 L~~~fe~~~~~~  366 (566)
                      |+++|+++|++.
T Consensus       252 L~~~f~~~~~~~  263 (311)
T 2r0y_A          252 LTNYFNYLIQKE  263 (311)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh
Confidence            999999999974

>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=100.00  E-value=6.4e-42  Score=360.02  Aligned_cols=204  Identities=24%  Similarity=0.356  Sum_probs=161.1

Q ss_pred             hhhhhhhhccccccccCCcccccCCCCCCHHHHHHHhhccCCC-CHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHH
Q psy245          132 YPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYW-SGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKL  210 (566)
Q Consensus       132 ~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~-s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~  210 (566)
                      ++.++.+|..+|++..+||||++|++||||+||++||  +.|. ++++|+.||+|||.||++||+++|.|+.+|..|+++
T Consensus        94 ~~~~~~~F~~p~~~~~~PdY~~iIk~Pmdl~tI~~kl--~~y~~~~~~f~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~  171 (361)
T 2r10_A           94 YKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVML  171 (361)
T ss_dssp             THHHHGGGSSCCCTTTCTTHHHHCSSCCCHHHHHTSC--CCSTTHHHHHHHHHHHHHHHHHHHBCSSSHHHHHHHHHHHH
T ss_pred             CCcccHHhcCCCCcccCCChHhhcCCCcCHHHHHHHh--hccCCCHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHH
Confidence            3344444444444555669999999999999999999  4554 899999999999999999999999999999999999


Q ss_pred             HHHHhhhhccccccccCCCCCCCCCCcccccccccCCCCCCCCCCCcchHHHHHHHHHHHHH-------HH----hc---
Q psy245          211 FLTKVSARRESGRQIKKPNRGSDEGSFTTQLATSVTSVGDQGSYAKPKLTESLKYCNEILKE-------LF----SK---  276 (566)
Q Consensus       211 f~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~c~~iL~~-------l~----~~---  276 (566)
                      |++.|.+.....    .+.       ..    .            ........+.|..++..       .+    ..   
T Consensus       172 ~~~~~~k~k~~~----~~~-------~i----~------------~~~k~~l~~~~~~l~~~~~~~i~~~~~~~r~~~~~  224 (361)
T 2r10_A          172 IEFEVLKAKNLK----RNY-------LI----N------------SEVKAKLLHYLNKLVDATEKKINQALLGASSPKNL  224 (361)
T ss_dssp             HHHHHHHHHTTT----TCC-------BC----C------------HHHHHHHHHHHHHHHHCCHHHHHHHHHGGGCCSSC
T ss_pred             HHHHHhhccccC----CcC-------cC----C------------HHHHHHHHHHHHHhhccchHHHHHHHhcccccccc
Confidence            999998653211    000       00    0            00011122334333321       11    00   


Q ss_pred             -cCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccCCCCCHHHHHHHHH
Q psy245          277 -KHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKL  355 (566)
Q Consensus       277 -~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~v~~~A~~L  355 (566)
                       ....++|||++|||..  ++||||+||++||||+||++||++|.|.++.+|.+||+|||+||+.||+++|.||.+|..|
T Consensus       225 ~~~~~~s~~F~~pvd~~--~~PdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L  302 (361)
T 2r10_A          225 DDKVKLSEPFMELVDKD--ELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTL  302 (361)
T ss_dssp             CCSSCTTGGGSSCCCTT--TCTHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHH
T ss_pred             ccCCcchhcccCCCChh--hcccHHHHhcCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence             1235899999999987  6999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcC
Q psy245          356 QDVFETKIAKA  366 (566)
Q Consensus       356 ~~~fe~~~~~~  366 (566)
                      +++|+.+|++.
T Consensus       303 ~~~f~~~~~~~  313 (361)
T 2r10_A          303 TNYFNYLIQKE  313 (361)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHh
Confidence            99999999974

>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=6.7e-30  Score=231.05  Aligned_cols=118  Identities=63%  Similarity=1.154  Sum_probs=107.0

Q ss_pred             CCCCCcchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHH
Q psy245          252 GSYAKPKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDV  331 (566)
Q Consensus       252 ~~~~~~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv  331 (566)
                      ...++.+++++++.|..||..|+++++..++|||.+|||+..+++||||++|++||||+||++||++|.|.++.+|.+||
T Consensus        13 ~~~k~~~~~~~l~~c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv   92 (130)
T 2ouo_A           13 APEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADV   92 (130)
T ss_dssp             ------CHHHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHH
T ss_pred             CCCCCcccHHHHHHHHHHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHH
Confidence            34567788999999999999999988766789999999998778999999999999999999999999999999999999


Q ss_pred             HHHHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCCC
Q psy245          332 RLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD  369 (566)
Q Consensus       332 ~Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~  369 (566)
                      +|||+||+.||+++|.||.+|..|+++|+++|++++.+
T Consensus        93 ~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~e  130 (130)
T 2ouo_A           93 RLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE  130 (130)
T ss_dssp             HHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHTSCC-
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHCCCC
Confidence            99999999999999999999999999999999999753

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

Probab=99.96  E-value=4.8e-29  Score=224.51  Aligned_cols=122  Identities=62%  Similarity=1.126  Sum_probs=115.1

Q ss_pred             CCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhcc
Q psy245           62 VQPPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALT  141 (566)
Q Consensus        62 ~~~~~~~~~~~~~~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~  141 (566)
                      +++|...++.+.++.+++|+++|+.|++.|++|+.+|||..|||...+++|                             
T Consensus         4 ~p~p~~~~~~~~~r~~~~l~~~~~~il~~L~~~~~a~~F~~PVd~~~~~~p-----------------------------   54 (127)
T 2oss_A            4 PPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLP-----------------------------   54 (127)
T ss_dssp             CCCCCCCCTTSCCCCCHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCT-----------------------------
T ss_pred             CCCCCcCCcCcCcccHHHHHHHHHHHHHHHHhCccchhhcCCCChhhccCc-----------------------------
Confidence            456677777888999999999999999999999999999999998766777                             


Q ss_pred             ccccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          142 VPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       142 lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                              |||++|++||||+||++||++|.|.++++|..||+|||+||++||+++|.++.+|..|++.|++.|++++.
T Consensus        55 --------dY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  125 (127)
T 2oss_A           55 --------DYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPT  125 (127)
T ss_dssp             --------THHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             --------cHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence                    99999999999999999999999999999999999999999999999999999999999999999999875

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

Probab=99.95  E-value=3.8e-29  Score=223.24  Aligned_cols=114  Identities=64%  Similarity=1.194  Sum_probs=107.5

Q ss_pred             cchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHh
Q psy245          257 PKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFT  336 (566)
Q Consensus       257 ~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~  336 (566)
                      .+++++++.|..||..|.++++..++|||.+|||+..+++||||++|++||||+||++||++|.|.++.+|.+||+|||+
T Consensus         5 ~~~~~~l~~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~   84 (120)
T 3jvl_A            5 SKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFS   84 (120)
T ss_dssp             CSSCHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHH
Confidence            46678999999999999999877789999999999988899999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCC
Q psy245          337 NCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV  370 (566)
Q Consensus       337 Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~  370 (566)
                      ||+.||+++|.||.+|..|+++|++.|++++.+.
T Consensus        85 Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~p~~~  118 (120)
T 3jvl_A           85 NCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEP  118 (120)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHTTCCC--
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            9999999999999999999999999999998754

>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=1.4e-28  Score=228.63  Aligned_cols=122  Identities=61%  Similarity=1.105  Sum_probs=109.0

Q ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhcccc
Q psy245           64 PPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVP  143 (566)
Q Consensus        64 ~~~~~~~~~~~~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP  143 (566)
                      .+.+++|.++++.+++|+.+|+.||+.|++++.+|||..|||...+++|                               
T Consensus        17 ~~~~~~p~~~~r~t~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~~~~P-------------------------------   65 (154)
T 4alg_A           17 GSHMSNPKKPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLP-------------------------------   65 (154)
T ss_dssp             ---------CCCCBHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCT-------------------------------
T ss_pred             CCCCCCCCCCCcchHHHHHHHHHHHHHHHhCcCchhhcCCCChhhccCC-------------------------------
Confidence            4566778889999999999999999999999999999999998777777                               


Q ss_pred             ccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcccc
Q psy245          144 VLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESG  222 (566)
Q Consensus       144 ~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~  222 (566)
                            |||++|++||||+||++||+++.|.++++|+.||+|||.||++||+++|.|+.+|..|++.|++.|.+++...
T Consensus        66 ------dY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~l~~~~  138 (154)
T 4alg_A           66 ------DYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEE  138 (154)
T ss_dssp             ------THHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHTTSCSSC
T ss_pred             ------CHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCchh
Confidence                  9999999999999999999999999999999999999999999999999999999999999999999998643

>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=99.94  E-value=3.5e-27  Score=212.38  Aligned_cols=112  Identities=42%  Similarity=0.797  Sum_probs=100.5

Q ss_pred             CCcchHHHHHH-HHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHH
Q psy245          255 AKPKLTESLKY-CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRL  333 (566)
Q Consensus       255 ~~~~~~~~~k~-c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~L  333 (566)
                      +.++....++. |..||..|.++.   .+|+|.+|||+..+++||||++|++||||+||++||++|.|.++.+|.+||+|
T Consensus        14 ~~~r~~~~l~~~~~~il~~L~~~~---~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~l   90 (127)
T 2oss_A           14 KPKRQTNQLQYLLRVVLKTLWKHQ---FAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNT   90 (127)
T ss_dssp             SCCCCCHHHHHHHHTHHHHHHTST---TCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHH
T ss_pred             cCcccHHHHHHHHHHHHHHHHhCc---cchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            33444455554 556999998876   78999999998767899999999999999999999999999999999999999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCCC
Q psy245          334 IFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD  369 (566)
Q Consensus       334 if~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~  369 (566)
                      ||+||+.||+++|.||.+|..|+++|+++|++++.+
T Consensus        91 i~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~~  126 (127)
T 2oss_A           91 MFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTE  126 (127)
T ss_dssp             HHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCC
Confidence            999999999999999999999999999999998753

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

Probab=99.94  E-value=1.1e-26  Score=208.14  Aligned_cols=107  Identities=23%  Similarity=0.394  Sum_probs=100.9

Q ss_pred             HHHHHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHh
Q psy245          260 TESLKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFT  336 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~  336 (566)
                      ..+.+.|..||+.|+.+++   ..++|+|.+||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+
T Consensus        12 ~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~   89 (123)
T 2dat_A           12 PKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRK--ELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCH   89 (123)
T ss_dssp             HHHHHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCTT--TSCHHHHHCSSCCCHHHHHHHHTTTCCCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhcccCCeeeHHhcCCCCcc--cCCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence            5778899999999999875   35799999999986  799999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          337 NCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       337 Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      ||+.||+++|.||.+|..|+++|+++++++|.
T Consensus        90 Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~ps  121 (123)
T 2dat_A           90 NAQTFNLEGSQIYEDSIVLQSVFKSARQSGPS  121 (123)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHcCC
Confidence            99999999999999999999999999999874

>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=99.94  E-value=6.3e-27  Score=217.40  Aligned_cols=115  Identities=42%  Similarity=0.821  Sum_probs=102.9

Q ss_pred             CCcchHHHHHHH-HHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHH
Q psy245          255 AKPKLTESLKYC-NEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRL  333 (566)
Q Consensus       255 ~~~~~~~~~k~c-~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~L  333 (566)
                      +.++++..++.| ..||+.|.++.   ++|||.+|||+..+++||||++|++||||+||++||++|.|.++.+|.+||+|
T Consensus        25 ~~~r~t~~l~~~~~~il~~l~~~~---~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~L  101 (154)
T 4alg_A           25 KPGRVTNQLQYLHKVVMKALWKHQ---FAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNT  101 (154)
T ss_dssp             -CCCCBHHHHHHHHTHHHHHHTST---TCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHHHHHHHhCc---CchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            344555666555 55788888875   78999999999988899999999999999999999999999999999999999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCC
Q psy245          334 IFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVPI  372 (566)
Q Consensus       334 if~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~~~  372 (566)
                      ||.||+.||+++|.||.+|..|+++|+++|++++.+..+
T Consensus       102 if~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~l~~~~~e  140 (154)
T 4alg_A          102 MFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQE  140 (154)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHTTSCSSCCB
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCchhcc
Confidence            999999999999999999999999999999999876543

>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=99.94  E-value=1e-26  Score=206.50  Aligned_cols=105  Identities=34%  Similarity=0.648  Sum_probs=99.0

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      .....++.|..||..|.+++   .+|||.+|||..  .+||||++|++||||+||++||++|.|.++++|.+||+|||.|
T Consensus        10 ~~~~~~~~c~~il~~l~~~~---~s~~F~~pv~~~--~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~N   84 (117)
T 3g0l_A           10 DDSKDLALCSMILTEMETHE---DAWPFLLPVNLK--LVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDN   84 (117)
T ss_dssp             CCTTHHHHHHHHHHHHHTST---TCGGGSSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhCC---CchhhcCcCChh--hcCChHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence            34467899999999999887   689999999997  5899999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       338 a~~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      |+.||+++|.+|.+|..|+++|+++|+++.
T Consensus        85 a~~yN~~~s~~~~~A~~L~~~f~~~~~~~~  114 (117)
T 3g0l_A           85 CETFNEDDSDIGRAGHNMRKYFEKKWTDTF  114 (117)
T ss_dssp             HHHHSCSSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999764

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

Probab=99.93  E-value=6.7e-27  Score=211.37  Aligned_cols=119  Identities=39%  Similarity=0.718  Sum_probs=101.1

Q ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhcCC---CCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhc
Q psy245           64 PPTVPPPHRPGRNTNQLAFISKNVLKPVMKHQH---AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFAL  140 (566)
Q Consensus        64 ~~~~~~~~~~~~~~~~l~~~~~~v~~~l~~~~~---~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~  140 (566)
                      .++.+++.+.++.++++++ |..||+.|+++++   +|||..|||...+++|                            
T Consensus         8 s~~~~~~~k~~~~~~~l~~-c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~p----------------------------   58 (130)
T 2ouo_A            8 SQQHPAPEKSSKVSEQLKC-CSGILKEMFAKKHAAYAWPFYKPVDVEALGLH----------------------------   58 (130)
T ss_dssp             -----------CHHHHHHH-HHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCT----------------------------
T ss_pred             CCCCCCCCCCcccHHHHHH-HHHHHHHHHhCCcchhHHHhcCCCChhhccCC----------------------------
Confidence            3444556677788888875 5679999999875   8999999998777777                            


Q ss_pred             cccccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          141 TVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       141 ~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                               |||++|++||||+||++||++|.|.++.+|..||+|||.||++||+++|.|+.+|..|++.|++.|.++|.
T Consensus        59 ---------dY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  129 (130)
T 2ouo_A           59 ---------DYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD  129 (130)
T ss_dssp             ---------THHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             ---------cHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence                     99999999999999999999999999999999999999999999999999999999999999999999874

>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=99.93  E-value=3.1e-26  Score=201.85  Aligned_cols=105  Identities=30%  Similarity=0.569  Sum_probs=99.6

Q ss_pred             hHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcc
Q psy245          259 LTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNC  338 (566)
Q Consensus       259 ~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  338 (566)
                      ...+...|..||..|.+++   .+|||.+|||+.  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+||
T Consensus         5 ~~~l~~~~~~il~~l~~~~---~~~~F~~pvd~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na   79 (112)
T 3d7c_A            5 PDQLYTTLKNLLAQIKSHP---SAWPFMEPVKKS--EAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANC   79 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHSG---GGGGGSSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCC---CchhhcCCCCcc--cccCHHHHccCCcCHHHHHHHHcCCCCcCHHHHHHHHHHHHHHH
Confidence            3567899999999999987   789999999987  69999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          339 YKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       339 ~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      +.||+++|.+|.+|..|++.|+++|+++..
T Consensus        80 ~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~  109 (112)
T 3d7c_A           80 REYNPPDSEYCRCASALEKFFYFKLKEGGL  109 (112)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            999999999999999999999999998764

>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=99.93  E-value=1.5e-26  Score=206.65  Aligned_cols=104  Identities=34%  Similarity=0.657  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      ...+.|..||..|..+.   .+|||.+|||..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+||+.
T Consensus        13 ~~~~~~~~il~~l~~~~---~a~~F~~pvd~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~   87 (121)
T 1e6i_A           13 PHDAAIQNILTELQNHA---AAWPFLQPVNKE--EVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRM   87 (121)
T ss_dssp             TTHHHHHHHHHHHHHST---TCGGGSSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCC---CchhhCCCCChh--hCcCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            34678999999999876   789999999987  6999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHcCCCC
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAKAPDD  369 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~~~~~  369 (566)
                      ||+++|.+|.+|..|+++|+++|++++.+
T Consensus        88 yN~~~s~i~~~A~~L~~~f~~~~~~~p~~  116 (121)
T 1e6i_A           88 YNGENTSYYKYANRLEKFFNNKVKEIPEY  116 (121)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHTSGGG
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence            99999999999999999999999998654

>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=99.93  E-value=5e-26  Score=204.11  Aligned_cols=108  Identities=23%  Similarity=0.349  Sum_probs=100.6

Q ss_pred             hHHHHHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHH
Q psy245          259 LTESLKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIF  335 (566)
Q Consensus       259 ~~~~~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif  335 (566)
                      ...+.+.|..||..|...++   ..++++|..||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||
T Consensus        13 ~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~--~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~   90 (124)
T 3mb4_A           13 MTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRS--ELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMF   90 (124)
T ss_dssp             CCHHHHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTT--TCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHhHhcccCCcccHHhhcCCCcc--ccCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            45677899999999998664   46889999999987  79999999999999999999999999999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          336 TNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       336 ~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      .||+.||+++|.||.+|..|+++|++.|+++..
T Consensus        91 ~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~  123 (124)
T 3mb4_A           91 NNACTYNEPESLIYKDALVLHKVLLETRRDLEG  123 (124)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999998854

>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=99.93  E-value=6.4e-26  Score=201.40  Aligned_cols=111  Identities=29%  Similarity=0.494  Sum_probs=102.2

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCC
Q psy245           70 PHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQ  149 (566)
Q Consensus        70 ~~~~~~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~p  149 (566)
                      .+++++........|..|++.|++|+.+|||..|||...  +|                                     
T Consensus         4 ~~k~~~~~~~~~~~c~~il~~l~~~~~s~~F~~pv~~~~--~p-------------------------------------   44 (117)
T 3g0l_A            4 VKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKL--VP-------------------------------------   44 (117)
T ss_dssp             CCCCCCCCTTHHHHHHHHHHHHHTSTTCGGGSSCCCTTT--ST-------------------------------------
T ss_pred             CcCCCcCCHHHHHHHHHHHHHHHhCCCchhhcCcCChhh--cC-------------------------------------
Confidence            445566666777888999999999999999999999643  56                                     


Q ss_pred             cccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          150 DYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       150 dY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      |||++|++||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.|.++-
T Consensus        45 dY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~  114 (117)
T 3g0l_A           45 GYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTF  114 (117)
T ss_dssp             THHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCSSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999998864

>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=99.93  E-value=6.2e-26  Score=204.82  Aligned_cols=109  Identities=22%  Similarity=0.334  Sum_probs=101.4

Q ss_pred             chHHHHHHHHHHHHHHHhccC----CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHH
Q psy245          258 KLTESLKYCNEILKELFSKKH----SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRL  333 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~----~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~L  333 (566)
                      ....+.+.|..||..|+.+++    ..++|+|..||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|
T Consensus         8 ~~~~l~~~~~~il~~l~~~~d~~~~~~~s~~F~~pv~~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~L   85 (129)
T 2grc_A            8 NPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRK--ELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVML   85 (129)
T ss_dssp             CCHHHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTT--TCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHhcccccccCeeeHHhcCCCCcc--cCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            345778999999999999874    35789999999976  799999999999999999999999999999999999999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          334 IFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       334 if~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      ||+||+.||+++|.||.+|..|+++|++.|+++..
T Consensus        86 i~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~  120 (129)
T 2grc_A           86 LCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEK  120 (129)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccC
Confidence            99999999999999999999999999999998854

>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=99.93  E-value=9.6e-26  Score=200.85  Aligned_cols=107  Identities=36%  Similarity=0.638  Sum_probs=99.4

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      ...+..+.|..+|..|+...  ..+|||.+|||+..+++||||++|++||||+||++||++|.|.++.+|.+||+|||+|
T Consensus         8 ~~~el~~~l~~~l~~l~~~~--~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~N   85 (119)
T 3p1f_A            8 KPEELRQALMPTLEALYRQD--PESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNN   85 (119)
T ss_dssp             CHHHHHHHHHHHHHHHHTCT--TTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhC--CCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            34567889999999998743  3789999999998878999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          338 CYKYNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       338 a~~yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      |+.||+++|.+|.+|..|+++|++.|.++
T Consensus        86 a~~yN~~~s~i~~~A~~L~~~f~~~~~~~  114 (119)
T 3p1f_A           86 AWLYNRKTSRVYKFCSKLAEVFEQEIDPV  114 (119)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999875

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

Probab=99.93  E-value=9.4e-26  Score=212.05  Aligned_cols=107  Identities=28%  Similarity=0.431  Sum_probs=97.6

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      ....+.+.|..||..|+++.   .+|||..|||+..+++||||++|++||||+||++||++|.|.++.+|.+||+|||.|
T Consensus        18 ~~~~~~~~~~~il~~L~~~~---~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~N   94 (166)
T 3fkm_X           18 GNKQWYLLANQLILSLSKYE---GGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDN   94 (166)
T ss_dssp             TTHHHHHHHHHHHHHHTTST---TGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhCC---CChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence            44688999999999999877   688999999998778999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       338 a~~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      |+.||+++|.|+.+|..|+++|++.|.++.
T Consensus        95 a~~yN~~~s~i~~~A~~L~~~f~~~l~~~~  124 (166)
T 3fkm_X           95 CSLYNTSNSVVAITGKNIETYFNNQLIVMG  124 (166)
T ss_dssp             HHHSSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            999999999999999999999999999875

>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=99.93  E-value=7.8e-26  Score=199.31  Aligned_cols=107  Identities=36%  Similarity=0.627  Sum_probs=101.3

Q ss_pred             CCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCccccc
Q psy245           75 RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKV  154 (566)
Q Consensus        75 ~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~i  154 (566)
                      +.+++|+..|..|++.|++|+.+|||..|||..  ++|                                     |||++
T Consensus         3 ~~~~~l~~~~~~il~~l~~~~~~~~F~~pvd~~--~~p-------------------------------------dY~~i   43 (112)
T 3d7c_A            3 EDPDQLYTTLKNLLAQIKSHPSAWPFMEPVKKS--EAP-------------------------------------DYYEV   43 (112)
T ss_dssp             CSHHHHHHHHHHHHHHHHHSGGGGGGSSCCCTT--TST-------------------------------------THHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCchhhcCCCCcc--ccc-------------------------------------CHHHH
Confidence            467899999999999999999999999999964  466                                     99999


Q ss_pred             CCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          155 IKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       155 Ik~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      |++||||+||++||++|.|.++.+|.+||+|||.||++||+++|.++.+|..|++.|++.|++++.
T Consensus        44 Ik~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~  109 (112)
T 3d7c_A           44 IRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEGGL  109 (112)
T ss_dssp             CSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             ccCCcCHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            999999999999999999999999999999999999999999999999999999999999998753

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

Probab=99.92  E-value=1.2e-25  Score=204.39  Aligned_cols=107  Identities=32%  Similarity=0.595  Sum_probs=99.6

Q ss_pred             hHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhC--CCCCCHHHHHHHHHHHHh
Q psy245          259 LTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA--REYKSSKEFADDVRLIFT  336 (566)
Q Consensus       259 ~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~--~~Y~s~~ef~~Dv~Lif~  336 (566)
                      ...+++.|..||..|+++.   .+|+|.+||+.   ++||||++|++||||+||++||++  |.|.++.+|.+||+|||+
T Consensus        18 ~p~~~~~c~~il~~L~~~~---~s~~F~~Pv~~---~~pdY~~iIk~PmDL~tI~~kL~~~~~~Y~s~~ef~~Dv~Lif~   91 (135)
T 2yyn_A           18 TPIDKRKCERLLLFLYCHE---MSLAFQDPVPL---TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQ   91 (135)
T ss_dssp             CHHHHHHHHHHHHHHHTSG---GGGGGSSCCCT---TSTTHHHHCSSCCCHHHHHHHHHSSSCCCSSHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhCc---cchhhcCCCcc---cCCCHHHHcCCCCCHHHHHHHHhccccCCCCHHHHHHHHHHHHH
Confidence            4567899999999999876   78999999997   489999999999999999999998  599999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCCC
Q psy245          337 NCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVP  371 (566)
Q Consensus       337 Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~~  371 (566)
                      ||+.||+++|.||.+|..|+++|+++|+++..+..
T Consensus        92 Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~~  126 (135)
T 2yyn_A           92 NCAEFNEPDSEVANAGIKLENYFEELLKNLYPEKR  126 (135)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHhccccC
Confidence            99999999999999999999999999999876653

>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=99.92  E-value=1.1e-25  Score=199.66  Aligned_cols=100  Identities=30%  Similarity=0.628  Sum_probs=95.7

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      ++.+.|..+|..|..++   .+|||..|||+.  .+||||++|++||||+||++||++|.|.++.+|.+||+|||.||+.
T Consensus        16 ~~~~~~~~il~~l~~~~---~s~~F~~pv~~~--~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~   90 (116)
T 3nxb_A           16 DDFTAMYKVLDVVKAHK---DSWPFLEPVDES--YAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRK   90 (116)
T ss_dssp             CHHHHHHHHHHHHHHST---TCGGGSSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCC---CcHhhcCcCChh--hccChHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            46789999999999987   678999999998  6899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHc
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAK  365 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~  365 (566)
                      ||+++|.++.+|..|+++|++.|.+
T Consensus        91 yN~~~s~~~~~A~~L~~~f~~~~~k  115 (116)
T 3nxb_A           91 YNGESSEYTKMSDNLERCFHRAMMK  115 (116)
T ss_dssp             HHCTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999975

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

Probab=99.92  E-value=1.7e-25  Score=198.32  Aligned_cols=106  Identities=29%  Similarity=0.361  Sum_probs=98.7

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      ......+.|..||+.|.++.   .+++|..|||+.  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+|
T Consensus         5 ~~~~l~~~l~~il~~L~~~~---~~~~F~~PVd~~--~~pdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Li~~N   79 (117)
T 2i7k_A            5 EQTPLQEALNQLMRQLQRKD---PSAFFSFPVTDF--IAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTN   79 (117)
T ss_dssp             THHHHHHHHHHHHHHHHTSS---GGGTSSSCCCTT--TSSSHHHHCSCCCCHHHHHHHHTTTSCCSHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHhCc---ccHHhcCCCCcc--ccCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence            45677899999999999876   678999999986  6899999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       338 a~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      |+.||+++|.+|.+|..|++.|++.|.....
T Consensus        80 a~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  110 (117)
T 2i7k_A           80 AMIYNKPETIYYKAAKKLLHSGMKILSQERL  110 (117)
T ss_dssp             HHHTSCSSSSHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999987644

>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=99.92  E-value=9.8e-26  Score=199.88  Aligned_cols=106  Identities=23%  Similarity=0.396  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          261 ESLKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      .+++.|..|+..|..+++   ..++|+|.+||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+|
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 DPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRR--NQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNN   82 (116)
T ss_dssp             CHHHHHHHHHHHHHHCBCTTCCBGGGGGSSCCCGG--GCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhccCCCeeeHHhcCCCCcc--cCCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence            467899999999999875   35799999999976  6999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       338 a~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      |+.||+++|.+|.+|..|+++|++.++++..
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            9999999999999999999999999998743

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

Probab=99.92  E-value=1.8e-25  Score=199.56  Aligned_cols=104  Identities=31%  Similarity=0.439  Sum_probs=97.6

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      .+...|..||..|.++.   .+|||.+|||+.  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+||+.
T Consensus         7 pl~~~l~~il~~l~~~~---~~~~F~~pv~~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~   81 (121)
T 2d9e_A            7 GFLILLRKTLEQLQEKD---TGNIFSEPVPLS--EVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLK   81 (121)
T ss_dssp             HHHHHHHHHHHHHHHHC---SSCSSSSCCCTT--TCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCC---ccHhhCCcCCcc--ccCCHHHHcCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            45678999999999987   678999999987  6999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHcCCCC
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAKAPDD  369 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~~~~~  369 (566)
                      ||+++|.+|.+|..|++.|+..|.++...
T Consensus        82 yN~~~s~~~~~A~~L~~~~~~~l~~~~~~  110 (121)
T 2d9e_A           82 YNAKDTIFYRAAVRLREQGGAVLRQARRQ  110 (121)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999987543

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

Probab=99.92  E-value=1.4e-25  Score=210.97  Aligned_cols=113  Identities=26%  Similarity=0.391  Sum_probs=100.6

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCc
Q psy245           71 HRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQD  150 (566)
Q Consensus        71 ~~~~~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pd  150 (566)
                      ....+.+.+|+..|..||+.|++++.+|||..|||+..+++|                                     |
T Consensus        13 ~~~~p~~~~~~~~~~~il~~L~~~~~s~~F~~PVd~~~~~~p-------------------------------------d   55 (166)
T 3fkm_X           13 NLYFQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCP-------------------------------------D   55 (166)
T ss_dssp             ----CTTHHHHHHHHHHHHHHTTSTTGGGGSSCCC-----CC-------------------------------------C
T ss_pred             cCCCcccHHHHHHHHHHHHHHHhCCCChhhcCCCChhhccCC-------------------------------------C
Confidence            344566789999999999999999999999999998776777                                     9


Q ss_pred             ccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          151 YHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       151 Y~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ||.+|++||||+||++||.+|.|.++.+|+.||+|||.||++||+++|.|+.+|..|++.|++.|.++..
T Consensus        56 Y~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~~~f~~~l~~~~~  125 (166)
T 3fkm_X           56 YYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFNNQLIVMGY  125 (166)
T ss_dssp             GGGCCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHHHSSCTTSHHHHHHHHHHHHHHHHHHHTTH
T ss_pred             HHHhcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999998763

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

Probab=99.92  E-value=2.2e-25  Score=199.55  Aligned_cols=108  Identities=21%  Similarity=0.317  Sum_probs=99.9

Q ss_pred             CCCcHHHHHHHHHHHHHHHhcC------CCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhcccccccc
Q psy245           74 GRNTNQLAFISKNVLKPVMKHQ------HAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLII  147 (566)
Q Consensus        74 ~~~~~~l~~~~~~v~~~l~~~~------~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~  147 (566)
                      ...+..|+..|+.||+.|++|+      .+|||..||+.  .++|                                   
T Consensus         8 ~~~~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~--~~~p-----------------------------------   50 (123)
T 2dat_A            8 SPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSR--KELP-----------------------------------   50 (123)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCT--TTSC-----------------------------------
T ss_pred             CCCCHHHHHHHHHHHHHHHhhhcccCCeeeHHhcCCCCc--ccCC-----------------------------------
Confidence            3456899999999999999997      48899999884  3456                                   


Q ss_pred             CCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          148 LQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       148 ~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                        |||++|++||||+||++||+++.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.++++|.
T Consensus        51 --dY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~ps  121 (123)
T 2dat_A           51 --EYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQSGPS  121 (123)
T ss_dssp             --HHHHHCSSCCCHHHHHHHHTTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             --CHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHcCC
Confidence              99999999999999999999999999999999999999999999999999999999999999999999885

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

Probab=99.92  E-value=1.9e-25  Score=200.08  Aligned_cols=106  Identities=38%  Similarity=0.689  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      ..+.+.|..||..|++++   .+|||..||++.  ++||||++|++||||+||++||++|.|.++.+|..||+|||.||+
T Consensus         9 ~~~~~~c~~il~~l~~~~---~s~~F~~pv~~~--~~pdY~~~I~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~   83 (123)
T 3q2e_A            9 SNWKKQCKELVNLIFQCE---DSEPFRQPVDLV--EYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAK   83 (123)
T ss_dssp             -CHHHHHHHHHHHHHTSG---GGGGGSSCCCTT--TCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCC---CcHhhcCCCChh--hcCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence            367889999999999988   678999999998  699999999999999999999999999999999999999999999


Q ss_pred             ccCCC-CCHHHHHHHHHHHHHHHHHHcCCCCC
Q psy245          340 KYNPP-DHDVVAMAKKLQDVFETKIAKAPDDV  370 (566)
Q Consensus       340 ~yN~~-~s~v~~~A~~L~~~fe~~~~~~~~~~  370 (566)
                      .||++ +|.||.+|..|+++|+++|+++..+.
T Consensus        84 ~yN~~~~s~i~~~A~~L~~~f~~~~~~~~~~~  115 (123)
T 3q2e_A           84 AYTPNKRSKIYSMTLRLSALFEEKMKKISSDF  115 (123)
T ss_dssp             HHSCCTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99996 99999999999999999999886543

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

Probab=99.92  E-value=1.7e-25  Score=203.57  Aligned_cols=105  Identities=35%  Similarity=0.631  Sum_probs=99.0

Q ss_pred             hHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcc
Q psy245          259 LTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNC  338 (566)
Q Consensus       259 ~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  338 (566)
                      +..+.+.|..||..|++++   .+|||..|||..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||.||
T Consensus        19 ~~~l~~~~~~il~~l~~~~---~s~~F~~pv~~~--~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na   93 (135)
T 3mb3_A           19 IQAWKKQCEELLNLIFQCE---DSEPFRQPVDLL--EYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNS   93 (135)
T ss_dssp             SSTHHHHHHHHHHHHHHSG---GGGGGSSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCC---CChhhcCCCChh--hCCCHHHHhCCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Confidence            4578899999999999988   588999999986  79999999999999999999999999999999999999999999


Q ss_pred             cccCCC-CCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          339 YKYNPP-DHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       339 ~~yN~~-~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      +.||++ +|.||.+|..|+++|++.|.++..
T Consensus        94 ~~yN~~~~s~i~~~A~~L~~~f~~~~~~~~~  124 (135)
T 3mb3_A           94 KAYTPSKRSRIYSMSLRLSAFFEEHISSVLS  124 (135)
T ss_dssp             HHHSCCTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999998 999999999999999999998643

>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=99.92  E-value=2.3e-25  Score=200.35  Aligned_cols=107  Identities=23%  Similarity=0.284  Sum_probs=98.7

Q ss_pred             hHHHHHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHH
Q psy245          259 LTESLKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIF  335 (566)
Q Consensus       259 ~~~~~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif  335 (566)
                      .....+.|..+++.|..+++   ..++|||.+||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||
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 AARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKK--KNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVF   84 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGG--GCTTHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCcCCCChhHHhcCCCCcc--cCCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            34567788999999988764   45799999999988  69999999999999999999999999999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          336 TNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       336 ~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      +||+.||+++|.+|.+|..|+++|++.|.++.
T Consensus        85 ~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~  116 (126)
T 3mqm_A           85 RNAEKYYGRKSPVGRDVCRLRKAYYNARHEAS  116 (126)
T ss_dssp             HHHHHHHCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999998764

>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=99.92  E-value=3.5e-25  Score=199.99  Aligned_cols=110  Identities=24%  Similarity=0.371  Sum_probs=99.7

Q ss_pred             cchHHHHHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHH
Q psy245          257 PKLTESLKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRL  333 (566)
Q Consensus       257 ~~~~~~~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~L  333 (566)
                      .....+..+|..+++.|....+   ..++|||.+||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|
T Consensus        13 ~~~~kl~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~--~~PdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~L   90 (130)
T 3k2j_A           13 LGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKK--KYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNL   90 (130)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTT--TCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHhcccCCCccHhhcCCCChh--hCccHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            3455667788888888887664   35799999999987  799999999999999999999999999999999999999


Q ss_pred             HHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          334 IFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       334 if~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      ||.||+.||+++|.||.+|..|+++|+++|+++..
T Consensus        91 if~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~  125 (130)
T 3k2j_A           91 MFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELAR  125 (130)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999998753

>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=99.92  E-value=3.3e-25  Score=197.41  Aligned_cols=111  Identities=28%  Similarity=0.482  Sum_probs=103.1

Q ss_pred             CCCCCcHHHHHHHHHHHHHHHh-cCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCc
Q psy245           72 RPGRNTNQLAFISKNVLKPVMK-HQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQD  150 (566)
Q Consensus        72 ~~~~~~~~l~~~~~~v~~~l~~-~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pd  150 (566)
                      +......+|...|..++..|++ ++.+|||..|||+..+++|                                     |
T Consensus         4 ~~~~~~~el~~~l~~~l~~l~~~~~~s~~F~~pv~~~~~~~p-------------------------------------d   46 (119)
T 3p1f_A            4 KKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIP-------------------------------------D   46 (119)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCT-------------------------------------T
T ss_pred             cccCCHHHHHHHHHHHHHHHHHhCCCCchhcCCCCchhccCC-------------------------------------C
Confidence            3345677899999999999998 7799999999998766777                                     9


Q ss_pred             ccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          151 YHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       151 Y~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      ||++|++||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.+.++.
T Consensus        47 Y~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  115 (119)
T 3p1f_A           47 YFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVM  115 (119)
T ss_dssp             HHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999998764

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

Probab=99.91  E-value=5.1e-25  Score=197.20  Aligned_cols=104  Identities=36%  Similarity=0.433  Sum_probs=96.2

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      ......+.|..+|..|..+.   .+++|..|||+.  .+||||++|++||||+||++||++|.|.++.+|.+||+|||.|
T Consensus        10 ~~~p~~~~l~~il~~l~~~~---~~~~F~~pv~~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~N   84 (123)
T 3hme_A           10 ESTPIQQLLEHFLRQLQRKD---PHGFFAFPVTDA--IAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDN   84 (123)
T ss_dssp             -CCHHHHHHHHHHHHHHTTC---TTCSSSSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhCC---ccHhhcCCCChh--hccCHHHHCCCCCCHHHHHHHhccCCCCCHHHHHHHHHHHHHH
Confidence            34466788999999999877   567999999987  6899999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          338 CYKYNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       338 a~~yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      |+.||+++|.+|.+|..|++.|++.|.+.
T Consensus        85 a~~yN~~~s~~~~~A~~L~~~~~~~~~~~  113 (123)
T 3hme_A           85 AMTYNRPDTVYYKLAKKILHAGFKMMSKE  113 (123)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999998753

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

Probab=99.91  E-value=5.3e-25  Score=196.49  Aligned_cols=106  Identities=25%  Similarity=0.389  Sum_probs=99.6

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           76 NTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        76 ~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      ....|+..|+.||+.|++|+.+|||..|||..  ++|                                     |||++|
T Consensus         4 ~~~pl~~~l~~il~~l~~~~~~~~F~~pv~~~--~~p-------------------------------------dY~~iI   44 (121)
T 2d9e_A            4 GSSGFLILLRKTLEQLQEKDTGNIFSEPVPLS--EVP-------------------------------------DYLDHI   44 (121)
T ss_dssp             CCCHHHHHHHHHHHHHHHHCSSCSSSSCCCTT--TCT-------------------------------------THHHHC
T ss_pred             cccHHHHHHHHHHHHHHcCCccHhhCCcCCcc--ccC-------------------------------------CHHHHc
Confidence            34578899999999999999999999999964  466                                     999999


Q ss_pred             CCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          156 KHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       156 k~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ++||||+||++||++|.|.++.+|..||+|||.||++||+++|.++.+|..|++.|+..|.++..
T Consensus        45 k~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~~~~~l~~~~~  109 (121)
T 2d9e_A           45 KKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARR  109 (121)
T ss_dssp             SSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999998765

>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=99.91  E-value=2.9e-25  Score=198.03  Aligned_cols=109  Identities=40%  Similarity=0.732  Sum_probs=100.3

Q ss_pred             CCCcHHHHHHHHHHHHHHHhcCC---CCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCc
Q psy245           74 GRNTNQLAFISKNVLKPVMKHQH---AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQD  150 (566)
Q Consensus        74 ~~~~~~l~~~~~~v~~~l~~~~~---~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pd  150 (566)
                      +..+.+++ .|..||..|++++.   +|||..|||...+++|                                     |
T Consensus         5 ~~~~~~l~-~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~p-------------------------------------d   46 (120)
T 3jvl_A            5 SKISEQLK-CCSGILKEMFAKKHAAYAWPFYKPVDVEALGLH-------------------------------------D   46 (120)
T ss_dssp             CSSCHHHH-HHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCT-------------------------------------T
T ss_pred             hhhHHHHH-HHHHHHHHHHhCcCccccchhcCCCCchhcCCC-------------------------------------C
Confidence            34455555 45679999999988   9999999998887777                                     9


Q ss_pred             ccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          151 YHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       151 Y~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ||++|++||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.|.+++.
T Consensus        47 Y~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~p~  116 (120)
T 3jvl_A           47 YCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD  116 (120)
T ss_dssp             HHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCcC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999874

>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=99.91  E-value=4.1e-25  Score=197.07  Aligned_cols=108  Identities=25%  Similarity=0.364  Sum_probs=99.3

Q ss_pred             hHHHHHHHHHHHHHHHhccC---CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHH
Q psy245          259 LTESLKYCNEILKELFSKKH---SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIF  335 (566)
Q Consensus       259 ~~~~~k~c~~iL~~l~~~~~---~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif  335 (566)
                      ...+.+.|..++..|...++   ..++++|.+||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||
T Consensus         6 p~~l~~~~~~ll~~l~~~~d~~g~~~s~~F~~~~~~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~   83 (120)
T 3ljw_A            6 PAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKV--QYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLA   83 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHCBCTTSCBTTGGGSSCCCTT--TCHHHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccCcCCCcccHHhcCCCCcc--cCCChHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence            34667889999999988765   34689999999987  79999999999999999999999999999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          336 TNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       336 ~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      +||+.||+++|.||.+|..|+++|+++|++++.
T Consensus        84 ~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~i~~  116 (120)
T 3ljw_A           84 KNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEH  116 (120)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999999999999999999999999998753

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

Probab=99.91  E-value=1e-24  Score=193.40  Aligned_cols=107  Identities=28%  Similarity=0.387  Sum_probs=100.2

Q ss_pred             CCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCccccc
Q psy245           75 RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKV  154 (566)
Q Consensus        75 ~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~i  154 (566)
                      .....|+..|..|++.|++++.+|+|..||+.  .++|                                     |||++
T Consensus         4 ~~~~~l~~~l~~il~~L~~~~~~~~F~~PVd~--~~~p-------------------------------------dY~~i   44 (117)
T 2i7k_A            4 VEQTPLQEALNQLMRQLQRKDPSAFFSFPVTD--FIAP-------------------------------------GYSMI   44 (117)
T ss_dssp             TTHHHHHHHHHHHHHHHHTSSGGGTSSSCCCT--TTSS-------------------------------------SHHHH
T ss_pred             cchHHHHHHHHHHHHHHHhCcccHHhcCCCCc--cccC-------------------------------------CHHHH
Confidence            45678999999999999999999999999995  3466                                     99999


Q ss_pred             CCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          155 IKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       155 Ik~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      |++||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.+....-
T Consensus        45 Ik~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  110 (117)
T 2i7k_A           45 IKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERL  110 (117)
T ss_dssp             CSCCCCHHHHHHHHTTTSCCSHHHHHHHHHHHHHHHHHTSCSSSSHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999987653

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

Probab=99.91  E-value=1.3e-24  Score=197.80  Aligned_cols=106  Identities=33%  Similarity=0.503  Sum_probs=99.2

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      ++..+...|..+|..|..++   .+|+|..||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+|
T Consensus        10 ~~~~l~~~l~~il~~l~~~~---~~~~F~~pv~~~--~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~N   84 (135)
T 3rcw_A           10 RLTPLTVLLRSVLDQLQDKD---PARIFAQPVSLK--EVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDN   84 (135)
T ss_dssp             CCCHHHHHHHHHHHHHHHTC---TTCSSSSCCCTT--TCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHhCC---cchhhcCCCChh--hcCCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            44567889999999999987   678999999998  7999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       338 a~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      |+.||+++|.+|.+|..|++.|++.|.++..
T Consensus        85 a~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~  115 (135)
T 3rcw_A           85 CMKYNARDTVFYRAAVRLRDQGGVVLRQARR  115 (135)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999997643

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

Probab=99.91  E-value=6.1e-25  Score=199.93  Aligned_cols=109  Identities=27%  Similarity=0.444  Sum_probs=100.6

Q ss_pred             CCCCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCccc
Q psy245           73 PGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYH  152 (566)
Q Consensus        73 ~~~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~  152 (566)
                      +......|+..|..||+.|++|+.+|||..|||.  .++|                                     |||
T Consensus        15 ~~~~~~~l~~~~~~il~~l~~~~~s~~F~~pv~~--~~~p-------------------------------------dY~   55 (135)
T 3mb3_A           15 QSYDIQAWKKQCEELLNLIFQCEDSEPFRQPVDL--LEYP-------------------------------------DYR   55 (135)
T ss_dssp             --CCSSTHHHHHHHHHHHHHHSGGGGGGSSCCCT--TTST-------------------------------------THH
T ss_pred             CCcCHHHHHHHHHHHHHHHHhCCCChhhcCCCCh--hhCC-------------------------------------CHH
Confidence            3445568999999999999999999999999996  3466                                     999


Q ss_pred             ccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCC-CCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          153 KVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKP-GEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       153 ~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~-~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ++|++||||+||++||++|.|.++++|..||+|||.||++||++ +|.|+.+|..|++.|++.|..+..
T Consensus        56 ~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~~s~i~~~A~~L~~~f~~~~~~~~~  124 (135)
T 3mb3_A           56 DIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLS  124 (135)
T ss_dssp             HHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCCTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999997 899999999999999999998765

>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=99.91  E-value=8.6e-25  Score=195.18  Aligned_cols=100  Identities=38%  Similarity=0.602  Sum_probs=94.7

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCCH
Q psy245           82 FISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDL  161 (566)
Q Consensus        82 ~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMdL  161 (566)
                      ..|..|++.|++|+.+|||..|||..  ++|                                     |||++|++||||
T Consensus        16 ~~~~~il~~l~~~~~a~~F~~pvd~~--~~p-------------------------------------dY~~iIk~PmdL   56 (121)
T 1e6i_A           16 AAIQNILTELQNHAAAWPFLQPVNKE--EVP-------------------------------------DYYDFIKEPMDL   56 (121)
T ss_dssp             HHHHHHHHHHHHSTTCGGGSSCCCTT--TST-------------------------------------THHHHCSSCCCH
T ss_pred             HHHHHHHHHHHcCCCchhhCCCCChh--hCc-------------------------------------CHHHHcCCCCCH
Confidence            45778999999999999999999964  466                                     999999999999


Q ss_pred             HHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          162 GTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       162 ~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      +||++||++|.|.++.+|..||+|||.||++||+++|.++.+|..|++.|++.+.++|.
T Consensus        57 ~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~p~  115 (121)
T 1e6i_A           57 STMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPE  115 (121)
T ss_dssp             HHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHTSGG
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccc
Confidence            99999999999999999999999999999999999999999999999999999999875

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

Probab=99.91  E-value=7.1e-25  Score=196.34  Aligned_cols=109  Identities=27%  Similarity=0.446  Sum_probs=99.1

Q ss_pred             CCCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccc
Q psy245           74 GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHK  153 (566)
Q Consensus        74 ~~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~  153 (566)
                      ++....|+..|..||+.|++|+.+|||..||+..  .+|                                     |||.
T Consensus         5 ~~~~~~~~~~c~~il~~l~~~~~s~~F~~pv~~~--~~p-------------------------------------dY~~   45 (123)
T 3q2e_A            5 NYVESNWKKQCKELVNLIFQCEDSEPFRQPVDLV--EYP-------------------------------------DYRD   45 (123)
T ss_dssp             -----CHHHHHHHHHHHHHTSGGGGGGSSCCCTT--TCT-------------------------------------THHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhCCCcHhhcCCCChh--hcC-------------------------------------CHHH
Confidence            4466789999999999999999999999999964  356                                     9999


Q ss_pred             cCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCC-CCHHHHHHHHHHHHHHHHhhhhccc
Q psy245          154 VIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKP-GEDVVVMAQTLEKLFLTKVSARRES  221 (566)
Q Consensus       154 iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~-~s~i~~~A~~L~~~f~~~~~~~~~~  221 (566)
                      +|++||||+||++||++|.|.++++|+.||+|||.||++||++ +|.|+.+|..|++.|++.|.++...
T Consensus        46 ~I~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~~s~i~~~A~~L~~~f~~~~~~~~~~  114 (123)
T 3q2e_A           46 IIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKISSD  114 (123)
T ss_dssp             HCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999996 9999999999999999999998763

>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=99.91  E-value=1.7e-24  Score=195.39  Aligned_cols=110  Identities=23%  Similarity=0.313  Sum_probs=100.4

Q ss_pred             CCCcHHHHHHHHHHHHHHHhcC-------CCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccc
Q psy245           74 GRNTNQLAFISKNVLKPVMKHQ-------HAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLI  146 (566)
Q Consensus        74 ~~~~~~l~~~~~~v~~~l~~~~-------~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~  146 (566)
                      +..+..|+..|..||+.|++++       .+|||..||+.  .++|                                  
T Consensus         6 ~~~~~~l~~~~~~il~~l~~~~d~~~~~~~s~~F~~pv~~--~~~p----------------------------------   49 (129)
T 2grc_A            6 SPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSR--KELP----------------------------------   49 (129)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCT--TTCH----------------------------------
T ss_pred             CCCcHHHHHHHHHHHHHHHhcccccccCeeeHHhcCCCCc--ccCC----------------------------------
Confidence            4556789999999999999986       47889999884  3456                                  


Q ss_pred             cCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcccc
Q psy245          147 ILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESG  222 (566)
Q Consensus       147 ~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~  222 (566)
                         |||.+|++||||+||++||.+|.|.++.+|..||+|||.||++||+++|.++.+|..|++.|++.+++++...
T Consensus        50 ---dY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~~  122 (129)
T 2grc_A           50 ---EYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKED  122 (129)
T ss_dssp             ---HHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ---CHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccCCC
Confidence               9999999999999999999999999999999999999999999999999999999999999999999987643

>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=99.90  E-value=1.9e-24  Score=192.71  Aligned_cols=107  Identities=27%  Similarity=0.420  Sum_probs=98.0

Q ss_pred             CCcHHHHHHHHHHHHHHHhcCC------CCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccC
Q psy245           75 RNTNQLAFISKNVLKPVMKHQH------AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIIL  148 (566)
Q Consensus        75 ~~~~~l~~~~~~v~~~l~~~~~------~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~  148 (566)
                      ..++.|+..|+.|++.|.++.+      ++||..||+.  .++|                                    
T Consensus         4 ~~p~~l~~~~~~ll~~l~~~~d~~g~~~s~~F~~~~~~--~~~p------------------------------------   45 (120)
T 3ljw_A            4 SSPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSK--VQYP------------------------------------   45 (120)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCBCTTSCBTTGGGSSCCCT--TTCH------------------------------------
T ss_pred             ccHHHHHHHHHHHHHHHHhccCcCCCcccHHhcCCCCc--ccCC------------------------------------
Confidence            4578999999999999999988      7777777663  2344                                    


Q ss_pred             CcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          149 QDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       149 pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                       |||.+|++||||+||++||.+|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.|++++.
T Consensus        46 -dY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~i~~  116 (120)
T 3ljw_A           46 -DYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEH  116 (120)
T ss_dssp             -HHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -ChHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence             99999999999999999999999999999999999999999999999999999999999999999999875

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

Probab=99.90  E-value=2.7e-24  Score=195.51  Aligned_cols=108  Identities=31%  Similarity=0.485  Sum_probs=99.3

Q ss_pred             CCCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccc
Q psy245           74 GRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHK  153 (566)
Q Consensus        74 ~~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~  153 (566)
                      ++.+...+..|..||..|++|+.+|||..||+.   ++|                                     |||+
T Consensus        15 ~~m~p~~~~~c~~il~~L~~~~~s~~F~~Pv~~---~~p-------------------------------------dY~~   54 (135)
T 2yyn_A           15 VKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPL---TVP-------------------------------------DYYK   54 (135)
T ss_dssp             -CCCHHHHHHHHHHHHHHHTSGGGGGGSSCCCT---TST-------------------------------------THHH
T ss_pred             CCCCHHHHHHHHHHHHHHHhCccchhhcCCCcc---cCC-------------------------------------CHHH
Confidence            345666777888999999999999999999985   467                                     9999


Q ss_pred             cCCCCCCHHHHHHHhhc--cCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccc
Q psy245          154 VIKHPMDLGTIKKRLEN--FYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRES  221 (566)
Q Consensus       154 iIk~PMdL~tI~~kL~~--~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~  221 (566)
                      +|++||||+||++||++  +.|.++.+|.+||+|||.||++||+++|.|+.+|..|++.|++.|.++...
T Consensus        55 iIk~PmDL~tI~~kL~~~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~  124 (135)
T 2yyn_A           55 IIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPE  124 (135)
T ss_dssp             HCSSCCCHHHHHHHHHSSSCCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHSSS
T ss_pred             HcCCCCCHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence            99999999999999998  599999999999999999999999999999999999999999999998753

>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=99.90  E-value=1.5e-24  Score=192.25  Aligned_cols=100  Identities=33%  Similarity=0.599  Sum_probs=93.5

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCC
Q psy245           79 QLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHP  158 (566)
Q Consensus        79 ~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~P  158 (566)
                      ++...|..||+.|++|+.+|||..|||..  .+|                                     |||.+|++|
T Consensus        16 ~~~~~~~~il~~l~~~~~s~~F~~pv~~~--~~p-------------------------------------dY~~~I~~P   56 (116)
T 3nxb_A           16 DDFTAMYKVLDVVKAHKDSWPFLEPVDES--YAP-------------------------------------NYYQIIKAP   56 (116)
T ss_dssp             CHHHHHHHHHHHHHHSTTCGGGSSCCCTT--TST-------------------------------------THHHHCSSC
T ss_pred             HHHHHHHHHHHHHHhCCCcHhhcCcCChh--hcc-------------------------------------ChHHHcCCC
Confidence            35566778999999999999999999965  356                                     999999999


Q ss_pred             CCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhh
Q psy245          159 MDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSA  217 (566)
Q Consensus       159 MdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  217 (566)
                      |||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.|.+
T Consensus        57 mdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~k  115 (116)
T 3nxb_A           57 MDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK  115 (116)
T ss_dssp             CCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999999999998864

>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=99.90  E-value=3.5e-24  Score=192.12  Aligned_cols=106  Identities=25%  Similarity=0.328  Sum_probs=96.3

Q ss_pred             CCcHHHHHHHHHHHHHHHhcCC------CCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccC
Q psy245           75 RNTNQLAFISKNVLKPVMKHQH------AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIIL  148 (566)
Q Consensus        75 ~~~~~l~~~~~~v~~~l~~~~~------~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~  148 (566)
                      +....|+..|+.|++.|+++.+      +|||..||+..  ++|                                    
T Consensus        11 k~~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~--~~p------------------------------------   52 (124)
T 3mb4_A           11 KYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRS--ELP------------------------------------   52 (124)
T ss_dssp             CCCCHHHHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTT--TCH------------------------------------
T ss_pred             ccChHHHHHHHHHHHHHHhHhcccCCcccHHhhcCCCcc--ccC------------------------------------
Confidence            3455899999999999999554      58888888743  355                                    


Q ss_pred             CcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          149 QDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       149 pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                       |||++|++||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.|+++.
T Consensus        53 -dY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~  122 (124)
T 3mb4_A           53 -DYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLE  122 (124)
T ss_dssp             -HHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             -CHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence             9999999999999999999999999999999999999999999999999999999999999999999875

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

Probab=99.90  E-value=4.7e-24  Score=190.93  Aligned_cols=103  Identities=27%  Similarity=0.403  Sum_probs=96.5

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           78 NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      ..++.+|..|++.|++++.+|||..||+..  .+|                                     |||++|++
T Consensus        12 ~p~~~~l~~il~~l~~~~~~~~F~~pv~~~--~~p-------------------------------------dY~~iIk~   52 (123)
T 3hme_A           12 TPIQQLLEHFLRQLQRKDPHGFFAFPVTDA--IAP-------------------------------------GYSMIIKH   52 (123)
T ss_dssp             CHHHHHHHHHHHHHHTTCTTCSSSSCCCTT--TST-------------------------------------THHHHCSS
T ss_pred             CHHHHHHHHHHHHHHhCCccHhhcCCCChh--hcc-------------------------------------CHHHHCCC
Confidence            357889999999999999999999999964  356                                     99999999


Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      ||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|.+.|.+..
T Consensus        53 PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~~  114 (123)
T 3hme_A           53 PMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKER  114 (123)
T ss_dssp             CCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTCHHH
T ss_pred             CCCHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999987643

>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=99.90  E-value=3.4e-24  Score=198.43  Aligned_cols=108  Identities=19%  Similarity=0.289  Sum_probs=98.4

Q ss_pred             HHHHHHHHHHHHHHhccC----CCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHh
Q psy245          261 ESLKYCNEILKELFSKKH----SSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFT  336 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~----~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~  336 (566)
                      ....+|..|+..|+...+    ..++++|..||+..  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+
T Consensus        24 ~~~~~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~~~--~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~  101 (150)
T 3tlp_A           24 IRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKK--DYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFR  101 (150)
T ss_dssp             HHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTT--TCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHhcccCCcccHHhcCCCchh--hCcCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence            346788899999988764    34689999999987  799999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCC
Q psy245          337 NCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV  370 (566)
Q Consensus       337 Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~  370 (566)
                      ||+.||+++|.||.+|..|+++|+++|.++...+
T Consensus       102 Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~p  135 (150)
T 3tlp_A          102 NARHYNEEGSQVYNDAHILEKLLKEKRKELGPLP  135 (150)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHHHCCC-
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHccCCC
Confidence            9999999999999999999999999999987553

>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=99.90  E-value=6.1e-24  Score=201.53  Aligned_cols=103  Identities=35%  Similarity=0.631  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      ....+.|..||..|..++   .+|||.+|||+.  ++|+||++|++||||+||++||++|.|.++.+|.+||+|||+||+
T Consensus        71 ~~~~~~l~~il~~l~~~~---~~~~F~~pv~~~--~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~  145 (174)
T 2ri7_A           71 EKDYEGLKRVLRSLQAHK---MAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCR  145 (174)
T ss_dssp             HHHHHHHHHHHHHHHTSG---GGTTTSSCCCTT--TCHHHHHHCSSCCCHHHHHHHHHTTCCCBHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhh---hhhhhhcCCCcc--cCCchHHHhCCcCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence            456788999999999887   788999999987  699999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      .||+++|.+|.+|..|+++|+++|++++
T Consensus       146 ~yN~~~s~~~~~A~~L~~~f~~~~~~~~  173 (174)
T 2ri7_A          146 YYNPSDSPFYQCAEVLESFFVQKLKGFK  173 (174)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHTTTCC
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence            9999999999999999999999998875

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

Probab=99.90  E-value=7e-24  Score=192.92  Aligned_cols=104  Identities=32%  Similarity=0.431  Sum_probs=98.4

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           78 NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      ..|+.+|..||+.|++|+.+|||..||+..  ++|                                     |||.+|++
T Consensus        12 ~~l~~~l~~il~~l~~~~~~~~F~~pv~~~--~~p-------------------------------------dY~~iI~~   52 (135)
T 3rcw_A           12 TPLTVLLRSVLDQLQDKDPARIFAQPVSLK--EVP-------------------------------------DYLDHIKH   52 (135)
T ss_dssp             CHHHHHHHHHHHHHHHTCTTCSSSSCCCTT--TCT-------------------------------------THHHHCSS
T ss_pred             hHHHHHHHHHHHHHHhCCcchhhcCCCChh--hcC-------------------------------------CHHHHhCC
Confidence            468999999999999999999999999964  456                                     99999999


Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|.+.|.++..
T Consensus        53 PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~  115 (135)
T 3rcw_A           53 PMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARR  115 (135)
T ss_dssp             CCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999998754

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

Probab=99.90  E-value=8.4e-24  Score=197.03  Aligned_cols=109  Identities=28%  Similarity=0.546  Sum_probs=98.3

Q ss_pred             chHHHHHHHHHHHHHHHhcc--CCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHH
Q psy245          258 KLTESLKYCNEILKELFSKK--HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIF  335 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~--~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif  335 (566)
                      .+......|..||..+...+  ....+|||..||+..  .+||||++|++||||+||++||++|.|.++.+|.+||+|||
T Consensus        22 ~~~d~~~~l~~iL~~i~~~kl~~~~~s~~F~~PVd~~--~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif   99 (158)
T 3uv4_A           22 SMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKK--FVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLIL   99 (158)
T ss_dssp             CCSHHHHHHHHHHHHHHHHTTTTSTTCGGGTSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHH
T ss_pred             cCCchHHHHHHHHHHHHHHHHHcCCCchhhcCcCChh--hcccHHHHcCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            34456778888888887643  335799999999987  69999999999999999999999999999999999999999


Q ss_pred             hcccccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          336 TNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       336 ~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      .||+.||+++|.||.+|..|+++|++.|.++..
T Consensus       100 ~Na~~yN~~~s~i~~~A~~L~~~~~~~l~e~~~  132 (158)
T 3uv4_A          100 ANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDE  132 (158)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999998854

>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=99.90  E-value=6e-24  Score=191.09  Aligned_cols=105  Identities=23%  Similarity=0.235  Sum_probs=96.2

Q ss_pred             cHHHHHHHHHHHHHHHhcCC------CCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCc
Q psy245           77 TNQLAFISKNVLKPVMKHQH------AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQD  150 (566)
Q Consensus        77 ~~~l~~~~~~v~~~l~~~~~------~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pd  150 (566)
                      +..|+..|+.|++.|+++.+      +|||..||+..  ++|                                     |
T Consensus         7 ~~~l~~~~~~i~~~l~~~~d~~g~~~s~~F~~pv~~~--~~p-------------------------------------d   47 (126)
T 3mqm_A            7 AARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKK--KNA-------------------------------------D   47 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGG--GCT-------------------------------------T
T ss_pred             HHHHHHHHHHHHHHHHHHhCcCCCChhHHhcCCCCcc--cCC-------------------------------------C
Confidence            45788999999999999876      78888888753  355                                     9


Q ss_pred             ccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          151 YHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       151 Y~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ||++|++||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.+.++..
T Consensus        48 Y~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~  117 (126)
T 3mqm_A           48 YYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEASA  117 (126)
T ss_dssp             HHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999988654

>2jns_A Bromodomain-containing protein 4; ET-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.89  E-value=4.5e-24  Score=180.01  Aligned_cols=85  Identities=78%  Similarity=1.208  Sum_probs=80.2

Q ss_pred             CCCCCccccCCCCCHHHHHHHHHhccCCCCcchHHHHHHHHhhCCCCCCCCCCcEEEeCCCCChHHHHHHHHHHHHHhcc
Q psy245          481 MNDESDEESSKPMSYFEKQELSLDINKLPGKKLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVATCLRK  560 (566)
Q Consensus       481 ~~~s~~e~~~~pmT~eEK~~Ls~~I~~Lp~e~L~~Vv~II~~~~p~~~~~~~dEiEiDid~L~~~tLr~L~~yV~~cL~k  560 (566)
                      ..|+.++..+++||++||++|+.+|++||+++|.+||+||++++|++.+.+++|||||||+|++.|||+|++||.+||++
T Consensus         6 ~~d~~~e~~~~~mT~eEK~~Ls~~I~~Lp~e~L~~Vi~II~~~~p~l~~~~~dEIEiDid~L~~~TL~~L~~yV~~~l~~   85 (90)
T 2jns_A            6 SGESEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLRELERYVTSCLRK   85 (90)
T ss_dssp             CCCTTTTSSCCCCCHHHHHHHHHHHTTSCHHHHTTHHHHHHTTCGGGTTSCTTSCCCCTTTSCHHHHHHHHHHHHTTSCC
T ss_pred             CCcCCCCCCCCCCCHHHHHHHHHHHHHcCHHHHHHHHHHHHhcCccccCCCCCeEEEeccCCCHHHHHHHHHHHHHHHHh
Confidence            45777888999999999999999999999999999999999999999777889999999999999999999999999999


Q ss_pred             CCCCCC
Q psy245          561 KPRKPN  566 (566)
Q Consensus       561 k~~kp~  566 (566)
                      | |||.
T Consensus        86 k-~k~~   90 (90)
T 2jns_A           86 K-RKPQ   90 (90)
T ss_dssp             C-CCCC
T ss_pred             h-cCCC
Confidence            8 9985

>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=99.89  E-value=1.2e-23  Score=189.91  Aligned_cols=108  Identities=27%  Similarity=0.357  Sum_probs=98.6

Q ss_pred             CCcHHHHHHHHHHHHHHHhcCC------CCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccC
Q psy245           75 RNTNQLAFISKNVLKPVMKHQH------AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIIL  148 (566)
Q Consensus        75 ~~~~~l~~~~~~v~~~l~~~~~------~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~  148 (566)
                      .....|...|+.|++.|.++.+      +|||..||+.  .++|                                    
T Consensus        13 ~~~~kl~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~--~~~P------------------------------------   54 (130)
T 3k2j_A           13 LGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSK--KKYP------------------------------------   54 (130)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCT--TTCH------------------------------------
T ss_pred             cchHHHHHHHHHHHHHHHHHhcccCCCccHhhcCCCCh--hhCc------------------------------------
Confidence            3456888899999999999876      8888888874  3455                                    


Q ss_pred             CcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccc
Q psy245          149 QDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRES  221 (566)
Q Consensus       149 pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~  221 (566)
                       |||++|++||||+||++||+++.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.|+++...
T Consensus        55 -dY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~  126 (130)
T 3k2j_A           55 -DYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARR  126 (130)
T ss_dssp             -HHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -cHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence             999999999999999999999999999999999999999999999999999999999999999999998753

>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=99.89  E-value=1e-23  Score=186.95  Aligned_cols=102  Identities=23%  Similarity=0.297  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHHHHhcCC------CCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccc
Q psy245           80 LAFISKNVLKPVMKHQH------AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHK  153 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~------~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~  153 (566)
                      ....|+.|++.|+++.+      +|||..||+.  .++|                                     |||.
T Consensus         6 ~~~~c~~il~~l~~~~d~~g~~~s~~F~~p~~~--~~~p-------------------------------------dY~~   46 (116)
T 3iu5_A            6 PIAVCHELYNTIRDYKDEQGRLLCELFIRAPKR--RNQP-------------------------------------DYYE   46 (116)
T ss_dssp             HHHHHHHHHHHHHHCBCTTCCBGGGGGSSCCCG--GGCH-------------------------------------HHHH
T ss_pred             HHHHHHHHHHHHHHhhccCCCeeeHHhcCCCCc--ccCC-------------------------------------CHHH
Confidence            44567889999999865      7888888774  3355                                     9999


Q ss_pred             cCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          154 VIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       154 iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      +|++||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|++.|++.++++..
T Consensus        47 iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~l~~  113 (116)
T 3iu5_A           47 VVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQ  113 (116)
T ss_dssp             HCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999999999999998865

>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=99.88  E-value=6.4e-23  Score=196.23  Aligned_cols=105  Identities=32%  Similarity=0.599  Sum_probs=97.7

Q ss_pred             cchHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhC--CCCCCHHHHHHHHHHH
Q psy245          257 PKLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA--REYKSSKEFADDVRLI  334 (566)
Q Consensus       257 ~~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~--~~Y~s~~ef~~Dv~Li  334 (566)
                      .....+.+.|..||..|+.+.   .+++|..||+.   ++|+||++|++||||+||++||++  |.|.++.+|.+||+||
T Consensus        77 ~l~~~~~~~c~~il~~l~~~~---~s~~F~~Pv~~---~~pdY~~iIk~PmdL~tI~~kl~~~~~~Y~s~~ef~~Dv~li  150 (184)
T 3o36_A           77 KLTPIDKRKCERLLLFLYCHE---MSLAFQDPVPL---TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLI  150 (184)
T ss_dssp             CCCHHHHHHHHHHHHHHHHST---TCHHHHSCCCT---TSTTHHHHCSSCCCHHHHHHHHHSTTCSCCSHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHhch---hhhhhcccccc---CCCchhhhcCCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence            345678899999999999987   67899999996   489999999999999999999998  7999999999999999


Q ss_pred             HhcccccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          335 FTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       335 f~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      |+||+.||+++|.||.+|..|+++|+++|+++.
T Consensus       151 ~~Na~~yN~~~s~v~~~a~~L~~~f~~~~~~~~  183 (184)
T 3o36_A          151 FQNCAEFNEPDSEVANAGIKLENYFEELLKNLY  183 (184)
T ss_dssp             HHHHHHHSCTTCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999999999998763

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

Probab=99.88  E-value=2.4e-23  Score=193.99  Aligned_cols=105  Identities=32%  Similarity=0.575  Sum_probs=96.8

Q ss_pred             cHHHHHHHHHHHHH-HHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           77 TNQLAFISKNVLKP-VMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        77 ~~~l~~~~~~v~~~-l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      ..+|..+|+.|+.. |+.++.+|||..||+..  .+|                                     |||.+|
T Consensus        27 ~~~l~~iL~~i~~~kl~~~~~s~~F~~PVd~~--~~P-------------------------------------dY~~iI   67 (158)
T 3uv4_A           27 QVAFSFILDNIVTQKMMAVPDSWPFHHPVNKK--FVP-------------------------------------DYYKVI   67 (158)
T ss_dssp             HHHHHHHHHHHHHHTTTTSTTCGGGTSCCCTT--TST-------------------------------------THHHHC
T ss_pred             HHHHHHHHHHHHHHHHHcCCCchhhcCcCChh--hcc-------------------------------------cHHHHc
Confidence            45778888887765 88899999999999964  356                                     999999


Q ss_pred             CCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          156 KHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       156 k~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ++||||+||++||++|.|.++.+|..||+|||.||++||+++|.|+.+|..|...|.+.|.++..
T Consensus        68 k~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~~~~~~~l~e~~~  132 (158)
T 3uv4_A           68 VNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDE  132 (158)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             CCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999875

>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=99.88  E-value=8.6e-23  Score=184.49  Aligned_cols=100  Identities=32%  Similarity=0.457  Sum_probs=91.7

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      ......|..+|..|..++   .+|||..|||+.  ++||||++|++||||+||++||++|.|.++.+|.+||+|||+||+
T Consensus         9 ~~l~~~l~~il~~l~~~~---~~~~F~~pv~~~--~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~   83 (130)
T 3dai_A            9 RELRIFLRNVTHRLAIDK---RFRVFTKPVDPD--EVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNAL   83 (130)
T ss_dssp             HHHHHHHHHHHHHHHTSG---GGGGGSSCCCTT--TCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCC---ccHhhcCCCChh--hcCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH
Confidence            345667888898888877   688999999998  699999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHH----HHHHHHHHHHHHHHHH
Q psy245          340 KYNPPDHDV----VAMAKKLQDVFETKIA  364 (566)
Q Consensus       340 ~yN~~~s~v----~~~A~~L~~~fe~~~~  364 (566)
                      .||+++|++    +.+|..|++.+...+.
T Consensus        84 ~yN~~~s~~~~~i~~~A~~L~~~~~~~i~  112 (130)
T 3dai_A           84 EYNPDRDPGDRLIRHRACALRDTAYAIIK  112 (130)
T ss_dssp             HHCCSSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCChhHHHHHHHHHHHHHHHHHHHH
Confidence            999999866    7899999999999986

>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=99.88  E-value=7.9e-23  Score=193.87  Aligned_cols=105  Identities=36%  Similarity=0.601  Sum_probs=97.7

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           76 NTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        76 ~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      .+......|+.||+.|++|+.+|||..|||..  ++|                                     |||++|
T Consensus        69 l~~~~~~~l~~il~~l~~~~~~~~F~~pv~~~--~~p-------------------------------------dY~~~I  109 (174)
T 2ri7_A           69 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPN--DAP-------------------------------------DYYGVI  109 (174)
T ss_dssp             CCHHHHHHHHHHHHHHHTSGGGTTTSSCCCTT--TCH-------------------------------------HHHHHC
T ss_pred             CCHHHHHHHHHHHHHHHhhhhhhhhhcCCCcc--cCC-------------------------------------chHHHh
Confidence            34566677889999999999999999999964  466                                     999999


Q ss_pred             CCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          156 KHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       156 k~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      ++||||+||++||++|.|.++.+|.+||+|||+||++||+++|.++.+|..|++.|++.|++++
T Consensus       110 ~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~  173 (174)
T 2ri7_A          110 KEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK  173 (174)
T ss_dssp             SSCCCHHHHHHHHHTTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCcCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence            9999999999999999999999999999999999999999999999999999999999998875

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

Probab=99.87  E-value=5.8e-23  Score=197.07  Aligned_cols=103  Identities=25%  Similarity=0.410  Sum_probs=95.2

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhcc--CCCChHHHHHHhhCC---CCCCHHHHHHHHH
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIK--KPMDLGTVKAKMDAR---EYKSSKEFADDVR  332 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk--~PMDL~tIk~kL~~~---~Y~s~~ef~~Dv~  332 (566)
                      .....++.|..||..|+.+.   .+|||.+||+      |+||++|+  +||||+||++||++|   .|.++++|.+||+
T Consensus        73 m~~~~~~~c~~iL~~l~~~~---~s~pF~~pV~------~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~Y~s~~eF~~Dv~  143 (189)
T 2ro1_A           73 LSPANQRKCERVLLALFCHE---PCRPLHQLAT------DSTFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVG  143 (189)
T ss_dssp             SCHHHHHHHHHHHHHHHHST---THHHHHSCSC------CTTCSSSCSSCCCCHHHHHHHHHTSSSSCCSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhhcccCc---cchhhcCCCC------hhhhccccCCCcccHHHHHHHHhcCCCcccCCHHHHHHHHH
Confidence            44567889999999999976   7899999998      57999998  899999999999999   9999999999999


Q ss_pred             HHHhcccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCC
Q psy245          333 LIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDV  370 (566)
Q Consensus       333 Lif~Na~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~  370 (566)
                      |||+||++|| +++.+|.+|..|+++|+++|+++..+.
T Consensus       144 Lif~N~~~yN-~~s~~~~~a~~L~~~Fe~~~~~~~~~~  180 (189)
T 2ro1_A          144 RMFKQFNKLT-EDKADVQSIIGLQRFFETRMNEAFGDT  180 (189)
T ss_dssp             HHHHHHHHHC-CSSCSSHHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHhcCcc
Confidence            9999999999 589999999999999999999987764

>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=99.87  E-value=2e-22  Score=182.12  Aligned_cols=100  Identities=25%  Similarity=0.397  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           78 NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      .+|+.+|+.|++.|++|+.+|||..|||..  ++|                                     |||.+|++
T Consensus         9 ~~l~~~l~~il~~l~~~~~~~~F~~pv~~~--~~p-------------------------------------dY~~iI~~   49 (130)
T 3dai_A            9 RELRIFLRNVTHRLAIDKRFRVFTKPVDPD--EVP-------------------------------------DYVTVIKQ   49 (130)
T ss_dssp             HHHHHHHHHHHHHHHTSGGGGGGSSCCCTT--TCT-------------------------------------THHHHCSS
T ss_pred             HHHHHHHHHHHHHHHcCCccHhhcCCCChh--hcC-------------------------------------CHHHHcCC
Confidence            578889999999999999999999999965  356                                     99999999


Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHH----HHHHHHHHHHHHHHhh
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDV----VVMAQTLEKLFLTKVS  216 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i----~~~A~~L~~~f~~~~~  216 (566)
                      ||||+||++||.+|.|.++++|..||+|||.||++||+++|.+    +.+|..|+..+...+.
T Consensus        50 PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~i~~~A~~L~~~~~~~i~  112 (130)
T 3dai_A           50 PMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIK  112 (130)
T ss_dssp             CCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999865    7889999999988886

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

Probab=99.87  E-value=4.3e-22  Score=179.82  Aligned_cols=98  Identities=37%  Similarity=0.555  Sum_probs=89.8

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      .+.++...|..||..|..++   .+|||.+|       +||||++|++||||+||++||++|.|.++.+|.+||+|||+|
T Consensus         9 ~~~~L~~~~~~il~~l~~~~---~~~~F~~P-------~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~Li~~N   78 (131)
T 2dkw_A            9 TLRELRLFLRDVTKRLATDK---RFNIFSKP-------VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSN   78 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHSG---GGCTTSSC-------CSSCTTSCSSCCCHHHHHHHHHTTCCCSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCc---cchhhcCc-------CccHHhHcCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence            34566678999999999987   67899998       699999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCH----HHHHHHHHHHHHHHHHHc
Q psy245          338 CYKYNPPDHD----VVAMAKKLQDVFETKIAK  365 (566)
Q Consensus       338 a~~yN~~~s~----v~~~A~~L~~~fe~~~~~  365 (566)
                      |+.||+++|+    |+.+|..|++.|...++.
T Consensus        79 a~~yN~~~s~~~~~i~~~A~~L~~~~~~~l~~  110 (131)
T 2dkw_A           79 ALEYNPDKDPGDKIIRHRACTLKDTAHAIIAA  110 (131)
T ss_dssp             HHHSCCCSSTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCChhHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999995    679999999999999863

>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=99.86  E-value=1.4e-22  Score=187.67  Aligned_cols=102  Identities=28%  Similarity=0.301  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHHHHhcCC-------CCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCccc
Q psy245           80 LAFISKNVLKPVMKHQH-------AWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYH  152 (566)
Q Consensus        80 l~~~~~~v~~~l~~~~~-------~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~  152 (566)
                      -...|+.|++.|+++.+       ++||..||+                                       +..+||||
T Consensus        25 ~~~~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~---------------------------------------~~~~pdY~   65 (150)
T 3tlp_A           25 RKQRMKILFNVVLEAREPGSGRRLCDLFMVKPS---------------------------------------KKDYPDYY   65 (150)
T ss_dssp             HHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCC---------------------------------------TTTCHHHH
T ss_pred             hHHHHHHHHHHHHHHHhcccCCcccHHhcCCCc---------------------------------------hhhCcCHH
Confidence            35677888888888765       555555555                                       44455999


Q ss_pred             ccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          153 KVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       153 ~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ++|++||||+||++||++|.|.++++|+.||+|||.||++||+++|.|+.+|..|++.|++.|.++..
T Consensus        66 ~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~  133 (150)
T 3tlp_A           66 KIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKELGP  133 (150)
T ss_dssp             HHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999874

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

Probab=99.86  E-value=9.2e-22  Score=177.65  Aligned_cols=99  Identities=25%  Similarity=0.430  Sum_probs=92.2

Q ss_pred             CCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCccccc
Q psy245           75 RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKV  154 (566)
Q Consensus        75 ~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~i  154 (566)
                      ....+|+.+|..|++.|++|+.+|||..|       +|                                     |||++
T Consensus         8 ~~~~~L~~~~~~il~~l~~~~~~~~F~~P-------~p-------------------------------------dY~~i   43 (131)
T 2dkw_A            8 NTLRELRLFLRDVTKRLATDKRFNIFSKP-------VS-------------------------------------DYLEV   43 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSGGGCTTSSC-------CS-------------------------------------SCTTS
T ss_pred             HHHHHHHHHHHHHHHHHHhCccchhhcCc-------Cc-------------------------------------cHHhH
Confidence            44578999999999999999999999999       57                                     99999


Q ss_pred             CCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCH----HHHHHHHHHHHHHHHhhh
Q psy245          155 IKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGED----VVVMAQTLEKLFLTKVSA  217 (566)
Q Consensus       155 Ik~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~----i~~~A~~L~~~f~~~~~~  217 (566)
                      |++||||+||++||.+|.|.++.+|..||+|||.||++||+++|.    |+.+|..|++.|...++.
T Consensus        44 Ik~PmDL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s~~~~~i~~~A~~L~~~~~~~l~~  110 (131)
T 2dkw_A           44 IKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAA  110 (131)
T ss_dssp             CSSCCCHHHHHHHHHTTCCCSSHHHHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999985    678999999999988853

>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=99.86  E-value=6.5e-22  Score=192.72  Aligned_cols=106  Identities=36%  Similarity=0.630  Sum_probs=98.8

Q ss_pred             chHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhC---CCCCCHHHHHHHHHHH
Q psy245          258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDA---REYKSSKEFADDVRLI  334 (566)
Q Consensus       258 ~~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~---~~Y~s~~ef~~Dv~Li  334 (566)
                      ....+.+.|..||..|+.++   .+|||.+||+.   ++|+||++|++||||+||++||++   |.|.++.+|.+||+||
T Consensus        78 ls~~~~~~c~~il~~l~~~~---~s~~F~~Pv~~---~~pdY~~iIk~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li  151 (207)
T 3u5n_A           78 LSPVDQRKCERLLLYLYCHE---LSIEFQEPVPA---SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLI  151 (207)
T ss_dssp             SCHHHHHHHHHHHHHHHTST---TCGGGSSCCCT---TSTTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhcc---chhhhhccCCh---hhccHhHHhCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHH
Confidence            44677899999999999887   78899999987   489999999999999999999997   7999999999999999


Q ss_pred             HhcccccCC-----------------CCCHHHHHHHHHHHHHHHHHHcCCCC
Q psy245          335 FTNCYKYNP-----------------PDHDVVAMAKKLQDVFETKIAKAPDD  369 (566)
Q Consensus       335 f~Na~~yN~-----------------~~s~v~~~A~~L~~~fe~~~~~~~~~  369 (566)
                      |+||+.||+                 +++.|+.+|..|+.+|+++|+++..+
T Consensus       152 ~~Na~~yN~~~s~v~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~~~~~~p~  203 (207)
T 3u5n_A          152 FKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSD  203 (207)
T ss_dssp             HHHHHHHHHHHHHHC----------CCCCHHHHHHHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHCCCcchHHHHHHHHHhcccccCHHHHHHHHHHHHHHHHHHHhCCC
Confidence            999999999                 99999999999999999999998654

>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=99.86  E-value=7.3e-22  Score=188.89  Aligned_cols=105  Identities=32%  Similarity=0.511  Sum_probs=98.5

Q ss_pred             CCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCccccc
Q psy245           75 RNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKV  154 (566)
Q Consensus        75 ~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~i  154 (566)
                      .....++..|..||..|+.|+.+|||..||+.   ++|                                     |||++
T Consensus        77 ~l~~~~~~~c~~il~~l~~~~~s~~F~~Pv~~---~~p-------------------------------------dY~~i  116 (184)
T 3o36_A           77 KLTPIDKRKCERLLLFLYCHEMSLAFQDPVPL---TVP-------------------------------------DYYKI  116 (184)
T ss_dssp             CCCHHHHHHHHHHHHHHHHSTTCHHHHSCCCT---TST-------------------------------------THHHH
T ss_pred             ccCHHHHHHHHHHHHHHHhchhhhhhcccccc---CCC-------------------------------------chhhh
Confidence            45678888999999999999999999999983   366                                     99999


Q ss_pred             CCCCCCHHHHHHHhhc--cCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          155 IKHPMDLGTIKKRLEN--FYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       155 Ik~PMdL~tI~~kL~~--~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      |++||||+||++||++  +.|.++.+|++||+|||+||++||+++|.|+.+|..|++.|++.|+++.
T Consensus       117 Ik~PmdL~tI~~kl~~~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~v~~~a~~L~~~f~~~~~~~~  183 (184)
T 3o36_A          117 IKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLY  183 (184)
T ss_dssp             CSSCCCHHHHHHHHHSTTCSCCSHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            9999999999999998  7999999999999999999999999999999999999999999998864

>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=99.86  E-value=9.9e-22  Score=198.38  Aligned_cols=105  Identities=29%  Similarity=0.557  Sum_probs=99.1

Q ss_pred             hHHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcc
Q psy245          259 LTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNC  338 (566)
Q Consensus       259 ~~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na  338 (566)
                      ...+...|..||..|.+++   .+|||..||+..  .+||||++|++||||+||++||++|.|.++.+|.+||+|||+||
T Consensus        12 ~~~l~~~l~~il~~l~~~~---~~~~F~~pv~~~--~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na   86 (265)
T 3uv5_A           12 MVTLSSILESIINDMRDLP---NTYPFHTPVNAK--VVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNS   86 (265)
T ss_dssp             HHHHHHHHHHHHHHHHTST---TCGGGTSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCC---CchhhhCCCChh--hcCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHhhh
Confidence            4577889999999999987   678999999998  58999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          339 YKYNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       339 ~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      +.||+++|.|+.+|..|+++|++.|.++..
T Consensus        87 ~~yN~~~s~i~~~A~~l~~~~~~~~~~~~~  116 (265)
T 3uv5_A           87 ATYNGPKHSLTQISQSMLDLCDEKLKEKED  116 (265)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             hhcCCCCChHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999998754

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

Probab=99.84  E-value=9.2e-22  Score=188.71  Aligned_cols=102  Identities=21%  Similarity=0.225  Sum_probs=93.6

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           76 NTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        76 ~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      ....-+..|..||..|+.|+.+|||.+||+      |                                     +||.+|
T Consensus        73 m~~~~~~~c~~iL~~l~~~~~s~pF~~pV~------~-------------------------------------~Yy~iI  109 (189)
T 2ro1_A           73 LSPANQRKCERVLLALFCHEPCRPLHQLAT------D-------------------------------------STFSLD  109 (189)
T ss_dssp             SCHHHHHHHHHHHHHHHHSTTHHHHHSCSC------C-------------------------------------TTCSSS
T ss_pred             CCHHHHHHHHHHHhhcccCccchhhcCCCC------h-------------------------------------hhhccc
Confidence            344555678889999999999999999998      4                                     999999


Q ss_pred             C--CCCCHHHHHHHhhcc---CCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccc
Q psy245          156 K--HPMDLGTIKKRLENF---YYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRES  221 (566)
Q Consensus       156 k--~PMdL~tI~~kL~~~---~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~  221 (566)
                      +  +||||+||++||+++   .|.++++|++||+|||+||++|| +++.++.+|..|++.|++.|+++...
T Consensus       110 k~~~PMDL~tIk~kL~~~~~~~Y~s~~eF~~Dv~Lif~N~~~yN-~~s~~~~~a~~L~~~Fe~~~~~~~~~  179 (189)
T 2ro1_A          110 QPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLT-EDKADVQSIIGLQRFFETRMNEAFGD  179 (189)
T ss_dssp             CSSCCCCHHHHHHHHHTSSSSCCSCHHHHHHHHHHHHHHHHHHC-CSSCSSHHHHHHHHHHHHHHHHHTTT
T ss_pred             cCCCcccHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHhcCc
Confidence            8  899999999999999   99999999999999999999999 48888999999999999999998764

>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=99.83  E-value=4.1e-21  Score=196.34  Aligned_cols=103  Identities=28%  Similarity=0.543  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      ......|..||..|.++.   .+|||.+||+..  .+||||++|++||||+||++||++|.|.++.+|.+||+|||+||+
T Consensus        46 ~~l~~~~~~il~~l~~~~---~a~~F~~pV~~~--~~pdY~~iIk~PmDL~tIk~kl~~~~Y~s~~~f~~D~~li~~Na~  120 (292)
T 3aad_A           46 VTLSSILESIINDMRDLP---NTYPFHTPVNAK--VVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSA  120 (292)
T ss_dssp             HHHHHHHHHHHHHHSSST---TCGGGSSSCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCC---cchhhcCCCCch--hcccHHHHcCCcCCHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHH
Confidence            445678999999999876   789999999998  689999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      .||+++|.++.+|..|+++|++.|+++.
T Consensus       121 ~yN~~~s~i~~~A~~L~~~~~~~~~~~~  148 (292)
T 3aad_A          121 TYNGPKHSLTQISQSMLDLCDEKLKEKE  148 (292)
T ss_dssp             HHTCSSSHHHHHHTHHHHTTTTTGGGSH
T ss_pred             HHcCCchHHHHHHHHHHHHHHhhhhcch
Confidence            9999999999999999999999998764

>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=99.83  E-value=8.3e-21  Score=184.88  Aligned_cols=105  Identities=27%  Similarity=0.445  Sum_probs=97.9

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           76 NTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        76 ~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      ....++..|..||..|++|+.+|||..||+.   ++|                                     |||.+|
T Consensus        78 ls~~~~~~c~~il~~l~~~~~s~~F~~Pv~~---~~p-------------------------------------dY~~iI  117 (207)
T 3u5n_A           78 LSPVDQRKCERLLLYLYCHELSIEFQEPVPA---SIP-------------------------------------NYYKII  117 (207)
T ss_dssp             SCHHHHHHHHHHHHHHHTSTTCGGGSSCCCT---TST-------------------------------------THHHHC
T ss_pred             ccHHHHHHHHHHHHHHHhccchhhhhccCCh---hhc-------------------------------------cHhHHh
Confidence            4567778889999999999999999999984   466                                     999999


Q ss_pred             CCCCCHHHHHHHhhc---cCCCCHHHHHHHHHHhhhhccccCC-----------------CCCHHHHHHHHHHHHHHHHh
Q psy245          156 KHPMDLGTIKKRLEN---FYYWSGKEAISDFNTMFTNCYVYNK-----------------PGEDVVVMAQTLEKLFLTKV  215 (566)
Q Consensus       156 k~PMdL~tI~~kL~~---~~Y~s~~ef~~Dv~lif~N~~~yN~-----------------~~s~i~~~A~~L~~~f~~~~  215 (566)
                      ++||||+||++||++   |.|.++++|..||+|||+||++||+                 +++.++++|..|+..|++.|
T Consensus       118 k~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~v~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~~  197 (207)
T 3u5n_A          118 KKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKL  197 (207)
T ss_dssp             SSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHHHHHHHHHHHHC----------CCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHHHHHCCCcchHHHHHHHHHhcccccCHHHHHHHHHHHHHHHHH
Confidence            999999999999997   7999999999999999999999999                 99999999999999999999


Q ss_pred             hhhcc
Q psy245          216 SARRE  220 (566)
Q Consensus       216 ~~~~~  220 (566)
                      +++.+
T Consensus       198 ~~~~p  202 (207)
T 3u5n_A          198 TEIYS  202 (207)
T ss_dssp             HHHST
T ss_pred             HHhCC
Confidence            98764

>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=99.79  E-value=2.3e-19  Score=162.87  Aligned_cols=110  Identities=18%  Similarity=0.228  Sum_probs=101.8

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccC
Q psy245           76 NTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVI  155 (566)
Q Consensus        76 ~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iI  155 (566)
                      .+..++.+++.|++.|++|.+.                                 .||.+++.|+.||+++  |+||.  
T Consensus         4 v~~~lq~~l~~l~~~v~~~~De---------------------------------~GR~lsd~F~~LPsk~--pdYY~--   46 (147)
T 3iu6_A            4 VTLLIQELIHNLFVSVMSHQDD---------------------------------EGRCYSDSLAEIPAVD--PNFPN--   46 (147)
T ss_dssp             CCCHHHHHHHHHHHHHHTCBCT---------------------------------TSCBGGGGGTTCCSSC--TTSTT--
T ss_pred             HHHHHHHHHHHHHHHHHhhcCC---------------------------------CCCcchHHHhHCCCCC--ccccC--
Confidence            3457889999999999999886                                 2788999999999998  79998  


Q ss_pred             CCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcccc
Q psy245          156 KHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESG  222 (566)
Q Consensus       156 k~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~~  222 (566)
                      ++||+|.+|++||.+|.|+++++|..||.+||+||++||.++|.||.+|..|+.+|.+...++-..+
T Consensus        47 k~Pi~l~~Ikkri~~~~Y~sld~f~~D~~lmf~NAr~yN~e~S~IyeDAv~Lq~~f~~~r~eL~~~g  113 (147)
T 3iu6_A           47 KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCKNG  113 (147)
T ss_dssp             SCCCCHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            9999999999999999999999999999999999999999999999999999999999999886543

>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=99.77  E-value=2.2e-19  Score=184.75  Aligned_cols=70  Identities=27%  Similarity=0.386  Sum_probs=68.3

Q ss_pred             CCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhh
Q psy245          148 LQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSA  217 (566)
Q Consensus       148 ~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  217 (566)
                      +||||++|++||||+||++||++|.|.++.+|..||+|||+||++||+++|.|+.+|..|++.|++.|++
T Consensus       193 ~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  262 (311)
T 2r0y_A          193 LPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQK  262 (311)
T ss_dssp             CHHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHhCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3499999999999999999999999999999999999999999999999999999999999999999998

>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=99.76  E-value=3.9e-19  Score=186.71  Aligned_cols=79  Identities=24%  Similarity=0.296  Sum_probs=71.8

Q ss_pred             hccccccccCCcccccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhh
Q psy245          139 ALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSA  217 (566)
Q Consensus       139 f~~lP~~~~~pdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  217 (566)
                      |..++....+||||++|++||||+||++||++|.|.++.+|..||+|||+||++||+++|.||.+|..|+..|+..|.+
T Consensus       234 F~~pvd~~~~PdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  312 (361)
T 2r10_A          234 FMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQK  312 (361)
T ss_dssp             GSSCCCTTTCTHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCChhhcccHHHHhcCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3333333345599999999999999999999999999999999999999999999999999999999999999999998

>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=99.72  E-value=8.6e-18  Score=152.58  Aligned_cols=105  Identities=11%  Similarity=0.230  Sum_probs=94.2

Q ss_pred             HHHHHHHHHHHHHHhccCC---CCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhc
Q psy245          261 ESLKYCNEILKELFSKKHS---SYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTN  337 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~---~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~N  337 (566)
                      .....+..|+..++.+++.   .++.+|.+.++..    |+||+  ++||+|.+|++||+.|.|+++++|..||.|||+|
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            3455678888899888754   5788999998876    78998  9999999999999999999999999999999999


Q ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHcCCCCCC
Q psy245          338 CYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVP  371 (566)
Q Consensus       338 a~~yN~~~s~v~~~A~~L~~~fe~~~~~~~~~~~  371 (566)
                      |++||.+||.||.+|..|+++|.+.+.++.....
T Consensus        81 Ar~yN~e~S~IyeDAv~Lq~~f~~~r~eL~~~g~  114 (147)
T 3iu6_A           81 ARRMNRTDSEIYEDAVELQQFFIKIRDELCKNGE  114 (147)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence            9999999999999999999999999999866533

>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=99.44  E-value=1.3e-13  Score=130.83  Aligned_cols=93  Identities=19%  Similarity=0.282  Sum_probs=81.9

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      .....+||..|..++   .+|||+..             .++.||||.||++||+.|.|.++.+|.+||+|||.||..||
T Consensus        77 ~~~l~~vl~~L~~~~---~s~~~~~y-------------~~k~PmDL~~i~kKl~~~~Y~s~~eF~~Dv~lIf~n~~~~~  140 (183)
T 3lqh_A           77 QISLKQVLTALLNSR---TTSHLLRY-------------RQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSD  140 (183)
T ss_dssp             HHHHHHHHHHHHTCH---HHHHHHTC-------------CC--CCSHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhcc---ccHhhhhh-------------hhcCCccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhcc
Confidence            445678899888876   67898662             14999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHcCCCCCC
Q psy245          343 PPDHDVVAMAKKLQDVFETKIAKAPDDVP  371 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~fe~~~~~~~~~~~  371 (566)
                      .+++++..++..|+.+|+++++++.++..
T Consensus       141 ~~~~e~~~ag~~l~~~f~~~l~~vfpwf~  169 (183)
T 3lqh_A          141 GGQPEIKKANSMVKSFFIRQMERVFPWFS  169 (183)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHCTTSC
T ss_pred             CCChhhhhhhhHHHHHHHHHHHHHCCCCC
Confidence            99999999999999999999999988864

>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=99.40  E-value=1.8e-13  Score=129.80  Aligned_cols=93  Identities=15%  Similarity=0.251  Sum_probs=81.9

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           78 NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      ..|+..+..||+.|..|+.+|||.                                                .|.  ++.
T Consensus        74 ~el~~~l~~vl~~L~~~~~s~~~~------------------------------------------------~y~--~k~  103 (183)
T 3lqh_A           74 KELQISLKQVLTALLNSRTTSHLL------------------------------------------------RYR--QQQ  103 (183)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHH------------------------------------------------TCC--C--
T ss_pred             HHHHHHHHHHHHHHHhccccHhhh------------------------------------------------hhh--hcC
Confidence            466777888999999998887663                                                332  599


Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ||||.+|++||++|.|.++.+|+.||.|||+||..||+.++.+.+++..|+.+|++.|+++-+
T Consensus       104 PmDL~~i~kKl~~~~Y~s~~eF~~Dv~lIf~n~~~~~~~~~e~~~ag~~l~~~f~~~l~~vfp  166 (183)
T 3lqh_A          104 PLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFP  166 (183)
T ss_dssp             CCSHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhccCCChhhhhhhhHHHHHHHHHHHHHCC
Confidence            999999999999999999999999999999999999999999999999999999999998765

>2lm0_A AF4/FMR2 family member 1/protein AF-9 chimera; intrinsically disordered, nuclear protein; NMR {Homo sapiens}

Probab=95.53  E-value=0.019  Score=49.67  Aligned_cols=60  Identities=22%  Similarity=0.347  Sum_probs=50.4

Q ss_pred             CHHHHHHHHHhccCCCCc-chHHHHHHHHhhCCCCCCCCCCcEEEeCCCCChHHHHHHHHHHH
Q psy245          494 SYFEKQELSLDINKLPGK-KLGRVVHIIQSREPSLRDSNPDEIEIDFETLKPSTLRELEKYVA  555 (566)
Q Consensus       494 T~eEK~~Ls~~I~~Lp~e-~L~~Vv~II~~~~p~~~~~~~dEiEiDid~L~~~tLr~L~~yV~  555 (566)
                      =.+|-++|...|-.|... .|.+||++|.+. ..+. .....+.||+.+||..|+++|+.|+.
T Consensus        60 y~~~L~~l~~rim~l~d~~~lq~iv~li~~t-G~~~-it~~tfDFDLc~LD~~Tv~klq~~l~  120 (125)
T 2lm0_A           60 YLDELVELHRRLMTLRERHILQQIVNLIEET-GHFH-ITNTTFDFDLCSLDKTTVRKLQSYLE  120 (125)
T ss_dssp             THHHHHHHHHHHHTCCCCSSHHHHHHHHHTS-CCEE-ECSSCEEECTTTSCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhccccHHHHHHHHHHHHhc-Ccee-eecccccceeeccCHHHHHHHHHHHH
Confidence            357889999999999887 699999999863 3443 34488999999999999999999874

---

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	566
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	2e-30
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	3e-21
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	7e-30
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	5e-24
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	7e-30
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	3e-21
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	2e-29
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	3e-23
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	1e-28
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	4e-23
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	4e-27
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	8e-23

>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 =  112 bits (282), Expect = 2e-30
 Identities = 37/102 (36%), Positives = 56/102 (54%), Gaps = 2/102 (1%)

Query: 264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKS 323
           +     L+ L+  +    + PF +PVD   LG+ DY +I+K PMDL T+K K+D  +Y+ 
Sbjct: 9   QALMPTLEALY--RQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQE 66

Query: 324 SKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
             ++ DDV L+F N + YN     V     KL +VFE +I  
Sbjct: 67  PWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDP 108

>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 = 86.9 bits (215), Expect = 3e-21
 Identities = 31/138 (22%), Positives = 52/138 (37%), Gaps = 38/138 (27%)

Query: 85  KNVLKPVMKHQ-HAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVP 143
              L+ + +    + PF QPVD   L +P                               
Sbjct: 12  MPTLEALYRQDPESLPFRQPVDPQLLGIP------------------------------- 40

Query: 144 VLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVM 203
                 DY  ++K+PMDL TIK++L+   Y    + + D   MF N ++YN+    V   
Sbjct: 41  ------DYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKF 94

Query: 204 AQTLEKLFLTKVSARRES 221
              L ++F  ++    +S
Sbjct: 95  CSKLAEVFEQEIDPVMQS 112

>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 =  112 bits (281), Expect = 7e-30
 Identities = 32/118 (27%), Positives = 63/118 (53%), Gaps = 3/118 (2%)

Query: 255 AKPKLTESLKYCNEILKELFSK-KHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVK 313
              + T+ +   + IL+ + +  +     +PF+ PV+A    + DY++II +PMDL T++
Sbjct: 16  IHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAK--VVKDYYKIITRPMDLQTLR 73

Query: 314 AKMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVP 371
             +  R Y S +EF + + LI  N   YN P H +  +++ + D+ + K+ +  D + 
Sbjct: 74  ENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLA 131

>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 = 95.4 bits (237), Expect = 5e-24
 Identities = 30/163 (18%), Positives = 58/163 (35%), Gaps = 39/163 (23%)

Query: 65  PTVPPPHRPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHW 124
           P      R       L+ I ++++  +    + +PFH PV+A                  
Sbjct: 12  PHKSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAK----------------- 54

Query: 125 VLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFN 184
                                    DY+K+I  PMDL T+++ +    Y S +E      
Sbjct: 55  ------VVK----------------DYYKIITRPMDLQTLRENVRKRLYPSREEFREHLE 92

Query: 185 TMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRESGRQIKK 227
            +  N   YN P   +  ++Q++  L   K+  + +   +++K
Sbjct: 93  LIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEK 135

>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 =  111 bits (278), Expect = 7e-30
 Identities = 35/106 (33%), Positives = 58/106 (54%), Gaps = 5/106 (4%)

Query: 264 KYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKS 323
                IL EL +      AWPF +PV+     + DY++ IK+PMDL T++ K+++ +Y+ 
Sbjct: 6   AAIQNILTELQNHAA---AWPFLQPVN--KEEVPDYYDFIKEPMDLSTMEIKLESNKYQK 60

Query: 324 SKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDD 369
            ++F  D RL+F NC  YN  +      A +L+  F  K+ + P+ 
Sbjct: 61  MEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPEY 106

>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 = 86.9 bits (215), Expect = 3e-21
 Identities = 39/136 (28%), Positives = 52/136 (38%), Gaps = 39/136 (28%)

Query: 85  KNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPV 144
           +N+L  +  H  AWPF QPV+                         E P           
Sbjct: 9   QNILTELQNHAAAWPFLQPVNKE-----------------------EVP----------- 34

Query: 145 LIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMA 204
                DY+  IK PMDL T++ +LE+  Y   ++ I D   +F NC +YN         A
Sbjct: 35  -----DYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYA 89

Query: 205 QTLEKLFLTKVSARRE 220
             LEK F  KV    E
Sbjct: 90  NRLEKFFNNKVKEIPE 105

>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 =  110 bits (277), Expect = 2e-29
 Identities = 31/110 (28%), Positives = 58/110 (52%), Gaps = 4/110 (3%)

Query: 264 KYCNEILKELFSKKHSSY--AWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREY 321
              + IL  + ++K  +   +WPF+ PV+     + DY+++I  PMDL T++  +   +Y
Sbjct: 8   VAFSFILDNIVTQKMMAVPDSWPFHHPVN--KKFVPDYYKVIVNPMDLETIRKNISKHKY 65

Query: 322 KSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKAPDDVP 371
           +S + F DDV LI  N  KYN P+      A+++ +V    + +  + + 
Sbjct: 66  QSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLT 115

>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 = 93.1 bits (231), Expect = 3e-23
 Identities = 37/149 (24%), Positives = 55/149 (36%), Gaps = 40/149 (26%)

Query: 80  LAFISKN-VLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAF 138
            +FI  N V + +M    +WPFH PV+                           P     
Sbjct: 10  FSFILDNIVTQKMMAVPDSWPFHHPVNKK-----------------------FVP----- 41

Query: 139 ALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGE 198
                      DY+KVI +PMDL TI+K +    Y S +  + D N +  N   YN P  
Sbjct: 42  -----------DYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPES 90

Query: 199 DVVVMAQTLEKLFLTKVSARRESGRQIKK 227
                AQ +  +    ++   E   Q++K
Sbjct: 91  QYTKTAQEIVNVCYQTLTEYDEHLTQLEK 119

>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 =  107 bits (268), Expect = 1e-28
 Identities = 34/108 (31%), Positives = 58/108 (53%), Gaps = 8/108 (7%)

Query: 258 KLTESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMD 317
           +L  +LK    +L ++ S   +   WPF +PV        DY+E+I+ P+DL T+  ++ 
Sbjct: 2   QLYTTLK---NLLAQIKSHPSA---WPFMEPVKK--SEAPDYYEVIRFPIDLKTMTERLR 53

Query: 318 AREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAK 365
           +R Y + K F  D++ +  NC +YNPPD +    A  L+  F  K+ +
Sbjct: 54  SRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKE 101

>d3d7ca1 a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: GCN5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.0 bits (228), Expect = 4e-23
 Identities = 39/138 (28%), Positives = 56/138 (40%), Gaps = 39/138 (28%)

Query: 78  NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLA 137
           +QL    KN+L  +  H  AWPF +PV                          E P    
Sbjct: 1   DQLYTTLKNLLAQIKSHPSAWPFMEPVKKS-----------------------EAP---- 33

Query: 138 FALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPG 197
                       DY++VI+ P+DL T+ +RL + YY + K  ++D   +  NC  YN P 
Sbjct: 34  ------------DYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPD 81

Query: 198 EDVVVMAQTLEKLFLTKV 215
            +    A  LEK F  K+
Sbjct: 82  SEYCRCASALEKFFYFKL 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 =  103 bits (259), Expect = 4e-27
 Identities = 38/112 (33%), Positives = 62/112 (55%), Gaps = 6/112 (5%)

Query: 256 KPKLTESLKY-CNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKA 314
           +P+  + L      IL+++ S + +   WPF +PV         Y+E+I+ PMDL T+  
Sbjct: 7   EPRDPDQLYSTLKSILQQVKSHQSA---WPFMEPVKR--TEAPGYYEVIRFPMDLKTMSE 61

Query: 315 KMDAREYKSSKEFADDVRLIFTNCYKYNPPDHDVVAMAKKLQDVFETKIAKA 366
           ++  R Y S K F  D++ +FTNC +YNPP+ +    A  L+  F +KI +A
Sbjct: 62  RLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEA 113

>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 = 91.6 bits (227), Expect = 8e-23
 Identities = 45/144 (31%), Positives = 64/144 (44%), Gaps = 39/144 (27%)

Query: 72  RPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIE 131
           +  R+ +QL    K++L+ V  HQ AWPF +PV                          E
Sbjct: 6   KEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRT-----------------------E 42

Query: 132 YPILLAFALTVPVLIILQDYHKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCY 191
            P                 Y++VI+ PMDL T+ +RL+N YY S K  ++D   +FTNC 
Sbjct: 43  AP----------------GYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCK 86

Query: 192 VYNKPGEDVVVMAQTLEKLFLTKV 215
            YN P  +    A  LEK F +K+
Sbjct: 87  EYNPPESEYYKCANILEKFFFSKI 110

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	566
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.93
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.92
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.92
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.92
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.91
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.91
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.91
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.91
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.91
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.91
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.9
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.89

>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=99.93  E-value=6.4e-26  Score=194.44  Aligned_cols=100  Identities=32%  Similarity=0.622  Sum_probs=94.7

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      ++...|..||..|.+++   .+|||..||++.  ++|+||++|++||||+||++||++|.|.|+.+|.+||+|||.||+.
T Consensus         2 ~L~~~l~~il~~l~~~~---~s~~F~~pv~~~--~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~   76 (102)
T d3d7ca1           2 QLYTTLKNLLAQIKSHP---SAWPFMEPVKKS--EAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCRE   76 (102)
T ss_dssp             HHHHHHHHHHHHHHHSG---GGGGGSSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCC---CCCccCCCCChh--hCcCHHHHcCCccCHHHHHHHhccCccCCHHHHHHHHHHHHHHHHH
Confidence            45678999999999987   688999999986  6899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHc
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAK  365 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~  365 (566)
                      ||+++|.+|.+|..|+++|+++|++
T Consensus        77 yN~~~s~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          77 YNPPDSEYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999875

>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=99.92  E-value=5.2e-26  Score=197.97  Aligned_cols=102  Identities=34%  Similarity=0.672  Sum_probs=96.8

Q ss_pred             HHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccccC
Q psy245          263 LKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKYN  342 (566)
Q Consensus       263 ~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN  342 (566)
                      .+.|..||..|.+++   .||||..|||+.  .+|+||++|++||||+||++||.+|.|.|+.+|.+||+|||.||+.||
T Consensus         5 ~~~l~~il~~l~~~~---~a~pF~~pvd~~--~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN   79 (111)
T d1e6ia_           5 DAAIQNILTELQNHA---AAWPFLQPVNKE--EVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYN   79 (111)
T ss_dssp             HHHHHHHHHHHHHST---TCGGGSSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhCC---CChhhcCCCCch--hCcCHHHHcCCchhHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHC
Confidence            578999999999987   688999999987  689999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHcCCCC
Q psy245          343 PPDHDVVAMAKKLQDVFETKIAKAPDD  369 (566)
Q Consensus       343 ~~~s~v~~~A~~L~~~fe~~~~~~~~~  369 (566)
                      +++|.++.+|..|+++|+++|++++..
T Consensus        80 ~~~s~i~~~A~~l~~~f~~~~~~ipe~  106 (111)
T d1e6ia_          80 GENTSYYKYANRLEKFFNNKVKEIPEY  106 (111)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHTSGGG
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence            999999999999999999999998643

>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=99.92  E-value=1.9e-25  Score=195.26  Aligned_cols=105  Identities=36%  Similarity=0.647  Sum_probs=97.7

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      .++.+.|..+|+.|+++.  ..||||..|||+...++||||++|++||||+||++||++|.|.|+.+|.+||+|||+||+
T Consensus         5 ~el~~~l~~~l~~l~~~~--p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~   82 (114)
T d3dwya1           5 EELRQALMPTLEALYRQD--PESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAW   82 (114)
T ss_dssp             HHHHHHHHHHHHHHHTCT--TTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcC--cCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCccccHHHHHHHHHHHHHHHH
Confidence            456778899999998653  367899999999877899999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHcC
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKIAKA  366 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~~~~  366 (566)
                      .||+++|.++.+|..|++.|++.+.++
T Consensus        83 ~yN~~~s~~~~~A~~L~~~f~~~~~~i  109 (114)
T d3dwya1          83 LYNRKTSRVYKFCSKLAEVFEQEIDPV  109 (114)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999865

>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=99.92  E-value=1.6e-25  Score=191.85  Aligned_cols=101  Identities=38%  Similarity=0.671  Sum_probs=95.8

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           78 NQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        78 ~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      ++|...|+.|+..|++|+.+|||..||+..  ++|                                     |||++|++
T Consensus         1 d~L~~~l~~il~~l~~~~~s~~F~~pv~~~--~~p-------------------------------------dY~~~I~~   41 (102)
T d3d7ca1           1 DQLYTTLKNLLAQIKSHPSAWPFMEPVKKS--EAP-------------------------------------DYYEVIRF   41 (102)
T ss_dssp             HHHHHHHHHHHHHHHHSGGGGGGSSCCCTT--TST-------------------------------------THHHHCSS
T ss_pred             ChHHHHHHHHHHHHHhCCCCCccCCCCChh--hCc-------------------------------------CHHHHcCC
Confidence            478899999999999999999999999953  466                                     99999999


Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhh
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSA  217 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  217 (566)
                      ||||+||++||++|.|.++.+|.+||+|||.||++||+++|.++.+|..|++.|+++|++
T Consensus        42 PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          42 PIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             CCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHhccCccCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999999999999999998864

>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=99.91  E-value=2.1e-25  Score=196.20  Aligned_cols=109  Identities=40%  Similarity=0.692  Sum_probs=102.0

Q ss_pred             CCCCCcHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcc
Q psy245           72 RPGRNTNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDY  151 (566)
Q Consensus        72 ~~~~~~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY  151 (566)
                      +.++.+.+|...|+.|++.|++|+.++||..||+..  .+|                                     ||
T Consensus         6 ~~~~~~~~l~~~l~~il~~l~~~~~a~~F~~pv~~~--~~p-------------------------------------dY   46 (118)
T d1wuma1           6 KEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRT--EAP-------------------------------------GY   46 (118)
T ss_dssp             SCCCSHHHHHHHHHHHHHHHHHSSSCHHHHSCCCSS--SSS-------------------------------------SC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCcCcccCCCChh--hCc-------------------------------------CH
Confidence            445678899999999999999999999999999953  356                                     99


Q ss_pred             cccCCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhc
Q psy245          152 HKVIKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARR  219 (566)
Q Consensus       152 ~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~  219 (566)
                      |++|++||||+||++||++|.|.++.+|+.||+|||.||+.||+++|.++.+|..|++.|.+.|+++.
T Consensus        47 ~~iI~~PmdL~~I~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yn~~~s~~~~~A~~l~~~f~~~~~e~~  114 (118)
T d1wuma1          47 YEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAG  114 (118)
T ss_dssp             TTTCSSCCCHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHHHSCTTSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHcCChhhHHHHHHHhcccccCchHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            99999999999999999999999999999999999999999999999999999999999999998764

>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=99.91  E-value=3.4e-25  Score=193.68  Aligned_cols=108  Identities=29%  Similarity=0.521  Sum_probs=101.0

Q ss_pred             CcHHHHHHHHHHHHHHHhc-CCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCccccc
Q psy245           76 NTNQLAFISKNVLKPVMKH-QHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKV  154 (566)
Q Consensus        76 ~~~~l~~~~~~v~~~l~~~-~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~i  154 (566)
                      .+.+|+..|..+++.|+++ +.+|||..|||+...++|                                     |||++
T Consensus         3 ~p~el~~~l~~~l~~l~~~~p~a~pF~~pvd~~~~~~p-------------------------------------dY~~i   45 (114)
T d3dwya1           3 KPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIP-------------------------------------DYFDI   45 (114)
T ss_dssp             CHHHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCT-------------------------------------THHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCcCCCccCCCCChhhccCC-------------------------------------CHHHH
Confidence            3678999999999999987 589999999998766677                                     99999


Q ss_pred             CCCCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          155 IKHPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       155 Ik~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      |++||||+||++||.+|.|.++++|.+||+|||+||+.||+++|.++.+|..|++.|++.+..+..
T Consensus        46 I~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~i~~  111 (114)
T d3dwya1          46 VKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQ  111 (114)
T ss_dssp             CSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHcCccccHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999987653

>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=99.91  E-value=2.5e-25  Score=193.59  Aligned_cols=102  Identities=37%  Similarity=0.583  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCCCCC
Q psy245           81 AFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKHPMD  160 (566)
Q Consensus        81 ~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~PMd  160 (566)
                      ...|..||..|++|+++|||..|||..  .+|                                     |||++|++|||
T Consensus         5 ~~~l~~il~~l~~~~~a~pF~~pvd~~--~~p-------------------------------------dY~~vI~~Pmd   45 (111)
T d1e6ia_           5 DAAIQNILTELQNHAAAWPFLQPVNKE--EVP-------------------------------------DYYDFIKEPMD   45 (111)
T ss_dssp             HHHHHHHHHHHHHSTTCGGGSSCCCTT--TST-------------------------------------THHHHCSSCCC
T ss_pred             HHHHHHHHHHHHhCCCChhhcCCCCch--hCc-------------------------------------CHHHHcCCchh
Confidence            466788999999999999999999964  356                                     99999999999


Q ss_pred             HHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhccc
Q psy245          161 LGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRES  221 (566)
Q Consensus       161 L~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~~  221 (566)
                      |+||++||.+|.|.++.+|..||+|||.||+.||+++|.++.+|..|++.|++.|++++..
T Consensus        46 L~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~i~~~A~~l~~~f~~~~~~ipe~  106 (111)
T d1e6ia_          46 LSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPEY  106 (111)
T ss_dssp             HHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHTSGGG
T ss_pred             HHHHHHHHHccccchHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999999999999999999999999999999999999999998764

>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=99.91  E-value=7.5e-25  Score=197.99  Aligned_cols=105  Identities=26%  Similarity=0.456  Sum_probs=98.7

Q ss_pred             cHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCC
Q psy245           77 TNQLAFISKNVLKPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIK  156 (566)
Q Consensus        77 ~~~l~~~~~~v~~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk  156 (566)
                      ...|+.+|..|++.|++|+.+|||..|||...  +|                                     |||++|+
T Consensus        24 ~~~l~~~l~~il~~l~~~~~s~pF~~Pvd~~~--~p-------------------------------------dY~~iI~   64 (139)
T d1eqfa1          24 MVTLSSILESIINDMRDLPNTYPFHTPVNAKV--VK-------------------------------------DYYKIIT   64 (139)
T ss_dssp             HHHHHHHHHHHHHHHHTSTTCGGGTSCCCTTT--ST-------------------------------------THHHHCS
T ss_pred             HHHHHHHHHHHHHHHHcCCCchhhhCCCChhh--cc-------------------------------------CHHHHcC
Confidence            34688999999999999999999999999643  56                                     9999999


Q ss_pred             CCCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          157 HPMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       157 ~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      +||||+||++||++|.|.++++|..||+|||.||++||+++|.++.+|..|+..|++.|+++..
T Consensus        65 ~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~~~~~~~~~~~  128 (139)
T d1eqfa1          65 RPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKED  128 (139)
T ss_dssp             SCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             ChhhHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999988764

>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=99.91  E-value=8.2e-25  Score=192.35  Aligned_cols=103  Identities=36%  Similarity=0.629  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccc
Q psy245          260 TESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCY  339 (566)
Q Consensus       260 ~~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~  339 (566)
                      .++...|..||..|..++   .++||..||+..  .+|+||++|++||||+||++||++|.|.++.+|.+||+|||+||+
T Consensus        12 ~~l~~~l~~il~~l~~~~---~a~~F~~pv~~~--~~pdY~~iI~~PmdL~~I~~kl~~~~Y~s~~ef~~Dv~li~~Na~   86 (118)
T d1wuma1          12 DQLYSTLKSILQQVKSHQ---SAWPFMEPVKRT--EAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCK   86 (118)
T ss_dssp             HHHHHHHHHHHHHHHHSS---SCHHHHSCCCSS--SSSSCTTTCSSCCCHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCC---CcCcccCCCChh--hCcCHHHHcCChhhHHHHHHHhcccccCchHHHHHHHHHHHHHHH
Confidence            355688999999999987   678999999987  689999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          340 KYNPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       340 ~yN~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      .||+++|.++.+|..|+++|++.|+++.
T Consensus        87 ~yn~~~s~~~~~A~~l~~~f~~~~~e~~  114 (118)
T d1wuma1          87 EYNPPESEYYKCANILEKFFFSKIKEAG  114 (118)
T ss_dssp             HHSCTTSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            9999999999999999999999998753

>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=99.91  E-value=2.2e-24  Score=194.86  Aligned_cols=103  Identities=29%  Similarity=0.559  Sum_probs=95.8

Q ss_pred             HHHHHHHHHHHHHHhccCCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhcccc
Q psy245          261 ESLKYCNEILKELFSKKHSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYK  340 (566)
Q Consensus       261 ~~~k~c~~iL~~l~~~~~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~  340 (566)
                      .+...|..||+.|..+.   .+|||..|||+.  .+||||++|++||||+||++||++|.|.|+.+|.+||+|||+||+.
T Consensus        26 ~l~~~l~~il~~l~~~~---~s~pF~~Pvd~~--~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~  100 (139)
T d1eqfa1          26 TLSSILESIINDMRDLP---NTYPFHTPVNAK--VVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSAT  100 (139)
T ss_dssp             HHHHHHHHHHHHHHTST---TCGGGTSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCC---CchhhhCCCChh--hccCHHHHcCChhhHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHH
Confidence            34567888999998776   678999999998  6899999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy245          341 YNPPDHDVVAMAKKLQDVFETKIAKAPD  368 (566)
Q Consensus       341 yN~~~s~v~~~A~~L~~~fe~~~~~~~~  368 (566)
                      ||+++|.++.+|..|+++|+++|+++..
T Consensus       101 yN~~~s~i~~~A~~L~~~~~~~~~~~~~  128 (139)
T d1eqfa1         101 YNGPKHSLTQISQSMLDLCDEKLKEKED  128 (139)
T ss_dssp             HTCTTSHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999998743

>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=99.90  E-value=2e-24  Score=192.43  Aligned_cols=102  Identities=30%  Similarity=0.559  Sum_probs=91.8

Q ss_pred             HHHHHHHHHHHhcc--CCCCCcCcccCCCccccCCCchhhhccCCCChHHHHHHhhCCCCCCHHHHHHHHHHHHhccccc
Q psy245          264 KYCNEILKELFSKK--HSSYAWPFYKPVDAAWLGLNDYHEIIKKPMDLGTVKAKMDAREYKSSKEFADDVRLIFTNCYKY  341 (566)
Q Consensus       264 k~c~~iL~~l~~~~--~~~~a~pF~~PVd~~~~~~pdY~~iIk~PMDL~tIk~kL~~~~Y~s~~ef~~Dv~Lif~Na~~y  341 (566)
                      ..+..||..|...+  ....||||++|||+.  .+|+||++|++||||+||++||.+|.|.|+.+|.+||+|||+||+.|
T Consensus         8 ~~~~~il~~l~~~~~~~~p~a~pF~~pVd~~--~~PdY~~vIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~y   85 (128)
T d1eqfa2           8 VAFSFILDNIVTQKMMAVPDSWPFHHPVNKK--FVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKY   85 (128)
T ss_dssp             HHHHHHHHHHHHHTTTTSTTCGGGTSCCCTT--TSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCChhcCCCCcc--cCcCHHHHcCCcccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHH
Confidence            45667777765443  334699999999987  68999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHcCC
Q psy245          342 NPPDHDVVAMAKKLQDVFETKIAKAP  367 (566)
Q Consensus       342 N~~~s~v~~~A~~L~~~fe~~~~~~~  367 (566)
                      |+++|.++.+|..|++.|++.+.++.
T Consensus        86 N~~~s~i~~~A~~L~~~~~~~l~~~~  111 (128)
T d1eqfa2          86 NGPESQYTKTAQEIVNVCYQTLTEYD  111 (128)
T ss_dssp             HCTTCHHHHHHHHHHHHHHHHHHHTH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhH
Confidence            99999999999999999999999874

>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=99.89  E-value=2e-24  Score=192.43  Aligned_cols=103  Identities=33%  Similarity=0.596  Sum_probs=94.4

Q ss_pred             HHHHHHHHHH-HHHHhcCCCCCCCCCCcccccCCchhHHHHHHHHHHHHhhhhhhhhhhhhhccccccccCCcccccCCC
Q psy245           79 QLAFISKNVL-KPVMKHQHAWPFHQPVDAIDLNLPFLIFRFLVFQHWVLSMYIEYPILLAFALTVPVLIILQDYHKVIKH  157 (566)
Q Consensus        79 ~l~~~~~~v~-~~l~~~~~~~~f~~pv~~~~~~~p~~~~~~~~~~~~~l~~~~~~r~~~~~f~~lP~~~~~pdY~~iIk~  157 (566)
                      ++.+++..|+ +.+++++.||||..|||..  .+|                                     |||++|++
T Consensus         9 ~~~~il~~l~~~~~~~~p~a~pF~~pVd~~--~~P-------------------------------------dY~~vIk~   49 (128)
T d1eqfa2           9 AFSFILDNIVTQKMMAVPDSWPFHHPVNKK--FVP-------------------------------------DYYKVIVN   49 (128)
T ss_dssp             HHHHHHHHHHHHTTTTSTTCGGGTSCCCTT--TST-------------------------------------THHHHCSS
T ss_pred             HHHHHHHHHHHHHHHcCCCCChhcCCCCcc--cCc-------------------------------------CHHHHcCC
Confidence            5777777764 6678889999999999954  366                                     99999999


Q ss_pred             CCCHHHHHHHhhccCCCCHHHHHHHHHHhhhhccccCCCCCHHHHHHHHHHHHHHHHhhhhcc
Q psy245          158 PMDLGTIKKRLENFYYWSGKEAISDFNTMFTNCYVYNKPGEDVVVMAQTLEKLFLTKVSARRE  220 (566)
Q Consensus       158 PMdL~tI~~kL~~~~Y~s~~ef~~Dv~lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  220 (566)
                      ||||+||++||++|.|.++.+|..||+|||+||+.||+++|.++.+|..|.+.|.+.+.+++.
T Consensus        50 PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~L~~~~~~~l~~~~~  112 (128)
T d1eqfa2          50 PMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDE  112 (128)
T ss_dssp             CCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             cccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhHH
Confidence            999999999999999999999999999999999999999999999999999999999988764