Psyllid ID: psy1225

---

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------
Protein Sequence
MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIECQVYLISDELTHYQVVLTGTAEQVRLSGLPDGDWLAFTLPVVSGKASST
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHcccccHHHccccccccccccHHHHHHHHHccccccccccccccccccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccEccccccccccHcccccHHHHHcccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHcccccccccHcHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHEEcccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccHHccHHcccccccccHHHHHHHHHHHHHHHcccccHccccccccccccccc
Coil and Loop (DISEMBL)
mrpqknqteggnlsepflklpakrynpdyyriiknprslltigktlksghySTLNELTGELNLMFEnakkfnpadsrlYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFEnakkfnpadsrlYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENakkfnpadlRLYRDAVKLQKLMQRKVQEVMILDIECQVYLISDELTHYQVVLTGTAEQvrlsglpdgdwlaftlpvvsgkasst
Flexible Loop (DISEMBL)
mrpqknqteggnlsepflklpakryNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKkfnpadsrLYRDAVKLQKLmqrkvqenprslltigktlksghYSTLNELTGELNLMFENAKkfnpadsrLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIECQVYLISDELTHYQVVLTGTAEQVRLSGLPDGDWLAFTlpvvsgkasst
Low Complexity Region (SEG)
MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIECQVYLISDELTHYQVVLTGTAEQVRLSGLPDGDWLAFTLPVVSGKASST
Disordered region (IsUnstruct)
*****************LKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKL**********SLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIECQVYLISDELTHYQVVLTGTAEQVRLSGLPDGDWLAFTLPVV*******
Disordered Region (DISOPRED)
********EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE********************************************************
Disordered Region (DISEMBL)
***********NLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIECQVYLISDELTHYQVVLTGTAEQVRLSGLPDGDWLAFTLPV********
Disordered Region (DISPRO)
*******TEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIECQVYLISDELTHYQVVLTGTAEQVRLSGLPDGDWLAFT***********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIECQVYLISDELTHYQVVLTGTAEQVRLSGLPDGDWLAFTLPVVSGKASST
Positional Conservation
no confident homologs detected

---

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	256	2.2.26 [Sep-21-2011]
Q90941	1633	Protein polybromo-1 OS=Ga	yes	N/A	0.753	0.118	0.292	1e-17
Q8BSQ9	1634	Protein polybromo-1 OS=Mu	yes	N/A	0.753	0.118	0.318	7e-17
Q86U86	1689	Protein polybromo-1 OS=Ho	no	N/A	0.753	0.114	0.318	8e-17
Q9UTN6	1199	Chromatin structure-remod	yes	N/A	0.304	0.065	0.418	1e-11
P25439	1638	ATP-dependent helicase br	no	N/A	0.328	0.051	0.392	5e-11
P32597	1359	Nuclear protein STH1/NPS1	yes	N/A	0.375	0.070	0.375	7e-11
O74964	803	Chromatin structure-remod	no	N/A	0.257	0.082	0.438	1e-10
Q09948	542	Chromatin structure-remod	no	N/A	0.285	0.134	0.419	1e-10
P51532	1647	Transcription activator B	no	N/A	0.328	0.051	0.333	1e-08
A7Z019	1606	Transcription activator B	no	N/A	0.328	0.052	0.333	1e-08

>sp|Q90941|PB1_CHICK Protein polybromo-1 OS=Gallus gallus GN=PBRM1 PE=1 SV=1

 Score = 90.5 bits (223), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 115/226 (50%), Gaps = 33/226 (14%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  +SEPF +LP+K+  PDYY+ IK P SL  I   LK+  Y TL++L  +LNLMFENA
Sbjct: 398 QGQLISEPFFQLPSKKKYPDYYQQIKTPISLQQIRAKLKNHEYETLDQLEADLNLMFENA 457

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQENPR--------SLLT--IGKTLKSGHYSTLNEL 118
           K++N  +S +Y+  +K+Q++MQ K +E  R        S+++     T  S   S  N  
Sbjct: 458 KRYNVPNSAIYKRVLKMQQVMQAKKKELARRDDIEDGDSMISSATSDTGSSKRKSKKNMR 517

Query: 119 TGELNLMF---------------------ENAKKFNPADSRLYRDAVKLQKLMQ--RKVQ 155
              + +++                     + +KK  P   ++  + + L+ +    R  +
Sbjct: 518 KQRMKILYNAVLEARESGTGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKMIEHNIRNDK 577

Query: 156 EFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
                 +  ++ LMF NA+ +N    ++Y DA  L+K+++ K +E+
Sbjct: 578 YVGEEAMIDDMKLMFRNARHYNEEGSQVYNDAHMLEKILKEKRKEL 623

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).
Gallus gallus (taxid: 9031)

>sp|Q8BSQ9|PB1_MOUSE Protein polybromo-1 OS=Mus musculus GN=Pbrm1 PE=1 SV=4

 Score = 87.8 bits (216), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 115/226 (50%), Gaps = 33/226 (14%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +LNLMFENA
Sbjct: 400 QGQLIAEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENA 459

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQENPR--------SLLT--IGKTLKSGHYSTLNEL 118
           K++N  +S +Y+  +KLQ++MQ K +E  R        S+++     T  +   S  N  
Sbjct: 460 KRYNVPNSAIYKRVLKLQQVMQAKKKELARRDDIEDGDSMISSATSDTGSAKRKSKKNIR 519

Query: 119 TGELNLMFENA-KKFNPADSRL-------------YRDAVKLQ-KLMQRKVQEFSL--NE 161
              + ++F    +   P   R              Y D  K+  + M  K+ E ++  ++
Sbjct: 520 KQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDK 579

Query: 162 LTGE------LSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
             GE      + LMF NA+ +N    ++Y DA  L+KL++ K +E+
Sbjct: 580 YAGEEGMMEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKDKRKEL 625

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology) (By similarity). Act as a negative regulator of cell proliferation.

Mus musculus (taxid: 10090)

>sp|Q86U86|PB1_HUMAN Protein polybromo-1 OS=Homo sapiens GN=PBRM1 PE=1 SV=1

 Score = 87.4 bits (215), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 115/226 (50%), Gaps = 33/226 (14%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +LNLMFENA
Sbjct: 400 QGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENA 459

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQENPR--------SLLT--IGKTLKSGHYSTLNEL 118
           K++N  +S +Y+  +KLQ++MQ K +E  R        S+++     T  +   S  N  
Sbjct: 460 KRYNVPNSAIYKRVLKLQQVMQAKKKELARRDDIEDGDSMISSATSDTGSAKRKSKKNIR 519

Query: 119 TGELNLMFENA-KKFNPADSRL-------------YRDAVKLQ-KLMQRKVQEFSL--NE 161
              + ++F    +   P   R              Y D  K+  + M  K+ E ++  ++
Sbjct: 520 KQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDK 579

Query: 162 LTGE------LSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
             GE      + LMF NA+ +N    ++Y DA  L+KL++ K +E+
Sbjct: 580 YAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKEL 625

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Act as a negative regulator of cell proliferation.

Homo sapiens (taxid: 9606)

>sp|Q9UTN6|SNF21_SCHPO Chromatin structure-remodeling complex subunit snf21 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=snf21 PE=1 SV=1

 Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 36/86 (41%), Positives = 53/86 (61%)

Query: 10   GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
            G  L++ FL+LP+K+  PDYY IIK+P +L  I K +    Y TL  +  +L  MF NA+
Sbjct: 1085 GRPLNKLFLELPSKKLYPDYYMIIKSPIALDAIRKHINGTFYKTLEAMKSDLMTMFNNAR 1144

Query: 70   KFNPADSRLYRDAVKLQKLMQRKVQE 95
             +N   S +Y DA K+Q  M+ K++E
Sbjct: 1145 TYNEEGSFVYEDANKMQTAMETKIEE 1170

Helicase. Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. Controls particularly membrane and organelle development genes.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|P25439|BRM_DROME ATP-dependent helicase brm OS=Drosophila melanogaster GN=brm PE=1 SV=2

 Score = 68.2 bits (165), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 53/84 (63%)

Query: 5    KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
            K+  +G  LSEPF+KLP+++  PDYY IIK P  +  I + ++   Y+ LNEL  +   +
Sbjct: 1439 KHNQDGRTLSEPFMKLPSRQRLPDYYEIIKRPVDIKKILQRIEDCKYADLNELEKDFMQL 1498

Query: 65   FENAKKFNPADSRLYRDAVKLQKL 88
             +NA+ +N   S +Y D++ LQK+
Sbjct: 1499 CQNAQIYNEEASLIYLDSIALQKV 1522

Transcriptional regulator. Act as coactivator, assisting one or more dedicated transcriptional activators of ANTC and BXC homeotic gene clusters. Can counteract the repressive effect of Polycomb protein. ATPase subunit of the Brahma complex, a multiprotein complex which is the equivalent of the yeast SWI/SNF complex and acts by remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. This complex can both serve as a transcriptional coactivator or corepressor, depending on the context.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P32597|STH1_YEAST Nuclear protein STH1/NPS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=STH1 PE=1 SV=1

 Score = 67.8 bits (164), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 55/96 (57%)

Query: 1    MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
            MR Q ++ +    +  F KLP+KR  PDY+++I+ P ++  I K  K+G Y TL E+   
Sbjct: 1262 MREQLDEVDSHPRTSIFEKLPSKRDYPDYFKVIEKPMAIDIILKNCKNGTYKTLEEVRQA 1321

Query: 61   LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEN 96
            L  MFENA+ +N   S +Y DA KL +      +E+
Sbjct: 1322 LQTMFENARFYNEEGSWVYVDADKLNEFTDEWFKEH 1357

Catalytic component of the chromatin structure-remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is the essential ATPase of the complex. It is a DNA translocase capable of nucleosome remodeling. Required for full expression of early meiotic genes. Essential for mitotic growth and repression of CHA1 expression. Also involved in G2 phase control.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|O74964|RSC1_SCHPO Chromatin structure-remodeling complex subunit rsc1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rsc1 PE=1 SV=1

 Score = 67.0 bits (162), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/73 (43%), Positives = 43/73 (58%)

Query: 10  GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
           G  L  PF +LP  R  P+YY+ I+ P +L  I K L    Y T+ +   + NLMF+NAK
Sbjct: 230 GRQLFAPFERLPDPRMFPEYYQAIEQPMALEVIQKKLSKHRYETIEQFVDDFNLMFDNAK 289

Query: 70  KFNPADSRLYRDA 82
            FN   S++YRDA
Sbjct: 290 SFNDPSSQVYRDA 302

Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. Controls particularly membrane and organelle development genes.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q09948|RSC4_SCHPO Chromatin structure-remodeling complex subunit rsc4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rsc4 PE=1 SV=1

 Score = 67.0 bits (162), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 48/81 (59%)

Query: 4   QKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNL 63
           ++   +G  L + F+ LP+KR  PDYY IIK+P ++  + K  K G Y+TL     +LN 
Sbjct: 157 EEKDEQGRFLIDIFIDLPSKRLYPDYYEIIKSPMTIKMLEKRFKKGEYTTLESFVKDLNQ 216

Query: 64  MFENAKKFNPADSRLYRDAVK 84
           MF NAK +N   S +Y DA K
Sbjct: 217 MFINAKTYNAPGSFVYEDAEK 237

Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. Controls particularly membrane and organelle development genes.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P51532|SMCA4_HUMAN Transcription activator BRG1 OS=Homo sapiens GN=SMARCA4 PE=1 SV=2

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 53/84 (63%)

Query: 5    KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
            K+ + G  LSE F++LP+++  P+YY +I+ P     I + +++  Y +LN+L  ++ L+
Sbjct: 1473 KDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLL 1532

Query: 65   FENAKKFNPADSRLYRDAVKLQKL 88
             +NA+ FN   S +Y D++ LQ +
Sbjct: 1533 CQNAQTFNLEGSLIYEDSIVLQSV 1556

Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. SMARCA4/BAF190A may promote neural stem cell self-renewal/proliferation by enhancing Notch-dependent proliferative signals, while concurrently making the neural stem cell insensitive to SHH-dependent differentiating cues (By similarity). Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Acts as a corepressor of ZEB1 to regulate E-cadherin transcription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|A7Z019|SMCA4_BOVIN Transcription activator BRG1 OS=Bos taurus GN=SMARCA4 PE=2 SV=1

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 53/84 (63%)

Query: 5    KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
            K+ + G  LSE F++LP+++  P+YY +I+ P     I + +++  Y +LN+L  ++ L+
Sbjct: 1432 KDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLL 1491

Query: 65   FENAKKFNPADSRLYRDAVKLQKL 88
             +NA+ FN   S +Y D++ LQ +
Sbjct: 1492 CQNAQTFNLEGSLIYEDSIVLQSV 1515

Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-fOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. SMARCA4/BAF190A may promote neural stem cell self-renewal/proliferation by enhancing Notch-dependent proliferative signals, while concurrently making the neural stem cell insensitive to SHH-dependent differentiating cues. Acts as a corepressor of ZEB1 to regulate E-cadherin transcription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

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	256
242010994	1673	predicted protein [Pediculus humanus cor	0.761	0.116	0.355	3e-28
383852643	1651	PREDICTED: protein polybromo-1-like [Meg	0.753	0.116	0.371	3e-25
322790256	1587	hypothetical protein SINV_09840 [Solenop	0.753	0.121	0.363	1e-24
307180267	1644	Protein polybromo-1 [Camponotus floridan	0.753	0.117	0.363	1e-24
380016641	1651	PREDICTED: protein polybromo-1-like [Api	0.753	0.116	0.363	3e-24
189234458	1648	PREDICTED: similar to polybromo-1 [Tribo	0.738	0.114	0.340	3e-24
328793686	1651	PREDICTED: protein polybromo-1 [Apis mel	0.753	0.116	0.358	9e-24
350415036	1651	PREDICTED: protein polybromo-1-like [Bom	0.753	0.116	0.358	1e-23
307207938	1647	Protein polybromo-1 [Harpegnathos saltat	0.753	0.117	0.358	1e-23
328719779	1680	PREDICTED: protein polybromo-1-like [Acy	0.753	0.114	0.326	2e-23

>gi|242010994|ref|XP_002426242.1| predicted protein [Pediculus humanus corporis] gi|212510305|gb|EEB13504.1| predicted protein [Pediculus humanus corporis]

 Score =  131 bits (329), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 87/245 (35%), Positives = 129/245 (52%), Gaps = 50/245 (20%)

Query: 5   KNQTEGGN--LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELN 62
           KN T  G   L EPF KLP++R+ PDYY+ IKNP SLL I   LK G Y T++E+ G+LN
Sbjct: 341 KNTTNNGGYALCEPFWKLPSRRHYPDYYKEIKNPVSLLQIRNKLKKGEYGTVSEVAGDLN 400

Query: 63  LMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE--------------------------- 95
           +MFENAKK+N  +SRLYRDA+KLQK+MQ KV+E                           
Sbjct: 401 IMFENAKKYNRPESRLYRDAIKLQKVMQHKVKELLDFDQESESDTDSDNSPIIKKDTSPI 460

Query: 96  --------------NP---RSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSR 138
                         NP   +  L+I K L    Y    +    L  M + +KK  P   +
Sbjct: 461 AKKRGRKSAAFIRDNPSLRKRFLSICKALTEYTYEDGRQPI--LMFMEKPSKKLYPEYYK 518

Query: 139 LYRDAVKLQKLMQR-KVQEFSL-NELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQR 196
           +  + + L ++    K ++++  ++L  +L LMF N +KFN  +  +Y+DA  L+K++  
Sbjct: 519 IIAEPIDLLQIQGNIKAEKYTTEDQLISDLKLMFSNCRKFNEENSVIYKDANNLEKVLND 578

Query: 197 KVQEV 201
           K++E+
Sbjct: 579 KLKEL 583

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383852643|ref|XP_003701836.1| PREDICTED: protein polybromo-1-like [Megachile rotundata]

 Score =  121 bits (303), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 87/234 (37%), Positives = 127/234 (54%), Gaps = 41/234 (17%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  +SE F KLP+KR  PDYY++IKNP SLL I   +K G Y T++E+ G++N+MFENA
Sbjct: 368 QGVRMSEYFWKLPSKRLYPDYYKMIKNPISLLQIRTKIKKGEYGTVSEVAGDMNIMFENA 427

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE-------------------NPR------SLLTI 103
           KK+N   SRLY+ AVKLQK+MQ KVQE                    P+      +LLT 
Sbjct: 428 KKYNIHTSRLYKCAVKLQKIMQEKVQELLEFDQDSDSDSEFENNSQQPKLIKRASNLLTR 487

Query: 104 GK-----TLKSGHYS---TLNELTGE------LNLMFENAKKFNPADSRLYRDAVKLQKL 149
           GK      LK   Y+    + E   E      L  M + +KK  P   ++  + + +  +
Sbjct: 488 GKYKDNIPLKRRLYALVKCVMEYVCEDGRQPMLMFMEKPSKKLYPDYYQVIAEPIDMLAI 547

Query: 150 MQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
               KV+++ S NEL  +  LMF N +++N     +Y DA  L+K++  KV+E+
Sbjct: 548 EANIKVEKYQSENELIQDFKLMFNNCRQYNEEGSLIYEDANTLEKVLMDKVKEL 601

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322790256|gb|EFZ15255.1| hypothetical protein SINV_09840 [Solenopsis invicta]

 Score =  119 bits (298), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 127/234 (54%), Gaps = 41/234 (17%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  +SE F KLP+KR  PDYY++IKNP SLL I   +K G Y T++E+ G++N+MFENA
Sbjct: 368 QGVRMSEYFWKLPSKRLYPDYYKMIKNPISLLQIRTKIKKGEYGTVSEVAGDMNIMFENA 427

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE-------------------NPR------SLLTI 103
           KK+N   SRLY+ AVKLQK+MQ KVQE                    P+      +LLT 
Sbjct: 428 KKYNMHTSRLYKCAVKLQKIMQEKVQELLEFDQDSDSDSESENSSQQPKLIKRASNLLTR 487

Query: 104 GK-----TLKSGHYSTLN---ELTGE------LNLMFENAKKFNPADSRLYRDAVKLQKL 149
           GK      LK   Y+ +    E   E      L  M + +KK  P   ++  + + +  +
Sbjct: 488 GKYKDNIPLKKRLYTLVKCVIEYVCEDGRQPMLMFMEKPSKKLYPDYYQVIAEPIDMLAI 547

Query: 150 MQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
               KV+++ + NEL  +  LMF N +++N     +Y DA  L+K++  K++E+
Sbjct: 548 EANIKVEKYQNENELIQDFKLMFNNCRQYNEEGSLIYEDANTLEKVLMDKIKEL 601

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307180267|gb|EFN68300.1| Protein polybromo-1 [Camponotus floridanus]

 Score =  119 bits (298), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 126/234 (53%), Gaps = 41/234 (17%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  +SE F KLP+KR  PDYY++IKNP SLL I   +K G Y T++E+ G++N+MFENA
Sbjct: 368 QGVRMSEYFWKLPSKRLYPDYYKMIKNPISLLQIRTKIKKGEYGTVSEVAGDMNIMFENA 427

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE-------------------NPR------SLLTI 103
           KK+N   SRLY+ AVKLQK+MQ KVQE                    P+      +LLT 
Sbjct: 428 KKYNIHTSRLYKCAVKLQKIMQEKVQELLEFDQDSDSDSESENSSYQPKLIKRASNLLTR 487

Query: 104 GK-----TLKSGHYSTLN---ELTGE------LNLMFENAKKFNPADSRLYRDAVKLQKL 149
           GK      LK   Y+ +    E   E      L  M + +KK  P   ++  + + +  +
Sbjct: 488 GKYKDNIPLKKRLYTLVKCVIEYVCEDGRQPMLMFMEKPSKKLYPDYYQVIAEPIDMLAI 547

Query: 150 MQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
               K +++ S NEL  +  LMF N +++N     +Y DA  L++++  KV+E+
Sbjct: 548 EANIKAEKYQSENELIQDFKLMFNNCRQYNEEGSLIYEDANTLERVLMDKVKEL 601

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380016641|ref|XP_003692286.1| PREDICTED: protein polybromo-1-like [Apis florea]

 Score =  118 bits (295), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 125/234 (53%), Gaps = 41/234 (17%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  +SE F KLP+KR  PDYY+ IKNP SLL I   +K G Y T++E+ G++N+MFENA
Sbjct: 368 QGVRMSEYFWKLPSKRLYPDYYKTIKNPISLLQIRTKIKKGEYGTVSEVAGDMNIMFENA 427

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE-------------------NPR------SLLTI 103
           KK+N   SRLY+ AVKLQK+MQ KVQE                    P+      +LLT 
Sbjct: 428 KKYNIHTSRLYKCAVKLQKIMQEKVQELLEFDQDSDSDSEFENSSHQPKLIKRASNLLTR 487

Query: 104 GK-----TLKSGHYSTLN---ELTGE------LNLMFENAKKFNPADSRLYRDAVKLQKL 149
           GK      LK   Y+ +    E   E      L  M + +KK  P   ++  + + +  +
Sbjct: 488 GKYKDNIPLKKRLYALVKCVIEYVCEDGRQPMLMFMEKPSKKLYPDYYQVIAEPIDMLAI 547

Query: 150 MQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
               K +++ S NEL  +  LMF N +++N     +Y DA  L++++  KV+E+
Sbjct: 548 EANIKAEKYQSENELIQDFKLMFNNCRQYNEEGSLIYEDANTLERVLMDKVKEL 601

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189234458|ref|XP_001808258.1| PREDICTED: similar to polybromo-1 [Tribolium castaneum]

 Score =  117 bits (294), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 80/235 (34%), Positives = 116/235 (49%), Gaps = 46/235 (19%)

Query: 10  GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
           G +LSEPF KLP+KR+ PDYYR IKNP SL  I + L    Y T++E+ G++ +MFENAK
Sbjct: 378 GVSLSEPFWKLPSKRFYPDYYREIKNPVSLTQIKRKLTKHAYGTISEVAGDMTIMFENAK 437

Query: 70  KFNPADSRLYRDAVKLQKLMQRKVQE------------------------NPRSLLTIGK 105
           K+N   SRLY+DAVKLQK+MQ KVQE                         P++  + G 
Sbjct: 438 KYNLPSSRLYKDAVKLQKVMQMKVQELLDIDQDTDSEADSEVVVRKKPGPKPKNTQSSGS 497

Query: 106 TLKSGHYS--------------------TLNELTGELNLMFENAKKFNPADSRLYRDAVK 145
           T + G                       T+N     L  M + +KK       +  + + 
Sbjct: 498 TPQRGRPPRDPIPLKKRLHALAKYMLDYTVNGRKPMLGFMEKPSKKLYSEYYEVISEPID 557

Query: 146 LQKLMQ--RKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKV 198
             ++ Q  R  Q  S ++L  +  LMF N ++FN  +  +Y D++ L+K +  KV
Sbjct: 558 FLEIEQKIRADQYSSESDLVKDFKLMFSNCRQFNEENSPIYEDSLVLEKHLLDKV 612

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328793686|ref|XP_625055.3| PREDICTED: protein polybromo-1 [Apis mellifera]

 Score =  116 bits (291), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 125/234 (53%), Gaps = 41/234 (17%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  +SE F KLP+KR  PDYY+ IKNP SLL I   +K G Y T++E+ G++N+MFENA
Sbjct: 368 QGVRMSEYFWKLPSKRLYPDYYKTIKNPISLLQIRTKIKKGEYGTVSEVAGDMNIMFENA 427

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE-------------------NPR------SLLTI 103
           KK+N   SRLY+ AVKLQK+MQ KVQE                    P+      +LLT 
Sbjct: 428 KKYNIHTSRLYKCAVKLQKIMQEKVQELLEFDQDSDSDSEFENSSHQPKLIKRASNLLTR 487

Query: 104 GK-----TLKSGHYSTLN---ELTGE------LNLMFENAKKFNPADSRLYRDAVKLQKL 149
           GK      LK   Y+ +    E   E      L  M + +KK  P   ++  + + +  +
Sbjct: 488 GKYKDNIPLKKRLYALVKCVIEYVCEDGRQPMLMFMEKPSKKLYPDYYQVIAEPIDMLAI 547

Query: 150 MQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
               K +++ + NEL  +  LMF N +++N     +Y DA  L++++  KV+E+
Sbjct: 548 EANIKAEKYQNENELIQDFKLMFNNCRQYNEEGSLIYEDANTLERVLMDKVKEL 601

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350415036|ref|XP_003490512.1| PREDICTED: protein polybromo-1-like [Bombus impatiens]

 Score =  116 bits (290), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 124/234 (52%), Gaps = 41/234 (17%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  +SE F KLP+KR  PDYY+ IKNP SLL I   +K G Y T++E+ G++N+MFENA
Sbjct: 368 QGVRMSEYFWKLPSKRLYPDYYKTIKNPISLLQIRTKIKKGEYGTVSEVAGDMNIMFENA 427

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE-------------------NPR------SLLTI 103
           KK+N   SRLY+ AVKLQK+MQ KV E                    P+      +LLT 
Sbjct: 428 KKYNIHTSRLYKCAVKLQKIMQEKVHELLEFDQDSDSDSEFENSSHQPKLIKRASNLLTR 487

Query: 104 GK-----TLKSGHYSTLN---ELTGE------LNLMFENAKKFNPADSRLYRDAVKLQKL 149
           GK      LK   Y+ +    E   E      L  M + +KK  P   ++  + + +  +
Sbjct: 488 GKYKDNIPLKKRLYALVKCVIEYVCEDGRQPMLMFMEKPSKKLYPDYYQVIAEPIDMLAI 547

Query: 150 MQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
               K +++ S NEL  +  LMF N +++N     +Y DA  L++++  KV+E+
Sbjct: 548 EANIKAEKYQSENELIQDFKLMFNNCRQYNEEGSLIYEDANTLERVLMDKVKEL 601

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307207938|gb|EFN85497.1| Protein polybromo-1 [Harpegnathos saltator]

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 123/234 (52%), Gaps = 41/234 (17%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  +SE F KLP KR  PDYY+ IKNP  LL I   +K G Y T++E+ G++N+MFENA
Sbjct: 368 QGLRISEYFWKLPPKRLYPDYYKTIKNPICLLQIHTKIKKGEYGTVSEVAGDMNIMFENA 427

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE-------------------NPR------SLLTI 103
           KK+N   SRLY+ AVKLQK+MQ KVQE                    P+      +LLT 
Sbjct: 428 KKYNVHTSRLYKSAVKLQKIMQEKVQELLEFDQDSDSDSESENSSQQPKLIKRASNLLTR 487

Query: 104 GK-----TLKSGHYSTLN---ELTGE------LNLMFENAKKFNPADSRLYRDAVKLQKL 149
           GK      LK   Y+ +    E   E      L  M + +KK  P   ++  + + +  +
Sbjct: 488 GKYKDNIPLKKRLYALVKCVIEYVCEDGRQPMLMFMEKPSKKLYPDYYQVIAEPIDMLAI 547

Query: 150 MQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
               K +++ S +EL  +  LMF N +++N     +Y DA  L+K++  KV+E+
Sbjct: 548 EANIKAEKYQSESELIQDFKLMFNNCRQYNEEGSLIYEDANTLEKVLMDKVKEL 601

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328719779|ref|XP_001944619.2| PREDICTED: protein polybromo-1-like [Acyrthosiphon pisum]

 Score =  115 bits (288), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 125/242 (51%), Gaps = 49/242 (20%)

Query: 8   TEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN 67
           ++G  LS+ F KLP+KRY P+YY  I+NP SL+ IGK L++G Y T++E+ G++N+M EN
Sbjct: 369 SQGNLLSDTFWKLPSKRYYPNYYHEIRNPLSLMQIGKKLRNGDYGTVSEVAGDMNVMLEN 428

Query: 68  AKKFNPADSRLYRDAVKLQKLMQRKVQE-------------------------------- 95
           AKK+   D++ Y+DAVKLQK+MQ K QE                                
Sbjct: 429 AKKYFTIDTKQYKDAVKLQKVMQTKAQELLDLGHQYSDSEDDSADDDLQSTSRTSKKFAR 488

Query: 96  NPRSLLTIGKTLKS--------------GHYSTLNELTGELNLMFENAKKFNPADSRLYR 141
           +PR  LT GK L +                Y+T +     L  M   +KK  PA  ++  
Sbjct: 489 SPR-CLTRGKYLNNIPLKRRLYALCKCLMDYTTEHGRVPMLMFMEIPSKKLYPAYYKVIS 547

Query: 142 DAVKLQKLMQRKVQE--FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQ 199
           + + +  + ++  QE   S +E+  +  LMF+N ++FN     +Y DA  L+K++  + +
Sbjct: 548 EPIDMLTIEEKIKQEKYKSEDEILQDFKLMFDNCRQFNEEGSLIYEDANTLEKVLLDRSK 607

Query: 200 EV 201
           E+
Sbjct: 608 EL 609

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	256
ZFIN|ZDB-GENE-010501-3	1648	pbrm1l "polybromo 1, like" [Da	0.328	0.050	0.452	3.5e-27
UNIPROTKB|F1NLL8	1630	PBRM1 "Protein polybromo-1" [G	0.378	0.059	0.459	5.7e-23
UNIPROTKB|Q90941	1633	PBRM1 "Protein polybromo-1" [G	0.378	0.059	0.459	5.8e-23
UNIPROTKB|H0Y5B5	1085	PBRM1 "Protein polybromo-1" [H	0.378	0.089	0.459	1.4e-22
UNIPROTKB|E7EVG2	1461	PBRM1 "Protein polybromo-1" [H	0.378	0.066	0.459	3.1e-22
UNIPROTKB|Q86U86	1689	PBRM1 "Protein polybromo-1" [H	0.378	0.057	0.459	4.4e-22
MGI|MGI:1923998	1634	Pbrm1 "polybromo 1" [Mus muscu	0.378	0.059	0.459	6.5e-22
UNIPROTKB|E2RRR3	1635	PBRM1 "Uncharacterized protein	0.378	0.059	0.459	6.5e-22
UNIPROTKB|E2RRL7	1689	PBRM1 "Uncharacterized protein	0.378	0.057	0.459	7.1e-22
RGD|1565549	1704	Pbrm1 "polybromo 1" [Rattus no	0.378	0.056	0.459	7.2e-22

ZFIN|ZDB-GENE-010501-3 pbrm1l "polybromo 1, like" [Danio rerio (taxid:7955)]

 Score = 203 (76.5 bits), Expect = 3.5e-27, Sum P(3) = 3.5e-27
 Identities = 38/84 (45%), Positives = 61/84 (72%)

Query:     9 EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
             +G  LSEPFL+LP++R  PDYY  IKNP SL  I + +K+G Y  + ++  +L++MFENA
Sbjct:   379 QGLLLSEPFLQLPSRREYPDYYHQIKNPISLQQIREKMKNGDYEAVEQIEADLSVMFENA 438

Query:    69 KKFNPADSRLYRDAVKLQKLMQRK 92
             +++N  +S +Y+ A +LQ +MQ++
Sbjct:   439 RRYNMPNSTIYKRAQRLQLIMQQQ 462

GO:0003677 "DNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|F1NLL8 PBRM1 "Protein polybromo-1" [Gallus gallus (taxid:9031)]

 Score = 219 (82.2 bits), Expect = 5.7e-23, Sum P(2) = 5.7e-23
 Identities = 45/98 (45%), Positives = 67/98 (68%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  +SEPF +LP+K+  PDYY+ IK P SL  I   LK+  Y TL++L  +
Sbjct:   391 VRSCRNN-QGQLISEPFFQLPSKKKYPDYYQQIKTPISLQQIRAKLKNHEYETLDQLEAD 449

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +K+Q++MQ K +E  R
Sbjct:   450 LNLMFENAKRYNVPNSAIYKRVLKMQQVMQAKKKELAR 487

GO:0003677 "DNA binding" evidence=IEA

GO:0000776 "kinetochore" evidence=IEA

GO:0001890 "placenta development" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0007507 "heart development" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

UNIPROTKB|Q90941 PBRM1 "Protein polybromo-1" [Gallus gallus (taxid:9031)]

 Score = 219 (82.2 bits), Expect = 5.8e-23, Sum P(2) = 5.8e-23
 Identities = 45/98 (45%), Positives = 67/98 (68%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  +SEPF +LP+K+  PDYY+ IK P SL  I   LK+  Y TL++L  +
Sbjct:   391 VRSCRNN-QGQLISEPFFQLPSKKKYPDYYQQIKTPISLQQIRAKLKNHEYETLDQLEAD 449

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +K+Q++MQ K +E  R
Sbjct:   450 LNLMFENAKRYNVPNSAIYKRVLKMQQVMQAKKKELAR 487

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0016568 "chromatin modification" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|H0Y5B5 PBRM1 "Protein polybromo-1" [Homo sapiens (taxid:9606)]

 Score = 208 (78.3 bits), Expect = 1.4e-22, Sum P(2) = 1.4e-22
 Identities = 45/98 (45%), Positives = 65/98 (66%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +
Sbjct:   337 VRSCRNN-QGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECD 395

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct:   396 LNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELAR 433

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E7EVG2 PBRM1 "Protein polybromo-1" [Homo sapiens (taxid:9606)]

 Score = 208 (78.3 bits), Expect = 3.1e-22, Sum P(2) = 3.1e-22
 Identities = 45/98 (45%), Positives = 65/98 (66%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +
Sbjct:   393 VRSCRNN-QGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECD 451

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct:   452 LNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELAR 489

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q86U86 PBRM1 "Protein polybromo-1" [Homo sapiens (taxid:9606)]

 Score = 208 (78.3 bits), Expect = 4.4e-22, Sum P(2) = 4.4e-22
 Identities = 45/98 (45%), Positives = 65/98 (66%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +
Sbjct:   393 VRSCRNN-QGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECD 451

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct:   452 LNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELAR 489

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0000776 "kinetochore" evidence=IEA

GO:0001890 "placenta development" evidence=IEA

GO:0007507 "heart development" evidence=IEA

GO:0006338 "chromatin remodeling" evidence=TAS

GO:0003682 "chromatin binding" evidence=NAS

GO:0007067 "mitosis" evidence=TAS

GO:0000228 "nuclear chromosome" evidence=NAS

GO:0008285 "negative regulation of cell proliferation" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:1923998 Pbrm1 "polybromo 1" [Mus musculus (taxid:10090)]

 Score = 209 (78.6 bits), Expect = 6.5e-22, Sum P(2) = 6.5e-22
 Identities = 45/98 (45%), Positives = 65/98 (66%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +
Sbjct:   393 VRSCRNH-QGQLIAEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECD 451

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct:   452 LNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELAR 489

GO:0000776 "kinetochore" evidence=IDA

GO:0001890 "placenta development" evidence=IMP

GO:0001974 "blood vessel remodeling" evidence=TAS

GO:0003007 "heart morphogenesis" evidence=TAS

GO:0003349 "epicardium-derived cardiac endothelial cell differentiation" evidence=TAS

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IC

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

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

GO:0007507 "heart development" evidence=IMP

GO:0008285 "negative regulation of cell proliferation" evidence=ISO

GO:0016568 "chromatin modification" evidence=IEA

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

GO:0060948 "cardiac vascular smooth muscle cell development" evidence=TAS

GO:0060979 "vasculogenesis involved in coronary vascular morphogenesis" evidence=TAS

UNIPROTKB|E2RRR3 PBRM1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 209 (78.6 bits), Expect = 6.5e-22, Sum P(2) = 6.5e-22
 Identities = 45/98 (45%), Positives = 65/98 (66%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +
Sbjct:   393 VRSCRNN-QGQLIAEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECD 451

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct:   452 LNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELAR 489

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RRL7 PBRM1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 209 (78.6 bits), Expect = 7.1e-22, Sum P(2) = 7.1e-22
 Identities = 45/98 (45%), Positives = 65/98 (66%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +
Sbjct:   393 VRSCRNN-QGQLIAEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECD 451

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct:   452 LNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELAR 489

GO:0003677 "DNA binding" evidence=IEA

RGD|1565549 Pbrm1 "polybromo 1" [Rattus norvegicus (taxid:10116)]

 Score = 209 (78.6 bits), Expect = 7.2e-22, Sum P(2) = 7.2e-22
 Identities = 45/98 (45%), Positives = 65/98 (66%)

Query:     1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
             +R  +N  +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +
Sbjct:   393 VRSCRNN-QGQLIAEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECD 451

Query:    61 LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
             LNLMFENAK++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct:   452 LNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELAR 489

GO:0000776 "kinetochore" evidence=IEA;ISO

GO:0001890 "placenta development" evidence=IEA;ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005575 "cellular_component" evidence=ND

GO:0007507 "heart development" evidence=IEA;ISO

GO:0008150 "biological_process" evidence=ND

GO:0008285 "negative regulation of cell proliferation" evidence=IEA;ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	256
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	3e-32
smart00297	107	smart00297, BROMO, bromo domain	1e-23
cd04369	99	cd04369, Bromodomain, Bromodomain	6e-23
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	5e-22
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	2e-21
COG5076	371	COG5076, COG5076, Transcription factor involved in	7e-20
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	1e-19
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	5e-18
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	1e-17
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	1e-17
cd05517	103	cd05517, Bromo_polybromo_II, Bromodomain, polybrom	2e-17
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	9e-17
pfam00439	84	pfam00439, Bromodomain, Bromodomain	1e-16
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	5e-15
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	2e-14
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	2e-13
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	4e-13
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	5e-13
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	8e-13
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	9e-13
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	1e-12
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	1e-12
cd04369	99	cd04369, Bromodomain, Bromodomain	2e-12
smart00297	107	smart00297, BROMO, bromo domain	3e-12
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	1e-11
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	2e-11
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	7e-11
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	8e-11
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	2e-10
COG5076	371	COG5076, COG5076, Transcription factor involved in	6e-10
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	6e-10
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	9e-10
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	1e-09
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	2e-09
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	3e-09
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	4e-09
pfam00439	84	pfam00439, Bromodomain, Bromodomain	1e-08
cd05517	103	cd05517, Bromo_polybromo_II, Bromodomain, polybrom	6e-08
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	1e-07
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	3e-07
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	3e-07
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	5e-07
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	5e-07
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	9e-07
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	1e-06
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	1e-06
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	2e-06
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	3e-06
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	4e-06
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	4e-06
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	5e-06
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	6e-06
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	6e-06
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	1e-05
smart00297	107	smart00297, BROMO, bromo domain	2e-05
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	3e-05
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	4e-05
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	5e-05
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	9e-05
cd04369	99	cd04369, Bromodomain, Bromodomain	2e-04
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	2e-04
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	2e-04
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	2e-04
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	3e-04
cd05526	110	cd05526, Bromo_polybromo_VI, Bromodomain, polybrom	7e-04
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	0.002
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	0.002
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	0.002
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	0.002
cd05526	110	cd05526, Bromo_polybromo_VI, Bromodomain, polybrom	0.003

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

 Score =  113 bits (286), Expect = 3e-32
 Identities = 53/86 (61%), Positives = 64/86 (74%)

Query: 8   TEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN 67
            +G  L+EPFLKLP+KR  PDYY+ IKNP SL  I   LK+G Y TL EL  +LNLMFEN
Sbjct: 18  NQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFEN 77

Query: 68  AKKFNPADSRLYRDAVKLQKLMQRKV 93
           AK++N  +SR+Y+DA KLQKLMQ K 
Sbjct: 78  AKRYNVPNSRIYKDAEKLQKLMQAKK 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|197636 smart00297, BROMO, bromo domain

 Score = 91.2 bits (227), Expect = 1e-23
 Identities = 40/83 (48%), Positives = 57/83 (68%)

Query: 13  LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
           LS PFLK  +++  PDYY IIK P  L TI K L++G YS++ E   + NLMF NA+ +N
Sbjct: 24  LSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

Query: 73  PADSRLYRDAVKLQKLMQRKVQE 95
             DS +Y+DA KL+K  ++K++E
Sbjct: 84  GPDSEVYKDAKKLEKFFEKKLRE 106

Length = 107

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score = 89.4 bits (222), Expect = 6e-23
 Identities = 38/81 (46%), Positives = 53/81 (65%)

Query: 13 LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
          LSEPFL+    +  PDYY +IKNP  L TI K LK+G Y +L E   ++ L+F NAK +N
Sbjct: 19 LSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYN 78

Query: 73 PADSRLYRDAVKLQKLMQRKV 93
             S +Y+DA KL+KL ++ +
Sbjct: 79 GPGSPIYKDAKKLEKLFEKLL 99

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

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

 Score = 87.4 bits (217), Expect = 5e-22
 Identities = 36/93 (38%), Positives = 58/93 (62%), Gaps = 2/93 (2%)

Query: 5   KNQTEGGN--LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELN 62
           KN T+G    LS  F++LP+K   PDYY +IK P  +  I   ++   Y +L+++  +  
Sbjct: 13  KNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFV 72

Query: 63  LMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 95
           LMF+NA K+N  DS++Y+DA+ LQK++    +E
Sbjct: 73  LMFDNACKYNEPDSQIYKDALTLQKVLLETKRE 105

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

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

 Score = 85.3 bits (212), Expect = 2e-21
 Identities = 32/80 (40%), Positives = 50/80 (62%)

Query: 16  PFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 75
           PFL+   K   PDYY +IK P  L T+ + L++G+Y TL E   +L L+F+N + +N  D
Sbjct: 21  PFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

Query: 76  SRLYRDAVKLQKLMQRKVQE 95
           +  Y+ A KL+K   +K++E
Sbjct: 81  TEYYKCANKLEKFFWKKLKE 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|227408 COG5076, COG5076, Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]

 Score = 87.2 bits (216), Expect = 7e-20
 Identities = 52/173 (30%), Positives = 75/173 (43%), Gaps = 12/173 (6%)

Query: 1   MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
            + Q    +G  LS  FL LP+KR  PDYY IIK+P  LLTI K LK+G Y +  E   +
Sbjct: 153 FKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSD 212

Query: 61  LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNEL-- 118
           LNLMF+N K +N  DS +Y DA +L+K   + ++E P  +L +              +  
Sbjct: 213 LNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLELSIKPGREEREERESVLI 272

Query: 119 ------TGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGE 165
                  G    +          D   Y   ++    +  K  +   N    E
Sbjct: 273 TNSQAHVGAWPFL-RPVSDEEVPD---YYKDIRDPMDLSTKELKLRNNYYRPE 321

Length = 371

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

 Score = 80.7 bits (200), Expect = 1e-19
 Identities = 38/87 (43%), Positives = 55/87 (63%), Gaps = 1/87 (1%)

Query: 1  MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
          +R ++++  G  L+  F KLP K   P+YY+ I NP SL  I K +K   Y + ++   +
Sbjct: 13 LRKERDE-NGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLND 71

Query: 61 LNLMFENAKKFNPADSRLYRDAVKLQK 87
          LNLMFENAK +N  DS+ Y+DAV L+K
Sbjct: 72 LNLMFENAKLYNENDSQEYKDAVLLEK 98

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 = 76.6 bits (189), Expect = 5e-18
 Identities = 36/59 (61%), Positives = 43/59 (72%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
           NP SL  I   LK+G Y TL EL  +LNLMFENAK++N  +SR+Y+DA KLQKLMQ K 
Sbjct: 45  NPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKLMQAKK 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|99947 cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like subfamily, specific to animals

 Score = 75.9 bits (187), Expect = 1e-17
 Identities = 25/83 (30%), Positives = 51/83 (61%)

Query: 6  NQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMF 65
            ++G  L+E F++LP+++  P+YY +I+ P     I + +++  Y +L +L  ++ L+ 
Sbjct: 17 KDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLC 76

Query: 66 ENAKKFNPADSRLYRDAVKLQKL 88
          +NA+ FN   S +Y D++ LQ +
Sbjct: 77 QNAQTFNLEGSLIYEDSIVLQSV 99

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

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

 Score = 75.5 bits (186), Expect = 1e-17
 Identities = 34/84 (40%), Positives = 52/84 (61%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
            G  LSE FL+ P+K+  PDYY IIK P +L  I + ++   Y +L E   + +LMF NA
Sbjct: 19  TGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANA 78

Query: 69  KKFNPADSRLYRDAVKLQKLMQRK 92
           + +N   S +Y DAV+++K  ++K
Sbjct: 79  RTYNQEGSIVYEDAVEMEKAFKKK 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|99948 cd05517, Bromo_polybromo_II, Bromodomain, polybromo repeat II

 Score = 75.2 bits (185), Expect = 2e-17
 Identities = 34/80 (42%), Positives = 54/80 (67%)

Query: 13  LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
           +SE F KLP+K   PDYY +IK P  L TI + ++SG+Y ++ ++  +L+LM +NAK FN
Sbjct: 23  ISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82

Query: 73  PADSRLYRDAVKLQKLMQRK 92
              S++Y+DA  ++K+   K
Sbjct: 83  EPGSQVYKDANAIKKIFTAK 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|99954 cd05524, Bromo_polybromo_I, Bromodomain, polybromo repeat I

 Score = 73.5 bits (181), Expect = 9e-17
 Identities = 33/95 (34%), Positives = 54/95 (56%), Gaps = 1/95 (1%)

Query: 1   MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
           +R  K+  +G  L E F+++P +R  P+YY ++ NP  LL I + LK+  Y  +++LT +
Sbjct: 14  IRNYKS-EDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTAD 72

Query: 61  LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 95
             L+  NAK +   DS  ++DA KL +L      E
Sbjct: 73  FELLINNAKAYYKPDSPEHKDACKLWELFLSARNE 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|215921 pfam00439, Bromodomain, Bromodomain

 Score = 72.4 bits (178), Expect = 1e-16
 Identities = 33/72 (45%), Positives = 44/72 (61%)

Query: 13 LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
          L+EPFL+       PDYY +IK P  L TI + LKSG Y +L E   ++ L+F NA  +N
Sbjct: 13 LAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKDVELIFSNAITYN 72

Query: 73 PADSRLYRDAVK 84
            DS +Y+DA K
Sbjct: 73 GEDSDIYKDAKK 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|99949 cd05518, Bromo_polybromo_IV, Bromodomain, polybromo repeat IV

 Score = 68.6 bits (168), Expect = 5e-15
 Identities = 32/84 (38%), Positives = 51/84 (60%)

Query: 10  GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
           G  L + F++ P+K+  PDYY+II  P  L TI   +++  Y+T  EL  +  LMF NA+
Sbjct: 20  GRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNAR 79

Query: 70  KFNPADSRLYRDAVKLQKLMQRKV 93
            +N   S++Y DA  L+K+++ K 
Sbjct: 80  HYNEEGSQVYEDANILEKVLKEKR 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|99955 cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-family

 Score = 67.4 bits (165), Expect = 2e-14
 Identities = 30/79 (37%), Positives = 47/79 (59%)

Query: 10  GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
           G +L+ PF+ LP+K+ NPDYY  I +P  L TI K + +G+Y T      ++  +F NA+
Sbjct: 22  GQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAE 81

Query: 70  KFNPADSRLYRDAVKLQKL 88
           K+    S + RD  +L+K 
Sbjct: 82  KYYGRKSPIGRDVCRLRKA 100

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|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 4/87 (4%)

Query: 12  NLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENA 68
            LS PF + P     P+YY+IIK P  L  I K L+     HYS+  E   ++ LMF+N 
Sbjct: 20  ELSLPFHE-PVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNC 78

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE 95
            KFN  DS + +   +L+   + +++E
Sbjct: 79  YKFNEEDSEVAQAGKELELFFEEQLKE 105

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|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score = 63.3 bits (155), Expect = 4e-13
 Identities = 22/61 (36%), Positives = 38/61 (62%)

Query: 97  PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 156
           P  L T+ + L++G+Y TL E   +L L+F+N + +N  D+  Y+ A KL+K   +K++E
Sbjct: 41  PMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKE 100

Query: 157 F 157
            
Sbjct: 101 L 101

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

 Score = 63.4 bits (155), Expect = 5e-13
 Identities = 27/87 (31%), Positives = 43/87 (49%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K+  PDYY+IIK P  L TI K +    Y +  E   ++ L+ +N+  +N 
Sbjct: 18  SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNG 77

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSL 100
            DS   + A ++ +L +  + E    L
Sbjct: 78  PDSVYTKKAKEMLELAEELLAEREEKL 104

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

 Score = 62.7 bits (153), Expect = 8e-13
 Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 2/85 (2%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
            G  +   F  LP ++  PDYY+IIKNP SL T+ K L   HY+   E   +L  +  NA
Sbjct: 20  NGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNA 77

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKV 93
           + +N   S +Y+ A+ L+K +   +
Sbjct: 78  RLYNTKGSVIYKYALILEKYINDVI 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|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 62.8 bits (153), Expect = 9e-13
 Identities = 28/70 (40%), Positives = 37/70 (52%)

Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
          S PFL   +KR  PDYY IIK P  L T+ K LK+  Y +  E   +LNL+++N   +N 
Sbjct: 26 STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNS 85

Query: 74 ADSRLYRDAV 83
            S   R   
Sbjct: 86 DPSHPLRRHA 95

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

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 25/66 (37%), Positives = 37/66 (56%)

Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
            DY+ IIK+P  L TI K L +  Y+   E   ++ LMF N  K+NP D  ++  A KLQ
Sbjct: 36  HDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQ 95

Query: 87  KLMQRK 92
            + + +
Sbjct: 96  DVFEDR 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|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 28/82 (34%), Positives = 44/82 (53%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PFL+  +K   PDYY IIK P  L TI + L  G Y    E   ++ L+F N   +NP
Sbjct: 30  SWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNP 89

Query: 74  ADSRLYRDAVKLQKLMQRKVQE 95
             + +Y+   +LQ+   ++ ++
Sbjct: 90  EHTSVYKAGTRLQRFFIKRCRK 111

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 = 61.6 bits (150), Expect = 2e-12
 Identities = 27/64 (42%), Positives = 41/64 (64%)

Query: 91  RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLM 150
            +V +NP  L TI K LK+G Y +L E   ++ L+F NAK +N   S +Y+DA KL+KL 
Sbjct: 36  YEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLF 95

Query: 151 QRKV 154
           ++ +
Sbjct: 96  EKLL 99

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

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

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 27/63 (42%), Positives = 42/63 (66%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
           + P  L TI K L++G YS++ E   + NLMF NA+ +N  DS +Y+DA KL+K  ++K+
Sbjct: 45  KKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKL 104

Query: 155 QEF 157
           +E 
Sbjct: 105 REL 107

Length = 107

>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 12  NLSEPFLKLP-AKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
             + PFL        N P+Y+ IIK P  L TI K L++G Y +  E   ++ L+F+N  
Sbjct: 19  AYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCY 78

Query: 70  KFNPADSRLYRDAVKLQKLMQRK 92
            FNP  + +Y    +L+++   K
Sbjct: 79  TFNPEGTDVYMMGHQLEEVFNDK 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|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 58.5 bits (142), Expect = 2e-11
 Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 14  SEPFLKL--PAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKF 71
           + PFL    P K   P Y  IIK P  L TI + LKS  Y+++ E T + NLM +N   F
Sbjct: 22  ARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTF 81

Query: 72  NPADSRLYRDAVKLQKLMQRK 92
           N  +  + +   +LQ   ++ 
Sbjct: 82  NGPEHPVSQMGKRLQAAFEKH 102

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|99951 cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 30/71 (42%), Positives = 47/71 (66%), Gaps = 2/71 (2%)

Query: 130 KKFNPADSRLYRDAVKLQKLMQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDA 187
           K+  P   +  ++ + LQ++  + K  E+ +L EL  +L+LMFENAK++N  + R+Y+DA
Sbjct: 33  KRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDA 92

Query: 188 VKLQKLMQRKV 198
            KLQKLMQ K 
Sbjct: 93  EKLQKLMQAKK 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|99935 cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BAZ2B_like subfamily

 Score = 57.0 bits (138), Expect = 8e-11
 Identities = 27/77 (35%), Positives = 43/77 (55%)

Query: 16 PFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 75
          PFL+    +  P Y +IIK P    TI + L+SG Y TL E   ++ L+F+N + FN  D
Sbjct: 20 PFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDD 79

Query: 76 SRLYRDAVKLQKLMQRK 92
          S + R    ++K  +++
Sbjct: 80 SEVGRAGHNMRKFFEKR 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|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 20/62 (32%), Positives = 38/62 (61%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
           + P  +  I   ++   Y +L+++  +  LMF+NA K+N  DS++Y+DA+ LQK++    
Sbjct: 44  KKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLLETK 103

Query: 155 QE 156
           +E
Sbjct: 104 RE 105

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

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

 Score = 58.7 bits (142), Expect = 6e-10
 Identities = 29/85 (34%), Positives = 45/85 (52%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
           ++P  LLTI K LK+G Y +  E   +LNLMF+N K +N  DS +Y DA +L+K   + +
Sbjct: 186 KSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLI 245

Query: 155 QEFSLNELTGELSLMFENAKKFNPA 179
           +E     L   +    E  ++    
Sbjct: 246 EEIPEEMLELSIKPGREEREERESV 270

Length = 371

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

 Score = 54.8 bits (132), Expect = 6e-10
 Identities = 28/82 (34%), Positives = 47/82 (57%), Gaps = 2/82 (2%)

Query: 14  SEPFLK-LPAKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKF 71
           S PF + +  K    PDY+ I+KNP  L TI + L +G Y    +   ++ LMF+NA  +
Sbjct: 22  SLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLY 81

Query: 72  NPADSRLYRDAVKLQKLMQRKV 93
           N   SR+Y+   KL ++ ++++
Sbjct: 82  NRKTSRVYKYCTKLAEVFEQEI 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|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily

 Score = 54.8 bits (132), Expect = 9e-10
 Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           SEPF +       PDY  II  P  L T+ +TL  G+Y    E   ++ L+F N+K + P
Sbjct: 23  SEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTP 82

Query: 74  -ADSRLYRDAVKLQKLMQRKV 93
              SR+Y   ++L  L +  +
Sbjct: 83  NKRSRIYSMTLRLSALFEEHI 103

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

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 24/62 (38%), Positives = 37/62 (59%)

Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
          PDY+ IIK P  L T+ K L+ G YS+  E   ++ L F NA ++NP  + ++  A +L 
Sbjct: 33 PDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELL 92

Query: 87 KL 88
          K+
Sbjct: 93 KI 94

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 26/54 (48%), Positives = 35/54 (64%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 148
            NP SL  I K +K   Y + ++   +LNLMFENAK +N  DS+ Y+DAV L+K
Sbjct: 45  SNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEK 98

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|99944 cd05512, Bromo_brd1_like, Bromodomain; brd1_like subfamily

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 23/60 (38%), Positives = 32/60 (53%)

Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
          PDY   IK P    T+ K L+S  Y TL +   + NL+  N   +N  D+  YR AV+L+
Sbjct: 32 PDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 24/69 (34%), Positives = 38/69 (55%)

Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY++IIK P  L TI K L++ +Y + +E   + N MF N   +N     +   A  L+
Sbjct: 38  PDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLE 97

Query: 87  KLMQRKVQE 95
           KL  +K+ +
Sbjct: 98  KLFLQKLAQ 106

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

>gnl|CDD|215921 pfam00439, Bromodomain, Bromodomain

 Score = 50.9 bits (122), Expect = 1e-08
 Identities = 22/51 (43%), Positives = 31/51 (60%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVK 145
           + P  L TI + LKSG Y +L E   ++ L+F NA  +N  DS +Y+DA K
Sbjct: 34  KEPMDLSTIRQKLKSGKYKSLAEFLKDVELIFSNAITYNGEDSDIYKDAKK 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|99948 cd05517, Bromo_polybromo_II, Bromodomain, polybromo repeat II

 Score = 49.4 bits (118), Expect = 6e-08
 Identities = 22/61 (36%), Positives = 40/61 (65%)

Query: 93  VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
           V + P  L TI + ++SG+Y ++ ++  +L+LM +NAK FN   S++Y+DA  ++K+   
Sbjct: 42  VIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTA 101

Query: 153 K 153
           K
Sbjct: 102 K 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|99954 cd05524, Bromo_polybromo_I, Bromodomain, polybromo repeat I

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 23/65 (35%), Positives = 34/65 (52%)

Query: 93  VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
           V  NP  LL I + LK+  Y  +++LT +  L+  NAK +   DS  ++DA KL +L   
Sbjct: 44  VVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLS 103

Query: 153 KVQEF 157
              E 
Sbjct: 104 ARNEV 108

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|99949 cd05518, Bromo_polybromo_IV, Bromodomain, polybromo repeat IV

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 22/63 (34%), Positives = 36/63 (57%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           K+   P  L TI   +++  Y+T  EL  +  LMF NA+ +N   S++Y DA  L+K+++
Sbjct: 41  KIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVLK 100

Query: 152 RKV 154
            K 
Sbjct: 101 EKR 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|99937 cd05505, Bromo_WSTF_like, Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like)

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 20/63 (31%), Positives = 31/63 (49%)

Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
          S PF +        DY ++I NP  L T+      G YS++ E   ++ L+F NA+K+  
Sbjct: 18 SWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYE 77

Query: 74 ADS 76
            S
Sbjct: 78 NGS 80

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

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 20/62 (32%), Positives = 33/62 (53%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
            + ++P  L TI K L +  Y+   E   ++ LMF N  K+NP D  ++  A KLQ + +
Sbjct: 40  DIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFE 99

Query: 152 RK 153
            +
Sbjct: 100 DR 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|99945 cd05513, Bromo_brd7_like, Bromodomain, brd7_like subgroup

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 22/59 (37%), Positives = 33/59 (55%)

Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKL 85
          P Y  IIK+P    T+ + +K+  Y ++ E   +  LM ENA K+N  D+  Y+ A KL
Sbjct: 32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 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|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 96  NPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
            P  L  I K L+     HYS+  E   ++ LMF+N  KFN  DS + +   +L+   + 
Sbjct: 42  TPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEE 101

Query: 153 KVQEF 157
           +++E 
Sbjct: 102 QLKEI 106

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|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 75  DSRLYR---DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKK 131
           D+R +    D VKL       + + P  L TI + LKS  Y+++ E T + NLM +N   
Sbjct: 21  DARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLT 80

Query: 132 FNPADSRLYRDAVKLQKLMQRK 153
           FN  +  + +   +LQ   ++ 
Sbjct: 81  FNGPEHPVSQMGKRLQAAFEKH 102

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

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 21/63 (33%), Positives = 36/63 (57%)

Query: 91  RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLM 150
           RK+ + P    TI + L+SG Y TL E   ++ L+F+N + FN  DS + R    ++K  
Sbjct: 34  RKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF 93

Query: 151 QRK 153
           +++
Sbjct: 94  EKR 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|99950 cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfamily, specific to fungi

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 19/59 (32%), Positives = 35/59 (59%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK 153
           + P +L  I + ++   Y +L E   + +LMF NA+ +N   S +Y DAV+++K  ++K
Sbjct: 44  KRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKKK 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|99957 cd05528, Bromo_AAA, Bromodomain; sub-family co-occurring with AAA domains

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 19/49 (38%), Positives = 28/49 (57%)

Query: 27 PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 75
          PDYY IIK P  L TI + L +  Y T  +   +++L+  NA ++NP  
Sbjct: 34 PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDR 82

Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver. Length = 112

>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 18/62 (29%), Positives = 33/62 (53%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
            + + P  L TI K L++G Y +  E   ++ L+F+N   FNP  + +Y    +L+++  
Sbjct: 40  SIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFN 99

Query: 152 RK 153
            K
Sbjct: 100 DK 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|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily

 Score = 44.8 bits (106), Expect = 4e-06
 Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 12/98 (12%)

Query: 61  LNLMF--ENAKKF-NPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNE 117
           +NLM+  E+++ F  P D   Y D         R + + P  L T+ +TL  G+Y    E
Sbjct: 14  VNLMWDCEDSEPFRQPVDLLKYPD--------YRDIIDTPMDLGTVKETLFGGNYDDPME 65

Query: 118 LTGELNLMFENAKKFNP-ADSRLYRDAVKLQKLMQRKV 154
              ++ L+F N+K + P   SR+Y   ++L  L +  +
Sbjct: 66  FAKDVRLIFSNSKSYTPNKRSRIYSMTLRLSALFEEHI 103

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|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score = 43.7 bits (104), Expect = 5e-06
 Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           M+ K++     +L E   +L L+F+N + +N  D   Y+ A KL+K   +K++E+
Sbjct: 47  MEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL 101

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|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 147 QKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
            K+   + Q  SL+++  +  LMF+NA K+N  D ++Y+DA+ LQK++    +E
Sbjct: 54  SKIEGNQYQ--SLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLLETKRE 105

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

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

 Score = 43.6 bits (103), Expect = 6e-06
 Identities = 26/109 (23%), Positives = 52/109 (47%), Gaps = 9/109 (8%)

Query: 56  ELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK-------VQENPRSLLTIGKTLK 108
           ELT ++N + +   K+  +D R   +     +L  RK       +   P     I + ++
Sbjct: 1   ELTKKMNKIVDVVIKYKDSDGRQLAEV--FIQLPSRKELPEYYELIRKPVDFKKIKERIR 58

Query: 109 SGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF 157
           +  Y +L +L  ++ L+ +NA+ FN   S +Y D++ LQ + +   Q+ 
Sbjct: 59  NHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKSARQKI 107

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 24/76 (31%), Positives = 38/76 (50%)

Query: 81  DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 140
           DAVKL      K+ + P  L TI K L++ +Y + +E   + N MF N   +N     + 
Sbjct: 31  DAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVV 90

Query: 141 RDAVKLQKLMQRKVQE 156
             A  L+KL  +K+ +
Sbjct: 91  LMAQTLEKLFLQKLAQ 106

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|197636 smart00297, BROMO, bromo domain

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 19/57 (33%), Positives = 37/57 (64%), Gaps = 3/57 (5%)

Query: 148 KLMQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           K +++K++     S+ E   + +LMF NA+ +N  D  +Y+DA KL+K  ++K++E+
Sbjct: 51  KTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

Length = 107

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

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 18/51 (35%), Positives = 27/51 (52%)

Query: 97  PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 147
           P    T+ K L+S  Y TL +   + NL+  N   +N  D+  YR AV+L+
Sbjct: 41  PMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91

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|99939 cd05507, Bromo_brd8_like, Bromodomain, brd8_like subgroup

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 23/73 (31%), Positives = 40/73 (54%)

Query: 14 SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
          +  FLK   +   P Y+ ++  P  L TI K +++G   +  E   ++ LMF+NA  +N 
Sbjct: 21 ASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNS 80

Query: 74 ADSRLYRDAVKLQ 86
          +D  +Y  AV++Q
Sbjct: 81 SDHDVYLMAVEMQ 93

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

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 21/69 (30%), Positives = 35/69 (50%)

Query: 81  DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 140
           D V L       + + P  L T+ K L+ G YS+  E   ++ L F NA ++NP  + ++
Sbjct: 26  DVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVH 85

Query: 141 RDAVKLQKL 149
             A +L K+
Sbjct: 86  TMAKELLKI 94

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

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 17/65 (26%), Positives = 31/65 (47%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P  L TI + L  G Y    E   ++ L+F N   +NP  + +Y+   +LQ+   ++ +
Sbjct: 51  KPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCR 110

Query: 156 EFSLN 160
           +  L 
Sbjct: 111 KLGLP 115

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 = 39.3 bits (92), Expect = 2e-04
 Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 6/65 (9%)

Query: 140 YRDAVKLQ---KLMQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKL 193
           Y + +K       +++K++     SL E   ++ L+F NAK +N     +Y+DA KL+KL
Sbjct: 35  YYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKL 94

Query: 194 MQRKV 198
            ++ +
Sbjct: 95  FEKLL 99

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

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 17/54 (31%), Positives = 29/54 (53%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKL 149
           +P  L TI K + +G+Y T      ++  +F NA+K+    S + RD  +L+K 
Sbjct: 47  DPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLRKA 100

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 16/66 (24%), Positives = 32/66 (48%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           K+ + P  L TI K +    Y +  E   ++ L+ +N+  +N  DS   + A ++ +L +
Sbjct: 35  KIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAE 94

Query: 152 RKVQEF 157
             + E 
Sbjct: 95  ELLAER 100

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 = 39.3 bits (92), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 38/74 (51%)

Query: 81  DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 140
           D   L       + +NP  L TI + L +G Y    +   ++ LMF+NA  +N   SR+Y
Sbjct: 30  DPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVY 89

Query: 141 RDAVKLQKLMQRKV 154
           +   KL ++ ++++
Sbjct: 90  KYCTKLAEVFEQEI 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|99952 cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           K+ +NP SL T+ K L   HY+   E   +L  +  NA+ +N   S +Y+ A+ L+K + 
Sbjct: 42  KIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKYIN 99

Query: 152 RKV 154
             +
Sbjct: 100 DVI 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|99956 cd05526, Bromo_polybromo_VI, Bromodomain, polybromo repeat VI

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 9  EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
          EG   S+   +LP    +    + I  P +L  I + +  G Y  L++   ++  + E A
Sbjct: 22 EGRCYSDSLAELPELAVDGVGPKKI--PLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERA 79

Query: 69 KKFNPADSRLYRDAVKLQK 87
          ++ +  DS +Y DAV+LQ+
Sbjct: 80 RRLSRTDSEIYEDAVELQQ 98

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 = 110

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 20/45 (44%), Positives = 31/45 (68%), Gaps = 2/45 (4%)

Query: 148 KLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQK 192
           K+ +RK + F  ++   +L+LMFENAK +N  D + Y+DAV L+K
Sbjct: 56  KVKRRKYKSF--DQFLNDLNLMFENAKLYNENDSQEYKDAVLLEK 98

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 = 36.5 bits (85), Expect = 0.002
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 140 YRDAVK----LQKLMQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKL 193
           Y + V     L K+ Q+ K +E+  +++LT +  L+  NAK +   D   ++DA KL +L
Sbjct: 41  YYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWEL 100

Query: 194 MQRKVQEVM 202
                 EV+
Sbjct: 101 FLSARNEVL 109

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|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 11/76 (14%)

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN 128
            K +  ++  Y D +K            P  L T+ K LK+  Y +  E   +LNL+++N
Sbjct: 31  TKVSKREAPDYYDIIK-----------KPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKN 79

Query: 129 AKKFNPADSRLYRDAV 144
              +N   S   R   
Sbjct: 80  CLLYNSDPSHPLRRHA 95

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 15  EPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA 74
           E  + L A    PDY+  +  P  L TI   L++ +Y +L  L  ++ L+  NA+ FN  
Sbjct: 49  EYPVDLRAW--YPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEP 106

Query: 75  DSRLYRDAVKLQKLMQR 91
           +S + + A +L   + R
Sbjct: 107 NSEIAKKAKRLSDWLLR 123

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|99956 cd05526, Bromo_polybromo_VI, Bromodomain, polybromo repeat VI

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 16/55 (29%), Positives = 32/55 (58%)

Query: 94  QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 148
           ++ P +L  I + +  G Y  L++   ++  + E A++ +  DS +Y DAV+LQ+
Sbjct: 44  KKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTDSEIYEDAVELQQ 98

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 = 110

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	256
KOG1827|consensus	629		99.97
COG5076	371	Transcription factor involved in chromatin remodel	99.96
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.93
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.93
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.93
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.93
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.93
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.93
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.93
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.93
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.93
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.93
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.92
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.92
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.92
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.92
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.92
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.92
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.92
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.91
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.91
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.91
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.91
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.91
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.9
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.9
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.9
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.89
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.89
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.89
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.88
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.88
smart00297	107	BROMO bromo domain.	99.88
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.88
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.86
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.84
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.83
KOG1474|consensus	640		99.83
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.83
KOG1474|consensus	640		99.82
KOG1472|consensus	720		99.65
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.63
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.63
KOG0008|consensus	1563		99.62
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.62
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.62
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.61
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.6
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.6
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.59
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.59
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.59
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.58
KOG1245|consensus	1404		99.58
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.58
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.58
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.57
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.57
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.56
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.56
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.56
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.54
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.53
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.53
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.53
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.52
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.51
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.51
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.51
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.5
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.49
smart00297	107	BROMO bromo domain.	99.49
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.49
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.48
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.47
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.46
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.46
KOG1472|consensus	720		99.4
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.37
cd04717	121	BAH_polybromo BAH, or Bromo Adjacent Homology doma	99.36
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.35
cd04718	148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	99.28
KOG1828|consensus	418		99.27
COG5076	371	Transcription factor involved in chromatin remodel	99.24
KOG0386|consensus	1157		99.23
cd04714	121	BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain,	99.18
KOG0008|consensus	1563		99.17
KOG1827|consensus	629		99.17
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	99.09
cd04715	159	BAH_Orc1p_like BAH, or Bromo Adjacent Homology dom	99.07
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	99.0
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	98.91
KOG0955|consensus	1051		98.83
cd04370	123	BAH BAH, or Bromo Adjacent Homology domain (also c	98.77
smart00439	120	BAH Bromo adjacent homology domain.	98.6
KOG1245|consensus	1404		98.53
cd04713	146	BAH_plant_3 BAH, or Bromo Adjacent Homology domain	98.33
cd04712	130	BAH_DCM_I BAH, or Bromo Adjacent Homology domain,	98.31
cd04716	122	BAH_plantDCM_I BAH, or Bromo Adjacent Homology dom	98.28
cd04760	124	BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain	98.27
PF01426	119	BAH: BAH domain; InterPro: IPR001025 The BAH (brom	98.22
cd04721	130	BAH_plant_1 BAH, or Bromo Adjacent Homology domain	97.91
KOG1828|consensus	418		97.64
cd04709	164	BAH_MTA BAH, or Bromo Adjacent Homology domain, as	97.55
KOG0386|consensus	1157		97.5
cd04708	202	BAH_plantDCM_II BAH, or Bromo Adjacent Homology do	97.11
cd04719	128	BAH_Orc1p_animal BAH, or Bromo Adjacent Homology d	97.01
KOG0955|consensus	1051		96.98
cd04711	137	BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domai	96.6
cd04710	135	BAH_fungalPHD BAH, or Bromo Adjacent Homology doma	96.44
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	96.24
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	95.47
KOG0644|consensus	1113		91.93
KOG1886|consensus	464		89.37
KOG0644|consensus	1113		89.37
cd04720	179	BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology do	89.27
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	81.01

>KOG1827|consensus

Probab=99.97  E-value=2.5e-33  Score=262.71  Aligned_cols=202  Identities=21%  Similarity=0.257  Sum_probs=165.7

Q ss_pred             ccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHH
Q psy1225           6 NQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKL   85 (256)
Q Consensus         6 ~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L   85 (256)
                      .+..|+.++..|.++|+++..|+||.+|.+||+|..|++|+.++.|.+.+.|..|+.+|+.||+.||.++|.+++++..|
T Consensus        68 ~d~~gk~~~d~feklp~~~~~p~yy~~i~~pisl~~ik~kv~k~~y~~~~~f~~D~~lm~ena~~~n~~ds~~~~~s~~l  147 (629)
T KOG1827|consen   68 KDDEGKQLFDKFEKLPSRKEFPEYYYVIQQPISLDQIKRKVKKGRYKRLSFFQLDFLLMTENARLYNRPDSLIYKDSGEL  147 (629)
T ss_pred             ccccCcccchhHhhccccccCCCcceeecCcccHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhcCcchhhhhhhhhh
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCChhhhhch
Q psy1225          86 QKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGE  165 (256)
Q Consensus        86 ~~~f~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~~~~~~~d  165 (256)
                      ++.|.....+. .|+               +....+...                             ++   .-.+-..
T Consensus       148 ~~~~~~~~~~~-~d~---------------e~s~~~~~~-----------------------------l~---~~~l~~~  179 (629)
T KOG1827|consen  148 EKYFISLEDEK-KDG---------------ELSMESNEE-----------------------------LK---AGGLHYH  179 (629)
T ss_pred             hcchhhhhccc-cch---------------hhccccccc-----------------------------cc---cCCCCcc
Confidence            98886644320 000               000000000                             00   0000000


Q ss_pred             hhh-hhccchhcCCccccccccHHH-----HHHHHHHHHHHhcCCCC-ccceeecccceeEe-------EEeecCccccc
Q psy1225         166 LSL-MFENAKKFNPADLRLYRDAVK-----LQKLMQRKVQEVMILDI-ECQVYLISDELTHY-------QVVLTGTAEQV  231 (256)
Q Consensus       166 ~~~-~~~n~~~yn~~~~~i~~~a~~-----l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-------ev~kt~~~~~~  231 (256)
                      ... +-.++-.|+.++|+...++++     +.+|++.|...+|.+|+ +||||||+||+|..       |||||++|++|
T Consensus       180 ~~~~~~i~~~~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~  259 (629)
T KOG1827|consen  180 ELGPVEIDGTKYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDD  259 (629)
T ss_pred             cCCCccccCcccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccccchhcccceeccccccc
Confidence            001 234778999999999888887     23599999999999999 69999999999995       99999999999


Q ss_pred             ccCCCCCCceeeeeecccccCCCC
Q psy1225         232 RLSGLPDGDWLAFTLPVVSGKASS  255 (256)
Q Consensus       232 ~~~~i~~~~~v~f~~~~~~g~~~~  255 (256)
                      +++.|+|+|+||++++|++|+|..
T Consensus       260 ~~q~l~g~c~v~~~~~yi~~~p~~  283 (629)
T KOG1827|consen  260 LVQRLLGKCYVMKPTEYISGDPEN  283 (629)
T ss_pred             HHHHhhcceEEeehhHhhhcCccc
Confidence            999999999999999999999974

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

Probab=99.96  E-value=5e-30  Score=234.39  Aligned_cols=201  Identities=27%  Similarity=0.394  Sum_probs=165.7

Q ss_pred             ccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHH
Q psy1225           4 QKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAV   83 (256)
Q Consensus         4 ~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~   83 (256)
                      .+....|+.++.+|+.+|++..+|+||.+|+.||||.+|+++|+.+.|+++++|..|+.|||.||+.||+++|.++.+|.
T Consensus       156 ~~~~~~~~~~s~~F~~~p~k~~~PdYy~iIk~Pm~L~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~  235 (371)
T COG5076         156 QLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAK  235 (371)
T ss_pred             HhhcccccccccccccCCccccCCChheeecchhhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhccCCCcchhhhhH
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCChhhhh
Q psy1225          84 KLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELT  163 (256)
Q Consensus        84 ~L~~~f~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~~~~~~  163 (256)
                      .|++.+...+..+|-..  +......+.                         .....             +        
T Consensus       236 ~l~~~~~~~i~~~~~~~--~~~~~~~~~-------------------------~~~~~-------------~--------  267 (371)
T COG5076         236 ELEKYFLKLIEEIPEEM--LELSIKPGR-------------------------EEREE-------------R--------  267 (371)
T ss_pred             HHHHHHHHHHHhccccc--hhhccCccc-------------------------ccccc-------------c--------
Confidence            99999999998774431  111111111                         00000             0        


Q ss_pred             chhhhhhccchhcCCccccccccHH-----HHHHHHHHHHHHhcCCCC-ccceeecccceeEe-------EEeecCcccc
Q psy1225         164 GELSLMFENAKKFNPADLRLYRDAV-----KLQKLMQRKVQEVMILDI-ECQVYLISDELTHY-------QVVLTGTAEQ  230 (256)
Q Consensus       164 ~d~~~~~~n~~~yn~~~~~i~~~a~-----~l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-------ev~kt~~~~~  230 (256)
                       . ..+. .+...+.+.|...+.+.     +..++++.|.+..+..|. +||||+|++|+|.-       +|.++|.+++
T Consensus       268 -~-~~~i-~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (371)
T COG5076         268 -E-SVLI-TNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTD  344 (371)
T ss_pred             -h-hhcc-cccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhh
Confidence             0 0112 22266777887777666     445699999999999888 79999999999983       9999999999


Q ss_pred             cccCCCCCCceeeeeecccccCCCC
Q psy1225         231 VRLSGLPDGDWLAFTLPVVSGKASS  255 (256)
Q Consensus       231 ~~~~~i~~~~~v~f~~~~~~g~~~~  255 (256)
                      |++....+.|+|.+.+|++||.+..
T Consensus       345 ~~~~~~~~~~~~~~~~~~~~~~~~~  369 (371)
T COG5076         345 YYKNANVLEDFVIKKTRLIREYPKL  369 (371)
T ss_pred             hhhhccchhhhHhhhhhhhhccccc
Confidence            9999999999999999999998764

>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III

Probab=99.93  E-value=3.3e-26  Score=172.28  Aligned_cols=86  Identities=62%  Similarity=0.951  Sum_probs=83.3

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..|++++++|+++|++..+||||++|++||||+||++||++|.|.++++|..|++|||.||+.||+++|.++.+|..|+
T Consensus        17 ~~~g~~~s~pF~~~p~~~~~PdYy~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~L~   96 (103)
T cd05520          17 NNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQ   96 (103)
T ss_pred             CCCCCCccHhhhcCCCcccCCCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q psy1225          87 KLMQRK   92 (256)
Q Consensus        87 ~~f~~~   92 (256)
                      ++|.++
T Consensus        97 ~~f~~~  102 (103)
T cd05520          97 KLMQAK  102 (103)
T ss_pred             HHHHHh
Confidence            999875

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.

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

Probab=99.93  E-value=3.8e-26  Score=173.26  Aligned_cols=90  Identities=29%  Similarity=0.624  Sum_probs=86.3

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +.+|+++|++|.+||++..+||||++|++||||+||++||++|.|.++++|..|+.|||.||+.||+++|.++.+|..|+
T Consensus        18 d~~g~~~s~~F~~~p~~~~~pdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~l~   97 (107)
T cd05516          18 DSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQ   97 (107)
T ss_pred             CcCCCEeeHHhhcCCCcccCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            44699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      +.|.+.++++
T Consensus        98 ~~f~~~~~~~  107 (107)
T cd05516          98 SVFKSARQKI  107 (107)
T ss_pred             HHHHHHHhcC
Confidence            9999987653

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.

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.93  E-value=3.4e-26  Score=173.36  Aligned_cols=94  Identities=28%  Similarity=0.337  Sum_probs=89.0

Q ss_pred             ccccccccCCccccccccCCCCC--CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKR--YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~--~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      +.+++....++.|++|..||+..  ++||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++
T Consensus        11 ~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~   90 (107)
T cd05497          11 KVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVV   90 (107)
T ss_pred             HHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            45678888999999999999865  7999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhc
Q psy1225          80 RDAVKLQKLMQRKVQE   95 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~k   95 (256)
                      .+|..|++.|.+++.+
T Consensus        91 ~~A~~l~~~f~~~l~~  106 (107)
T cd05497          91 LMAQTLEKLFLQKLAQ  106 (107)
T ss_pred             HHHHHHHHHHHHHHHc
Confidence            9999999999998765

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.

>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family

Probab=99.93  E-value=5.2e-26  Score=171.92  Aligned_cols=87  Identities=34%  Similarity=0.612  Sum_probs=83.9

Q ss_pred             ccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHH
Q psy1225           6 NQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKL   85 (256)
Q Consensus         6 ~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L   85 (256)
                      ++.+|+++|++|+++|++..+||||++|++||||++|++||++|.|.++++|..|+.+||.||+.||+++|.++.+|..|
T Consensus        18 kd~~g~~~s~~F~~lp~k~~~pdYy~~I~~P~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f~Na~~yn~~~S~i~~~A~~L   97 (106)
T cd05525          18 KDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRL   97 (106)
T ss_pred             hccCCCcccHhhccCCCcccCCchhhhCCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q psy1225          86 QKLMQRK   92 (256)
Q Consensus        86 ~~~f~~~   92 (256)
                      ++.|.+.
T Consensus        98 ~~~f~~~  104 (106)
T cd05525          98 RKAYYQA  104 (106)
T ss_pred             HHHHHHc
Confidence            9999764

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.

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

Probab=99.93  E-value=5.1e-26  Score=169.36  Aligned_cols=91  Identities=23%  Similarity=0.312  Sum_probs=86.9

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      .++++....++.|++|..||+...+||||++|++||||+||++||++|.|.|+++|.+|+.|||.||+.||+++|.++.+
T Consensus         6 ~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~   85 (97)
T cd05505           6 EEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVLSC   85 (97)
T ss_pred             HHHHHHHHhCCCcccccCCCChhhcccHHHHcCCcCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            35677888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q psy1225          82 AVKLQKLMQRK   92 (256)
Q Consensus        82 A~~L~~~f~~~   92 (256)
                      |..|++.|.+.
T Consensus        86 a~~le~~f~~~   96 (97)
T cd05505          86 MRKTEQCCVNL   96 (97)
T ss_pred             HHHHHHHHHHh
Confidence            99999999865

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.

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.93  E-value=8.3e-26  Score=170.92  Aligned_cols=88  Identities=36%  Similarity=0.705  Sum_probs=84.4

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..||++|.+|++||++.++||||++|++||||+||++||.++.|.++++|..|+.|||.||+.||+++|.++.+|..|+
T Consensus        17 d~~~~~~a~~F~~~p~~~~~pdYy~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~~yN~~~s~i~~~A~~L~   96 (105)
T cd05515          17 DGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQ   96 (105)
T ss_pred             CcCCCcccHHhccCCCcccCCcHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHh
Q psy1225          87 KLMQRKVQ   94 (256)
Q Consensus        87 ~~f~~~~~   94 (256)
                      ++|.+...
T Consensus        97 ~~~~~~~~  104 (105)
T cd05515          97 KVLLETKR  104 (105)
T ss_pred             HHHHHHHc
Confidence            99987654

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

>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV

Probab=99.93  E-value=7.5e-26  Score=170.30  Aligned_cols=86  Identities=37%  Similarity=0.699  Sum_probs=83.3

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..|++++.+|+.+|++..+||||++|++||||+||++||.+|.|.|+++|..|+.|||.||+.||+++|.++.+|..|+
T Consensus        17 d~~gr~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le   96 (103)
T cd05518          17 EGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILE   96 (103)
T ss_pred             ccCCCcccHHHhcCCCcccCccHHHHcCCCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q psy1225          87 KLMQRK   92 (256)
Q Consensus        87 ~~f~~~   92 (256)
                      +.|.++
T Consensus        97 ~~~~~~  102 (103)
T cd05518          97 KVLKEK  102 (103)
T ss_pred             HHHHhc
Confidence            998764

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

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.93  E-value=7.4e-26  Score=170.40  Aligned_cols=85  Identities=40%  Similarity=0.723  Sum_probs=82.5

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..||+++++|+++|++..+||||++|++||||+||++||+++.|.++++|..|++|||.||+.||+++|.++.+|..|+
T Consensus        17 d~~gr~~~~~F~~lp~~~~~pdYy~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~l~   96 (103)
T cd05517          17 DPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIK   96 (103)
T ss_pred             CcCCCChhHHHhcCCCCCCCCCHHHHcCCCcCHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHH
Q psy1225          87 KLMQR   91 (256)
Q Consensus        87 ~~f~~   91 (256)
                      +.|..
T Consensus        97 ~~f~~  101 (103)
T cd05517          97 KIFTA  101 (103)
T ss_pred             HHHHh
Confidence            99875

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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.93  E-value=8.7e-26  Score=168.57  Aligned_cols=91  Identities=22%  Similarity=0.367  Sum_probs=85.7

Q ss_pred             CccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHH
Q psy1225           1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYR   80 (256)
Q Consensus         1 l~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~   80 (256)
                      |+.+++... ++.|++|..||+...+||||.+|++||||+||++||++|.|+++++|.+|++|||.||..||+++|.++.
T Consensus         8 L~~~~~~~~-~~~s~~F~~PV~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~Na~~YN~~~s~i~~   86 (99)
T cd05508           8 LKFALERMK-QPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQ   86 (99)
T ss_pred             HHHHHHHHh-CcCcchhcCCCChhhCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            455677777 9999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy1225          81 DAVKLQKLMQRK   92 (256)
Q Consensus        81 ~A~~L~~~f~~~   92 (256)
                      +|..|.+.+...
T Consensus        87 ~A~~l~~~~~~e   98 (99)
T cd05508          87 AAKAIVKICEQE   98 (99)
T ss_pred             HHHHHHHHHHhh
Confidence            999999988654

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.

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.93  E-value=9.5e-26  Score=173.63  Aligned_cols=104  Identities=28%  Similarity=0.405  Sum_probs=95.4

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCC-CchhHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA-DSRLYR   80 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~-~S~i~~   80 (256)
                      +++++....++.|++|..||+...+||||++|++||||+||++||.+|.|.++++|..|++|||.||+.||++ +|.++.
T Consensus        11 ~~il~~l~~~~~s~~F~~PVd~~~~pdY~~iIk~PmDL~tIk~kL~~~~Y~~~~ef~~D~~lif~Na~~yN~~~~s~i~~   90 (119)
T cd05496          11 KELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNKRSRIYS   90 (119)
T ss_pred             HHHHHHHHhCCccccccCCCChhhcCcHHHHhCCcccHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHH
Confidence            4577888899999999999999999999999999999999999999999999999999999999999999985 899999


Q ss_pred             HHHHHHHHHHHHHhcccccHHHHHH
Q psy1225          81 DAVKLQKLMQRKVQENPRSLLTIGK  105 (256)
Q Consensus        81 ~A~~L~~~f~~~~~klP~dl~~I~~  105 (256)
                      +|..|++.|.+.+.+++-.+..+.+
T Consensus        91 ~a~~L~~~F~~~~~~l~~~~~~~~~  115 (119)
T cd05496          91 MTLRLSALFEEHIKKIISDWKSALK  115 (119)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999888555554443

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.

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.92  E-value=2.2e-25  Score=170.58  Aligned_cols=90  Identities=34%  Similarity=0.644  Sum_probs=86.3

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..|++++.+|.++|++..+||||++|++||||+||++||+++.|.|+++|.+|+.|||.||+.||+++|.++++|..|+
T Consensus        19 ~~~g~~l~~~F~~~p~~~~~PdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~~~~~A~~L~   98 (113)
T cd05524          19 SEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLW   98 (113)
T ss_pred             ccCCCchhHHHhcCCCcccCCCHHHHhCCccCHHHHHHHhCcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      +.|.+.+.++
T Consensus        99 ~~f~~~~~~~  108 (113)
T cd05524          99 ELFLSARNEV  108 (113)
T ss_pred             HHHHHHHHHh
Confidence            9999887665

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.

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.92  E-value=3.3e-25  Score=169.41  Aligned_cols=106  Identities=27%  Similarity=0.405  Sum_probs=99.9

Q ss_pred             CccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHH
Q psy1225           1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYR   80 (256)
Q Consensus         1 l~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~   80 (256)
                      |++++++...++.|.+|..||+...+|+||++|++||||+||++||++|.|+++++|.+|+++||.||..||+++|.++.
T Consensus         5 l~~ii~~l~~~~~s~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~   84 (112)
T cd05511           5 LDEIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTK   84 (112)
T ss_pred             HHHHHHHHHhCCCchhhcCCCChhhcccHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            46788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcccccHHHHHHH
Q psy1225          81 DAVKLQKLMQRKVQENPRSLLTIGKT  106 (256)
Q Consensus        81 ~A~~L~~~f~~~~~klP~dl~~I~~k  106 (256)
                      +|..|.+.+...+.++|-.+++..+.
T Consensus        85 ~A~~l~~~~~~~~~~~~~~~~~~~~~  110 (112)
T cd05511          85 KAKEMLELAEELLAEREEKLTQLEKN  110 (112)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence            99999999999999887777766654

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.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.92  E-value=3.1e-25  Score=165.51  Aligned_cols=92  Identities=30%  Similarity=0.543  Sum_probs=88.3

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ++++++...++.+.+|+.||+...+|+||++|++||||+||++||++|.|+|+++|.+|++|||.||+.||+++|.++++
T Consensus         6 ~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~   85 (97)
T cd05503           6 ETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRA   85 (97)
T ss_pred             HHHHHHHHcCCCchhhcCCCCccccCCHHHHhCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            46788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy1225          82 AVKLQKLMQRKV   93 (256)
Q Consensus        82 A~~L~~~f~~~~   93 (256)
                      |..|++.|++.+
T Consensus        86 a~~l~~~f~~~~   97 (97)
T cd05503          86 GHNMRKFFEKRW   97 (97)
T ss_pred             HHHHHHHHHHhC
Confidence            999999998764

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.

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.92  E-value=4e-25  Score=166.90  Aligned_cols=94  Identities=26%  Similarity=0.398  Sum_probs=89.1

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      .++++....++.|.+|.+||+...+|+||++|++||||+||++||++|.|.+++||.+|+.|||.||..||+++|.++.+
T Consensus         9 ~~il~~l~~~~~a~~F~~pV~~~~~p~Y~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~v~~~   88 (104)
T cd05507           9 LLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLM   88 (104)
T ss_pred             HHHHHHHHcCCCCHhhcCCCCccccCCHHHHhCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            45778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhc
Q psy1225          82 AVKLQKLMQRKVQE   95 (256)
Q Consensus        82 A~~L~~~f~~~~~k   95 (256)
                      |..|++.+...+..
T Consensus        89 A~~l~~~~~~~~~~  102 (104)
T cd05507          89 AVEMQREVMSQIQQ  102 (104)
T ss_pred             HHHHHHHHHHHhhc
Confidence            99999998887653

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.

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

Probab=99.92  E-value=5.7e-25  Score=165.92  Aligned_cols=86  Identities=40%  Similarity=0.711  Sum_probs=83.4

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..|++++++|.+||++..+||||++|++||||++|++||++|.|.|+++|.+|+++||.||+.||+++|.++.+|..|+
T Consensus        17 ~~~~~~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l~   96 (103)
T cd05519          17 DETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEME   96 (103)
T ss_pred             CcCCCchhHHhcCCCCCCCCcCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            55699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q psy1225          87 KLMQRK   92 (256)
Q Consensus        87 ~~f~~~   92 (256)
                      +.|.++
T Consensus        97 ~~f~~~  102 (103)
T cd05519          97 KAFKKK  102 (103)
T ss_pred             HHHHHh
Confidence            999875

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.92  E-value=5e-25  Score=169.12  Aligned_cols=95  Identities=29%  Similarity=0.496  Sum_probs=90.9

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      .++++....++.+.+|..||+...+||||++|++||||+||++||++|.|.|+++|.+|+.|||.||..||+++|.++.+
T Consensus        18 ~~il~~l~~~~~s~~F~~pvd~~~~pdY~~vI~~PmDL~tI~~kL~~~~Y~s~~~f~~Dv~LI~~Na~~yN~~~s~i~~~   97 (115)
T cd05504          18 EQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKA   97 (115)
T ss_pred             HHHHHHHHhCCCchhhcCCCCccccccHHHHhcCcccHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            35777888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      |..|++.|.+.++++
T Consensus        98 A~~l~~~f~~~~~~~  112 (115)
T cd05504          98 GTRLQRFFIKRCRKL  112 (115)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999998875

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.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.92  E-value=6.2e-25  Score=167.58  Aligned_cols=96  Identities=34%  Similarity=0.455  Sum_probs=89.3

Q ss_pred             ccccccccCC-ccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCc-hhH
Q psy1225           2 RPQKNQTEGG-NLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADS-RLY   79 (256)
Q Consensus         2 ~~~~~~~~~~-~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S-~i~   79 (256)
                      +++++....+ +.|.+|..||++..+||||++|++||||+||++||++|.|+|+++|.+|++|||.||+.||+++| .++
T Consensus        13 ~~il~~l~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~Li~~N~~~yN~~~s~~~~   92 (112)
T cd05510          13 DKVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLR   92 (112)
T ss_pred             HHHHHHHHhcCccccchhcCCChhhcCCHHHHhcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            4677888888 89999999999999999999999999999999999999999999999999999999999999866 678


Q ss_pred             HHHHHHHHHHHHHHhccc
Q psy1225          80 RDAVKLQKLMQRKVQENP   97 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~klP   97 (256)
                      ++|..|++.+...+..+|
T Consensus        93 ~~A~~l~~~~~~~~~~~~  110 (112)
T cd05510          93 RHANFMKKKAEHLLKLIP  110 (112)
T ss_pred             HHHHHHHHHHHHHHHHCC
Confidence            999999999999887764

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

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.91  E-value=8.2e-25  Score=164.55  Aligned_cols=96  Identities=33%  Similarity=0.593  Sum_probs=91.6

Q ss_pred             CccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHH
Q psy1225           1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYR   80 (256)
Q Consensus         1 l~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~   80 (256)
                      |+.+++....++.+.+|.+||+...+|+||++|++||||+||++||++|.|.|+++|.+|+++||.||+.||+++|.++.
T Consensus         6 ~~~il~~l~~~~~a~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~   85 (101)
T cd05509           6 LKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYK   85 (101)
T ss_pred             HHHHHHHHHhCCCchhhcCCCChhhcCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            35678888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcc
Q psy1225          81 DAVKLQKLMQRKVQEN   96 (256)
Q Consensus        81 ~A~~L~~~f~~~~~kl   96 (256)
                      +|..|++.|.+.++++
T Consensus        86 ~a~~l~~~f~~~~~~~  101 (101)
T cd05509          86 CANKLEKFFWKKLKEL  101 (101)
T ss_pred             HHHHHHHHHHHHHhhC
Confidence            9999999999988764

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.

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

Probab=99.91  E-value=1.3e-24  Score=164.13  Aligned_cols=87  Identities=43%  Similarity=0.634  Sum_probs=83.5

Q ss_pred             ccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHH
Q psy1225           6 NQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKL   85 (256)
Q Consensus         6 ~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L   85 (256)
                      ++.+|++++.+|+++|++..+||||++|++||||++|++||+++.|.++++|..|+.+||.||+.||+++|.++.+|..|
T Consensus        17 ~d~~g~~l~~~F~~~p~~~~~pdYy~~I~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l   96 (104)
T cd05522          17 RDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL   96 (104)
T ss_pred             hCcCCCcccHHHhcCCCccccCcHHHHhCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q psy1225          86 QKLMQRK   92 (256)
Q Consensus        86 ~~~f~~~   92 (256)
                      ++.|...
T Consensus        97 ~~~f~~l  103 (104)
T cd05522          97 EKEARLL  103 (104)
T ss_pred             HHHHHHh
Confidence            9998763

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.

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.91  E-value=9.7e-25  Score=165.76  Aligned_cols=94  Identities=30%  Similarity=0.488  Sum_probs=87.0

Q ss_pred             ccccccccCC-ccccccccCCCCC--CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchh
Q psy1225           2 RPQKNQTEGG-NLSEPFLKLPAKR--YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRL   78 (256)
Q Consensus         2 ~~~~~~~~~~-~~s~~F~~~p~~~--~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i   78 (256)
                      .++++....+ +.|++|..||+..  ++||||++|++||||+||++||.+|.|.++.+|.+|++|||.||+.||+++|.+
T Consensus         9 ~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i   88 (108)
T cd05495           9 MPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRV   88 (108)
T ss_pred             HHHHHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHH
Confidence            3456667677 9999999998865  799999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q psy1225          79 YRDAVKLQKLMQRKVQE   95 (256)
Q Consensus        79 ~~~A~~L~~~f~~~~~k   95 (256)
                      +++|..|++.|.+.+..
T Consensus        89 ~~~a~~l~~~F~~~~~~  105 (108)
T cd05495          89 YKYCTKLAEVFEQEIDP  105 (108)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999988764

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.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.91  E-value=9.3e-25  Score=162.97  Aligned_cols=89  Identities=30%  Similarity=0.476  Sum_probs=85.3

Q ss_pred             CccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHH
Q psy1225           1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYR   80 (256)
Q Consensus         1 l~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~   80 (256)
                      |+.+++....++.+.+|..||+...+||||++|++||||+||++||.++.|+++++|..|++|||.||..||+++|.+++
T Consensus         6 l~~il~~l~~~~~~~~F~~pVd~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~~~~   85 (98)
T cd05512           6 LRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYR   85 (98)
T ss_pred             HHHHHHHHHhCCCchhhcCCCCccccCCHHHHhcCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH
Q psy1225          81 DAVKLQKLM   89 (256)
Q Consensus        81 ~A~~L~~~f   89 (256)
                      +|..|++.-
T Consensus        86 ~A~~l~~~~   94 (98)
T cd05512          86 AAVRLRDQG   94 (98)
T ss_pred             HHHHHHHhh
Confidence            999998753

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.

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

Probab=99.91  E-value=2.3e-24  Score=162.87  Aligned_cols=86  Identities=34%  Similarity=0.535  Sum_probs=82.5

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..|++++.+|+.+|+++.+||||++|++||||+||++||++  |.++++|.+|+.+||.||+.||+++|.++.+|..|+
T Consensus        18 ~~~g~~~~~~F~~lp~~~~~pdYy~iI~~PmdL~tI~~kl~~--Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le   95 (106)
T cd05521          18 EENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILE   95 (106)
T ss_pred             CcCCCCchHhhhcCCccccCccHHHHhcCCCCHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            556999999999999999999999999999999999999997  999999999999999999999999999999999999


Q ss_pred             HHHHHHHh
Q psy1225          87 KLMQRKVQ   94 (256)
Q Consensus        87 ~~f~~~~~   94 (256)
                      +.|.+++.
T Consensus        96 ~~~~~~~~  103 (106)
T cd05521          96 KYINDVII  103 (106)
T ss_pred             HHHHHhhc
Confidence            99988754

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.

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.90  E-value=3.4e-24  Score=159.69  Aligned_cols=88  Identities=27%  Similarity=0.383  Sum_probs=83.4

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      .++++....++.+.+|..||+...+||||++|++||||+||++||+++.|.|+++|.+|++|||.||..||+++|.++++
T Consensus         7 ~~il~~l~~~~~~~~F~~PV~~~~~pdY~~vIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~   86 (98)
T cd05513           7 EQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKA   86 (98)
T ss_pred             HHHHHHHHcCCccccccCcCCccccccHHHHHcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            46778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHH
Q psy1225          82 AVKLQKLM   89 (256)
Q Consensus        82 A~~L~~~f   89 (256)
                      |..|...-
T Consensus        87 A~~L~~~~   94 (98)
T cd05513          87 AKKLLHSG   94 (98)
T ss_pred             HHHHHHhh
Confidence            99997653

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.

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

Probab=99.90  E-value=4.7e-24  Score=162.80  Aligned_cols=96  Identities=25%  Similarity=0.413  Sum_probs=90.5

Q ss_pred             CccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC----c
Q psy1225           1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD----S   76 (256)
Q Consensus         1 l~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~----S   76 (256)
                      |+.+++....++.+.+|.+||+...+||||++|++||||+||++||++|.|.|+++|.+|+++||.||+.||+++    |
T Consensus         8 L~~il~~l~~~~~~~~F~~pv~~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~~~s   87 (112)
T cd05528           8 LRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDPADK   87 (112)
T ss_pred             HHHHHHHHHhCCCchhhcCCCCccccCcHHHHHcCCCCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHCCCCCcccc
Confidence            467788889999999999999999999999999999999999999999999999999999999999999999994    6


Q ss_pred             hhHHHHHHHHHHHHHHHhcc
Q psy1225          77 RLYRDAVKLQKLMQRKVQEN   96 (256)
Q Consensus        77 ~i~~~A~~L~~~f~~~~~kl   96 (256)
                      .++.+|..|++.+..++.+.
T Consensus        88 ~i~~~A~~L~~~~~~~~~~~  107 (112)
T cd05528          88 LIRSRACELRDEVHAMIEAE  107 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999887654

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

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.90  E-value=8e-24  Score=159.43  Aligned_cols=84  Identities=31%  Similarity=0.554  Sum_probs=80.4

Q ss_pred             CCccccccccCCCCC--CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHH
Q psy1225          10 GGNLSEPFLKLPAKR--YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK   87 (256)
Q Consensus        10 ~~~~s~~F~~~p~~~--~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~   87 (256)
                      .+++|++|+.||+..  .+||||++|++||||++|++||++|.|+++++|.+|+++||.||+.||+++|.++.+|..|++
T Consensus        17 ~~~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I~~kl~~~~Y~s~~ef~~D~~li~~N~~~yn~~~s~~~~~a~~l~~   96 (102)
T cd05499          17 HSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEE   96 (102)
T ss_pred             CCcccchhcCCCCccccCCCCHHHHhcCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            478999999998877  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q psy1225          88 LMQRKV   93 (256)
Q Consensus        88 ~f~~~~   93 (256)
                      .|+.++
T Consensus        97 ~fe~~~  102 (102)
T cd05499          97 VFNDKW  102 (102)
T ss_pred             HHHHhC
Confidence            998764

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.89  E-value=2.2e-23  Score=158.77  Aligned_cols=93  Identities=32%  Similarity=0.493  Sum_probs=87.9

Q ss_pred             cccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           3 PQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKS---GHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         3 ~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~---~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      +++.+...++.|.+|..||+. .+|+||++|++||||+||++||++   |.|.++++|.+|++|||.||+.||+++|.++
T Consensus        11 ~il~~l~~~~~s~~F~~pv~~-~~p~Y~~iI~~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~   89 (109)
T cd05502          11 RLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVA   89 (109)
T ss_pred             HHHHHHHhCCCChhhcCCCCC-CCCCHHHHCCCCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            567777889999999999998 899999999999999999999998   6999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcc
Q psy1225          80 RDAVKLQKLMQRKVQEN   96 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~kl   96 (256)
                      .+|..|++.|.+.+.++
T Consensus        90 ~~a~~l~~~f~~~~~~~  106 (109)
T cd05502          90 QAGKELELFFEEQLKEI  106 (109)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999988764

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.

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.89  E-value=2.8e-23  Score=154.98  Aligned_cols=90  Identities=24%  Similarity=0.326  Sum_probs=83.2

Q ss_pred             cccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHH
Q psy1225           3 PQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDA   82 (256)
Q Consensus         3 ~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A   82 (256)
                      .+|...-.++.|.+|...|  ..+||||++|++||||+||++||.+|.|.|+++|.+|++|||.||+.||+++ .++..|
T Consensus         9 ~il~~l~~~~~s~~f~~~p--~~~pdY~~iIk~PMDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~N~~~yN~~~-~~~~~a   85 (102)
T cd05501           9 FLLLKVYCMSKSGFFISKP--YYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-DFGQVG   85 (102)
T ss_pred             HHHHHHHhCcccccccCCC--CCCCchHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHcCCC-HHHHHH
Confidence            4667777889999997765  4889999999999999999999999999999999999999999999999999 999999


Q ss_pred             HHHHHHHHHHHhc
Q psy1225          83 VKLQKLMQRKVQE   95 (256)
Q Consensus        83 ~~L~~~f~~~~~k   95 (256)
                      ..|++.|++++.+
T Consensus        86 ~~L~~~Fek~~~~   98 (102)
T cd05501          86 ITLEKKFEKNFKE   98 (102)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998765

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.89  E-value=4.4e-23  Score=155.38  Aligned_cols=90  Identities=31%  Similarity=0.413  Sum_probs=81.9

Q ss_pred             ccccccC---CccccccccCCCCC--CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchh
Q psy1225           4 QKNQTEG---GNLSEPFLKLPAKR--YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRL   78 (256)
Q Consensus         4 ~~~~~~~---~~~s~~F~~~p~~~--~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i   78 (256)
                      +++....   ++++.+|..||+..  .+|+||++|++||||++|++||++|.|.|+++|..|+++||.||+.||+++|.+
T Consensus         8 il~~l~~~~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~yn~~~s~i   87 (102)
T cd05498           8 ILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPV   87 (102)
T ss_pred             HHHHHHhCCCccccCcccCcCCccccCCCcHHHHccCCCcHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHH
Confidence            4444444   49999999998754  699999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy1225          79 YRDAVKLQKLMQRKV   93 (256)
Q Consensus        79 ~~~A~~L~~~f~~~~   93 (256)
                      +.+|..|++.|++++
T Consensus        88 ~~~a~~l~~~fe~~~  102 (102)
T cd05498          88 HAMARKLQDVFEDRW  102 (102)
T ss_pred             HHHHHHHHHHHHHhC
Confidence            999999999998764

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.88  E-value=6.7e-23  Score=153.59  Aligned_cols=92  Identities=27%  Similarity=0.379  Sum_probs=85.8

Q ss_pred             ccccccccCCccccccccCCCCC--CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKR--YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~--~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      +++++....++.+.+|..|++..  .+|+||++|++||||+||++||+++.|.++++|.+|+.+||.||..||+++|.++
T Consensus         6 ~~il~~l~~~~~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yn~~~s~i~   85 (99)
T cd05506           6 GTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVH   85 (99)
T ss_pred             HHHHHHHHhCCCCccccCCCCccccCCCCHHHHHcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            35677788899999999998754  7999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q psy1225          80 RDAVKLQKLMQRKV   93 (256)
Q Consensus        80 ~~A~~L~~~f~~~~   93 (256)
                      .+|..|++.|++++
T Consensus        86 ~~a~~l~~~fe~~w   99 (99)
T cd05506          86 TMAKELLKIFETRW   99 (99)
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999998764

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.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.88  E-value=7.7e-23  Score=154.29  Aligned_cols=91  Identities=29%  Similarity=0.399  Sum_probs=85.6

Q ss_pred             ccccccccCCccccccccCCCC--CCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAK--RYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~--~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      .++++....++.|.+|..||+.  ..+|+||++|++||||++|++||++|.|.++++|.+|+++||.||..||+++|.++
T Consensus        10 ~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~   89 (103)
T cd05500          10 LSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVS   89 (103)
T ss_pred             HHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            4577888899999999999885  47999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q psy1225          80 RDAVKLQKLMQRK   92 (256)
Q Consensus        80 ~~A~~L~~~f~~~   92 (256)
                      .+|..|++.|++.
T Consensus        90 ~~A~~l~~~fe~~  102 (103)
T cd05500          90 QMGKRLQAAFEKH  102 (103)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999864

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.

>smart00297 BROMO bromo domain

Probab=99.88  E-value=1e-22  Score=154.43  Aligned_cols=94  Identities=43%  Similarity=0.740  Sum_probs=88.8

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ..+++....++++.+|..||++..+|+||.+|++||||++|++||++|.|.|+++|.+|+.+||.||..||+++|.++.+
T Consensus        13 ~~i~~~~~~~~~~~~F~~~~~~~~~p~Y~~~i~~P~dl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~~n~~~s~~~~~   92 (107)
T smart00297       13 KAVLDKLDSHRLSWPFLKPVDRKEAPDYYDIIKKPMDLSTIKKKLENGKYSSVEEFVADVQLMFSNAKTYNGPDSEVYKD   92 (107)
T ss_pred             HHHHHHHHhCccchhhccCCChhhccCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            34666777889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhc
Q psy1225          82 AVKLQKLMQRKVQE   95 (256)
Q Consensus        82 A~~L~~~f~~~~~k   95 (256)
                      |..|.+.|...+.+
T Consensus        93 a~~l~~~f~~~~~~  106 (107)
T smart00297       93 AKKLEKFFEKKLRE  106 (107)
T ss_pred             HHHHHHHHHHHHhh
Confidence            99999999988765

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.88  E-value=1.7e-22  Score=157.95  Aligned_cols=87  Identities=26%  Similarity=0.416  Sum_probs=83.7

Q ss_pred             cCCccccccccCCCCC-CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHH
Q psy1225           9 EGGNLSEPFLKLPAKR-YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK   87 (256)
Q Consensus         9 ~~~~~s~~F~~~p~~~-~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~   87 (256)
                      .+++.+.+|..||+.. .+|+||++|++||||+||++||++|.|+++++|..|++|||.||..||+++|.++.+|..|++
T Consensus        40 ~~~~~~~~F~~pv~~~~~~p~Y~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~Na~~yN~~~s~i~~~A~~l~~  119 (128)
T cd05529          40 LQLEIAEYFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSD  119 (128)
T ss_pred             ccCcccccccCCCCccccCCcHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            4999999999999999 999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhc
Q psy1225          88 LMQRKVQE   95 (256)
Q Consensus        88 ~f~~~~~k   95 (256)
                      .|...+..
T Consensus       120 ~~~~~l~~  127 (128)
T cd05529         120 WLLRILSS  127 (128)
T ss_pred             HHHHHhcc
Confidence            99887653

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.

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.86  E-value=7.3e-22  Score=148.96  Aligned_cols=87  Identities=28%  Similarity=0.444  Sum_probs=81.4

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +.+|+.+|++|+++|++  .|+||.+|+.||||.+|++||++|.|.++++|..|+.+||.||+.||+++|.+|.+|..|+
T Consensus        20 D~~Gr~~s~~f~~LP~~--~~~~~~~ik~Pi~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NAr~yN~~~S~iy~dA~eLq   97 (110)
T cd05526          20 DEEGRCYSDSLAELPEL--AVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTDSEIYEDAVELQ   97 (110)
T ss_pred             CCCCCCchHHHHHCCCc--ccCchhhhcCCccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHHHHhCcccCHHHHHHHHHH
Confidence            56799999999999994  4778899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhc
Q psy1225          87 KLMQRKVQE   95 (256)
Q Consensus        87 ~~f~~~~~k   95 (256)
                      ++|.....+
T Consensus        98 ~~f~~~rd~  106 (110)
T cd05526          98 QFFIKIRDE  106 (110)
T ss_pred             HHHHHHHHH
Confidence            999876543

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.

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

Probab=99.84  E-value=4.8e-21  Score=138.94  Aligned_cols=82  Identities=39%  Similarity=0.690  Sum_probs=77.0

Q ss_pred             cccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHH
Q psy1225           3 PQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDA   82 (256)
Q Consensus         3 ~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A   82 (256)
                      ++++....++.+.+|..+|+...+|+|+++|++||||++|++||++|.|+++++|.+|+++||.||..||+++|.++.+|
T Consensus         3 ~il~~l~~~~~~~~F~~~~~~~~~p~y~~~i~~P~dL~~I~~kl~~~~Y~s~~~f~~Dv~~i~~Na~~yn~~~s~~~~~A   82 (84)
T PF00439_consen    3 EILEELMKHPISSPFSKPVDPKEYPDYYEIIKNPMDLSTIRKKLENGKYKSIEEFEADVRLIFQNARRYNPPDSPIYKAA   82 (84)
T ss_dssp             HHHHHHHTSTTGGGGSSSTHTTTSTTHHHHSSSS--HHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHH
T ss_pred             HHHHHHHcCCCchhhcCCCChhhCCCHHHHHhhccchhhhhHHhhccchhhHHHHHHHHHHHHHHHHHHCCCcCHHHHHh
Confidence            57788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HH
Q psy1225          83 VK   84 (256)
Q Consensus        83 ~~   84 (256)
                      ..
T Consensus        83 ~~   84 (84)
T PF00439_consen   83 EK   84 (84)
T ss_dssp             HH
T ss_pred             cC
Confidence            74

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

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.83  E-value=1.7e-20  Score=141.95  Aligned_cols=85  Identities=21%  Similarity=0.255  Sum_probs=75.9

Q ss_pred             ccccccccCC-----CCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225          12 NLSEPFLKLP-----AKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus        12 ~~s~~F~~~p-----~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      |-+.||..++     .+..+|+|+.+|++||||+||++||++|.|++++||.+|+.+||+||..||+++|.++..|..|.
T Consensus        17 p~~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~N~~~yNg~~s~~~~~A~~l~   96 (109)
T cd05492          17 PPDTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWLY   96 (109)
T ss_pred             cccccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            3456777775     44579999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      +...+.+.++
T Consensus        97 ~d~~~el~Ei  106 (109)
T cd05492          97 RDTCHDLREL  106 (109)
T ss_pred             HHHHHHHHHH
Confidence            8877766554

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.

>KOG1474|consensus

Probab=99.83  E-value=7.8e-21  Score=183.91  Aligned_cols=152  Identities=30%  Similarity=0.484  Sum_probs=138.5

Q ss_pred             ccccCCccccccccCCCC--CCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHH
Q psy1225           6 NQTEGGNLSEPFLKLPAK--RYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAV   83 (256)
Q Consensus         6 ~~~~~~~~s~~F~~~p~~--~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~   83 (256)
                      +....+.++++|..|++.  -..|+||.+|++|||+++|++++.+..|.+..+-.+|+..+|.||..||.+...+...+.
T Consensus         2 ~~~~~~~~~~~f~~~v~~v~l~~~~~~~~~~~~~d~~~~~~~~e~n~~~~~~~~~~~f~~~~sn~~~~~~~~~~v~~~~~   81 (640)
T KOG1474|consen    2 KEARKHKLAWPFLEPVDAVALNLPAYYEIIKRPMDIGTIEKRVENNYYFSASECIADFKTKFSNCYLFNDSGDDVVRMKQ   81 (640)
T ss_pred             cccccccccccccCccchhhccchhhhcccCCCCCchhhhhhhccCccccHhhhhhhccccccchhcccCCccchhhccc
Confidence            345578899999999885  458999999999999999999999999999999999999999999999999888888888


Q ss_pred             HHHHHHHHHHhcc-------------------------------------------------------------------
Q psy1225          84 KLQKLMQRKVQEN-------------------------------------------------------------------   96 (256)
Q Consensus        84 ~L~~~f~~~~~kl-------------------------------------------------------------------   96 (256)
                      .+.+.+.......                                                                   
T Consensus        82 ~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (640)
T KOG1474|consen   82 SLEKLFPKKLRSMPSDEEDKSSVGPKASKIPLDKDSSSQVRKLSERLKQELQQVRPLTKAVEFSPEPSVVSPVSPASQPF  161 (640)
T ss_pred             cchhhcccccccccccccCCcccccccccCcCCCCchhhhhhhhhccccccccCCcccccccccccccccCCCCCccccc
Confidence            8888775433322                                                                   


Q ss_pred             --------------------------------------------------------------------------------
Q psy1225          97 --------------------------------------------------------------------------------   96 (256)
Q Consensus        97 --------------------------------------------------------------------------------   96 (256)
                                                                                                      
T Consensus       162 ~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lk~C~~iLk~l~~~k~aw  241 (640)
T KOG1474|consen  162 KSKNGVKKVADTCVKSYKSKSEREPSPGQKREGTVAPNSSRESGDSAAEEEAKPKSKLTVELLKQCLSILKRLMKHKHAW  241 (640)
T ss_pred             ccccchhhhhccccccccccCcCCCCccccccccccCccccccccccccccccccccccHHHHHHHHHHHHHHHhccCCC
Confidence                                                                                            


Q ss_pred             ----------------------cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHH
Q psy1225          97 ----------------------PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV  154 (256)
Q Consensus        97 ----------------------P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~  154 (256)
                                            ||||+||++|+.++.|.++.+|..||+|||.||++||++++.||.+|..|+++|+.+|
T Consensus       242 pF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~Y~~~~eF~~DVRL~F~Ncm~YNp~g~dV~~Ma~~L~~~Fe~rw  321 (640)
T KOG1474|consen  242 PFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGEYKSAEEFAADVRLTFDNCMTYNPEGSDVYAMAKKLQEVFEERW  321 (640)
T ss_pred             CcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccccCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence                                  9999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcC
Q psy1225         155 QEF  157 (256)
Q Consensus       155 ~~~  157 (256)
                      ..+
T Consensus       322 ~~~  324 (640)
T KOG1474|consen  322 ASM  324 (640)
T ss_pred             hhc
Confidence            875

>cd04369 Bromodomain Bromodomain

Probab=99.83  E-value=8.4e-21  Score=140.77  Aligned_cols=90  Identities=42%  Similarity=0.704  Sum_probs=84.3

Q ss_pred             cccccccCC--ccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHH
Q psy1225           3 PQKNQTEGG--NLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYR   80 (256)
Q Consensus         3 ~~~~~~~~~--~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~   80 (256)
                      .+++....+  +.+.+|..||+...+|+|+++|++||||++|++||.+|.|.++++|.+|+.+|+.||..||+++|.++.
T Consensus         7 ~i~~~l~~~~~~~~~~F~~~~~~~~~~~Y~~~i~~P~~l~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~~n~~~~~~~~   86 (99)
T cd04369           7 SLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYK   86 (99)
T ss_pred             HHHHHHHhhcccccHHHhcCCChhcCCCHHHHHhCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            455566666  999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy1225          81 DAVKLQKLMQRK   92 (256)
Q Consensus        81 ~A~~L~~~f~~~   92 (256)
                      .|..|...+.+.
T Consensus        87 ~a~~l~~~~~~~   98 (99)
T cd04369          87 DAKKLEKLFEKL   98 (99)
T ss_pred             HHHHHHHHHHHh
Confidence            999999998764

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

>KOG1474|consensus

Probab=99.82  E-value=1.4e-20  Score=182.17  Aligned_cols=94  Identities=30%  Similarity=0.425  Sum_probs=90.0

Q ss_pred             cccccccCCccccccccCCCC--CCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHH
Q psy1225           3 PQKNQTEGGNLSEPFLKLPAK--RYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYR   80 (256)
Q Consensus         3 ~~~~~~~~~~~s~~F~~~p~~--~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~   80 (256)
                      .+|+....|..++||..|||.  -++|||++||++||||+||++||.+|.|.++.||.+||+|||.||.+||.+++.+|.
T Consensus       229 ~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~Y~~~~eF~~DVRL~F~Ncm~YNp~g~dV~~  308 (640)
T KOG1474|consen  229 SILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGEYKSAEEFAADVRLTFDNCMTYNPEGSDVYA  308 (640)
T ss_pred             HHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccccCCHHHHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            578888999999999999885  579999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcc
Q psy1225          81 DAVKLQKLMQRKVQEN   96 (256)
Q Consensus        81 ~A~~L~~~f~~~~~kl   96 (256)
                      +|..|+++|+..|..+
T Consensus       309 Ma~~L~~~Fe~rw~~~  324 (640)
T KOG1474|consen  309 MAKKLQEVFEERWASM  324 (640)
T ss_pred             HHHHHHHHHHHHHhhc
Confidence            9999999999999986

>KOG1472|consensus

Probab=99.65  E-value=1.4e-16  Score=152.46  Aligned_cols=68  Identities=40%  Similarity=0.616  Sum_probs=64.2

Q ss_pred             CccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchh
Q psy1225          11 GNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRL   78 (256)
Q Consensus        11 ~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i   78 (256)
                      +..+.+|..++++...|+||.+|+-||||.++.+|+..+.|.+.++|+.|+.+||.||..||...+..
T Consensus       301 ~~~s~~~~~kvs~~~a~~y~~i~k~pmdl~t~~~k~~~~~y~~~~~fv~d~~~~~~n~~~~n~ee~~~  368 (720)
T KOG1472|consen  301 TEHSTPFLEKVSKEDAPNYYQIIKAPMDLSTELKKLKSGPYCSKEEFVNDLMLIWRNCEKYNSEESHG  368 (720)
T ss_pred             cccccccccCCChhhCcchHHhhhcchHHHHHHHHhccccccchhHHHHHHHHHHhcchhhccccchh
Confidence            57789999999999999999999999999999999999999999999999999999999999976533

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.63  E-value=1.8e-15  Score=114.69  Aligned_cols=63  Identities=29%  Similarity=0.387  Sum_probs=60.2

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||+||++|++++.|.++++|.+|+.|||.||+.||+++|.++..|..|++.|.++++++
T Consensus        45 k~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~l~~~f~~~l~~~  107 (107)
T cd05497          45 KTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQM  107 (107)
T ss_pred             cCcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHcC
Confidence            349999999999999999999999999999999999999999999999999999999998764

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

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

Probab=99.63  E-value=1.1e-15  Score=113.78  Aligned_cols=59  Identities=25%  Similarity=0.388  Sum_probs=56.7

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      +-||||+||++|++++.|.|+++|.+|+.|||.||+.||+++|.++..|..|++.|.++
T Consensus        38 k~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~le~~f~~~   96 (97)
T cd05505          38 TNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKTEQCCVNL   96 (97)
T ss_pred             CCcCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHh
Confidence            33999999999999999999999999999999999999999999999999999999875

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.

>KOG0008|consensus

Probab=99.62  E-value=8e-16  Score=152.79  Aligned_cols=154  Identities=26%  Similarity=0.372  Sum_probs=134.2

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ..+.|+...-+-+.+|..|++...++|||.||+.||+|.++++.+.++.|.+-+.|..|+.+|+.|...||++-+.....
T Consensus      1267 ~~i~n~~~~~~~t~~f~~Pv~~k~v~dyy~vi~~P~~lq~~kk~v~kr~y~~r~~fle~~~~~~~ns~~yng~~~~~t~~ 1346 (1563)
T KOG0008|consen 1267 ETIINQARSSPNTYPFPTPVNAKEVKDYYRVITPPMDLQTQKKLVRKRLYESREHFLEELPLIVSNSTKYNGPLASLTRQ 1346 (1563)
T ss_pred             HHHHHHHhcCCCCcCCCCccchhhccchhhccCCCcchHHHHHHHHHHHHHHHHHHHHHhHHHhhchhhhcCchHHHHHH
Confidence            34567778888999999999999999999999999999999999999999999999999999999999999999988887


Q ss_pred             HHHHHHHHHHHHhcc------------------------------------------------------------cccHH
Q psy1225          82 AVKLQKLMQRKVQEN------------------------------------------------------------PRSLL  101 (256)
Q Consensus        82 A~~L~~~f~~~~~kl------------------------------------------------------------P~dl~  101 (256)
                      +..+.......+.+-                                                            |||+.
T Consensus      1347 ~q~mls~~~~~~~ekedk~~~lEk~Inplld~~d~v~~~~~d~~vs~~~~ipes~~f~~~v~~k~~~~yy~kik~pmdl~ 1426 (1563)
T KOG0008|consen 1347 QQSMLSLCFEKLKEKEDKLWRLEKAINPLLDDDDQVAFFILDNIVSQMKEIPESWPFHEPVNKKRVPDYYKKIKNPMDLE 1426 (1563)
T ss_pred             HHHHHHHHHHhhchhHHHHHHHHhhcCcccCccchhhHhhhhhHHHHHHhcchhcccccccchhhchHHHHHhcChhhHH
Confidence            777655443333211                                                            99999


Q ss_pred             HHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHh
Q psy1225         102 TIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ  155 (256)
Q Consensus       102 ~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~  155 (256)
                      +|.+++..++|.+.++|.+|+++++.|+..||+.+|..-.-|.++-.+....+.
T Consensus      1427 ~i~~n~~~~~y~s~~e~l~dv~~i~~n~~~~ng~e~~y~~k~~k~~ev~~~~~~ 1480 (1563)
T KOG0008|consen 1427 TILKNIPPHKYDSRSEFLDDVNLIYVNSVEYNGAESAYTKKARKIGEVGLANLL 1480 (1563)
T ss_pred             HHhhcCCccccccHHHHhhhhHhhcccceeecCccccccHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999887777776665554443

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.62  E-value=2.1e-15  Score=112.69  Aligned_cols=60  Identities=23%  Similarity=0.416  Sum_probs=57.9

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      -||||+||++|+++++|.|+++|.+|++|||+||+.||+++ .++..|..|++.|++++++
T Consensus        39 ~PMDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~N~~~yN~~~-~~~~~a~~L~~~Fek~~~~   98 (102)
T cd05501          39 EPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-DFGQVGITLEKKFEKNFKE   98 (102)
T ss_pred             CCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHHHHHHH
Confidence            39999999999999999999999999999999999999999 9999999999999998874

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.

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.62  E-value=1.7e-15  Score=116.75  Aligned_cols=100  Identities=25%  Similarity=0.447  Sum_probs=74.2

Q ss_pred             HHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHHHH-HHHHhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhC
Q psy1225          55 NELTGELNLMFENAKKFNPADSRLYRDAVKLQKLM-QRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN  133 (256)
Q Consensus        55 ~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~~f-~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN  133 (256)
                      .+|.+-+..|+.....  .+.|..+........+- ...+.+-||||+||++||.++.|.++++|.+|+.|||.||+.||
T Consensus         4 ~~w~~~c~~il~~l~~--~~~s~~F~~PVd~~~~pdY~~iIk~PmDL~tIk~kL~~~~Y~~~~ef~~D~~lif~Na~~yN   81 (119)
T cd05496           4 SDWKKQCKELVNLMWD--CEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT   81 (119)
T ss_pred             HHHHHHHHHHHHHHHh--CCccccccCCCChhhcCcHHHHhCCcccHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            3555555555555443  34454444433322110 01223339999999999999999999999999999999999999


Q ss_pred             CC-CCHHHHHHHHHHHHHHHHHhc
Q psy1225         134 PA-DSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus       134 ~~-~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      ++ +|.+|.+|..|++.|.++++.
T Consensus        82 ~~~~s~i~~~a~~L~~~F~~~~~~  105 (119)
T cd05496          82 PNKRSRIYSMTLRLSALFEEHIKK  105 (119)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHH
Confidence            85 999999999999999999875

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

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.61  E-value=3.4e-15  Score=113.39  Aligned_cols=63  Identities=30%  Similarity=0.537  Sum_probs=59.7

Q ss_pred             hcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          94 QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      .+-||||+||++|+++|.|.++.+|.+|+.|||.||+.||+++|.++++|..|++.|.++++.
T Consensus        43 Ik~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~F~~~~~~  105 (108)
T cd05495          43 VKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQEIDP  105 (108)
T ss_pred             hCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            344999999999999999999999999999999999999999999999999999999998764

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.

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.60  E-value=4e-15  Score=112.35  Aligned_cols=63  Identities=27%  Similarity=0.521  Sum_probs=59.4

Q ss_pred             hcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          94 QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      .+.||+|++|++|+++|+|.++++|..|+.+||+||++||.++|++|++|..|++.|..+.++
T Consensus        44 ik~Pi~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NAr~yN~~~S~iy~dA~eLq~~f~~~rd~  106 (110)
T cd05526          44 KKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTDSEIYEDAVELQQFFIKIRDE  106 (110)
T ss_pred             hcCCccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHHHHhCcccCHHHHHHHHHHHHHHHHHHH
Confidence            344999999999999999999999999999999999999999999999999999999887654

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.

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

Probab=99.60  E-value=3.2e-15  Score=113.38  Aligned_cols=60  Identities=27%  Similarity=0.516  Sum_probs=58.5

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      ||||++|++|+++|.|.++++|..|+.|||.||+.||+++|.+|.+|..|++.|.++++.
T Consensus        47 Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~f~~~~~~  106 (107)
T cd05516          47 PVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKSARQK  106 (107)
T ss_pred             CCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999999999999999988764

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.59  E-value=5.6e-15  Score=113.40  Aligned_cols=63  Identities=25%  Similarity=0.575  Sum_probs=60.5

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||++|++|++++.|.|+++|.+|+.|||.||+.||+++|.++.+|..|++.|.++++++
T Consensus        50 ~~PmDL~tI~~kL~~~~Y~s~~~f~~Dv~LI~~Na~~yN~~~s~i~~~A~~l~~~f~~~~~~~  112 (115)
T cd05504          50 KKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL  112 (115)
T ss_pred             cCcccHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            339999999999999999999999999999999999999999999999999999999999875

Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.59  E-value=4.3e-15  Score=110.77  Aligned_cols=58  Identities=33%  Similarity=0.627  Sum_probs=56.6

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV  154 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~  154 (256)
                      ||||++|++|++++.|.|+++|.+|+.|||.||+.||+++|.++++|..|++.|.++|
T Consensus        40 PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~f~~~~   97 (97)
T cd05503          40 PMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFFEKRW   97 (97)
T ss_pred             CCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999999999999998764

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.

>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family

Probab=99.59  E-value=6.5e-15  Score=111.36  Aligned_cols=57  Identities=30%  Similarity=0.445  Sum_probs=55.6

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      ||||++|++|++++.|.|+++|..|+.|||.||+.||+++|.++++|..|++.|.+.
T Consensus        48 P~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f~Na~~yn~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          48 PVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             CcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999999999999999999999999999999999764

ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV

Probab=99.58  E-value=4.6e-15  Score=111.65  Aligned_cols=57  Identities=37%  Similarity=0.658  Sum_probs=55.5

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      ||||++|++|++++.|.|+++|.+|+.|||.||+.||+++|.+|.+|..|++.|.++
T Consensus        46 Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le~~~~~~  102 (103)
T cd05518          46 PIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVLKEK  102 (103)
T ss_pred             CcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999999999999998764

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

>KOG1245|consensus

Probab=99.58  E-value=1.1e-15  Score=157.05  Aligned_cols=91  Identities=27%  Similarity=0.485  Sum_probs=86.7

Q ss_pred             cccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHH
Q psy1225           3 PQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDA   82 (256)
Q Consensus         3 ~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A   82 (256)
                      .+|.+..-|..|+||++||+...+||||+||++||||+||+.|+..|.|.++++|..|+.|||.||..||.+ |.+.++.
T Consensus      1308 ~il~e~~~~~~awPFlepVn~~~vp~Y~~IIk~Pmdl~tir~k~~~~~Y~~~eef~~Di~lvf~Nc~~yN~~-s~i~~ag 1386 (1404)
T KOG1245|consen 1308 DILHELVVHKAAWPFLEPVNPKEVPDYYDIIKKPMDLSTIREKLSKGIYPSPEEFATDIELVFDNCETYNED-SEIGRAG 1386 (1404)
T ss_pred             HHHHHHHHhhhcchhhccCChhhcccHHHHhcChhHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHhccc-hhhhhhc
Confidence            577888899999999999999999999999999999999999999999999999999999999999999999 9999999


Q ss_pred             HHHHHHHHHHHh
Q psy1225          83 VKLQKLMQRKVQ   94 (256)
Q Consensus        83 ~~L~~~f~~~~~   94 (256)
                      ..|.+.|...+.
T Consensus      1387 ~~l~~ff~~~~~ 1398 (1404)
T KOG1245|consen 1387 TCLRRFFHKRWR 1398 (1404)
T ss_pred             chHHHHHHHHHH
Confidence            999999987543

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.58  E-value=5.8e-15  Score=112.96  Aligned_cols=61  Identities=34%  Similarity=0.535  Sum_probs=59.0

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      ||||++|++|++++.|.|+++|.+|+.|||+||+.||+++|.+|++|..|++.|.+.++++
T Consensus        48 Pmdl~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~  108 (113)
T cd05524          48 PIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLSARNEV  108 (113)
T ss_pred             ccCHHHHHHHhCcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999999888753

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=99.58  E-value=5.8e-15  Score=111.12  Aligned_cols=57  Identities=61%  Similarity=0.904  Sum_probs=55.9

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      ||||++|++|++++.|.++++|.+|+.|||+||+.||+++|.+|.+|..|++.|+++
T Consensus        46 PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~L~~~f~~~  102 (103)
T cd05520          46 PISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKLMQAK  102 (103)
T ss_pred             CcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999875

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

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.57  E-value=6.9e-15  Score=111.19  Aligned_cols=59  Identities=32%  Similarity=0.657  Sum_probs=57.5

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHh
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ  155 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~  155 (256)
                      ||||++|++|++++.|.++++|.+|+.|||.||+.||+++|.+|.+|..|++.|.++.+
T Consensus        46 PmdL~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~~yN~~~s~i~~~A~~L~~~~~~~~~  104 (105)
T cd05515          46 PIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLLETKR  104 (105)
T ss_pred             CcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999999999999999999999988765

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=99.57  E-value=1e-14  Score=109.57  Aligned_cols=62  Identities=35%  Similarity=0.664  Sum_probs=59.8

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      -||||++|++|++++.|.|+++|.+|+.+||.||+.||+++|.++.+|..|++.|.++++++
T Consensus        40 ~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~a~~l~~~f~~~~~~~  101 (101)
T cd05509          40 KPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL  101 (101)
T ss_pred             CCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhC
Confidence            39999999999999999999999999999999999999999999999999999999998764

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.56  E-value=1.2e-14  Score=108.86  Aligned_cols=59  Identities=31%  Similarity=0.531  Sum_probs=57.0

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHH
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV  154 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~  154 (256)
                      -||||++|++||+++.|.++++|.+|+.+||.||+.||+++|.++.+|..|++.|+++|
T Consensus        41 ~P~dl~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yn~~~s~i~~~a~~l~~~fe~~w   99 (99)
T cd05506          41 KPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETRW   99 (99)
T ss_pred             CCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            39999999999999999999999999999999999999999999999999999999874

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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.56  E-value=9.7e-15  Score=109.01  Aligned_cols=59  Identities=20%  Similarity=0.373  Sum_probs=55.6

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      +-||||+||++|+++|.|.++++|.+|+.|||.||+.||+++|.++..|..|.+.+...
T Consensus        40 k~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~Na~~YN~~~s~i~~~A~~l~~~~~~e   98 (99)
T cd05508          40 FKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKICEQE   98 (99)
T ss_pred             CCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhh
Confidence            33999999999999999999999999999999999999999999999999999987653

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

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.56  E-value=1.3e-14  Score=109.46  Aligned_cols=62  Identities=31%  Similarity=0.494  Sum_probs=59.0

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||+||++|++++.|.++++|.+|+.|||.||+.||+++|.++.+|..|++.+.+++..
T Consensus        41 k~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~v~~~A~~l~~~~~~~~~~  102 (104)
T cd05507          41 YRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEMQREVMSQIQQ  102 (104)
T ss_pred             CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHhhc
Confidence            33999999999999999999999999999999999999999999999999999999888764

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.

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.54  E-value=1.5e-14  Score=108.87  Aligned_cols=56  Identities=36%  Similarity=0.683  Sum_probs=54.9

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR  152 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~  152 (256)
                      ||||++|++|++++.|.++++|.+|+.|||.||+.||+++|.++.+|..|++.|..
T Consensus        46 PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          46 PIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             CcCHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999875

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.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.53  E-value=2.1e-14  Score=108.09  Aligned_cols=59  Identities=31%  Similarity=0.580  Sum_probs=57.0

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHH
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV  154 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~  154 (256)
                      -||||++|++|++++.|.++++|.+|+.|||.||+.||+++|.++.+|..|++.|+++|
T Consensus        44 ~P~dL~~I~~kl~~~~Y~s~~ef~~D~~li~~N~~~yn~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          44 KPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             CCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            39999999999999999999999999999999999999999999999999999998764

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=99.53  E-value=3.4e-14  Score=105.87  Aligned_cols=54  Identities=31%  Similarity=0.565  Sum_probs=52.0

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHH
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKL  149 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~  149 (256)
                      -||||+||++|++++.|.|+++|.+|+.|||.||+.||+++|.+|++|..|.+.
T Consensus        40 ~PmDL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~   93 (98)
T cd05513          40 HPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKLLHS   93 (98)
T ss_pred             CccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHh
Confidence            399999999999999999999999999999999999999999999999999764

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.53  E-value=2.6e-14  Score=107.56  Aligned_cols=58  Identities=34%  Similarity=0.545  Sum_probs=56.6

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV  154 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~  154 (256)
                      ||||++|+++++++.|.|+++|..|+.|||.||+.||+++|.++.+|..|++.|+++|
T Consensus        45 Pmdl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~yn~~~s~i~~~a~~l~~~fe~~~  102 (102)
T cd05498          45 PMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDRW  102 (102)
T ss_pred             CCcHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999999999999998764

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

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.52  E-value=9.8e-14  Score=105.89  Aligned_cols=64  Identities=28%  Similarity=0.364  Sum_probs=58.5

Q ss_pred             hcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCC-HHHHHHHHHHHHHHHHHhcC
Q psy1225          94 QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADS-RLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s-~i~~~a~~L~~~~~~~~~~~  157 (256)
                      .+-||||++|++|++++.|.|+++|.+|+.|||.||+.||+++| .++++|..|++.++..+..+
T Consensus        45 Ik~PmdL~tI~~kl~~~~Y~s~~ef~~D~~Li~~N~~~yN~~~s~~~~~~A~~l~~~~~~~~~~~  109 (112)
T cd05510          45 IKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHANFMKKKAEHLLKLI  109 (112)
T ss_pred             hcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence            33499999999999999999999999999999999999999877 57789999999999988764

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.51  E-value=6.2e-14  Score=106.75  Aligned_cols=62  Identities=32%  Similarity=0.565  Sum_probs=59.0

Q ss_pred             cccccHHHHHHHhhc---CCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKS---GHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~---~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||++|++||++   +.|.++++|.+|+.|||.||+.||+++|.++.+|..|++.|.+++++
T Consensus        41 ~~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~a~~l~~~f~~~~~~  105 (109)
T cd05502          41 KTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKE  105 (109)
T ss_pred             CCCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            349999999999998   69999999999999999999999999999999999999999999875

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.

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

Probab=99.51  E-value=3.6e-14  Score=106.95  Aligned_cols=57  Identities=33%  Similarity=0.633  Sum_probs=55.8

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      ||||++|++|++++.|.|+.+|.+|+.|||.||+.||+++|.++.+|..|++.|.++
T Consensus        46 Pmdl~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l~~~f~~~  102 (103)
T cd05519          46 PIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKKK  102 (103)
T ss_pred             CcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999865

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.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.51  E-value=6.7e-14  Score=104.40  Aligned_cols=56  Identities=32%  Similarity=0.581  Sum_probs=53.1

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHH
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLM  150 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~  150 (256)
                      +-||||+||++|++++.|.++++|..|+.|||.||+.||+++|.+|++|..|++.-
T Consensus        39 k~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~~~~~A~~l~~~~   94 (98)
T cd05512          39 KQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLRDQG   94 (98)
T ss_pred             cCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHhh
Confidence            33999999999999999999999999999999999999999999999999998853

BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

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

Probab=99.50  E-value=1.5e-13  Score=104.96  Aligned_cols=61  Identities=23%  Similarity=0.413  Sum_probs=57.9

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCC----CHHHHHHHHHHHHHHHHHhc
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD----SRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~----s~i~~~a~~L~~~~~~~~~~  156 (256)
                      -||||+||++|++++.|.|+++|.+|+.|||.||+.||+++    |.++.+|..|++.+.+++.+
T Consensus        42 ~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~~~s~i~~~A~~L~~~~~~~~~~  106 (112)
T cd05528          42 QPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDPADKLIRSRACELRDEVHAMIEA  106 (112)
T ss_pred             CCCCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHCCCCCccccHHHHHHHHHHHHHHHHHHh
Confidence            39999999999999999999999999999999999999994    79999999999999988875

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

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.49  E-value=9.3e-14  Score=106.16  Aligned_cols=63  Identities=24%  Similarity=0.389  Sum_probs=60.2

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||++|++|++++.|.++++|..|+.|||.||+.||+++|.++.+|..|.+.+.++++++
T Consensus        38 ~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~l~~~~~~~~~~~  100 (112)
T cd05511          38 KRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELLAER  100 (112)
T ss_pred             cCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            339999999999999999999999999999999999999999999999999999999998865

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.

>smart00297 BROMO bromo domain

Probab=99.49  E-value=2.2e-13  Score=103.04  Aligned_cols=61  Identities=44%  Similarity=0.789  Sum_probs=59.2

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      -||||++|++|++++.|.++++|.+|+.+||.||..||+++|.++..|..|++.|.+++++
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            3999999999999999999999999999999999999999999999999999999999875

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.49  E-value=1e-13  Score=104.91  Aligned_cols=64  Identities=23%  Similarity=0.340  Sum_probs=58.9

Q ss_pred             hcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          94 QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      .+-||||+||++|+++++|.++++|..|+.|||.||..||+++|.++..|..|-+.....+.|+
T Consensus        43 Ik~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~N~~~yNg~~s~~~~~A~~l~~d~~~el~Ei  106 (109)
T cd05492          43 IHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWLYRDTCHDLREL  106 (109)
T ss_pred             hCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            3349999999999999999999999999999999999999999999999999998887776653

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

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

Probab=99.48  E-value=1.2e-13  Score=104.32  Aligned_cols=57  Identities=30%  Similarity=0.430  Sum_probs=55.2

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHh
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ  155 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~  155 (256)
                      ||||++|++|+++  |.++++|.+|+.|||+||+.||+++|.+|.+|..|++.|.+++.
T Consensus        47 PmdL~tI~~kl~~--Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le~~~~~~~~  103 (106)
T cd05521          47 PLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKYINDVII  103 (106)
T ss_pred             CCCHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHhhc
Confidence            9999999999998  99999999999999999999999999999999999999988764

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.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.47  E-value=1.4e-13  Score=103.75  Aligned_cols=57  Identities=32%  Similarity=0.521  Sum_probs=55.7

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      ||||++|++|++++.|.++.+|..|+.+||.||+.||+++|.++.+|..|++.|++.
T Consensus        46 P~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~l~~~fe~~  102 (103)
T cd05500          46 PMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAFEKH  102 (103)
T ss_pred             CCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999865

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.

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.46  E-value=1.9e-13  Score=106.81  Aligned_cols=62  Identities=27%  Similarity=0.448  Sum_probs=59.1

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +.||||++|++|++++.|.+.++|..|+.|||.||+.||+++|.++..|..|++.|...+++
T Consensus        66 ~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~Na~~yN~~~s~i~~~A~~l~~~~~~~l~~  127 (128)
T cd05529          66 PVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRILSS  127 (128)
T ss_pred             CCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHhcc
Confidence            34999999999999999999999999999999999999999999999999999999988764

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.

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

Probab=99.46  E-value=1.9e-13  Score=103.12  Aligned_cols=57  Identities=44%  Similarity=0.622  Sum_probs=55.5

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      ||||++|++|++++.|.++.+|.+|+.+||.||+.||+++|.+|.+|..|++.|.+.
T Consensus        47 Pmdl~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l~~~f~~l  103 (104)
T cd05522          47 PISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKEARLL  103 (104)
T ss_pred             CcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999998864

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=99.40  E-value=1.5e-13  Score=132.02  Aligned_cols=94  Identities=30%  Similarity=0.481  Sum_probs=89.2

Q ss_pred             cccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHH
Q psy1225           3 PQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDA   82 (256)
Q Consensus         3 ~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A   82 (256)
                      .++.+...|..++||.+|+...+.||||++|++||||.||+.+|+.+.|..+++|.+|+.++|.||+.||++.+..+++|
T Consensus       613 ~il~~l~~h~~awPf~~Pv~~~e~pdyy~~I~~pmDl~tM~~~l~~~~y~~~~~f~ad~~~vf~ncr~yn~~~~~y~k~~  692 (720)
T KOG1472|consen  613 NILDQLQNHGDAWPFLKPVNKKEVPDYYDVIKHPMDLRTMQNRLKDNQYTEVELFMADVVRVFANCRMYNGSDTQYYKCA  692 (720)
T ss_pred             hHHhhhhcCCccCCccCccccccCCcHHHHhcccccHHHHhhhccccchhhHHHHHHHHHHHHhhhhccCCccchheecc
Confidence            46788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcc
Q psy1225          83 VKLQKLMQRKVQEN   96 (256)
Q Consensus        83 ~~L~~~f~~~~~kl   96 (256)
                      ..|...+..++...
T Consensus       693 ~~le~~~~~k~~~~  706 (720)
T KOG1472|consen  693 QALEKFFLFKLNEL  706 (720)
T ss_pred             cchhhhhcchhhhh
Confidence            99999988776544

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

Probab=99.37  E-value=1.8e-12  Score=93.74  Aligned_cols=51  Identities=41%  Similarity=0.821  Sum_probs=46.7

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHH
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVK  145 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~  145 (256)
                      +.||||++|++|+++|.|.++++|..|+.+||.||+.||+++|.+|.+|.+
T Consensus        34 ~~P~dL~~I~~kl~~~~Y~s~~~f~~Dv~~i~~Na~~yn~~~s~~~~~A~~   84 (84)
T PF00439_consen   34 KNPMDLSTIRKKLENGKYKSIEEFEADVRLIFQNARRYNPPDSPIYKAAEK   84 (84)
T ss_dssp             SSS--HHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHH
T ss_pred             hhccchhhhhHHhhccchhhHHHHHHHHHHHHHHHHHHCCCcCHHHHHhcC
Confidence            449999999999999999999999999999999999999999999999974

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 ....

>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2

Probab=99.36  E-value=8e-15  Score=113.69  Aligned_cols=81  Identities=10%  Similarity=0.050  Sum_probs=69.0

Q ss_pred             hhcCCccccccccHHH-----HHHHHHHHHHHhcCCCC-ccceeecccceeEe-------EEeecCcccccccCCCCCCc
Q psy1225         174 KKFNPADLRLYRDAVK-----LQKLMQRKVQEVMILDI-ECQVYLISDELTHY-------QVVLTGTAEQVRLSGLPDGD  240 (256)
Q Consensus       174 ~~yn~~~~~i~~~a~~-----l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-------ev~kt~~~~~~~~~~i~~~~  240 (256)
                      ..|+.++++..+.++.     +.+|.+.|....|..++ ++|||||++|.|..       |||+|+++.++|++.|+|+|
T Consensus         2 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~~d~~~~~~I~~kc   81 (121)
T cd04717           2 LQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKC   81 (121)
T ss_pred             CEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCceEEcCccccccHHHhcCee
Confidence            3466777777665554     45688889888898899 69999999998742       99999999999999999999


Q ss_pred             eeeeeecccccCCC
Q psy1225         241 WLAFTLPVVSGKAS  254 (256)
Q Consensus       241 ~v~f~~~~~~g~~~  254 (256)
                      .||++.-|.+|+|.
T Consensus        82 ~Vl~~~~y~~~~p~   95 (121)
T cd04717          82 AVMDVKDYIKGRPT   95 (121)
T ss_pred             EEEehHHHhcCCCC
Confidence            99999999999985

The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04369 Bromodomain Bromodomain

Probab=99.35  E-value=2.4e-12  Score=95.07  Aligned_cols=58  Identities=45%  Similarity=0.758  Sum_probs=55.9

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHH
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~  153 (256)
                      -||||++|+.|++++.|.++.+|.+|+.+||.||+.||+++|.++..|..|+..+.+.
T Consensus        41 ~P~~l~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~~n~~~~~~~~~a~~l~~~~~~~   98 (99)
T cd04369          41 NPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKL   98 (99)
T ss_pred             CcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHh
Confidence            3999999999999999999999999999999999999999999999999999998765

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

>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

Probab=99.28  E-value=9.4e-13  Score=103.74  Aligned_cols=65  Identities=6%  Similarity=-0.084  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHHhcCCCC-ccceeecccceeEe-------EEeecCcccccccCCCCCCceeeeeecccccCCC
Q psy1225         189 KLQKLMQRKVQEVMILDI-ECQVYLISDELTHY-------QVVLTGTAEQVRLSGLPDGDWLAFTLPVVSGKAS  254 (256)
Q Consensus       189 ~l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-------ev~kt~~~~~~~~~~i~~~~~v~f~~~~~~g~~~  254 (256)
                      -+.+|.+.|.+. |..|+ ++||||||+|.|.-       |||+|.+|.+.+++-|+|+|+||++..|.+.++.
T Consensus        54 ~vArIekiW~~~-G~~~~~grWy~rPEET~~gr~~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~~  126 (148)
T cd04718          54 WLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASND  126 (148)
T ss_pred             HHHHHHHHHhcc-CceEEEEEEEeCchhccCccccccccceeeeccccccccHHHHhcccEEcCHHHcccccCC
Confidence            467899999976 88899 69999999997773       9999999999999999999999999999987654

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG1828|consensus

Probab=99.27  E-value=8e-13  Score=117.45  Aligned_cols=137  Identities=19%  Similarity=0.180  Sum_probs=119.7

Q ss_pred             CccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHHHHH
Q psy1225          11 GNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ   90 (256)
Q Consensus        11 ~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~~f~   90 (256)
                      +.+-.-|.-|+-....|+|.++|+.|||+.|++.|+..+.|.++.+|..|.+++..||..||.....++..|+.|..+..
T Consensus        34 Kdp~q~fafplt~~map~y~~iis~Pmd~~t~r~kidd~~yl~L~~m~~d~kl~~~na~~yn~~~Tv~~~aaKrL~~v~~  113 (418)
T KOG1828|consen   34 KDPKQKFAFPLTDKMAPNYLEIISEPMDRITKRSKIDDTRYLVLSQMEFDRKLPDGNATLYNLHPTVPIVAAKRLCPVRL  113 (418)
T ss_pred             cChhhhhccccchhhccchHhhhhcccccccccccCCCccceechhhhhhhcccccchhhhhcCCccccccccccchhhc
Confidence            33445566666667789999999999999999999999999999999999999999999999999999999998876544


Q ss_pred             HHHhcc--------------------------------------------------------------------------
Q psy1225          91 RKVQEN--------------------------------------------------------------------------   96 (256)
Q Consensus        91 ~~~~kl--------------------------------------------------------------------------   96 (256)
                      ....+-                                                                          
T Consensus       114 ~~~qe~~l~f~~~slg~y~~~rn~~~~v~~la~~~~sr~~~~d~~a~~s~ee~~l~v~~~e~~~~~~~~fs~k~~e~~~e  193 (418)
T KOG1828|consen  114 GMTQERLLSFVNTSLGFYEDKRNKVTPVLYLAYGPYSRYHYDDTFANISKEESDLIVSTYEEDSDLPSDFSHKFLETCQE  193 (418)
T ss_pred             chhhHHHHHhhhcccchhhhcccccCceeeeccCCccchhhhhhcCCCcccccccccccccccccccccccccccccCcc
Confidence            332211                                                                          


Q ss_pred             ------------------------------------------------------cccHHHHHHHhhcCCCCCHHHHHHHH
Q psy1225          97 ------------------------------------------------------PRSLLTIGKTLKSGHYSTLNELTGEL  122 (256)
Q Consensus        97 ------------------------------------------------------P~dl~~I~~kl~~~~Y~s~~~f~~D~  122 (256)
                                                                            |++.+|.+.+..++.|.| -+|..|.
T Consensus       194 ~~~~lgds~g~lqtg~~~l~~~q~~kl~~~~p~~~lnyg~tas~aP~YSm~Ik~~~~~~Tygdk~~andy~S-~~f~~D~  272 (418)
T KOG1828|consen  194 RVVTLGDSVGDLQTGGQQLQTLQEDKLNRVDPVAYLNYGPTASFAPGYSMTITEVEPPGTYGDKSSANDYES-LSFTQDR  272 (418)
T ss_pred             ceEehhhhhhhhccccHHHHHHHHHHhcccCchhhhcccchhhhcccccccccccCCCcchhhhhhhhhhhh-hhhhccc
Confidence                                                                  678889999999999999 8999999


Q ss_pred             HHHHHhhhhhCCCCCHHHHHHHHHHH
Q psy1225         123 NLMFENAKKFNPADSRLYRDAVKLQK  148 (256)
Q Consensus       123 ~lmf~Na~~yN~~~s~i~~~a~~L~~  148 (256)
                      .+|+.||.+||++....|+.|..+..
T Consensus       273 kl~~l~amT~gehsk~yyelank~lh  298 (418)
T KOG1828|consen  273 KLIALKAVTNGEHSKSYYELANKQLH  298 (418)
T ss_pred             chhhHHHHhcCCcchHHHHHHHhhhh
Confidence            99999999999999999999887665

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

Probab=99.24  E-value=2.5e-11  Score=111.34  Aligned_cols=66  Identities=42%  Similarity=0.700  Sum_probs=62.0

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCChhhh
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNEL  162 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~~~~~  162 (256)
                      ||+|.+|+++|++++|.++++|..|+.|||+||+.||+++|.+|.+|..|++.+...++.+.....
T Consensus       188 Pm~L~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~~~~~i~~~~~~~~  253 (371)
T COG5076         188 PMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEML  253 (371)
T ss_pred             hhhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHHHHHHHHHHhccccch
Confidence            999999999999999999999999999999999999999999999999999999999987544443

>KOG0386|consensus

Probab=99.23  E-value=8.1e-12  Score=122.25  Aligned_cols=90  Identities=41%  Similarity=0.723  Sum_probs=86.4

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..|+++++.|..+|+++.+||||.+|+.|+++..|.+++.++.|.+..+...|+.++|.||+.||..+|.+|.+|..|+
T Consensus      1041 ~~~~r~~~~~~~~~~s~k~~~d~~~~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~na~~~~~egs~~y~d~~~l~ 1120 (1157)
T KOG0386|consen 1041 DSAGRELSEVFLKLPSRKEYPDYYEIIKKPVAIDKIKKRIENHKYNSLKELEKDFMLLFNNARTYNEEGSRVYEDAIVLQ 1120 (1157)
T ss_pred             cccccccchhcccCcccccccchHHHhcchhhHHHHhhhccccccchHHHHHHHHHhhcchhhhhccCCceechhHHHHH
Confidence            44699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      .++.....++
T Consensus      1121 ~~~~~~~~~~ 1130 (1157)
T KOG0386|consen 1121 SVFKSARQEI 1130 (1157)
T ss_pred             HHHhhhHHHH
Confidence            9998877766

>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins

Probab=99.18  E-value=2.2e-13  Score=105.60  Aligned_cols=79  Identities=4%  Similarity=-0.041  Sum_probs=65.6

Q ss_pred             hcCCccccccccHHH-----HHHHHHHHHHHhcCCCC-ccceeecccceeEe-------EEeecCcccccccCCCCCCce
Q psy1225         175 KFNPADLRLYRDAVK-----LQKLMQRKVQEVMILDI-ECQVYLISDELTHY-------QVVLTGTAEQVRLSGLPDGDW  241 (256)
Q Consensus       175 ~yn~~~~~i~~~a~~-----l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-------ev~kt~~~~~~~~~~i~~~~~  241 (256)
                      .|+.+|++..+.+..     +.+|.+.|.+.+|..++ ++|||||++|.|..       |||+|+++.++|++.|+|+|.
T Consensus         3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S~~~d~~~~~~I~gkc~   82 (121)
T cd04714           3 IIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHKCY   82 (121)
T ss_pred             EEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcccccCCCCceEecCCcccccHHHhCcccE
Confidence            456667776665443     34578888877788888 69999999997652       999999999999999999999


Q ss_pred             eeeeecccccCC
Q psy1225         242 LAFTLPVVSGKA  253 (256)
Q Consensus       242 v~f~~~~~~g~~  253 (256)
                      |+++..|.++++
T Consensus        83 V~~~~ey~~~~~   94 (121)
T cd04714          83 VLTFAEYERLAR   94 (121)
T ss_pred             EEehhHheeccc
Confidence            999999999885

BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG0008|consensus

Probab=99.17  E-value=4.5e-12  Score=126.57  Aligned_cols=130  Identities=28%  Similarity=0.380  Sum_probs=113.5

Q ss_pred             cccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHH
Q psy1225           5 KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVK   84 (256)
Q Consensus         5 ~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~   84 (256)
                      +.....-+-|++|.++++++..|+||.+|++||||.+|.+++....|.+.+||.+|+++|+.|+..||++++.....|+.
T Consensus      1391 vs~~~~ipes~~f~~~v~~k~~~~yy~kik~pmdl~~i~~n~~~~~y~s~~e~l~dv~~i~~n~~~~ng~e~~y~~k~~k 1470 (1563)
T KOG0008|consen 1391 VSQMKEIPESWPFHEPVNKKRVPDYYKKIKNPMDLETILKNIPPHKYDSRSEFLDDVNLIYVNSVEYNGAESAYTKKARK 1470 (1563)
T ss_pred             HHHHHhcchhcccccccchhhchHHHHHhcChhhHHHHhhcCCccccccHHHHhhhhHhhcccceeecCccccccHHHHH
Confidence            33456678899999999999999999999999999999999999999999999999999999999999999988888877


Q ss_pred             HHHHHHHHHhcc-------------------------------cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhC
Q psy1225          85 LQKLMQRKVQEN-------------------------------PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN  133 (256)
Q Consensus        85 L~~~f~~~~~kl-------------------------------P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN  133 (256)
                      +-.+....+.+.                               |+|+.||..++..-.|.+-.+|..|+..+=.|+-.|-
T Consensus      1471 ~~ev~~~~~~e~~~~~~~le~~is~~~~~a~~~~ea~~~dd~~~~d~~t~~d~~~d~e~~~~~~~~~~~~q~~~n~~~~~ 1550 (1563)
T KOG0008|consen 1471 IGEVGLANLLEYIEHLLQLEENISTLFEAAVEKAEAPDYDDIVPGDLSTIPDDVRDTEYSDSMQRDADVWQIKSNAHVYD 1550 (1563)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCCccccCCCCCCCCcchhhccccchhhhcccceeeecccccccc
Confidence            666544433222                               8999999999999999999999999999888887773


Q ss_pred             C
Q psy1225         134 P  134 (256)
Q Consensus       134 ~  134 (256)
                      +
T Consensus      1551 g 1551 (1563)
T KOG0008|consen 1551 G 1551 (1563)
T ss_pred             C
Confidence            3

>KOG1827|consensus

Probab=99.17  E-value=4.3e-11  Score=113.53  Aligned_cols=140  Identities=26%  Similarity=0.212  Sum_probs=108.7

Q ss_pred             HHHHHHHHHHHHhhhCCCCchhHHHHHHHHHHHHHHHhcc----------------------------------------
Q psy1225          57 LTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEN----------------------------------------   96 (256)
Q Consensus        57 f~~D~~li~~Na~~yN~~~S~i~~~A~~L~~~f~~~~~kl----------------------------------------   96 (256)
                      .++|+.+|..|+..||++.+.+++.+..+++...+.....                                        
T Consensus         2 ~~~df~l~~e~~~~~~~p~s~p~k~~~~~~~~~~~~k~~~~~~d~p~i~~~~~~~f~~il~~~~~~~d~~gk~~~d~fek   81 (629)
T KOG1827|consen    2 VVADFPLMTENACSDNEPDSLPGKDAKNLQKTPLHDKTLMGRDDSPVIDPPLIPKFKTILASLLDLKDDEGKQLFDKFEK   81 (629)
T ss_pred             chhhhhHHhhccccccCCccccccCcchhhhchhhhhcccCCCCccccChHHHHHHHHHHHHHHhhccccCcccchhHhh
Confidence            3679999999999999999999999988877655444111                                        


Q ss_pred             ----------------cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHh-cCCh
Q psy1225          97 ----------------PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ-EFSL  159 (256)
Q Consensus        97 ----------------P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~-~~~~  159 (256)
                                      ||+|..|++|++.++|.+.+.|..|+.+|++||+.||.++|.+|+++..|+..|..+.. ..+.
T Consensus        82 lp~~~~~p~yy~~i~~pisl~~ik~kv~k~~y~~~~~f~~D~~lm~ena~~~n~~ds~~~~~s~~l~~~~~~~~~~~~d~  161 (629)
T KOG1827|consen   82 LPSRKEFPEYYYVIQQPISLDQIKRKVKKGRYKRLSFFQLDFLLMTENARLYNRPDSLIYKDSGELEKYFISLEDEKKDG  161 (629)
T ss_pred             ccccccCCCcceeecCcccHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhcCcchhhhhhhhhhhcchhhhhccccch
Confidence                            89999999999999999999999999999999999999999999999999999887554 2233


Q ss_pred             hhhhchhhhhhccchhcCCccccccccHHHHHHHHHHHHHHhcCCCC-ccceee
Q psy1225         160 NELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDI-ECQVYL  212 (256)
Q Consensus       160 ~~~~~d~~~~~~n~~~yn~~~~~i~~~a~~l~~i~~~~~~~~g~~~~-~c~y~r  212 (256)
                      +....+...+-..+-+|++.+-                ...+|...+ +||+|.
T Consensus       162 e~s~~~~~~l~~~~l~~~~~~~----------------~~i~~~~~~~gd~vlv  199 (629)
T KOG1827|consen  162 ELSMESNEELKAGGLHYHELGP----------------VEIDGTKYIVGDYVLV  199 (629)
T ss_pred             hhccccccccccCCCCcccCCC----------------ccccCcccccCceeee
Confidence            4333343333333344444332                233477777 699987

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=99.09  E-value=1.1e-10  Score=88.69  Aligned_cols=41  Identities=22%  Similarity=0.319  Sum_probs=39.3

Q ss_pred             CcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy1225          35 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD   75 (256)
Q Consensus        35 ~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~   75 (256)
                      .||||+||++||.+|.|.++++|++|+++||.||+.||.++
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            68999999999999999999999999999999999999863

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.

>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins

Probab=99.07  E-value=3.3e-12  Score=103.07  Aligned_cols=85  Identities=11%  Similarity=0.011  Sum_probs=69.3

Q ss_pred             ccchhcCCccccccccHHH---HHHHHHHHHHHh--cCCCC-ccceeecccceeE---------eEEeec-----Ccccc
Q psy1225         171 ENAKKFNPADLRLYRDAVK---LQKLMQRKVQEV--MILDI-ECQVYLISDELTH---------YQVVLT-----GTAEQ  230 (256)
Q Consensus       171 ~n~~~yn~~~~~i~~~a~~---l~~i~~~~~~~~--g~~~~-~c~y~rpeqt~h~---------~ev~kt-----~~~~~  230 (256)
                      .++..|+.+|++.++..+.   +.+|.+.|...+  |..++ ++|||||++|.+.         .|||+|     |++.+
T Consensus        25 ~~g~~y~lGD~Vlv~s~~~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~~~~~~~~~~~~nEvFlS~~~d~~~~~~  104 (159)
T cd04715          25 YDGVEYRLYDDVYVHNGDSEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIRMELKGEPKRHINEVFLACGRGEGLANI  104 (159)
T ss_pred             ECCEEEeCCCEEEEeCCCCCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhccccccCcccCCCcEEEecCcCcccccc
Confidence            3667899999998886542   234788887765  88888 6999999999631         299999     56799


Q ss_pred             cccCCCCCCceeeeeecccccCCCC
Q psy1225         231 VRLSGLPDGDWLAFTLPVVSGKASS  255 (256)
Q Consensus       231 ~~~~~i~~~~~v~f~~~~~~g~~~~  255 (256)
                      +|++.|+|+|.|++++.|+|.-|-|
T Consensus       105 n~l~sI~gKC~Vl~~~ey~~~~~~s  129 (159)
T cd04715         105 NLLESIIGKCNVVCISEDFRNPQPS  129 (159)
T ss_pred             CcHHHccceeEEEEehHhhhCCCCc
Confidence            9999999999999999999988764

Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=99.00  E-value=3.9e-10  Score=85.63  Aligned_cols=40  Identities=23%  Similarity=0.338  Sum_probs=38.8

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCC
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD  136 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~  136 (256)
                      ||||+||++||.+|.|.++++|..|++|||+||+.||.++
T Consensus        64 ~MDL~tIe~RL~ng~Y~tp~~F~~DiklI~~Nc~~ynd~d  103 (119)
T cd05491          64 NMDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKTIGDRE  103 (119)
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCHH
Confidence            9999999999999999999999999999999999999774

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.

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=98.91  E-value=2.6e-10  Score=87.29  Aligned_cols=69  Identities=19%  Similarity=0.095  Sum_probs=51.6

Q ss_pred             cccccCCccccccccCCCC--CCCcchhhhcCCcCcHHHHHHHHhcCCC-------CCHHHHHHHHHHHHHHHhhhCC
Q psy1225           5 KNQTEGGNLSEPFLKLPAK--RYNPDYYRIIKNPRSLLTIGKTLKSGHY-------STLNELTGELNLMFENAKKFNP   73 (256)
Q Consensus         5 ~~~~~~~~~s~~F~~~p~~--~~~pdYy~~I~~PmdL~tI~~kl~~~~Y-------~~~~ef~~D~~li~~Na~~yN~   73 (256)
                      +.....++.++||..||+.  ...||||++|++||||+||+++|.++.+       ..-....++...+..|+-.+|.
T Consensus        12 l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (114)
T cd05494          12 LKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGRRSPSNI   89 (114)
T ss_pred             HHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHccccccccccccccccccccccccccccCcccc
Confidence            4445567899999999998  8899999999999999999999998744       3333444455555555554444

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

>KOG0955|consensus

Probab=98.83  E-value=3.1e-09  Score=106.53  Aligned_cols=94  Identities=29%  Similarity=0.493  Sum_probs=85.3

Q ss_pred             cccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHH
Q psy1225           3 PQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDA   82 (256)
Q Consensus         3 ~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A   82 (256)
                      ..+....-......|..|++...+|||.++|++|||+.+++.++.+|.|+++++|..|+.+|+.||..||..+...+++|
T Consensus       572 ~~l~~lq~kD~~gif~~pvd~~e~pdy~~iik~pmd~~t~~~kl~s~~y~tle~ieed~~l~~~nc~~yn~~dtv~~r~a  651 (1051)
T KOG0955|consen  572 KSLDKLQKKDSYGIFAEPVDPSELPDYIDIIKKPMDFFTMRLKLESGAYSTLEPIEEDVNLIVSNCMEYNAKDTVYYRAA  651 (1051)
T ss_pred             HHHHHhhcccccCceeeccChhhcccHHHHhcCccchhhhhhhccccchhhhhHHHHhHhHhHhHHHHhhccCeehHhhh
Confidence            34455556667788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcc
Q psy1225          83 VKLQKLMQRKVQEN   96 (256)
Q Consensus        83 ~~L~~~f~~~~~kl   96 (256)
                      ..+++.....+.+.
T Consensus       652 v~~~e~~~~~~~~a  665 (1051)
T KOG0955|consen  652 VRLRELIKKDFRNA  665 (1051)
T ss_pred             HHHHhhhhhHHHhc
Confidence            99999887776555

>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif)

Probab=98.77  E-value=1.8e-10  Score=88.53  Aligned_cols=79  Identities=6%  Similarity=0.001  Sum_probs=63.8

Q ss_pred             hhcCCccccccccHHH-------HHHHHHHHHHHhcCCCC-ccceeecccceeE-------eEEeecCcccccccCCCCC
Q psy1225         174 KKFNPADLRLYRDAVK-------LQKLMQRKVQEVMILDI-ECQVYLISDELTH-------YQVVLTGTAEQVRLSGLPD  238 (256)
Q Consensus       174 ~~yn~~~~~i~~~a~~-------l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~-------~ev~kt~~~~~~~~~~i~~  238 (256)
                      ..|+.++++.....+.       +.+|.+.|....|..++ ++|||||++|.|.       .|||.|....++|++.|.|
T Consensus         2 ~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~v~~I~g   81 (123)
T cd04370           2 ITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIG   81 (123)
T ss_pred             CEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCccccCHHHhcc
Confidence            4566666666554443       34577777777788888 6899999999764       3999999999999999999


Q ss_pred             CceeeeeecccccC
Q psy1225         239 GDWLAFTLPVVSGK  252 (256)
Q Consensus       239 ~~~v~f~~~~~~g~  252 (256)
                      +|-|++...+..++
T Consensus        82 kc~V~~~~~~~~~~   95 (123)
T cd04370          82 KCKVLFVSEFEGLK   95 (123)
T ss_pred             ccEEEechHhhccc
Confidence            99999999998875

BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.

>smart00439 BAH Bromo adjacent homology domain

Probab=98.60  E-value=9e-10  Score=84.59  Aligned_cols=65  Identities=9%  Similarity=-0.021  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHhcC-CCC-ccceeecccceeE-------eEEeecCcccccccCCCCCCceeeeeecccccCCC
Q psy1225         190 LQKLMQRKVQEVMI-LDI-ECQVYLISDELTH-------YQVVLTGTAEQVRLSGLPDGDWLAFTLPVVSGKAS  254 (256)
Q Consensus       190 l~~i~~~~~~~~g~-~~~-~c~y~rpeqt~h~-------~ev~kt~~~~~~~~~~i~~~~~v~f~~~~~~g~~~  254 (256)
                      +.+|.+.|....|. .++ ++|||||++|.|.       .|||.|....+.+++.|+|+|.|++...|..+++.
T Consensus        21 i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~~~~I~~kc~V~~~~~~~~~~~~   94 (120)
T smart00439       21 IGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKCNVLSKSDYPGLRPE   94 (120)
T ss_pred             EEEEEEEEECCCCCEEEEEEEEEEChhhccccccccCCCcceEEEccCccCChHHeeeEEEEEEcchhcccccc
Confidence            34566677777777 688 6899999999654       29999999999999999999999999999887764

>KOG1245|consensus

Probab=98.53  E-value=2e-07  Score=97.00  Aligned_cols=58  Identities=26%  Similarity=0.537  Sum_probs=56.4

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHh
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ  155 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~  155 (256)
                      ||||+||+.|+..|.|.+.++|..|+.|||.||..||+. |.+++.+..|.++|+.+++
T Consensus      1341 Pmdl~tir~k~~~~~Y~~~eef~~Di~lvf~Nc~~yN~~-s~i~~ag~~l~~ff~~~~~ 1398 (1404)
T KOG1245|consen 1341 PMDLSTIREKLSKGIYPSPEEFATDIELVFDNCETYNED-SEIGRAGTCLRRFFHKRWR 1398 (1404)
T ss_pred             hhHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHhccc-hhhhhhcchHHHHHHHHHH
Confidence            999999999999999999999999999999999999999 9999999999999998765

>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

Probab=98.33  E-value=7.3e-09  Score=82.80  Aligned_cols=78  Identities=13%  Similarity=0.033  Sum_probs=61.4

Q ss_pred             cchhcCCccccccccHHH----HHHHHHHHHHHhcCCCC-ccceeecccceeE----------eEEeecCcccccccCCC
Q psy1225         172 NAKKFNPADLRLYRDAVK----LQKLMQRKVQEVMILDI-ECQVYLISDELTH----------YQVVLTGTAEQVRLSGL  236 (256)
Q Consensus       172 n~~~yn~~~~~i~~~a~~----l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~----------~ev~kt~~~~~~~~~~i  236 (256)
                      ++..|+.++.+....+..    +.+|.+.|...+|...+ ++|||||+++.+.          .|||.|.+.-+.|++.|
T Consensus        17 dg~~y~vgD~Vlv~~~~~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~~ElF~S~~~d~~~~~~I   96 (146)
T cd04713          17 DGNKYRLEDCVLLVPEDDQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDPRELFYSFHRDEVPAESV   96 (146)
T ss_pred             CCEEEECCCEEEEeCCCCCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCCCeEEEeCCCCcCCHHHC
Confidence            556788888887664332    23466667666677788 6899999999532          39999999999999999


Q ss_pred             CCCceeeeeeccc
Q psy1225         237 PDGDWLAFTLPVV  249 (256)
Q Consensus       237 ~~~~~v~f~~~~~  249 (256)
                      +|+|.|+++..+.
T Consensus        97 ~gkc~V~~~~~~~  109 (146)
T cd04713          97 LHPCKVAFVPKGK  109 (146)
T ss_pred             cceeEEEECCccc
Confidence            9999999988776

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1

Probab=98.31  E-value=1.5e-07  Score=73.69  Aligned_cols=60  Identities=12%  Similarity=-0.032  Sum_probs=52.7

Q ss_pred             HHHHHHHHHHHhcCCCC-ccceeecccceeEe-----EEeecCcccccccC----CCCCCceeeeeeccc
Q psy1225         190 LQKLMQRKVQEVMILDI-ECQVYLISDELTHY-----QVVLTGTAEQVRLS----GLPDGDWLAFTLPVV  249 (256)
Q Consensus       190 l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-----ev~kt~~~~~~~~~----~i~~~~~v~f~~~~~  249 (256)
                      +++|...|...+|.+.+ ..|||||++|++..     |||+|.++.+.+++    +|+++|.|.|+.++-
T Consensus        35 i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~~~~~~ElFLSd~c~~~~~~~~~~~I~~k~~V~~~~~~~  104 (130)
T cd04712          35 VQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGNYANERELFLTNECTCLELDLLSTEIKGVHKVDWSGTPW  104 (130)
T ss_pred             EEEEEEeeecCCCceEEEEEEEEcchhccccccCCCceEEEeccccccccccccceeEEEEEEEEecCcC
Confidence            34567778888898888 68999999998885     99999999999999    999999999987764

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants

Probab=98.28  E-value=1.7e-08  Score=78.06  Aligned_cols=62  Identities=13%  Similarity=-0.021  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHHhcCCCC-ccceeecccceeE--------eEEeecCcccccccCCCCCCceeeeeeccccc
Q psy1225         190 LQKLMQRKVQEVMILDI-ECQVYLISDELTH--------YQVVLTGTAEQVRLSGLPDGDWLAFTLPVVSG  251 (256)
Q Consensus       190 l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~--------~ev~kt~~~~~~~~~~i~~~~~v~f~~~~~~g  251 (256)
                      +.+|.+.|...+|..++ +-||||||+|++-        -|||.|....+-|++-|++||.|+.+..+..-
T Consensus        22 i~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~~~D~~pl~~I~~Kc~V~~~~~~~~~   92 (122)
T cd04716          22 ICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQATNHDKKRVFYSEIKNDNPLDCLISKVKILQVPPNVGT   92 (122)
T ss_pred             EEEEEEEEEcCCCceEEEEEEEEcHHHhccccccccCCCceEEEecccCccchhheeeeeEEEEeCCCCCc
Confidence            44577778777888888 5699999998543        19999999999999999999999998877654

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins

Probab=98.27  E-value=1.9e-07  Score=72.12  Aligned_cols=57  Identities=11%  Similarity=0.011  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHhcCCCC-ccceeecccceeEe-----EEeecCcccccccCCCCCCceeeeee
Q psy1225         190 LQKLMQRKVQEVMILDI-ECQVYLISDELTHY-----QVVLTGTAEQVRLSGLPDGDWLAFTL  246 (256)
Q Consensus       190 l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-----ev~kt~~~~~~~~~~i~~~~~v~f~~  246 (256)
                      +.+|-..|.+.+|.+.+ +||||||++||...     |||+|..+.+.++++|.++|.|.+-.
T Consensus        23 I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~~~~~kEvFlsd~c~d~~l~~I~~Kv~V~~~~   85 (124)
T cd04760          23 IARVTYMWKDSIGGKMFHAHWFCRGSDTVLGETSDPLELFLVDECEDMALSSIHGKVNVIYKA   85 (124)
T ss_pred             EEEEhhheecCCCCcEEEEEEEEECCcccccccCCCcEEEeecccCCcchHHheeeeEEEEeC
Confidence            34577888888899888 79999999998775     99999999999999999999998754

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation

Probab=98.22  E-value=3.4e-09  Score=81.30  Aligned_cols=62  Identities=5%  Similarity=-0.071  Sum_probs=49.9

Q ss_pred             HHHHHHHHhcC--CCC-ccceeecccceeE-----eEEeecCcccccccCCCCCCceeeeeecccccCCC
Q psy1225         193 LMQRKVQEVMI--LDI-ECQVYLISDELTH-----YQVVLTGTAEQVRLSGLPDGDWLAFTLPVVSGKAS  254 (256)
Q Consensus       193 i~~~~~~~~g~--~~~-~c~y~rpeqt~h~-----~ev~kt~~~~~~~~~~i~~~~~v~f~~~~~~g~~~  254 (256)
                      |.+.|....+.  .++ .+|||||++|.+.     .|||.|.+..++|++.|.|+|.|++...|..+++.
T Consensus        25 I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~~~~~~~~Elf~s~~~~~~~~~~I~gkc~V~~~~~~~~~~~~   94 (119)
T PF01426_consen   25 IEEIWEDKDGNKEKMVKVRWFYRPEDTSLGKTFSPRELFLSDHCDDIPVESIRGKCNVLHLEDYEQARPY   94 (119)
T ss_dssp             EEEEEEETTTSEEEEEEEEEEEEGGGSTTGGHSCTTEEEEEEEEEEEEGGGEEEEEEEEEHHHHTTGCCH
T ss_pred             EEEEEcCCCCCEEEEEEEEEeECcccccccccCCCCEEEEECcEeEEehhhEEeeeEEEECCcccccccc
Confidence            44445555555  577 6899999999222     39999999999999999999999999999887753

The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....

>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

Probab=97.91  E-value=1e-06  Score=69.01  Aligned_cols=82  Identities=4%  Similarity=-0.135  Sum_probs=61.2

Q ss_pred             cchhcCCccccccccHH---HHHHHHHHHHHHhcCCCC-ccceeecccceeE--------eEEeecCcccccccCCCCCC
Q psy1225         172 NAKKFNPADLRLYRDAV---KLQKLMQRKVQEVMILDI-ECQVYLISDELTH--------YQVVLTGTAEQVRLSGLPDG  239 (256)
Q Consensus       172 n~~~yn~~~~~i~~~a~---~l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~--------~ev~kt~~~~~~~~~~i~~~  239 (256)
                      |+..++.++.+..+.+.   -+.+|-+.|.+.+|..++ ++||+||++|.|.        .|||+|-++.+.|++.|+|+
T Consensus         4 ~~~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~~~d~i~~~~I~gk   83 (130)
T cd04721           4 NGVTISVHDFVYVLSEEEDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREIFLSPNLQVISVECIDGL   83 (130)
T ss_pred             CCEEEECCCEEEEeCCCCCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeEEEcCCccccchHHeeee
Confidence            34445555555444221   133466678777888888 5899999998662        29999999999999999999


Q ss_pred             ceeeeeecccccCC
Q psy1225         240 DWLAFTLPVVSGKA  253 (256)
Q Consensus       240 ~~v~f~~~~~~g~~  253 (256)
                      |.||..-.|..-.+
T Consensus        84 ~~Vls~~~y~k~~~   97 (130)
T cd04721          84 ATVLTREHYEKFQS   97 (130)
T ss_pred             eEECCHHHHhhhhc
Confidence            99999877776553

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG1828|consensus

Probab=97.64  E-value=2.5e-05  Score=70.22  Aligned_cols=77  Identities=17%  Similarity=0.131  Sum_probs=68.0

Q ss_pred             CCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHH
Q psy1225          10 GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK   87 (256)
Q Consensus        10 ~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~   87 (256)
                      .......|..+|-....|.|..+|++|++.+|.+.|..++.|.| -+|..|+.+|+.||.+||+++...|..|+.+..
T Consensus       222 ~~~p~~~lnyg~tas~aP~YSm~Ik~~~~~~Tygdk~~andy~S-~~f~~D~kl~~l~amT~gehsk~yyelank~lh  298 (418)
T KOG1828|consen  222 RVDPVAYLNYGPTASFAPGYSMTITEVEPPGTYGDKSSANDYES-LSFTQDRKLIALKAVTNGEHSKSYYELANKQLH  298 (418)
T ss_pred             ccCchhhhcccchhhhcccccccccccCCCcchhhhhhhhhhhh-hhhhcccchhhHHHHhcCCcchHHHHHHHhhhh
Confidence            33445566677777788999999999999999999999999999 999999999999999999999998888887655

>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins

Probab=97.55  E-value=1e-05  Score=65.66  Aligned_cols=57  Identities=7%  Similarity=0.012  Sum_probs=45.7

Q ss_pred             HHHHHHHHHhcCCCC-ccceeecccce--------------------------eEe---EEeecCcccccccCCCCCCce
Q psy1225         192 KLMQRKVQEVMILDI-ECQVYLISDEL--------------------------THY---QVVLTGTAEQVRLSGLPDGDW  241 (256)
Q Consensus       192 ~i~~~~~~~~g~~~~-~c~y~rpeqt~--------------------------h~~---ev~kt~~~~~~~~~~i~~~~~  241 (256)
                      +|.+.|....|..++ ++|||||+++.                          |.+   |||+|.++...|++-|.|||-
T Consensus        24 rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~~rELF~S~~~d~~p~~~IrGKC~  103 (164)
T cd04709          24 RIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLRHRELFLSRQVETLPATHIRGKCS  103 (164)
T ss_pred             EEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccCcceeEEecccccccHHHeeeeEE
Confidence            455556666777777 57999999852                          112   999999999999999999999


Q ss_pred             eeeeecc
Q psy1225         242 LAFTLPV  248 (256)
Q Consensus       242 v~f~~~~  248 (256)
                      |+++.-|
T Consensus       104 V~~~~d~  110 (164)
T cd04709         104 VTLLNDT  110 (164)
T ss_pred             EEEehhh
Confidence            9988755

The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG0386|consensus

Probab=97.50  E-value=8.2e-05  Score=74.16  Aligned_cols=62  Identities=35%  Similarity=0.622  Sum_probs=59.0

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCC
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFS  158 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~  158 (256)
                      |+++..|++++.++.|.+..+...|+.++|.||+.||+++|.+|.+|..|++++.....+++
T Consensus      1070 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~na~~~~~egs~~y~d~~~l~~~~~~~~~~~~ 1131 (1157)
T KOG0386|consen 1070 PVAIDKIKKRIENHKYNSLKELEKDFMLLFNNARTYNEEGSRVYEDAIVLQSVFKSARQEIS 1131 (1157)
T ss_pred             hhhHHHHhhhccccccchHHHHHHHHHhhcchhhhhccCCceechhHHHHHHHHhhhHHHHh
Confidence            99999999999999999999999999999999999999999999999999999988777653

>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants

Probab=97.11  E-value=0.00018  Score=60.06  Aligned_cols=44  Identities=9%  Similarity=-0.010  Sum_probs=37.2

Q ss_pred             cceeecccceeE-------eEEeecCcccccccCCCCCCceeeeeeccccc
Q psy1225         208 CQVYLISDELTH-------YQVVLTGTAEQVRLSGLPDGDWLAFTLPVVSG  251 (256)
Q Consensus       208 c~y~rpeqt~h~-------~ev~kt~~~~~~~~~~i~~~~~v~f~~~~~~g  251 (256)
                      =||||||+|+-.       .||+-|+.+.+.|++-|.|+|.|.+..-+..-
T Consensus        69 rwFYRPEdt~~~~~y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~  119 (202)
T cd04708          69 RRFYRPEDVSPEKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDS  119 (202)
T ss_pred             EEEechhhcCcccceecCceeEEEeccceeechhHcceEEEEEecCcchhh
Confidence            499999999332       19999999999999999999999988766443

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p

Probab=97.01  E-value=8.1e-05  Score=58.02  Aligned_cols=75  Identities=8%  Similarity=-0.039  Sum_probs=52.0

Q ss_pred             cCCccccccccHH----HHHHHHHHHHHHhcCCCC----ccceeecccce--------eEe---EEeecCccc---cccc
Q psy1225         176 FNPADLRLYRDAV----KLQKLMQRKVQEVMILDI----ECQVYLISDEL--------THY---QVVLTGTAE---QVRL  233 (256)
Q Consensus       176 yn~~~~~i~~~a~----~l~~i~~~~~~~~g~~~~----~c~y~rpeqt~--------h~~---ev~kt~~~~---~~~~  233 (256)
                      +..++.++.+.++    -+++|.+.+....|.+..    +=|||||++--        .+.   |||+|.++.   +..+
T Consensus         4 i~vGd~VlI~~~d~~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~~~~~~EvF~~~~~~~~~~i~~   83 (128)
T cd04719           4 IEVGDFVLIEGEDADGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGREPHSQEVFFYSRSSCDNDIDA   83 (128)
T ss_pred             EecCCEEEEECCCCCCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccCCCCCcEEEEecCccccCcEeH
Confidence            4445555555444    356677777665552222    24999999441        222   999999986   9999


Q ss_pred             CCCCCCceeeeeecccc
Q psy1225         234 SGLPDGDWLAFTLPVVS  250 (256)
Q Consensus       234 ~~i~~~~~v~f~~~~~~  250 (256)
                      +-|+|+|.|+.+..|..
T Consensus        84 etI~gkc~V~~~~~y~~  100 (128)
T cd04719          84 ETIIGKVRVEPVEPKTD  100 (128)
T ss_pred             HHcccEEEEEEcCCccc
Confidence            99999999999988864

Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG0955|consensus

Probab=96.98  E-value=0.00075  Score=68.65  Aligned_cols=59  Identities=34%  Similarity=0.660  Sum_probs=55.6

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHh
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ  155 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~  155 (256)
                      |||+.+++.++.++.|.++++|..|+.+|..||..||..+.-.|+.|..+++.....+.
T Consensus       605 pmd~~t~~~kl~s~~y~tle~ieed~~l~~~nc~~yn~~dtv~~r~av~~~e~~~~~~~  663 (1051)
T KOG0955|consen  605 PMDFFTMRLKLESGAYSTLEPIEEDVNLIVSNCMEYNAKDTVYYRAAVRLRELIKKDFR  663 (1051)
T ss_pred             ccchhhhhhhccccchhhhhHHHHhHhHhHhHHHHhhccCeehHhhhHHHHhhhhhHHH
Confidence            99999999999999999999999999999999999999999999999999987766554

>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins

Probab=96.60  E-value=0.0011  Score=51.84  Aligned_cols=37  Identities=8%  Similarity=0.025  Sum_probs=32.4

Q ss_pred             ccceeeccccee-------E--eEEeecCcccccccCCCCCCceee
Q psy1225         207 ECQVYLISDELT-------H--YQVVLTGTAEQVRLSGLPDGDWLA  243 (256)
Q Consensus       207 ~c~y~rpeqt~h-------~--~ev~kt~~~~~~~~~~i~~~~~v~  243 (256)
                      +-||||||+|--       .  .||+-|.+....|++.|-|||-|.
T Consensus        54 V~~fYRPEdi~~g~~~ayhsDirevy~Sd~~~~~~~~~I~GKC~V~   99 (137)
T cd04711          54 INKFYRPENTHKGFKATYHADINMLYWSDEEATVDFSAVQGRCTVE   99 (137)
T ss_pred             EEEEecccccccccccccccceeeEEeecceeecChhhccceEEEE
Confidence            369999998822       2  299999999999999999999998

DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains

Probab=96.44  E-value=0.00066  Score=53.47  Aligned_cols=78  Identities=6%  Similarity=-0.039  Sum_probs=51.4

Q ss_pred             hccchhcCCcccccccc--HH---HHHHHHHHHHHHhcC----------CC--C-ccceeecccceeEe-----EEeecC
Q psy1225         170 FENAKKFNPADLRLYRD--AV---KLQKLMQRKVQEVMI----------LD--I-ECQVYLISDELTHY-----QVVLTG  226 (256)
Q Consensus       170 ~~n~~~yn~~~~~i~~~--a~---~l~~i~~~~~~~~g~----------~~--~-~c~y~rpeqt~h~~-----ev~kt~  226 (256)
                      ..++..|+.+|.+....  +.   -+.+|...+...++.          ..  + ..|||||+++..+.     |||.|.
T Consensus         6 ~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~~~d~relf~S~   85 (135)
T cd04710           6 LKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRVVADSRLLYASM   85 (135)
T ss_pred             ccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcccCCceEEEEEe
Confidence            34566666666654332  21   123444444433332          12  3 36999999983332     999999


Q ss_pred             cccccccCCCCCCceeeeeec
Q psy1225         227 TAEQVRLSGLPDGDWLAFTLP  247 (256)
Q Consensus       227 ~~~~~~~~~i~~~~~v~f~~~  247 (256)
                      +....|++-|.|||-|.+..-
T Consensus        86 h~d~~p~~si~gKC~V~~~~d  106 (135)
T cd04710          86 HSDICPIGSVRGKCTVRHRDQ  106 (135)
T ss_pred             eEeeechHHEEeEEEEEEecc
Confidence            999999999999999988753

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

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

Probab=96.24  E-value=0.011  Score=46.00  Aligned_cols=45  Identities=18%  Similarity=0.436  Sum_probs=37.6

Q ss_pred             cCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHH
Q psy1225          36 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYR   80 (256)
Q Consensus        36 PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~   80 (256)
                      |.||.-|++|+..|.|+++.+|-.|+-.|+.-+..-.+....+-+
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~k  103 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKIIQAALNSEGGQPEIKK  103 (131)
T ss_pred             cccHHHHHHHHhccceehHHHHHHHHHHHHHHHHhhccCCccccC
Confidence            899999999999999999999999999999887765444343333

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=95.47  E-value=0.026  Score=43.95  Aligned_cols=60  Identities=13%  Similarity=0.345  Sum_probs=45.7

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      |.||..+++|+..|.|.|+.+|.+|+-.|+..+..-.+...++-+.....+.+|-+++.+
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~  118 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMES  118 (131)
T ss_pred             cccHHHHHHHHhccceehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHH
Confidence            899999999999999999999999999999887655554444444444455556665553

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

>KOG0644|consensus

Probab=91.93  E-value=0.17  Score=50.41  Aligned_cols=62  Identities=21%  Similarity=0.285  Sum_probs=51.5

Q ss_pred             hcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHHHHHHHH
Q psy1225          32 IIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV   93 (256)
Q Consensus        32 ~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~~f~~~~   93 (256)
                      --.-|.+|+.|+.+|++..|++.+.|..|+..|..||.+|.+.+..+...+..|...|...+
T Consensus      1049 ~fpvpls~evi~~rlEn~yYrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~Tl 1110 (1113)
T KOG0644|consen 1049 RFPVPLSLEVIRSRLENNYYRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRTL 1110 (1113)
T ss_pred             CCCCcccHHHHHHHHHhhhhhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhhhc
Confidence            35678999999999999999999999999999999999999887766666666666555443

>KOG1886|consensus

Probab=89.37  E-value=0.15  Score=47.69  Aligned_cols=59  Identities=10%  Similarity=-0.048  Sum_probs=45.3

Q ss_pred             HHHHHHHHhc-CCCCc-cceeecccceeEe----------EEeecCcccccccCCCCCCceeeeeeccccc
Q psy1225         193 LMQRKVQEVM-ILDIE-CQVYLISDELTHY----------QVVLTGTAEQVRLSGLPDGDWLAFTLPVVSG  251 (256)
Q Consensus       193 i~~~~~~~~g-~~~~~-c~y~rpeqt~h~~----------ev~kt~~~~~~~~~~i~~~~~v~f~~~~~~g  251 (256)
                      |...+..+.| ..-+. -|+||||++.-.-          |.|-+-+....+++-|.++|-|.||..|++=
T Consensus        73 i~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a~~~relF~SfH~De~~A~ti~~rC~V~fvp~~kql  143 (464)
T KOG1886|consen   73 IEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGAKQPRELFLSFHEDEAFAETILHRCKVHFVPAYKQL  143 (464)
T ss_pred             EeeeeccccCCCcceecccccCCCccCCCCCCCcccCCCccccccccccchhhhhhcccceeeeccccccc
Confidence            4444555554 33444 5999999884431          8999999999999999999999999998763

>KOG0644|consensus

Probab=89.37  E-value=0.26  Score=49.14  Aligned_cols=56  Identities=23%  Similarity=0.329  Sum_probs=47.0

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHH
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR  152 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~  152 (256)
                      |.+++.|+.+|++..|.+.+.|-.|+..|.+||..|.+-+-.+-..+..|...|..
T Consensus      1053 pls~evi~~rlEn~yYrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~ 1108 (1113)
T KOG0644|consen 1053 PLSLEVIRSRLENNYYRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDR 1108 (1113)
T ss_pred             cccHHHHHHHHHhhhhhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhh
Confidence            88899999999999999999999999999999999998776555555555554443

>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p

Probab=89.27  E-value=0.12  Score=42.78  Aligned_cols=75  Identities=11%  Similarity=0.124  Sum_probs=48.6

Q ss_pred             cchhcCCccccccccHHH----HHHHHHHHHHHhcC-CCCc-cceeecccc--------ee--------EeEEeecCccc
Q psy1225         172 NAKKFNPADLRLYRDAVK----LQKLMQRKVQEVMI-LDIE-CQVYLISDE--------LT--------HYQVVLTGTAE  229 (256)
Q Consensus       172 n~~~yn~~~~~i~~~a~~----l~~i~~~~~~~~g~-~~~~-c~y~rpeqt--------~h--------~~ev~kt~~~~  229 (256)
                      .+..++.+++++++++..    +..|-..+....+. .-+. -|||||.+=        .|        -.|+|.|-++.
T Consensus        49 d~~~~~vGD~Vlik~~~~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~d  128 (179)
T cd04720          49 DGLELSVGDTILVKDDVANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAELS  128 (179)
T ss_pred             CCeEEeCCCEEEEeCCCCCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEecccc
Confidence            446688888888877643    11122222111112 2333 499997722        33        25999999999


Q ss_pred             ccccCCCCCCceeeeee
Q psy1225         230 QVRLSGLPDGDWLAFTL  246 (256)
Q Consensus       230 ~~~~~~i~~~~~v~f~~  246 (256)
                      ..++.+|+++|-|+-+.
T Consensus       129 ~i~l~~Ii~k~~Vls~~  145 (179)
T cd04720         129 EIKLKDIIDKANVLSES  145 (179)
T ss_pred             eEEhhheeeeEEEecHH
Confidence            99999999999997433

The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=81.01  E-value=0.23  Score=37.93  Aligned_cols=42  Identities=10%  Similarity=-0.156  Sum_probs=29.0

Q ss_pred             hcccccHHHHHHHhhcCC-------CCCHHHHHHHHHHHHHhhhhhCCC
Q psy1225          94 QENPRSLLTIGKTLKSGH-------YSTLNELTGELNLMFENAKKFNPA  135 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~~~-------Y~s~~~f~~D~~lmf~Na~~yN~~  135 (256)
                      .+-||||+||++++.++.       |..-....++...+..||-.+|..
T Consensus        42 IK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (114)
T cd05494          42 IKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGRRSPSNIY   90 (114)
T ss_pred             cCCCCChHHHHHHHHccccccccccccccccccccccccccccCccccc
Confidence            334999999999999863       333444556666667776666653

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	256
3k2j_A	130	Crystal Structure Of The 3rd Bromodomain Of Human P		6e-17
3k2j_A	130	Crystal Structure Of The 3rd Bromodomain Of Human P		5e-09
3k2j_A	130	Crystal Structure Of The 3rd Bromodomain Of Human P		2e-04
3ljw_A	120	Crystal Structure Of The Second Bromodomain Of Huma		2e-11
3ljw_A	120	Crystal Structure Of The Second Bromodomain Of Huma		2e-04
2ktb_B	121	Solution Structure Of The Second Bromodomain Of Hum		2e-11
2ktb_B	121	Solution Structure Of The Second Bromodomain Of Hum		2e-04
3hmf_A	116	Crystal Structure Of The Second Bromodomain Of Huma		2e-11
3hmf_A	116	Crystal Structure Of The Second Bromodomain Of Huma		3e-04
3iu5_A	116	Crystal Structure Of The First Bromodomain Of Human		1e-10
3iu5_A	116	Crystal Structure Of The First Bromodomain Of Human		1e-04
2h60_A	128	Solution Structure Of Human Brg1 Bromodomain Length		3e-10
3uvd_A	124	Crystal Structure Of The Bromodomain Of Human Trans		3e-10
2grc_A	129	1.5 A Structure Of Bromodomain From Human Brg1 Prot		3e-10
2dat_A	123	Solution Structure Of The Bromodomain Of Human SwiS		5e-10
2r0v_A	346	Structure Of The Rsc4 Tandem Bromodomain Acetylated		3e-09
2r0v_A	346	Structure Of The Rsc4 Tandem Bromodomain Acetylated		9e-04
3tlp_A	150	Crystal Structure Of The Fourth Bromodomain Of Huma		3e-09
2r10_A	361	Structure Of An Acetylated Rsc4 Tandem Bromodomain		3e-09
2yqd_A	120	Solution Structure Of The Fifth Bromodomain From Mo		5e-09
3g0j_A	124	Crystal Structure Of The Fifth Bromodomain Of Human		7e-09
2r0s_A	285	Crystal Structure Of The Rsc4 Tandem Bromodomain Le		8e-09
3mqm_A	126	Crystal Structure Of The Bromodomain Of Human Ash1l		8e-09
2r0y_A	311	Structure Of The Rsc4 Tandem Bromodomain In Complex		9e-09
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		2e-08
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		4e-04
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		2e-08
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		6e-04
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		2e-08
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		3e-04
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		2e-08
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		4e-04
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		3e-08
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		5e-04
3nxb_A	116	Crystal Structure Of The Bromodomain Of Human Cecr2		1e-07
1f68_A	103	Nmr Solution Structure Of The Bromodomain From Huma		1e-07
2f6j_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		1e-07
3d7c_A	112	Crystal Structure Of The Bromodomain Of Human Gcn5,		1e-07
3dwy_A	119	Crystal Structure Of The Bromodomain Of Human Crebb		2e-07
1jsp_B	121	Nmr Structure Of Cbp Bromodomain In Complex With P5		2e-07
3o33_A	184	Crystal Structure Of Trim24 Phd-Bromo In The Free S		2e-07
1e6i_A	121	Bromodomain From Gcn5 Complexed With Acetylated H4		2e-07
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		3e-07
3fkm_X	166	Plasmodium Falciparum Bromodomain-Containing Protei		4e-07
2yyn_A	135	Crystal Sturcture Of Human Bromodomain Protein Leng		4e-07
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		4e-07
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		4e-07
3i3j_A	124	Crystal Structure Of The Bromodomain Of Human Ep300		6e-07
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		8e-07
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		8e-04
2nxb_A	123	Crystal Structure Of Human Bromodomain Containing P		9e-07
3jvl_A	120	Crystal Structure Of Bromodomain 2 Of Mouse Brd4 Le		1e-06
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		1e-06
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		8e-04
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		1e-06
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		5e-04
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		2e-06
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		8e-05
2wp2_A	120	Structure Of Brdt Bromodomain Bd1 Bound To A Diacet		2e-06
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		2e-06
2g4a_A	116	Solution Structure Of A Bromodomain From Ring3 Prot		2e-06
2lsp_B	128	Solution Structures Of Brd4 Second Bromodomain With		2e-06
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		2e-06
2ouo_A	130	Crystal Structure Of The Bromo Domain 2 In Human Br		2e-06
3jvj_A	131	Crystal Structure Of The Bromodomain 1 In Mouse Brd		2e-06
2oss_A	127	Crystal Structure Of The Bromo Domain 1 In Human Br		2e-06
2dvv_A	112	Crystal Structure Of The Second Bromodomain Of The		2e-06
3oni_A	114	Crystal Structure Of The Second Bromodomain Of Huma		2e-06
3hmh_A	155	Crystal Structure Of The Second Bromodomain Of Huma		3e-06
3uv4_A	158	Crystal Structure Of The Second Bromodomain Of Huma		3e-06
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		3e-06
2dww_A	114	Crystal Structure Of Bromodomain-Containing Protein		3e-06
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		6e-06
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		8e-05
2i8n_A	114	Solution Structure Of The Second Bromodomain Of Brd		7e-06
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		8e-06
2ydw_A	153	Crystal Structure Of The First Bromodomain Of Human		8e-06
2oo1_A	113	Crystal Structure Of The Bromo Domain 2 Of Human Br		8e-06
3g0l_A	117	Crystal Structure Of Human Bromodomain Adjacent To		8e-06
2e7o_A	112	Solution Structure Of The Bromodomain From Human Br		8e-06
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		9e-06
2e7n_A	117	Solution Structure Of The Second Bromodomain From H		3e-05
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		3e-05
2wp1_A	126	Structure Of Brdt Bromodomain 2 Bound To An Acetyla		5e-05
2d9e_A	121	Solution Structure Of The Bromodomain Of Peregrin L		6e-05
3u5m_A	207	Crystal Structure Of Trim33 Phd-Bromo In The Free S		6e-05
1x0j_A	122	Crystal Structure Analysis Of The N-Terminal Bromod		7e-05
3aqa_A	128	Crystal Structure Of The Human Brd2 Bd1 Bromodomain		8e-05

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

Iteration: 1
 Score = 84.3 bits (207), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 43/90 (47%), Positives = 61/90 (67%)
Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +LNLMFENA
Sbjct: 36  QGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENA 95
Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
           K++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct: 96  KRYNVPNSAIYKRVLKLQQVMQAKKKELAR 125

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 42/62 (67%)
Query: 97  PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 156
           P SL  I   LK+  Y TL+ L  +LNLMFENAK++N  +S +Y+  +KLQ++MQ K +E
Sbjct: 63  PISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKE 122
Query: 157 FS 158
            +
Sbjct: 123 LA 124

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 43/60 (71%), Gaps = 2/60 (3%)
Query: 144 VKLQKLMQR-KVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           + LQ++  + K QE+ +L+ L  +L+LMFENAK++N  +  +Y+  +KLQ++MQ K +E+
Sbjct: 64  ISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKEL 123

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 55/86 (63%)
Query: 10  GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
           G  +SE F KLP+K   PDYY IIK P  L TI + +++G Y +++ +  +++L+ +NAK
Sbjct: 28  GRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAK 87
Query: 70  KFNPADSRLYRDAVKLQKLMQRKVQE 95
            +N   S++++DA  ++K+   K  E
Sbjct: 88  TYNEPGSQVFKDANSIKKIFYMKKAE 113

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 41/67 (61%)
Query: 97  PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 156
           P  L TI + +++G Y +++ +  +++L+ +NAK +N   S++++DA  ++K+   K  E
Sbjct: 54  PIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAE 113
Query: 157 FSLNELT 163
              +E+ 
Sbjct: 114 IEHHEMA 120

>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 = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 55/86 (63%)
Query: 10  GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
           G  +SE F KLP+K   PDYY IIK P  L TI + +++G Y +++ +  +++L+ +NAK
Sbjct: 29  GRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAK 88
Query: 70  KFNPADSRLYRDAVKLQKLMQRKVQE 95
            +N   S++++DA  ++K+   K  E
Sbjct: 89  TYNEPGSQVFKDANSIKKIFYMKKAE 114

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 41/67 (61%)
Query: 97  PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 156
           P  L TI + +++G Y +++ +  +++L+ +NAK +N   S++++DA  ++K+   K  E
Sbjct: 55  PIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAE 114
Query: 157 FSLNELT 163
              +E+ 
Sbjct: 115 IEHHEMA 121

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 55/86 (63%)
Query: 10  GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
           G  +SE F KLP+K   PDYY IIK P  L TI + +++G Y +++ +  +++L+ +NAK
Sbjct: 26  GRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAK 85
Query: 70  KFNPADSRLYRDAVKLQKLMQRKVQE 95
            +N   S++++DA  ++K+   K  E
Sbjct: 86  TYNEPGSQVFKDANSIKKIFYMKKAE 111

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 40/65 (61%)
Query: 97  PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE 156
           P  L TI + +++G Y +++ +  +++L+ +NAK +N   S++++DA  ++K+   K  E
Sbjct: 52  PIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAE 111
Query: 157 FSLNE 161
              +E
Sbjct: 112 IEHHE 116

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 46/87 (52%)
Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  L E F++ P +R  PDYY ++  P  L+ I + LK   Y  +N LT +  L+F NA
Sbjct: 24  QGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNA 83
Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE 95
           K +   DS  Y+ A KL  L  R   E
Sbjct: 84  KSYYKPDSPEYKAACKLWDLYLRTRNE 110

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 33/66 (50%)
Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           +V   P  L+ I + LK   Y  +N LT +  L+F NAK +   DS  Y+ A KL  L  
Sbjct: 46  EVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYL 105
Query: 152 RKVQEF 157
           R   EF
Sbjct: 106 RTRNEF 111

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 62/99 (62%), Gaps = 3/99 (3%)
Query: 5   KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
           K+ + G  LSE F++LP+++  P+YY +I+ P     I + +++  Y +LN+L  ++ L+
Sbjct: 23  KDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLL 82
Query: 65  FENAKKFNPADSRLYRDAVKLQKL---MQRKVQENPRSL 100
            +NA+ FN   S +Y D++ LQ +   +++K+++   SL
Sbjct: 83  CQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSL 121

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 53/85 (62%)
Query: 5   KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
           K+ + G  LSE F++LP+++  P+YY +I+ P     I + +++  Y +LN+L  ++ L+
Sbjct: 28  KDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLL 87
Query: 65  FENAKKFNPADSRLYRDAVKLQKLM 89
            +NA+ FN   S +Y D++ LQ + 
Sbjct: 88  CQNAQTFNLEGSLIYEDSIVLQSVF 112

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 53/85 (62%)
Query: 5   KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
           K+ + G  LSE F++LP+++  P+YY +I+ P     I + +++  Y +LN+L  ++ L+
Sbjct: 27  KDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLL 86
Query: 65  FENAKKFNPADSRLYRDAVKLQKLM 89
            +NA+ FN   S +Y D++ LQ + 
Sbjct: 87  CQNAQTFNLEGSLIYEDSIVLQSVF 111

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 54/92 (58%)
Query: 8   TEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN 67
           + G  LSE F++LP+++  P+YY +I+ P     I + +++  Y +L +L  ++ L+  N
Sbjct: 31  SSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHN 90
Query: 68  AKKFNPADSRLYRDAVKLQKLMQRKVQENPRS 99
           A+ FN   S++Y D++ LQ + +   Q  P S
Sbjct: 91  AQTFNLEGSQIYEDSIVLQSVFKSARQSGPSS 122

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 50/90 (55%)
Query: 5   KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
           KN  +   LSEPF++L  K   P+YY I+ +P +L  + + L+ G YS + +   ++ L+
Sbjct: 207 KNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLV 266
Query: 65  FENAKKFNPADSRLYRDAVKLQKLMQRKVQ 94
           F+NA  FN   + +Y+DA  L       +Q
Sbjct: 267 FQNAHIFNDPSALIYKDATTLTNYFNYLIQ 296

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 7/86 (8%)
Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           ++  +P +L  + + L+ G YS + +   ++ L+F+NA  FN   + +Y+DA  L     
Sbjct: 233 EIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFN 292
Query: 152 RKVQ-EF-----SLNELTGELSLMFE 171
             +Q EF      LNE  GE++L F+
Sbjct: 293 YLIQKEFFPELQDLNE-RGEINLEFD 317

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 50/86 (58%)
Query: 10  GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
           G  L + F+  P+K+  PDYY+II  P  L  I   +++  Y+    +  ++ LMF NA+
Sbjct: 45  GRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNAR 104
Query: 70  KFNPADSRLYRDAVKLQKLMQRKVQE 95
            +N   S++Y DA  L+KL++ K +E
Sbjct: 105 HYNEEGSQVYNDAHILEKLLKEKRKE 130

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 39/123 (31%), Positives = 62/123 (50%), Gaps = 12/123 (9%)
Query: 5   KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
           KN  +   LSEPF++L  K   P+YY I+ +P +L  + + L+ G YS + +   ++ L+
Sbjct: 222 KNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLV 281
Query: 65  FENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNL 124
           F+NA  FN   + +Y+DA  L       +Q+     L             LNE  GE+NL
Sbjct: 282 FQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPEL-----------QDLNE-RGEINL 329
Query: 125 MFE 127
            F+
Sbjct: 330 EFD 332

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 2/87 (2%)
Query: 5   KNQTE--GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELN 62
           KN T+  G  LS  FL+LP++   PDYY  IK P  +  I   + +  Y  ++ +  +  
Sbjct: 28  KNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFV 87
Query: 63  LMFENAKKFNPADSRLYRDAVKLQKLM 89
           +MF NA  +N  +S +Y+DA+ L K++
Sbjct: 88  MMFNNACTYNEPESLIYKDALVLHKVL 114

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 2/87 (2%)
Query: 5   KNQTE--GGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELN 62
           KN T+  G  LS  FL+LP++   PDYY  IK P  +  I   + +  Y  ++ +  +  
Sbjct: 28  KNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFV 87
Query: 63  LMFENAKKFNPADSRLYRDAVKLQKLM 89
           +MF NA  +N  +S +Y+DA+ L K++
Sbjct: 88  MMFNNACTYNEPESLIYKDALVLHKVL 114

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 48/90 (53%)
Query: 5   KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
           KN  +   LSEPF +L  K   P+YY I+ +P +L  + + L+ G YS + +   +  L+
Sbjct: 166 KNLDDKVKLSEPFXELVDKDELPEYYEIVHSPXALSIVKQNLEIGQYSKIYDFIIDXLLV 225
Query: 65  FENAKKFNPADSRLYRDAVKLQKLMQRKVQ 94
           F+NA  FN   + +Y+DA  L       +Q
Sbjct: 226 FQNAHIFNDPSALIYKDATTLTNYFNYLIQ 255

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 44/75 (58%)
Query: 13  LSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
           L+ P L LP K+ N DYY  I +P  L+TI K + +G+Y T+     ++  +F NA+K+ 
Sbjct: 32  LAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYY 91
Query: 73  PADSRLYRDAVKLQK 87
              S + RD  +L+K
Sbjct: 92  GRKSPVGRDVCRLRK 106

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 48/90 (53%)
Query: 5   KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLM 64
           KN  +   LSEPF +L  K   P+YY I+ +P +L  + + L+ G YS + +   +  L+
Sbjct: 172 KNLDDKVKLSEPFXELVDKDELPEYYEIVHSPXALSIVKQNLEIGQYSKIYDFIIDXLLV 231
Query: 65  FENAKKFNPADSRLYRDAVKLQKLMQRKVQ 94
           F+NA  FN   + +Y+DA  L       +Q
Sbjct: 232 FQNAHIFNDPSALIYKDATTLTNYFNYLIQ 261

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%)
Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +   ++ PFL+       PDYY +IK P  L T+ + ++  +Y  L E   ++  +F+N 
Sbjct: 85  QAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNC 144
Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQ 94
           + +NP+DS  Y+ A  L+    +K++
Sbjct: 145 RYYNPSDSPFYQCAEVLESFFVQKLK 170

>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 = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 93  VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
           V + P  L T+ + ++  +Y  L E   ++  +F+N + +NP+DS  Y+ A  L+    +
Sbjct: 108 VIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQ 167
Query: 153 KVQEF 157
           K++ F
Sbjct: 168 KLKGF 172

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%)
Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +   ++ PFL+       PDYY +IK P  L T+ + ++  +Y  L E   ++  +F+N 
Sbjct: 33  QAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNC 92
Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQ 94
           + +NP+DS  Y+ A  L+    +K++
Sbjct: 93  RYYNPSDSPFYQCAEVLESFFVQKLK 118

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 93  VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
           V + P  L T+ + ++  +Y  L E   ++  +F+N + +NP+DS  Y+ A  L+    +
Sbjct: 56  VIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQ 115
Query: 153 KVQEF 157
           K++ F
Sbjct: 116 KLKGF 120

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%)
Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +   ++ PFL+       PDYY +IK P  L T+ + ++  +Y  L E   ++  +F+N 
Sbjct: 26  QAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTAIFDNC 85
Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQ 94
           + +NP+DS  Y+ A  L+    +K++
Sbjct: 86  RYYNPSDSPFYQCAEVLESFFVQKLK 111

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 93  VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
           V + P  L T+ + ++  +Y  L E   ++  +F+N + +NP+DS  Y+ A  L+    +
Sbjct: 49  VIKEPMDLATMEERVQRRYYEKLTEFVADMTAIFDNCRYYNPSDSPFYQCAEVLESFFVQ 108
Query: 153 KVQEF 157
           K++ F
Sbjct: 109 KLKGF 113

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%)
Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +   ++ PFL+       PDYY +IK P  L T+ + ++  +Y  L E   ++  +F+N 
Sbjct: 85  QAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNC 144
Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQ 94
           + +NP+DS  Y+ A  L+    +K++
Sbjct: 145 RYYNPSDSPFYQCAEVLESFFVQKLK 170

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 93  VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
           V + P  L T+ + ++  +Y  L E   ++  +F+N + +NP+DS  Y+ A  L+    +
Sbjct: 108 VIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQ 167
Query: 153 KVQEF 157
           K++ F
Sbjct: 168 KLKGF 172

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%)
Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +   ++ PFL+       PDYY +IK P  L T+ + ++  +Y  L E   ++  +F+N 
Sbjct: 26  QAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNC 85
Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQ 94
           + +NP+DS  Y+ A  L+    +K++
Sbjct: 86  RYYNPSDSPFYQCAEVLESFFVQKLK 111

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 93  VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
           V + P  L T+ + ++  +Y  L E   ++  +F+N + +NP+DS  Y+ A  L+    +
Sbjct: 49  VIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQ 108
Query: 153 KVQEF 157
           K++ F
Sbjct: 109 KLKGF 113

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 41/78 (52%)
Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PFL+   + Y P+YY+IIK P  + ++ K L  G Y T  E   ++  MF N +K+N 
Sbjct: 34  SWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNG 93
Query: 74  ADSRLYRDAVKLQKLMQR 91
             S   + +  L++   R
Sbjct: 94  ESSEYTKMSDNLERCFHR 111

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 46/89 (51%)
Query: 7   QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFE 66
           Q +    + PF++   K   PDYY +I+ P  L T+ + L+S +Y T      +L  +  
Sbjct: 14  QIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIA 73
Query: 67  NAKKFNPADSRLYRDAVKLQKLMQRKVQE 95
           N +++NP DS   R A  L+K    K++E
Sbjct: 74  NCREYNPPDSEYCRCASALEKFFYFKLKE 102

>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 = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 42/79 (53%)
Query: 16  PFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 75
           PFL+       PDYY +IK P  L T  + ++  +Y  L E   +   +F+N + +NP+D
Sbjct: 92  PFLEPVDPNDAPDYYGVIKEPXDLATXEERVQRRYYEKLTEFVADXTKIFDNCRYYNPSD 151
Query: 76  SRLYRDAVKLQKLMQRKVQ 94
           S  Y+ A  L+    +K++
Sbjct: 152 SPFYQCAEVLESFFVQKLK 170

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 46/89 (51%)
Query: 7   QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFE 66
           Q +    + PF++   K   PDYY +I+ P  L T+ + L+S +Y T      +L  +  
Sbjct: 18  QIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIA 77
Query: 67  NAKKFNPADSRLYRDAVKLQKLMQRKVQE 95
           N +++NP DS   R A  L+K    K++E
Sbjct: 78  NCREYNPPDSEYCRCASALEKFFYFKLKE 106

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY+ I+KNP  L TI + L +G Y    +   ++ LMF NA  +N   SR+Y+   KL 
Sbjct: 45  PDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLA 104
Query: 87  KLMQRKVQENPRSL 100
           ++ ++++    +SL
Sbjct: 105 EVFEQEIDPVMQSL 118

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY+ I+KNP  L TI + L +G Y    +   ++ LMF NA  +N   SR+Y+   KL 
Sbjct: 47  PDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLA 106
Query: 87  KLMQRKVQENPRSL 100
           ++ ++++    +SL
Sbjct: 107 EVFEQEIDPVMQSL 120

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGH--YSTLNELTGELNLMFENAKKFNPADSRLYRDAVK 84
           PDYY+IIKNP  L TI K L+  +  YS   +   +  L+F+N  +FN  DS +    +K
Sbjct: 111 PDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIK 170
Query: 85  LQKLMQR 91
           L+   + 
Sbjct: 171 LENYFEE 177

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 43/82 (52%)
Query: 16  PFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD 75
           PFL+   K   PDYY  IK P  L T+   L+S  Y  + +   +  L+F N + +N  +
Sbjct: 33  PFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGEN 92
Query: 76  SRLYRDAVKLQKLMQRKVQENP 97
           +  Y+ A +L+K    KV+E P
Sbjct: 93  TSYYKYANRLEKFFNNKVKEIP 114

>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 = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 40/72 (55%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDYY IIKNP  L TI K L++ +Y+  +E   + N MF N   +N     +   A  L+
Sbjct: 46  PDYYTIIKNPMDLNTIKKRLENKYYAKASECIEDFNTMFSNCYLYNKPGDDIVLMAQALE 105
Query: 87  KLMQRKVQENPR 98
           KL  +K+ + P+
Sbjct: 106 KLFMQKLSQMPQ 117

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 9   EGGNLSEPFLKLPAKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN 67
           EGG++ E  +   AK+ N PDYY +IKNP S   I   LK G Y+  +E   ++ L+F+N
Sbjct: 37  EGGHIFEKLV--DAKKQNCPDYYDVIKNPXSFSCIKTKLKKGQYAYPSEFVKDVQLIFDN 94
Query: 68  AKKFNPADS 76
              +N ++S
Sbjct: 95  CSLYNTSNS 103

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGH--YSTLNELTGELNLMFENAKKFNPADSRLYRDAVK 84
           PDYY+IIKNP  L TI K L+  +  YS   +   +  L+F+N  +FN  DS +    +K
Sbjct: 50  PDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIK 109
Query: 85  LQKLMQ 90
           L+   +
Sbjct: 110 LENYFE 115

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 2/90 (2%)
Query: 7   QTEGGNLSEPFLKLPAKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMF 65
           Q +    + PF++ P KR   P YY +I+ P  L T+ + LK+ +Y +      +L  +F
Sbjct: 24  QVKSHQSAWPFME-PVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVF 82
Query: 66  ENAKKFNPADSRLYRDAVKLQKLMQRKVQE 95
            N K++NP +S  Y+ A  L+K    K++E
Sbjct: 83  TNCKEYNPPESEYYKCANILEKFFFSKIKE 112

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 2/90 (2%)
Query: 7   QTEGGNLSEPFLKLPAKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMF 65
           Q +    + PF++ P KR   P YY +I+ P  L T+ + LK+ +Y +      +L  +F
Sbjct: 26  QVKSHQSAWPFME-PVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVF 84
Query: 66  ENAKKFNPADSRLYRDAVKLQKLMQRKVQE 95
            N K++NP +S  Y+ A  L+K    K++E
Sbjct: 85  TNCKEYNPPESEYYKCANILEKFFFSKIKE 114

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 43/74 (58%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY+ I+K+P  L TI + L +G Y    +   ++ LMF NA  +N   SR+Y+   KL 
Sbjct: 50  PDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLS 109
Query: 87  KLMQRKVQENPRSL 100
           ++ ++++    +SL
Sbjct: 110 EVFEQEIDPVMQSL 123

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY++IIKNP  + TI K L++ +Y + +E   + N MF N   +N     +   A  L+
Sbjct: 52  PDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALE 111
Query: 87  KLMQRKVQENPR 98
           K+  +KV + P+
Sbjct: 112 KIFLQKVAQMPQ 123

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 41/82 (50%)
Query: 81  DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 140
           DA+KL      K+ +NP  + TI K L++ +Y + +E   + N MF N   +N     + 
Sbjct: 45  DAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIV 104
Query: 141 RDAVKLQKLMQRKVQEFSLNEL 162
             A  L+K+  +KV +    E+
Sbjct: 105 LMAQALEKIFLQKVAQMPQEEV 126

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY++IIKNP  + TI K L++ +Y + +E   + N MF N   +N     +   A  L+
Sbjct: 50  PDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALE 109
Query: 87  KLMQRKVQENPR 98
           K+  +KV + P+
Sbjct: 110 KIFLQKVAQMPQ 121

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 36/70 (51%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY  IIK+P  + TI   L+S  Y    E   ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 46  DYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQD 105
Query: 88  LMQRKVQENP 97
           + + +  + P
Sbjct: 106 VFEMRFAKMP 115

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY++IIKNP  + TI K L++ +Y + +E   + N MF N   +N     +   A  L+
Sbjct: 54  PDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALE 113
Query: 87  KLMQRKVQENPR 98
           K+  +KV + P+
Sbjct: 114 KIFLQKVAQMPQ 125

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 41/82 (50%)
Query: 81  DAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 140
           DA+KL      K+ +NP  + TI K L++ +Y + +E   + N MF N   +N     + 
Sbjct: 47  DAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIV 106
Query: 141 RDAVKLQKLMQRKVQEFSLNEL 162
             A  L+K+  +KV +    E+
Sbjct: 107 LMAQALEKIFLQKVAQMPQEEV 128

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 46/86 (53%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY   IK+P    T+ K L++  Y  L+E   + +L+ +N  K+N  D+  YR AV+L+
Sbjct: 44  PDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLR 103
Query: 87  KLMQRKVQENPRSLLTIGKTLKSGHY 112
                 +++  R + +IG    SG +
Sbjct: 104 DQGGVVLRQARREVDSIGLEEASGMH 129

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ-------K 148
           +P    T+ K L++  Y  L+E   + +L+ +N  K+N  D+  YR AV+L+       +
Sbjct: 52  HPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLR 111
Query: 149 LMQRKVQEFSLNELTG 164
             +R+V    L E +G
Sbjct: 112 QARREVDSIGLEEASG 127

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           SEPF +       PDY  II  P    T+ +TL++G+Y +  EL  ++ L+F N+K + P
Sbjct: 39  SEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTP 98
Query: 74  AD-SRLYRDAVKLQKLMQRKV 93
           +  SR+Y  +++L    +  +
Sbjct: 99  SKRSRIYSMSLRLSAFFEEHI 119

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/96 (28%), Positives = 51/96 (53%), Gaps = 8/96 (8%)
Query: 61  LNLMFENAKKFNPADSRLYRDAVKLQKLMQ-RKVQENPRSLLTIGKTLKSGHYSTLNELT 119
           LNL+F+        DS  +R  V L +    R + + P    T+ +TL++G+Y +  EL 
Sbjct: 30  LNLIFQCE------DSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELC 83
Query: 120 GELNLMFENAKKFNPAD-SRLYRDAVKLQKLMQRKV 154
            ++ L+F N+K + P+  SR+Y  +++L    +  +
Sbjct: 84  KDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHI 119

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 38/72 (52%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDYY IIK P  L TI K L++ +Y   +E   + N MF N   +N     +   A  L+
Sbjct: 47  PDYYTIIKTPMDLNTIKKRLENKYYEKASECIEDFNTMFSNCYLYNKTGDDIVVMAQALE 106
Query: 87  KLMQRKVQENPR 98
           KL  +K+ + P+
Sbjct: 107 KLFMQKLSQMPQ 118

>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 = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 37/71 (52%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDYY+IIK P  + TI K L++ +Y    E   + N MF N   +N     +   A  L+
Sbjct: 74  PDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALE 133
Query: 87  KLMQRKVQENP 97
           KL  +K+ E P
Sbjct: 134 KLFLQKINELP 144

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 38/70 (54%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY+ IIK+P  L T+ + +++  Y    E   ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 38  DYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQD 97
Query: 88  LMQRKVQENP 97
           + + +  + P
Sbjct: 98  VFEFRYAKMP 107

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 36/70 (51%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY  IIK+P  + TI   L++  Y    E   ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 57  DYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQD 116
Query: 88  LMQRKVQENP 97
           + + +  + P
Sbjct: 117 VFEMRFAKMP 126

>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 = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 37/71 (52%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDYY+IIK P  + TI K L++ +Y    E   + N MF N   +N     +   A  L+
Sbjct: 54  PDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALE 113
Query: 87  KLMQRKVQENP 97
           KL  +K+ E P
Sbjct: 114 KLFLQKINELP 124

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 36/70 (51%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY  IIK+P  + TI   L++  Y    E   ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 59  DYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQD 118
Query: 88  LMQRKVQENP 97
           + + +  + P
Sbjct: 119 VFEMRFAKMP 128

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 37/71 (52%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDYY+IIK P  + TI K L++ +Y    E   + N MF N   +N     +   A  L+
Sbjct: 58  PDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALE 117
Query: 87  KLMQRKVQENP 97
           KL  +K+ E P
Sbjct: 118 KLFLQKINELP 128

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 37/71 (52%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDYY+IIK P  + TI K L++ +Y    E   + N MF N   +N     +   A  L+
Sbjct: 54  PDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALE 113
Query: 87  KLMQRKVQENP 97
           KL  +K+ E P
Sbjct: 114 KLFLQKINELP 124

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 38/70 (54%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY+ IIK+P  L T+ + +++  Y    E   ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 42  DYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQD 101
Query: 88  LMQRKVQENP 97
           + + +  + P
Sbjct: 102 VFEFRYAKMP 111

>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 = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 38/70 (54%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY+ IIK+P  L T+ + +++  Y    E   ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 44  DYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQD 103
Query: 88  LMQRKVQENP 97
           + + +  + P
Sbjct: 104 VFEFRYAKMP 113

>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 = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 48/97 (49%)
Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 45  SWPFHHPVNKKFVPDYYKMIVNPVDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 104
Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSG 110
            +S+  + A ++  +  + + E    L  + K + + 
Sbjct: 105 PESQYTKTAQEIVNICYQTITEYDEHLTQLEKDICTA 141

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 48/97 (49%)
Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 48  SWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 107
Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSG 110
            +S+  + A ++  +  + + E    L  + K + + 
Sbjct: 108 PESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTA 144

>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 = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/104 (26%), Positives = 51/104 (49%)
Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 188 SWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 247
Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNE 117
            +S+  + A ++  +  + + E    L  + K + +   + L E
Sbjct: 248 PESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEE 291

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 34/70 (48%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY  IIK+P    TI   L+S  Y    E   ++ L F N  K+NP D  +   A KLQ 
Sbjct: 44  DYCDIIKHPXDXSTIKSKLESREYRDAQEFGADVRLXFSNCYKYNPPDHEVVAXARKLQD 103
Query: 88  LMQRKVQENP 97
           + + +  + P
Sbjct: 104 VFEXRFAKXP 113

>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 = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           SEPF +       PDY  II  P    T+ +TL +G+Y +  E   ++ L+F NAK + P
Sbjct: 28  SEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTP 87
Query: 74  AD-SRLYRDAVKLQKLMQRKVQ 94
              S++Y   ++L  L + K++
Sbjct: 88  NKRSKIYSMTLRLSALFEEKMK 109

>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 = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/97 (27%), Positives = 50/97 (51%), Gaps = 2/97 (2%)
Query: 71  FNPADSRLYRDAVKLQKLMQ-RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 129
           F   DS  +R  V L +    R + + P    T+ +TL +G+Y +  E   ++ L+F NA
Sbjct: 23  FQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNA 82
Query: 130 KKFNPAD-SRLYRDAVKLQKLMQRKVQEFSLNELTGE 165
           K + P   S++Y   ++L  L + K+++ S +   G+
Sbjct: 83  KAYTPNKRSKIYSMTLRLSALFEEKMKKISSDFKIGQ 119

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 33/63 (52%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY  IIK+P  + TI   L++  Y    E   ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 38  DYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQD 97
Query: 88  LMQ 90
           + +
Sbjct: 98  VFE 100

>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 = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 48/97 (49%)
Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 155 SWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 214
Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSG 110
            +S+  + A ++  +  + + E    L  + K + + 
Sbjct: 215 PESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTA 251

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY++IIK P  + TI + L++ +Y   +E   + N MF N   +N     +   A  L+
Sbjct: 65  PDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLE 124
Query: 87  KLMQRKVQENPRS----LLTIGKTLKSG 110
           K+  +KV   P+     ++TI  + K G
Sbjct: 125 KIFLQKVASMPQEEQELVVTIPNSHKKG 152

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 35/70 (50%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY+ IIK+P  L T+ + +    Y        ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 44  DYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQD 103
Query: 88  LMQRKVQENP 97
           + + +  + P
Sbjct: 104 VFEMRFAKMP 113

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 16  PFLKLPAK-RYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA 74
           PFL LP   +  P Y ++IK P    TI + L SG Y  L     ++ L+F+N + FN  
Sbjct: 33  PFL-LPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNED 91
Query: 75  DSRLYRDAVKLQKLMQRK 92
           DS + R    ++K  ++K
Sbjct: 92  DSDIGRAGHNMRKYFEKK 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 = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 16  PFLKLPAK-RYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA 74
           PFL LP   +  P Y ++IK P    TI + L SG Y  L     ++ L+F+N + FN  
Sbjct: 30  PFL-LPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNED 88
Query: 75  DSRLYRDAVKLQKLMQRK 92
           DS + R    ++K  ++K
Sbjct: 89  DSDIGRAGHNMRKYFEKK 106

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 48/97 (49%)
Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 167 SWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 226
Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSG 110
            +S+  + A ++  +  + + E    L  + K + + 
Sbjct: 227 PESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTA 263

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 32/63 (50%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           DY+ IIK+P  L T+ + +    Y        ++ LMF N  K+NP D  +   A KLQ 
Sbjct: 49  DYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQD 108
Query: 88  LMQ 90
           + +
Sbjct: 109 VFE 111

>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 = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 38/72 (52%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY++IIK P  + TI + L++ +Y   +E   + N MF N   +N     +   A  L+
Sbjct: 65  PDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLE 124
Query: 87  KLMQRKVQENPR 98
           K+  +KV   P+
Sbjct: 125 KIFLQKVASMPQ 136

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 34/70 (48%)
Query: 28  DYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 87
           +YY ++KNP  L TI   + +  Y    E   ++ LMF N  K+NP D  +   A  LQ 
Sbjct: 51  NYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQD 110
Query: 88  LMQRKVQENP 97
           + +    + P
Sbjct: 111 VFELHFAKIP 120

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 41/84 (48%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY   IK P    T+ + L++  Y   ++   + NL+  N  K+N  D+  YR AV+L+
Sbjct: 38  PDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLR 97
Query: 87  KLMQRKVQENPRSLLTIGKTLKSG 110
           +     +++  R    +G    SG
Sbjct: 98  EQGGAVLRQARRQAEKMGSGPSSG 121

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 27  PDYYRIIKNPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENAKKFN 72
           P+YY+IIK P  L T+ K L+   S HY   ++   ++ L+F+N ++FN
Sbjct: 111 PNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFN 159

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 4/83 (4%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY++IIK P    TI + L++ +Y   +E   + N  F N   +N     +   A  L+
Sbjct: 39  PDYHKIIKQPXDXGTIKRRLENNYYWAASECXQDFNTXFTNCYIYNKPTDDIVLXAQTLE 98
Query: 87  KLMQRKVQENPRS----LLTIGK 105
           K+  +KV   P+     ++TI K
Sbjct: 99  KIFLQKVASXPQEEQELVVTIPK 121

>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 = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 36/72 (50%)
Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
           PDY++IIK P    TI + L++ +Y   +E   + N  F N   +N     +   A  L+
Sbjct: 45  PDYHKIIKQPXDXGTIKRRLENNYYWAASECXQDFNTXFTNCYIYNKPTDDIVLXAQTLE 104
Query: 87  KLMQRKVQENPR 98
           K+  +KV   P+
Sbjct: 105 KIFLQKVASXPQ 116

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	256
2dat_A	123	Possible global transcription activator SNF2L2; br	7e-32
2dat_A	123	Possible global transcription activator SNF2L2; br	2e-16
2dat_A	123	Possible global transcription activator SNF2L2; br	1e-07
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-31
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-17
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-08
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	4e-31
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	3e-17
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	2e-07
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	8e-31
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	8e-29
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	8e-31
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-16
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-08
2grc_A	129	Probable global transcription activator SNF2L4; br	2e-30
2grc_A	129	Probable global transcription activator SNF2L4; br	2e-15
2grc_A	129	Probable global transcription activator SNF2L4; br	5e-08
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	2e-30
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	1e-16
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	1e-07
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-30
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-16
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-07
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-29
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	4e-15
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	5e-07
2r10_A	361	Chromatin structure-remodeling complex protein RSC	5e-29
2r10_A	361	Chromatin structure-remodeling complex protein RSC	7e-28
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	5e-29
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	5e-26
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	5e-15
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	6e-29
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	4e-26
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	2e-15
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	4e-23
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	1e-12
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	3e-06
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	3e-22
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	4e-16
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	9e-06
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	3e-22
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	1e-13
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	4e-06
3d7c_A	112	General control of amino acid synthesis protein 5;	5e-22
3d7c_A	112	General control of amino acid synthesis protein 5;	1e-13
3d7c_A	112	General control of amino acid synthesis protein 5;	6e-07
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	1e-21
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	5e-12
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	4e-05
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	3e-21
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	2e-12
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	1e-05
3uv4_A	158	Second bromodomain of human transcription initiat	9e-21
3uv4_A	158	Second bromodomain of human transcription initiat	1e-11
3uv4_A	158	Second bromodomain of human transcription initiat	5e-05
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	1e-20
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	8e-12
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	5e-05
3p1f_A	119	CREB-binding protein; structural genomics consorti	1e-20
3p1f_A	119	CREB-binding protein; structural genomics consorti	5e-12
3p1f_A	119	CREB-binding protein; structural genomics consorti	4e-05
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	3e-20
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	3e-05
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	3e-20
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	9e-13
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	2e-05
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	6e-20
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	1e-11
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	8e-05
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	2e-19
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	5e-13
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	4e-06
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	2e-19
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	3e-11
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	8e-05
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	3e-19
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	2e-11
4alg_A	154	Bromodomain-containing protein 2; signaling protei	3e-19
4alg_A	154	Bromodomain-containing protein 2; signaling protei	6e-11
4alg_A	154	Bromodomain-containing protein 2; signaling protei	9e-05
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	4e-19
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	6e-10
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	7e-05
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	7e-19
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	5e-11
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	4e-04
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	2e-18
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	6e-11
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	4e-04
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	2e-18
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	4e-10
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	4e-18
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	1e-10
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	3e-04
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	4e-16
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	5e-10
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	6e-16
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	8e-11
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	5e-14
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	1e-07
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	8e-12
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	2e-10
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	6e-05
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	5e-11
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06

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

 Score =  112 bits (283), Expect = 7e-32
 Identities = 29/93 (31%), Positives = 54/93 (58%)

Query: 7   QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFE 66
            + G  LSE F++LP+++  P+YY +I+ P     I + +++  Y +L +L  ++ L+  
Sbjct: 30  DSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCH 89

Query: 67  NAKKFNPADSRLYRDAVKLQKLMQRKVQENPRS 99
           NA+ FN   S++Y D++ LQ + +   Q  P S
Sbjct: 90  NAQTFNLEGSQIYEDSIVLQSVFKSARQSGPSS 122

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

 Score = 72.4 bits (178), Expect = 2e-16
 Identities = 16/63 (25%), Positives = 32/63 (50%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
             P     I + +++  Y +L +L  ++ L+  NA+ FN   S++Y D++ LQ + +   
Sbjct: 57  RKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSAR 116

Query: 155 QEF 157
           Q  
Sbjct: 117 QSG 119

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

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
           ++ +++     SL +L  ++ L+  NA+ FN    ++Y D++ LQ + +   Q 
Sbjct: 65  IKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQS 118

>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 =  112 bits (282), Expect = 1e-31
 Identities = 43/90 (47%), Positives = 61/90 (67%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  ++EPF  LP+K+  PDYY+ IK P SL  I   LK+  Y TL+ L  +LNLMFENA
Sbjct: 36  QGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENA 95

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQENPR 98
           K++N  +S +Y+  +KLQ++MQ K +E  R
Sbjct: 96  KRYNVPNSAIYKRVLKLQQVMQAKKKELAR 125

>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 = 74.7 bits (184), Expect = 3e-17
 Identities = 29/66 (43%), Positives = 43/66 (65%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P SL  I   LK+  Y TL+ L  +LNLMFENAK++N  +S +Y+  +KLQ++MQ K +
Sbjct: 62  MPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKK 121

Query: 156 EFSLNE 161
           E +  +
Sbjct: 122 ELARRD 127

>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 = 50.1 bits (120), Expect = 3e-08
 Identities = 19/44 (43%), Positives = 33/44 (75%)

Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           +L+ L  +L+LMFENAK++N  +  +Y+  +KLQ++MQ K +E+
Sbjct: 80  TLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKEL 123

>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 =  110 bits (278), Expect = 4e-31
 Identities = 29/89 (32%), Positives = 45/89 (50%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
               L+ P L LP K+ N DYY  I +P  L+TI K + +G+Y T+     ++  +F NA
Sbjct: 28  SRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNA 87

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQENP 97
           +K+    S + RD  +L+K       E  
Sbjct: 88  EKYYGRKSPVGRDVCRLRKAYYNARHEAS 116

>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 = 74.3 bits (183), Expect = 3e-17
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
           +P  L+TI K + +G+Y T+     ++  +F NA+K+    S + RD  +L+K       
Sbjct: 54  DPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARH 113

Query: 156 EFS--LNELTGE 165
           E S  ++E+ GE
Sbjct: 114 EASAQIDEIVGE 125

>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 = 47.7 bits (114), Expect = 2e-07
 Identities = 9/55 (16%), Positives = 24/55 (43%), Gaps = 3/55 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           +++++      ++     ++  +F NA+K+      + RD  +L+K       E 
Sbjct: 61  IEKQILTGYYKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEA 115

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

 Score =  115 bits (289), Expect = 8e-31
 Identities = 37/229 (16%), Positives = 91/229 (39%), Gaps = 32/229 (13%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +  ++ + F+KLP+++++P YY  I+ P S+  I K+    +    +    ++ L+ +N 
Sbjct: 43  KYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEI-KSRDYEYEDGPSNFLLDVELLTKNC 101

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIG-------KTLKSGHYSTLNELTGE 121
           + +N  DS + ++++++  L++ +V +                K L   +          
Sbjct: 102 QAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKI 161

Query: 122 LNLMFENAKKFNPADSRL----------------YRDAVK----LQKLMQRKVQEF---S 158
              +   +   N  D                   Y + V     L   +++ ++      
Sbjct: 162 NQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSI-VKQNLEIGQYSK 220

Query: 159 LNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIE 207
           + +   ++ L+F+NA  FN     +Y+DA  L       +Q+    +++
Sbjct: 221 IYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQ 269

>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 =  110 bits (275), Expect = 8e-29
 Identities = 30/97 (30%), Positives = 51/97 (52%)

Query: 1   MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
               KN  +   LSEPF++L  K   P+YY I+ +P +L  + + L+ G YS + +   +
Sbjct: 168 ASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIID 227

Query: 61  LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENP 97
           + L+F+NA  FN   + +Y+DA  L       +Q+  
Sbjct: 228 MLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEF 264

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

 Score =  109 bits (275), Expect = 8e-31
 Identities = 33/87 (37%), Positives = 46/87 (52%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +G  L E F++ P +R  PDYY ++  P  L+ I + LK   Y  +N LT +  L+F NA
Sbjct: 24  QGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNA 83

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE 95
           K +   DS  Y+ A KL  L  R   E
Sbjct: 84  KSYYKPDSPEYKAACKLWDLYLRTRNE 110

>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 = 72.0 bits (177), Expect = 2e-16
 Identities = 24/62 (38%), Positives = 31/62 (50%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P  L+ I + LK   Y  +N LT +  L+F NAK +   DS  Y+ A KL  L  R   
Sbjct: 50  QPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRN 109

Query: 156 EF 157
           EF
Sbjct: 110 EF 111

>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 = 50.8 bits (122), Expect = 1e-08
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
           +Q+K++      +N LT +  L+F NAK +   D   Y+ A KL  L  R   E +
Sbjct: 57  IQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFV 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 =  109 bits (274), Expect = 2e-30
 Identities = 30/105 (28%), Positives = 60/105 (57%)

Query: 1   MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
           +   K+ + G  LSE F++LP+++  P+YY +I+ P     I + +++  Y +LN+L  +
Sbjct: 23  VIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKD 82

Query: 61  LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENPRSLLTIGK 105
           + L+ +NA+ FN   S +Y D++ LQ +     Q+  +   + G+
Sbjct: 83  VMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSEGE 127

>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 = 69.7 bits (171), Expect = 2e-15
 Identities = 17/62 (27%), Positives = 33/62 (53%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
             P     I + +++  Y +LN+L  ++ L+ +NA+ FN   S +Y D++ LQ +     
Sbjct: 56  RKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVR 115

Query: 155 QE 156
           Q+
Sbjct: 116 QK 117

>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 = 49.3 bits (118), Expect = 5e-08
 Identities = 25/125 (20%), Positives = 55/125 (44%), Gaps = 17/125 (13%)

Query: 89  MQRKVQENPRSLLTIGKTLKSGHYSTLNELTG-ELNLMFENAKKFNPADSRL---YRDAV 144
           M  K+  NP +L    K +        +  +G +L+ +F           +    Y + +
Sbjct: 1   MAEKLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQ-----LPSRKELPEYYELI 55

Query: 145 K----LQKLMQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRK 197
           +     +K ++ +++     SLN+L  ++ L+ +NA+ FN     +Y D++ LQ +    
Sbjct: 56  RKPVDFKK-IKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSV 114

Query: 198 VQEVM 202
            Q++ 
Sbjct: 115 RQKIE 119

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

 Score =  108 bits (272), Expect = 2e-30
 Identities = 32/87 (36%), Positives = 55/87 (63%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
            G  +SE F KLP+K   PDYY IIK P  L TI + +++G Y +++ +  +++L+ +NA
Sbjct: 27  SGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNA 86

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE 95
           K +N   S++++DA  ++K+   K  E
Sbjct: 87  KTYNEPGSQVFKDANSIKKIFYMKKAE 113

>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 = 72.8 bits (179), Expect = 1e-16
 Identities = 18/67 (26%), Positives = 41/67 (61%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P  L TI + +++G Y +++ +  +++L+ +NAK +N   S++++DA  ++K+   K  
Sbjct: 53  EPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKA 112

Query: 156 EFSLNEL 162
           E   +E+
Sbjct: 113 EIEHHEM 119

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 11/44 (25%), Positives = 27/44 (61%)

Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           S++ +  ++ L+ +NAK +N    ++++DA  ++K+   K  E+
Sbjct: 71  SIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEI 114

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

 Score =  108 bits (271), Expect = 5e-30
 Identities = 27/87 (31%), Positives = 47/87 (54%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
            G  LS  FL+LP++   PDYY  IK P  +  I   + +  Y  ++ +  +  +MF NA
Sbjct: 34  RGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNA 93

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE 95
             +N  +S +Y+DA+ L K++    ++
Sbjct: 94  CTYNEPESLIYKDALVLHKVLLETRRD 120

>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 = 71.2 bits (175), Expect = 5e-16
 Identities = 14/62 (22%), Positives = 31/62 (50%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P  +  I   + +  Y  ++ +  +  +MF NA  +N  +S +Y+DA+ L K++    +
Sbjct: 60  KPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRR 119

Query: 156 EF 157
           + 
Sbjct: 120 DL 121

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 10/43 (23%), Positives = 24/43 (55%)

Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
            ++ +  +  +MF NA  +N  +  +Y+DA+ L K++    ++
Sbjct: 78  DIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRD 120

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

 Score =  106 bits (267), Expect = 3e-29
 Identities = 30/97 (30%), Positives = 52/97 (53%)

Query: 1   MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
           +   +    G  L + F+  P+K+  PDYY+II  P  L  I   +++  Y+    +  +
Sbjct: 36  VLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIED 95

Query: 61  LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENP 97
           + LMF NA+ +N   S++Y DA  L+KL++ K +E  
Sbjct: 96  MKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKELG 132

>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 = 69.8 bits (171), Expect = 4e-15
 Identities = 19/62 (30%), Positives = 34/62 (54%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P  L  I   +++  Y+    +  ++ LMF NA+ +N   S++Y DA  L+KL++ K +
Sbjct: 70  EPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRK 129

Query: 156 EF 157
           E 
Sbjct: 130 EL 131

>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 = 47.1 bits (112), Expect = 5e-07
 Identities = 14/44 (31%), Positives = 26/44 (59%)

Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
               +  ++ LMF NA+ +N    ++Y DA  L+KL++ K +E+
Sbjct: 88  GEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKEL 131

>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 =  111 bits (279), Expect = 5e-29
 Identities = 36/229 (15%), Positives = 90/229 (39%), Gaps = 32/229 (13%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           +  ++ + F+KLP+++++P YY  I+ P S+  I K+    +    +    ++ L+ +N 
Sbjct: 93  KYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEI-KSRDYEYEDGPSNFLLDVELLTKNC 151

Query: 69  KKFNPADSRLYRDAVKLQKLMQR-------KVQENPRSLLTIGKTLKSGHYSTLNELTGE 121
           + +N  DS + ++++++  L++          +    +     K L   +          
Sbjct: 152 QAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKI 211

Query: 122 LNLMFENAKKFNPADSRL----------------YRDAVK----LQKLMQRKVQE---FS 158
              +   +   N  D                   Y + V     L   +++ ++      
Sbjct: 212 NQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSI-VKQNLEIGQYSK 270

Query: 159 LNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDIE 207
           + +   ++ L+F+NA  FN     +Y+DA  L       +Q+    +++
Sbjct: 271 IYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQ 319

>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 =  108 bits (271), Expect = 7e-28
 Identities = 30/97 (30%), Positives = 51/97 (52%)

Query: 1   MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGE 60
               KN  +   LSEPF++L  K   P+YY I+ +P +L  + + L+ G YS + +   +
Sbjct: 218 ASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIID 277

Query: 61  LNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQENP 97
           + L+F+NA  FN   + +Y+DA  L       +Q+  
Sbjct: 278 MLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEF 314

>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 =  110 bits (275), Expect = 5e-29
 Identities = 33/206 (16%), Positives = 75/206 (36%), Gaps = 18/206 (8%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PF      +   DYY+II  P  L T+ + ++   Y +  E    L L+ +N+  +N 
Sbjct: 65  TYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNG 124

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 133
               L + +  +  L   K++E    L  + K +              +       K   
Sbjct: 125 PKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMA 184

Query: 134 PADSRLYRDAVKLQKL---------------MQRKVQE---FSLNELTGELSLMFENAKK 175
             DS  +   V  + +               +++ + +    S      +++L+  N+ K
Sbjct: 185 VPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVK 244

Query: 176 FNPADLRLYRDAVKLQKLMQRKVQEV 201
           +N  + +  + A ++  +  + + E 
Sbjct: 245 YNGPESQYTKTAQEIVNVCYQTLTEY 270

>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 =  102 bits (254), Expect = 5e-26
 Identities = 28/104 (26%), Positives = 51/104 (49%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 188 SWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 247

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNE 117
            +S+  + A ++  +  + + E    L  + K + +   + L E
Sbjct: 248 PESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEE 291

>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 = 72.0 bits (176), Expect = 5e-15
 Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           KV  NP  L TI K +    Y +      ++NL+  N+ K+N  +S+  + A ++  +  
Sbjct: 205 KVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCY 264

Query: 152 RKVQEFS--LNELTGELSLMFENAKK 175
           + + E+   L +L  ++    E A +
Sbjct: 265 QTLTEYDEHLTQLEKDICTAKEAALE 290

>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 =  109 bits (273), Expect = 6e-29
 Identities = 33/206 (16%), Positives = 75/206 (36%), Gaps = 18/206 (8%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PF      +   DYY+II  P  L T+ + ++   Y +  E    L L+ +N+  +N 
Sbjct: 32  TYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNG 91

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 133
               L + +  +  L   K++E    L  + K +              +       K   
Sbjct: 92  PKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMA 151

Query: 134 PADSRLYRDAVKLQKL---------------MQRKVQEF---SLNELTGELSLMFENAKK 175
             DS  +   V  + +               +++ + +    S      +++L+  N+ K
Sbjct: 152 VPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVK 211

Query: 176 FNPADLRLYRDAVKLQKLMQRKVQEV 201
           +N  + +  + A ++  +  + + E 
Sbjct: 212 YNGPESQYTKTAQEIVNVCYQTLTEY 237

>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 =  101 bits (254), Expect = 4e-26
 Identities = 29/108 (26%), Positives = 52/108 (48%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 155 SWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 214

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGE 121
            +S+  + A ++  +  + + E    L  + K + +   + L E   E
Sbjct: 215 PESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELE 262

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

 Score = 72.7 bits (178), Expect = 2e-15
 Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           KV  NP  L TI K +    Y +      ++NL+  N+ K+N  +S+  + A ++  +  
Sbjct: 172 KVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCY 231

Query: 152 RKVQEFS--LNELTGELSLMFENAKK 175
           + + E+   L +L  ++    E A +
Sbjct: 232 QTLTEYDEHLTQLEKDICTAKEAALE 257

>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 = 90.1 bits (224), Expect = 4e-23
 Identities = 25/97 (25%), Positives = 43/97 (44%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
              F +       PDY   IK P    T+ + L++  Y   ++   + NL+  N  K+N 
Sbjct: 25  GNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNA 84

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSG 110
            D+  YR AV+L++     +++  R    +G    SG
Sbjct: 85  KDTIFYRAAVRLREQGGAVLRQARRQAEKMGSGPSSG 121

>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 = 62.0 bits (151), Expect = 1e-12
 Identities = 15/61 (24%), Positives = 31/61 (50%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P    T+ + L++  Y   ++   + NL+  N  K+N  D+  YR AV+L++     ++
Sbjct: 46  KPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLR 105

Query: 156 E 156
           +
Sbjct: 106 Q 106

>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 = 44.3 bits (105), Expect = 3e-06
 Identities = 11/55 (20%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           M++ ++     + ++   + +L+  N  K+N  D   YR AV+L++     +++ 
Sbjct: 53  MKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQA 107

>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 = 88.8 bits (220), Expect = 3e-22
 Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 4/87 (4%)

Query: 9   EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENA 68
           EG   S+   ++PA    P++    K P +   I K +++  Y  L+     +  + E A
Sbjct: 26  EGRCYSDSLAEIPAVD--PNFP--NKPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERA 81

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE 95
           ++ N  DS +Y DAV+LQ+   +   E
Sbjct: 82  RRMNRTDSEIYEDAVELQQFFIKIRDE 108

>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 = 72.2 bits (177), Expect = 4e-16
 Identities = 27/148 (18%), Positives = 59/148 (39%), Gaps = 10/148 (6%)

Query: 56  ELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK---VQENPRSLLTIGKTLKSGHY 112
            +   ++ +F +       + R Y D+  L ++         + P +   I K +++  Y
Sbjct: 7   LIQELIHNLFVSVMSHQDDEGRCYSDS--LAEIPAVDPNFPNKPPLTFDIIRKNVENNRY 64

Query: 113 STLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFEN 172
             L+     +  + E A++ N  DS +Y DAV+LQ+   +        EL     ++   
Sbjct: 65  RRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRD-----ELCKNGEILLSP 119

Query: 173 AKKFNPADLRLYRDAVKLQKLMQRKVQE 200
           A  +    L    +  + +KL +   ++
Sbjct: 120 ALSYTTKHLHNDVEKERKEKLPKEIEED 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 = 43.7 bits (103), Expect = 9e-06
 Identities = 12/44 (27%), Positives = 22/44 (50%)

Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
            L+     +  + E A++ N  D  +Y DAV+LQ+   +   E+
Sbjct: 66  RLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDEL 109

>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 = 89.2 bits (221), Expect = 3e-22
 Identities = 25/84 (29%), Positives = 45/84 (53%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PFL+       PDYY +IK P  L T+ + ++  +Y  L E   ++  +F+N + +NP
Sbjct: 90  AWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNP 149

Query: 74  ADSRLYRDAVKLQKLMQRKVQENP 97
           +DS  Y+ A  L+    +K++   
Sbjct: 150 SDSPFYQCAEVLESFFVQKLKGFK 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 = 66.4 bits (162), Expect = 1e-13
 Identities = 18/66 (27%), Positives = 36/66 (54%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
            V + P  L T+ + ++  +Y  L E   ++  +F+N + +NP+DS  Y+ A  L+    
Sbjct: 107 GVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFV 166

Query: 152 RKVQEF 157
           +K++ F
Sbjct: 167 QKLKGF 172

>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 = 44.9 bits (106), Expect = 4e-06
 Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
           M+ +VQ      L E   +++ +F+N + +NP+D   Y+ A  L+    +K++ 
Sbjct: 118 MEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKG 171

>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 = 87.0 bits (216), Expect = 5e-22
 Identities = 27/82 (32%), Positives = 44/82 (53%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PF++   K   PDYY +I+ P  L T+ + L+S +Y T      +L  +  N +++NP
Sbjct: 25  AWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNP 84

Query: 74  ADSRLYRDAVKLQKLMQRKVQE 95
            DS   R A  L+K    K++E
Sbjct: 85  PDSEYCRCASALEKFFYFKLKE 106

>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 = 64.6 bits (158), Expect = 1e-13
 Identities = 21/68 (30%), Positives = 34/68 (50%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           +V   P  L T+ + L+S +Y T      +L  +  N +++NP DS   R A  L+K   
Sbjct: 42  EVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFY 101

Query: 152 RKVQEFSL 159
            K++E  L
Sbjct: 102 FKLKEGGL 109

>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 = 46.1 bits (110), Expect = 6e-07
 Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILD 205
           M  +++     +      +L  +  N +++NP D    R A  L+K    K++E  ++D
Sbjct: 53  MTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEGGLID 111

>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 = 86.2 bits (214), Expect = 1e-21
 Identities = 26/83 (31%), Positives = 44/83 (53%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PFL+   + Y P+YY+IIK P  + ++ K L  G Y T  E   ++  MF N +K+N 
Sbjct: 34  SWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNG 93

Query: 74  ADSRLYRDAVKLQKLMQRKVQEN 96
             S   + +  L++   R + ++
Sbjct: 94  ESSEYTKMSDNLERCFHRAMMKH 116

>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 = 60.0 bits (146), Expect = 5e-12
 Identities = 15/61 (24%), Positives = 28/61 (45%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P  + ++ K L  G Y T  E   ++  MF N +K+N   S   + +  L++   R + 
Sbjct: 55  APMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMM 114

Query: 156 E 156
           +
Sbjct: 115 K 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 = 41.2 bits (97), Expect = 4e-05
 Identities = 10/54 (18%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 150 MQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
           M++K+      +  E   ++  MF N +K+N       + +  L++   R + +
Sbjct: 62  MEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 115

>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 = 85.1 bits (211), Expect = 3e-21
 Identities = 28/84 (33%), Positives = 44/84 (52%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PFL+   K   PDYY  IK P  L T+   L+S  Y  + +   +  L+F N + +N 
Sbjct: 31  AWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNG 90

Query: 74  ADSRLYRDAVKLQKLMQRKVQENP 97
            ++  Y+ A +L+K    KV+E P
Sbjct: 91  ENTSYYKYANRLEKFFNNKVKEIP 114

>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 = 61.6 bits (150), Expect = 2e-12
 Identities = 17/66 (25%), Positives = 32/66 (48%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
              + P  L T+   L+S  Y  + +   +  L+F N + +N  ++  Y+ A +L+K   
Sbjct: 48  DFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFN 107

Query: 152 RKVQEF 157
            KV+E 
Sbjct: 108 NKVKEI 113

>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 = 42.7 bits (101), Expect = 1e-05
 Identities = 13/55 (23%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           M+ K++      + +   +  L+F N + +N  +   Y+ A +L+K    KV+E+
Sbjct: 59  MEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 113

>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 = 84.9 bits (210), Expect = 9e-21
 Identities = 29/108 (26%), Positives = 52/108 (48%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 48  SWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 107

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGE 121
            +S+  + A ++  +  + + E    L  + K + +   + L E   E
Sbjct: 108 PESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELE 155

>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 = 60.6 bits (147), Expect = 1e-11
 Identities = 20/90 (22%), Positives = 39/90 (43%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           KV  NP  L TI K +    Y +      ++NL+  N+ K+N  +S+  + A ++  +  
Sbjct: 65  KVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCY 124

Query: 152 RKVQEFSLNELTGELSLMFENAKKFNPADL 181
           + + E+  +    E  +          A+L
Sbjct: 125 QTLTEYDEHLTQLEKDICTAKEAALEEAEL 154

>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 = 41.4 bits (97), Expect = 5e-05
 Identities = 7/56 (12%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 150 MQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
           +++ + +    S      +++L+  N+ K+N  + +  + A ++  +  + + E  
Sbjct: 76  IRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYD 131

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

 Score = 83.6 bits (207), Expect = 1e-20
 Identities = 28/97 (28%), Positives = 50/97 (51%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           +  F +  + +  PDY   IK+P    T+ K L++  Y  L+E   + +L+ +N  K+N 
Sbjct: 31  ARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNA 90

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSG 110
            D+  YR AV+L+      +++  R + +IG    SG
Sbjct: 91  RDTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASG 127

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

 Score = 60.1 bits (146), Expect = 8e-12
 Identities = 17/66 (25%), Positives = 34/66 (51%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
              ++P    T+ K L++  Y  L+E   + +L+ +N  K+N  D+  YR AV+L+    
Sbjct: 48  DHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGG 107

Query: 152 RKVQEF 157
             +++ 
Sbjct: 108 VVLRQA 113

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

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 13/55 (23%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           M+++++     +L+E   +  L+ +N  K+N  D   YR AV+L+      +++ 
Sbjct: 59  MRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQA 113

>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 = 83.1 bits (206), Expect = 1e-20
 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 4/90 (4%)

Query: 14  SEPFLKLP--AKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKK 70
           S PF + P   +    PDY+ I+KNP  L TI + L +G Y    +   ++ LMF NA  
Sbjct: 30  SLPFRQ-PVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWL 88

Query: 71  FNPADSRLYRDAVKLQKLMQRKVQENPRSL 100
           +N   SR+Y+   KL ++ ++++    +SL
Sbjct: 89  YNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 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 = 60.4 bits (147), Expect = 5e-12
 Identities = 19/63 (30%), Positives = 34/63 (53%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
           +NP  L TI + L +G Y    +   ++ LMF NA  +N   SR+Y+   KL ++ ++++
Sbjct: 52  KNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEI 111

Query: 155 QEF 157
              
Sbjct: 112 DPV 114

>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 = 41.1 bits (97), Expect = 4e-05
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 168 LMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
           LMF NA  +N    R+Y+   KL ++ ++++  VM
Sbjct: 81  LMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVM 115

>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 = 84.6 bits (209), Expect = 3e-20
 Identities = 28/86 (32%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKS--GHYSTLNELTGELNLMFENAKKF 71
           S  F   P     PDYY+IIKNP  L TI K L+     YS   +   +  L+F+N  +F
Sbjct: 99  SLAFQD-PVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEF 157

Query: 72  NPADSRLYRDAVKLQKLMQRKVQENP 97
           N  DS +    +KL+   +  ++   
Sbjct: 158 NEPDSEVANAGIKLENYFEELLKNLY 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 = 42.3 bits (99), Expect = 3e-05
 Identities = 9/55 (16%), Positives = 24/55 (43%)

Query: 147 QKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           ++L +         +   +  L+F+N  +FN  D  +    +KL+   +  ++ +
Sbjct: 128 KRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNL 182

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

 Score = 82.4 bits (204), Expect = 3e-20
 Identities = 22/88 (25%), Positives = 36/88 (40%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S  F         P Y  IIK+P    T+ + +K+  Y ++ EL     LM  NA  +N 
Sbjct: 26  SAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNK 85

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLL 101
            ++  Y+ A KL     + + +      
Sbjct: 86  PETIYYKAAKKLLHSGMKILSQERLEHH 113

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

 Score = 62.3 bits (152), Expect = 9e-13
 Identities = 16/67 (23%), Positives = 30/67 (44%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
           +P    T+ + +K+  Y ++ EL     LM  NA  +N  ++  Y+ A KL     + + 
Sbjct: 47  HPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILS 106

Query: 156 EFSLNEL 162
           +  L   
Sbjct: 107 QERLEHH 113

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 150 MQRKVQEF---SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
           M+ K++     S+ EL     LM  NA  +N  +   Y+ A KL     + + +
Sbjct: 54  MKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQ 107

>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 = 82.0 bits (203), Expect = 6e-20
 Identities = 29/86 (33%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 14  SEPFLK--LPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKF 71
           + PF +     K   PDYY+IIK P  + TI K L++ +Y    E   + N MF N   +
Sbjct: 39  AWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIY 98

Query: 72  NPADSRLYRDAVKLQKLMQRKVQENP 97
           N     +   A  L+KL  +K+ E P
Sbjct: 99  NKPGDDIVLMAEALEKLFLQKINELP 124

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 18/62 (29%), Positives = 28/62 (45%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P  + TI K L++ +Y    E   + N MF N   +N     +   A  L+KL  +K+ 
Sbjct: 62  TPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKIN 121

Query: 156 EF 157
           E 
Sbjct: 122 EL 123

>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 = 40.4 bits (95), Expect = 8e-05
 Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
           ++++++    ++  E   + + MF N   +N     +   A  L+KL  +K+ E+ 
Sbjct: 69  IKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELP 124

>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 = 80.5 bits (199), Expect = 2e-19
 Identities = 19/82 (23%), Positives = 34/82 (41%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
              F         P Y  IIK+P    T+   + +  Y ++ E   +  LM +NA  +N 
Sbjct: 31  HGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNR 90

Query: 74  ADSRLYRDAVKLQKLMQRKVQE 95
            D+  Y+ A K+     + + +
Sbjct: 91  PDTVYYKLAKKILHAGFKMMSK 112

>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 = 63.1 bits (154), Expect = 5e-13
 Identities = 16/72 (22%), Positives = 32/72 (44%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
           +P    T+   + +  Y ++ E   +  LM +NA  +N  D+  Y+ A K+     + + 
Sbjct: 52  HPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMS 111

Query: 156 EFSLNELTGELS 167
           +  L  L   +S
Sbjct: 112 KERLLALKRSMS 123

>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 = 43.9 bits (104), Expect = 4e-06
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILDI 206
           M+ K+      S+ E   +  LM +NA  +N  D   Y+ A K+     + + +  +L +
Sbjct: 59  MKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLAL 118

Query: 207 E 207
           +
Sbjct: 119 K 119

>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 = 80.0 bits (198), Expect = 2e-19
 Identities = 25/85 (29%), Positives = 42/85 (49%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PFL     +  P Y ++IK P    TI + L SG Y  L     ++ L+F+N + FN 
Sbjct: 31  AWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNE 90

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPR 98
            DS + R    ++K  ++K  +  +
Sbjct: 91  DDSDIGRAGHNMRKYFEKKWTDTFK 115

>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 = 58.5 bits (142), Expect = 3e-11
 Identities = 20/66 (30%), Positives = 33/66 (50%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           KV + P    TI + L SG Y  L     ++ L+F+N + FN  DS + R    ++K  +
Sbjct: 48  KVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFE 107

Query: 152 RKVQEF 157
           +K  + 
Sbjct: 108 KKWTDT 113

>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 = 40.4 bits (95), Expect = 8e-05
 Identities = 11/56 (19%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
           ++ K+      +L     ++ L+F+N + FN  D  + R    ++K  ++K  +  
Sbjct: 59  IREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTF 114

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

 Score = 81.1 bits (200), Expect = 3e-19
 Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 2/88 (2%)

Query: 14  SEPFLKL--PAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKF 71
              F KL    K+  PDYY +IKNP S   I   LK G Y+  +E   ++ L+F+N   +
Sbjct: 39  GHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLY 98

Query: 72  NPADSRLYRDAVKLQKLMQRKVQENPRS 99
           N ++S +      ++     ++     +
Sbjct: 99  NTSNSVVAITGKNIETYFNNQLIVMGYN 126

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

 Score = 60.3 bits (146), Expect = 2e-11
 Identities = 16/91 (17%), Positives = 38/91 (41%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
           NP S   I   LK G Y+  +E   ++ L+F+N   +N ++S +      ++     ++ 
Sbjct: 62  NPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFNNQLI 121

Query: 156 EFSLNELTGELSLMFENAKKFNPADLRLYRD 186
               N    +   + +  K     +++  ++
Sbjct: 122 VMGYNNFILKEKKINDMLKLVEEENIKWSKE 152

>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 = 80.5 bits (199), Expect = 3e-19
 Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 2/88 (2%)

Query: 14  SEPFLK--LPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKF 71
           + PF +     K   PDY++IIK P  + TI + L++ +Y   +E   + N MF N   +
Sbjct: 50  AWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIY 109

Query: 72  NPADSRLYRDAVKLQKLMQRKVQENPRS 99
           N     +   A  L+K+  +KV   P+ 
Sbjct: 110 NKPTDDIVLMAQTLEKIFLQKVASMPQE 137

>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 = 58.2 bits (141), Expect = 6e-11
 Identities = 16/62 (25%), Positives = 28/62 (45%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
            P  + TI + L++ +Y   +E   + N MF N   +N     +   A  L+K+  +KV 
Sbjct: 73  QPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVA 132

Query: 156 EF 157
             
Sbjct: 133 SM 134

>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 = 40.9 bits (96), Expect = 9e-05
 Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
           ++R+++    ++ +E   + + MF N   +N     +   A  L+K+  +KV  + 
Sbjct: 80  IKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMP 135

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

 Score = 79.7 bits (197), Expect = 4e-19
 Identities = 28/86 (32%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKS--GHYSTLNELTGELNLMFENAKKF 71
           S  F   P     PDYY+IIKNP  L TI K L+     YS   +   +  L+F+N  +F
Sbjct: 38  SLAFQD-PVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEF 96

Query: 72  NPADSRLYRDAVKLQKLMQRKVQENP 97
           N  DS +    +KL+   +  ++   
Sbjct: 97  NEPDSEVANAGIKLENYFEELLKNLY 122

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

 Score = 55.1 bits (133), Expect = 6e-10
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 96  NPRSLLTIGKTLKS--GHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRK 153
           NP  L TI K L+     YS   +   +  L+F+N  +FN  DS +    +KL+   +  
Sbjct: 58  NPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEEL 117

Query: 154 VQEFSLNE 161
           ++     +
Sbjct: 118 LKNLYPEK 125

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

 Score = 40.8 bits (96), Expect = 7e-05
 Identities = 9/55 (16%), Positives = 24/55 (43%)

Query: 147 QKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           ++L +         +   +  L+F+N  +FN  D  +    +KL+   +  ++ +
Sbjct: 67  KRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNL 121

>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 = 78.9 bits (195), Expect = 7e-19
 Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 12  NLSEPFLKL--PAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
             + PF K          DY  IIK+P  + TI   L++  Y    E   ++ LMF N  
Sbjct: 41  AYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCY 100

Query: 70  KFNPADSRLYRDAVKLQKLMQRKVQENP 97
           K+NP D  +   A KLQ + + +  + P
Sbjct: 101 KYNPPDHEVVAMARKLQDVFEMRFAKMP 128

>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 = 58.1 bits (141), Expect = 5e-11
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
           +P  + TI   L++  Y    E   ++ LMF N  K+NP D  +   A KLQ + + +  
Sbjct: 66  HPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFA 125

Query: 156 EF 157
           + 
Sbjct: 126 KM 127

>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 = 38.5 bits (90), Expect = 4e-04
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 168 LMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           LMF N  K+NP D  +   A KLQ + + +  ++
Sbjct: 94  LMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 127

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

 Score = 77.7 bits (192), Expect = 2e-18
 Identities = 28/88 (31%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 12  NLSEPFLKL--PAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK 69
             + PF K          DY  IIK+P  + TI   L+S  Y    E   ++ LMF N  
Sbjct: 28  AYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCY 87

Query: 70  KFNPADSRLYRDAVKLQKLMQRKVQENP 97
           K+NP D  +   A KLQ + + +  + P
Sbjct: 88  KYNPPDHEVVAMARKLQDVFEMRFAKMP 115

>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 = 57.3 bits (139), Expect = 6e-11
 Identities = 19/62 (30%), Positives = 30/62 (48%)

Query: 96  NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQ 155
           +P  + TI   L+S  Y    E   ++ LMF N  K+NP D  +   A KLQ + + +  
Sbjct: 53  HPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFA 112

Query: 156 EF 157
           + 
Sbjct: 113 KM 114

>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 = 38.4 bits (90), Expect = 4e-04
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 168 LMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
           LMF N  K+NP D  +   A KLQ + + +  ++
Sbjct: 81  LMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKM 114

>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 = 78.2 bits (193), Expect = 2e-18
 Identities = 28/97 (28%), Positives = 49/97 (50%), Gaps = 3/97 (3%)

Query: 14  SEPFLKLPAKRYN-PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
           SEPF + P      PDY  II  P    T+ +TL++G+Y +  EL  ++ L+F N+K + 
Sbjct: 39  SEPFRQ-PVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYT 97

Query: 73  PAD-SRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLK 108
           P+  SR+Y  +++L    +  +        +  +  K
Sbjct: 98  PSKRSRIYSMSLRLSAFFEEHISSVLSDYKSALRFHK 134

>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 = 55.5 bits (134), Expect = 4e-10
 Identities = 18/67 (26%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 91  RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD-SRLYRDAVKLQKL 149
           R + + P    T+ +TL++G+Y +  EL  ++ L+F N+K + P+  SR+Y  +++L   
Sbjct: 55  RDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAF 114

Query: 150 MQRKVQE 156
            +  +  
Sbjct: 115 FEEHISS 121

>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 = 77.0 bits (190), Expect = 4e-18
 Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           SEPF +       PDY  II  P    T+ +TL +G+Y +  E   ++ L+F NAK + P
Sbjct: 28  SEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTP 87

Query: 74  AD-SRLYRDAVKLQKLMQRKVQENPRSL 100
              S++Y   ++L  L + K+++     
Sbjct: 88  NKRSKIYSMTLRLSALFEEKMKKISSDF 115

>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 = 56.2 bits (136), Expect = 1e-10
 Identities = 24/88 (27%), Positives = 46/88 (52%), Gaps = 10/88 (11%)

Query: 91  RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPAD-SRLYRDAVKLQKL 149
           R + + P    T+ +TL +G+Y +  E   ++ L+F NAK + P   S++Y   ++L  L
Sbjct: 44  RDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSAL 103

Query: 150 MQRKVQEFSLNELTGELSLMFENAKKFN 177
            + K+++ S +         F+  +KFN
Sbjct: 104 FEEKMKKISSD---------FKIGQKFN 122

>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 = 38.5 bits (90), Expect = 3e-04
 Identities = 13/64 (20%), Positives = 30/64 (46%), Gaps = 5/64 (7%)

Query: 150 MQRKVQE---FSLNELTGELSLMFENAKKFNPADL-RLYRDAVKLQKLMQRKVQEVMILD 205
           ++  +      S  E   ++ L+F NAK + P    ++Y   ++L  L + K+++ +  D
Sbjct: 56  VRETLDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKK-ISSD 114

Query: 206 IECQ 209
            +  
Sbjct: 115 FKIG 118

>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 = 71.7 bits (176), Expect = 4e-16
 Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 2/89 (2%)

Query: 14  SEPFLKLPA-KRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 72
              F K P      PDY  +IK P  L ++   +    Y T+ +   +++L+  NA ++N
Sbjct: 28  FRVFTK-PVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYN 86

Query: 73  PADSRLYRDAVKLQKLMQRKVQENPRSLL 101
           P      R        ++       +  L
Sbjct: 87  PDRDPGDRLIRHRACALRDTAYAIIKEEL 115

>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 = 55.1 bits (133), Expect = 5e-10
 Identities = 13/81 (16%), Positives = 31/81 (38%)

Query: 95  ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKV 154
           + P  L ++   +    Y T+ +   +++L+  NA ++NP      R        ++   
Sbjct: 48  KQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTA 107

Query: 155 QEFSLNELTGELSLMFENAKK 175
                 EL  +   + E  ++
Sbjct: 108 YAIIKEELDEDFEQLCEEIQE 128

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

 Score = 71.3 bits (175), Expect = 6e-16
 Identities = 15/75 (20%), Positives = 30/75 (40%)

Query: 27  PDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 86
            DY  +IK P  L T+   +   +Y T  +   +++L+  NA ++NP      +      
Sbjct: 38  SDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRA 97

Query: 87  KLMQRKVQENPRSLL 101
             ++        + L
Sbjct: 98  CTLKDTAHAIIAAEL 112

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

 Score = 57.5 bits (139), Expect = 8e-11
 Identities = 17/88 (19%), Positives = 36/88 (40%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           +V + P  L T+   +   +Y T  +   +++L+  NA ++NP      +        ++
Sbjct: 42  EVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLK 101

Query: 152 RKVQEFSLNELTGELSLMFENAKKFNPA 179
                    EL  E + + E  K+  P+
Sbjct: 102 DTAHAIIAAELDPEFNKLCEEIKESGPS 129

>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 = 68.0 bits (165), Expect = 5e-14
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 4/81 (4%)

Query: 15  EPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENAKKF 71
             F + P     P+YY+IIK P  L T+ K L+   S HY   ++   ++ L+F+N ++F
Sbjct: 100 IEFQE-PVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERF 158

Query: 72  NPADSRLYRDAVKLQKLMQRK 92
           N     +   A   +  ++  
Sbjct: 159 NEMMKVVQVYADTQEINLKAD 179

>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 = 50.3 bits (119), Expect = 1e-07
 Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 6/85 (7%)

Query: 91  RKVQENPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ 147
            K+ + P  L T+ K L+   S HY   ++   ++ L+F+N ++FN     +   A   +
Sbjct: 114 YKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQE 173

Query: 148 KLMQRKVQEFSLNELTGELSLMFEN 172
             ++    +  + +    ++L FE+
Sbjct: 174 INLK---ADSEVAQAGKAVALYFED 195

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

 Score = 61.5 bits (148), Expect = 8e-12
 Identities = 8/76 (10%), Positives = 32/76 (42%)

Query: 20  LPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY 79
           L ++  +       + P  L  + + +  G+Y+++ E + ++  + + A   +     + 
Sbjct: 88  LNSRTTSHLLRYRQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIK 147

Query: 80  RDAVKLQKLMQRKVQE 95
           +    ++    R+++ 
Sbjct: 148 KANSMVKSFFIRQMER 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 = 57.7 bits (138), Expect = 2e-10
 Identities = 9/69 (13%), Positives = 31/69 (44%)

Query: 89  MQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK 148
           + R  Q+ P  L  + + +  G+Y+++ E + ++  + + A   +     + +    ++ 
Sbjct: 96  LLRYRQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKS 155

Query: 149 LMQRKVQEF 157
              R+++  
Sbjct: 156 FFIRQMERV 164

>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 = 41.9 bits (97), Expect = 6e-05
 Identities = 9/80 (11%), Positives = 33/80 (41%), Gaps = 4/80 (5%)

Query: 125 MFENAKKFNPADSRLYRDAVKLQKLMQRKVQE---FSLNELTGELSLMFENAKKFNPADL 181
              N++  +       +  + L+  ++RK+ +    S+ E + ++  + + A   +    
Sbjct: 86  ALLNSRTTSHLLRYRQQQPLDLEG-VKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQP 144

Query: 182 RLYRDAVKLQKLMQRKVQEV 201
            + +    ++    R+++ V
Sbjct: 145 EIKKANSMVKSFFIRQMERV 164

>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 = 59.1 bits (142), Expect = 5e-11
 Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 6/87 (6%)

Query: 12  NLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENA 68
               P  +L     +            L  I   L+   S  YS+  E   ++  MF+  
Sbjct: 92  EPCRPLHQLA--TDSTFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQF 149

Query: 69  KKFNPADSRLYRDAVKLQKLMQRKVQE 95
            K     +   +  + LQ+  + ++ E
Sbjct: 150 NKLTEDKA-DVQSIIGLQRFFETRMNE 175

>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 = 48.7 bits (115), Expect = 3e-07
 Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 4/65 (6%)

Query: 96  NPRSLLTIGKTLK---SGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQR 152
               L  I   L+   S  YS+  E   ++  MF+   K     +   +  + LQ+  + 
Sbjct: 113 GTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLTEDKA-DVQSIIGLQRFFET 171

Query: 153 KVQEF 157
           ++ E 
Sbjct: 172 RMNEA 176

>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 = 47.2 bits (111), Expect = 3e-06
 Identities = 43/315 (13%), Positives = 87/315 (27%), Gaps = 100/315 (31%)

Query: 13  LSEPFLKLPAKRYNPDYYR----------IIKNP----RSLLTIGKTLKSG--------- 49
             + F+     +   D  +          II +      +L      L            
Sbjct: 25  FEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVE 84

Query: 50  -----HYSTL-NELTGELNLMFENAKKFNPADSRLYRDAVKLQKL----------MQRKV 93
                +Y  L + +  E        + +     RLY D     K           +++ +
Sbjct: 85  EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQAL 144

Query: 94  QE-NPRSLLTI------GKT-LKSGHYSTLNELTGELNLMFE----NAKKFNPADSRLYR 141
            E  P   + I      GKT +             +  + F+    N K  N  ++ L  
Sbjct: 145 LELRPAKNVLIDGVLGSGKTWVAL---DVCLSYKVQCKMDFKIFWLNLKNCNSPETVL-- 199

Query: 142 DAVKLQKLMQRKVQEF-SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRK--- 197
               LQKL+ +    + S ++ +  + L   + +              +L++L++ K   
Sbjct: 200 --EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA-------------ELRRLLKSKPYE 244

Query: 198 --------VQEVMIL---DIECQVYLISDELTHYQVVLTGTAEQVRLSGLPDG------- 239
                   VQ        ++ C++ L +        +   T   + L             
Sbjct: 245 NCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK 304

Query: 240 ----DWL---AFTLP 247
                +L      LP
Sbjct: 305 SLLLKYLDCRPQDLP 319

>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 = 46.8 bits (110), Expect = 4e-06
 Identities = 36/212 (16%), Positives = 75/212 (35%), Gaps = 34/212 (16%)

Query: 37  RSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSR-LYRDAV--KLQKLMQRKV 93
           + LLT   T        L+  T     +  ++    P + + L    +  + Q L +  +
Sbjct: 267 KILLT---TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVL 323

Query: 94  QENPRSLLTIGKTLKSG-----HYSTLNELTGELNLMFENA-KKFNPADSR-LY------ 140
             NPR L  I ++++ G     ++  +N    +L  + E++     PA+ R ++      
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVN--CDKLTTIIESSLNVLEPAEYRKMFDRLSVF 381

Query: 141 RDAVK-----LQKL---MQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRD----AV 188
             +       L  +   + +      +N+L  + SL+ +  K+   +   +Y +      
Sbjct: 382 PPSAHIPTILLSLIWFDVIKSDVMVVVNKLH-KYSLVEKQPKESTISIPSIYLELKVKLE 440

Query: 189 KLQKLMQRKVQEVMILDIECQVYLISDELTHY 220
               L +  V    I        LI   L  Y
Sbjct: 441 NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY 472

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	256
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
2dat_A	123	Possible global transcription activator SNF2L2; br	99.94
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.94
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.94
3d7c_A	112	General control of amino acid synthesis protein 5;	99.93
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.93
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.93
2grc_A	129	Probable global transcription activator SNF2L4; br	99.93
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.93
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.93
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.92
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.92
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.92
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.92
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.92
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.92
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.92
3uv4_A	158	Second bromodomain of human transcription initiat	99.92
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.91
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.91
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.91
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.91
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.91
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.9
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.9
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.9
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.9
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.87
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.87
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.87
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.87
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.87
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.86
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.86
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.85
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.84
3d7c_A	112	General control of amino acid synthesis protein 5;	99.65
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.65
2dat_A	123	Possible global transcription activator SNF2L2; br	99.64
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.63
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.63
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.63
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.63
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.62
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.62
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.62
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.62
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.62
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.61
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.61
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.61
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.61
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.6
2grc_A	129	Probable global transcription activator SNF2L4; br	99.6
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.6
3uv4_A	158	Second bromodomain of human transcription initiat	99.6
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.59
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.58
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.58
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.57
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.57
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.55
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.54
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.54
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.47
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.47
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.46
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.45
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.38
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.33
1w4s_A	174	Polybromo, polybromo 1 protein; BAH, bromo-associa	99.29
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.17
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	97.59
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	97.18
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	97.04
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	95.38
4ft4_B	784	DNA (cytosine-5)-methyltransferase 1; chromodomain	94.03
4dov_A	163	ORC1, origin recognition complex subunit 1; DNA re	91.42

>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=6.2e-39  Score=279.40  Aligned_cols=156  Identities=22%  Similarity=0.393  Sum_probs=149.7

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+++....++.|++|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++.+
T Consensus        20 ~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~i~~~   99 (265)
T 3uv5_A           20 ESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQI   99 (265)
T ss_dssp             HHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHHHHHcCCCchhhhCCCChhhcCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhhhcCCCCChHHHH
Confidence            45778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc--------------------------------------------------------------ccc
Q psy1225          82 AVKLQKLMQRKVQEN--------------------------------------------------------------PRS   99 (256)
Q Consensus        82 A~~L~~~f~~~~~kl--------------------------------------------------------------P~d   99 (256)
                      |..|.+.+.+.+.++                                                              |||
T Consensus       100 A~~l~~~~~~~~~~~~~~~~~~ek~i~p~~dd~~~~~~~~il~~i~~~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~Pmd  179 (265)
T 3uv5_A          100 SQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMD  179 (265)
T ss_dssp             HHHHHHHHHHHHHHTHHHHHHHHHHHSTTTTCHHHHHHHHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCC
T ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhhhhhccccchhhHHHHHHHHHHHHHHHhhhhhHHHhCCCChhHhCcHHHHhCCccc
Confidence            999999998877654                                                              999


Q ss_pred             HHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225         100 LLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus       100 l~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      |+||++|+++|.|.++++|..|+.|||.||+.||+++|.+|++|..|++.|.+.++++
T Consensus       180 l~tI~~kl~~~~Y~~~~~f~~D~~lif~Na~~yN~~~s~~~~~A~~l~~~~~~~~~~~  237 (265)
T 3uv5_A          180 LETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEY  237 (265)
T ss_dssp             HHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999876

>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=1.1e-37  Score=274.88  Aligned_cols=156  Identities=22%  Similarity=0.393  Sum_probs=145.0

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ..+++....++.+++|+.||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++.+
T Consensus        53 ~~il~~l~~~~~a~~F~~pV~~~~~pdY~~iIk~PmDL~tIk~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~  132 (292)
T 3aad_A           53 ESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQI  132 (292)
T ss_dssp             HHHHHHHSSSTTCGGGSSSCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCSSSHHHHH
T ss_pred             HHHHHHHHhCCcchhhcCCCCchhcccHHHHcCCcCCHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHHHcCCchHHHHH
Confidence            45777888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc--------------------------------------------------------------ccc
Q psy1225          82 AVKLQKLMQRKVQEN--------------------------------------------------------------PRS   99 (256)
Q Consensus        82 A~~L~~~f~~~~~kl--------------------------------------------------------------P~d   99 (256)
                      |..|.+.|...+.++                                                              |||
T Consensus       133 A~~L~~~~~~~~~~~~~~~~~~e~~i~Pl~dd~~~~~~~~~l~~i~~~~l~~~~~s~~F~~pvd~~~~pdY~~iIk~Pmd  212 (292)
T 3aad_A          133 SQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMD  212 (292)
T ss_dssp             HTHHHHTTTTTGGGSHHHHHHHHHTTSSSTTCHHHHHHHHHHHHHHHHTGGGSTTCGGGTSCCCTTTSTTHHHHCSSCCC
T ss_pred             HHHHHHHHHhhhhcchhhhhhhhhccccccccchhHHHHHHHHHHhhhhhhcCcchhHHHhcccccccccHHHHcCCcCC
Confidence            998877654433221                                                              999


Q ss_pred             HHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225         100 LLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus       100 l~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      |+||++|++++.|.++++|.+|+.|||+||+.||+++|.+|.+|..|++.|.+.++++
T Consensus       213 L~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s~i~~~A~~L~~~~~~~~~~~  270 (292)
T 3aad_A          213 LETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEY  270 (292)
T ss_dssp             HHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999988765

>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=7.8e-37  Score=271.07  Aligned_cols=146  Identities=25%  Similarity=0.476  Sum_probs=136.5

Q ss_pred             cCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCC-CHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHH
Q psy1225           9 EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYS-TLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK   87 (256)
Q Consensus         9 ~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~-~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~   87 (256)
                      .|+.++++|++||++..+||||++|++||||+||++||  +.|. ++++|.+|++|||.||+.||+++|.++++|..|++
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            58899999999999999999999999999999999998  4555 89999999999999999999999999999999998


Q ss_pred             HHHHHHhc---------------------------------------------------c--------------------
Q psy1225          88 LMQRKVQE---------------------------------------------------N--------------------   96 (256)
Q Consensus        88 ~f~~~~~k---------------------------------------------------l--------------------   96 (256)
                      +|...+.+                                                   +                    
T Consensus       121 ~~~~~~~k~k~~~~~~~i~~~~k~~l~~~~~~l~~~~~~~i~~~l~~~r~~k~~~~~~~~s~~F~~pvd~~~~PdY~~iI  200 (311)
T 2r0y_A          121 LIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIV  200 (311)
T ss_dssp             HHHHHHHHHHTGGGCCBCCHHHHHHHHHHHHHHHHCCHHHHHHHHHGGGSCSSCCCSSCTTGGGSSCCCTTTCHHHHHHC
T ss_pred             HHHHHHhhcccCCCCCCCChHHHHHHHHHHHHHHhhhHHHHHHHHhccccccccccCCccHHHHhCCCChhhcccHHHHh
Confidence            88753210                                                   1                    


Q ss_pred             --cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          97 --PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        97 --P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                        ||||+||++||+++.|.++++|.+|++|||+||+.||+++|.+|.+|..|++.|.+++++
T Consensus       201 k~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  262 (311)
T 2r0y_A          201 HSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQK  262 (311)
T ss_dssp             SSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHH
Confidence              999999999999999999999999999999999999999999999999999999999886

>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=1.5e-35  Score=268.25  Aligned_cols=146  Identities=25%  Similarity=0.476  Sum_probs=136.0

Q ss_pred             cCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCC-CHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHH
Q psy1225           9 EGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYS-TLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK   87 (256)
Q Consensus         9 ~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~-~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~   87 (256)
                      .|++++++|++||++..+||||++|++||||+||++||  +.|. ++++|.+||+|||.||..||+++|.++.+|..|++
T Consensus        93 ~~~~~~~~F~~p~~~~~~PdY~~iIk~Pmdl~tI~~kl--~~y~~~~~~f~~D~~li~~Na~~yN~~~s~i~~~a~~l~~  170 (361)
T 2r10_A           93 KYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVM  170 (361)
T ss_dssp             HTHHHHGGGSSCCCTTTCTTHHHHCSSCCCHHHHHTSC--CCSTTHHHHHHHHHHHHHHHHHHHBCSSSHHHHHHHHHHH
T ss_pred             cCCcccHHhcCCCCcccCCChHhhcCCCcCHHHHHHHh--hccCCCHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHH
Confidence            57889999999999999999999999999999999998  4554 89999999999999999999999999999999998


Q ss_pred             HHHHHHhc---------------------------------------------------c--------------------
Q psy1225          88 LMQRKVQE---------------------------------------------------N--------------------   96 (256)
Q Consensus        88 ~f~~~~~k---------------------------------------------------l--------------------   96 (256)
                      +|...+.+                                                   +                    
T Consensus       171 ~~~~~~~k~k~~~~~~~i~~~~k~~l~~~~~~l~~~~~~~i~~~~~~~r~~~~~~~~~~~s~~F~~pvd~~~~PdY~~iI  250 (361)
T 2r10_A          171 LIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIV  250 (361)
T ss_dssp             HHHHHHHHHHTTTTCCBCCHHHHHHHHHHHHHHHHCCHHHHHHHHHGGGCCSSCCCSSCTTGGGSSCCCTTTCTHHHHHC
T ss_pred             HHHHHHhhccccCCcCcCCHHHHHHHHHHHHHhhccchHHHHHHHhccccccccccCCcchhcccCCCChhhcccHHHHh
Confidence            88753210                                                   1                    


Q ss_pred             --cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          97 --PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        97 --P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                        ||||+||++||+++.|.++++|..||.|||+||+.||+++|.+|.+|..|++.|++++++
T Consensus       251 k~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f~~~~~~  312 (361)
T 2r10_A          251 HSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQK  312 (361)
T ss_dssp             SSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence              999999999999999999999999999999999999999999999999999999999886

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

Probab=99.94  E-value=1.4e-26  Score=179.05  Aligned_cols=92  Identities=30%  Similarity=0.647  Sum_probs=88.4

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..|++++++|.+||++..+||||++|++||||+||++||+++.|.++++|.+|++|||.||..||+++|.++.+|..|+
T Consensus        30 d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~  109 (123)
T 2dat_A           30 DSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQ  109 (123)
T ss_dssp             CSSSCBSGGGGTSCCCTTTSCHHHHHCSSCCCHHHHHHHHTTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHH
T ss_pred             cccCCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            44689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccc
Q psy1225          87 KLMQRKVQENPR   98 (256)
Q Consensus        87 ~~f~~~~~klP~   98 (256)
                      ++|+..++++|-
T Consensus       110 ~~f~~~~~~~ps  121 (123)
T 2dat_A          110 SVFKSARQSGPS  121 (123)
T ss_dssp             HHHHHHHHSSSC
T ss_pred             HHHHHHHHHcCC
Confidence            999999998763

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

Probab=99.94  E-value=1.3e-26  Score=179.44  Aligned_cols=90  Identities=30%  Similarity=0.590  Sum_probs=86.9

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +.+||++|++|.+||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++++|..|+
T Consensus        32 d~~g~~~s~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~  111 (124)
T 3mb4_A           32 DKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLH  111 (124)
T ss_dssp             CTTSCBGGGGGSCCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHH
T ss_pred             cccCCcccHHhhcCCCccccCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      ++|.+.++++
T Consensus       112 ~~f~~~~~~l  121 (124)
T 3mb4_A          112 KVLLETRRDL  121 (124)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHH
Confidence            9999988765

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

Probab=99.94  E-value=1.2e-26  Score=180.88  Aligned_cols=90  Identities=47%  Similarity=0.763  Sum_probs=87.1

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..||++|++|.+||++..+||||++|++||||+||++||++|.|.++++|.+|++|||.||+.||+++|.++++|..|+
T Consensus        34 d~~g~~~s~~F~~pv~~~~~PdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~  113 (130)
T 3k2j_A           34 NNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQ  113 (130)
T ss_dssp             CSSSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHH
T ss_pred             cccCCCccHhhcCCCChhhCccHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      +.|.+.++++
T Consensus       114 ~~f~~~~~~l  123 (130)
T 3k2j_A          114 QVMQAKKKEL  123 (130)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999988765

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

Probab=99.94  E-value=1.1e-26  Score=177.92  Aligned_cols=90  Identities=37%  Similarity=0.636  Sum_probs=86.7

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +.+||++|++|.+||++..+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++++|..|+
T Consensus        22 d~~g~~~s~~F~~p~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~  101 (116)
T 3iu5_A           22 DEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLW  101 (116)
T ss_dssp             CTTCCBGGGGGSSCCCGGGCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHH
T ss_pred             ccCCCeeeHHhcCCCCcccCCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      +.|.+.++++
T Consensus       102 ~~f~~~~~~l  111 (116)
T 3iu5_A          102 DLYLRTRNEF  111 (116)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999987764

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

Probab=99.94  E-value=1.3e-26  Score=178.50  Aligned_cols=90  Identities=36%  Similarity=0.639  Sum_probs=87.3

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +.+||++|.+|.+||++..+||||++|++||||+||++||.+|.|.++++|.+|++|||.||..||+++|.++++|..|+
T Consensus        25 d~~g~~~s~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~  104 (120)
T 3ljw_A           25 NPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIK  104 (120)
T ss_dssp             CTTSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHH
T ss_pred             CcCCCcccHHhcCCCCcccCCChHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            55799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      ++|...+.++
T Consensus       105 ~~f~~~~~~i  114 (120)
T 3ljw_A          105 KIFYMKKAEI  114 (120)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999998876

>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=1.3e-26  Score=176.48  Aligned_cols=96  Identities=29%  Similarity=0.443  Sum_probs=91.8

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+++....++.+++|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++.+
T Consensus        13 ~~il~~l~~~~~~~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~   92 (112)
T 3d7c_A           13 KNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRC   92 (112)
T ss_dssp             HHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHH
T ss_pred             HHHHHHHHcCCCchhhcCCCCcccccCHHHHccCCcCHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            46778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhccc
Q psy1225          82 AVKLQKLMQRKVQENP   97 (256)
Q Consensus        82 A~~L~~~f~~~~~klP   97 (256)
                      |..|++.|.+.+++++
T Consensus        93 A~~L~~~f~~~~~~~~  108 (112)
T 3d7c_A           93 ASALEKFFYFKLKEGG  108 (112)
T ss_dssp             HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHCC
Confidence            9999999999988764

>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=178.41  Aligned_cols=97  Identities=29%  Similarity=0.510  Sum_probs=92.9

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ..+++...+++.+++|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++++
T Consensus        19 ~~il~~l~~~~~a~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~   98 (121)
T 1e6i_A           19 QNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKY   98 (121)
T ss_dssp             HHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHH
T ss_pred             HHHHHHHHcCCCchhhCCCCChhhCcCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            45778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcccc
Q psy1225          82 AVKLQKLMQRKVQENPR   98 (256)
Q Consensus        82 A~~L~~~f~~~~~klP~   98 (256)
                      |..|++.|.+.+.++|-
T Consensus        99 A~~L~~~f~~~~~~~p~  115 (121)
T 1e6i_A           99 ANRLEKFFNNKVKEIPE  115 (121)
T ss_dssp             HHHHHHHHHHHHHTSGG
T ss_pred             HHHHHHHHHHHHHHccc
Confidence            99999999999988864

>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=99.93  E-value=2.4e-26  Score=178.55  Aligned_cols=90  Identities=32%  Similarity=0.555  Sum_probs=86.9

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      +..|+++|++|.+||++..+||||++|++||||+||++||++|.|.++++|.+|++|||.||+.||+++|.++++|..|+
T Consensus        26 d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~  105 (126)
T 3mqm_A           26 DSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLR  105 (126)
T ss_dssp             CTTCCBTTGGGSSCCCGGGCTTHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHH
T ss_pred             CcCCCChhHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            55799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      +.|.+.+.++
T Consensus       106 ~~f~~~~~~~  115 (126)
T 3mqm_A          106 KAYYNARHEA  115 (126)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999988765

>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=3.5e-26  Score=178.23  Aligned_cols=89  Identities=31%  Similarity=0.623  Sum_probs=86.5

Q ss_pred             ccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHH
Q psy1225           8 TEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK   87 (256)
Q Consensus         8 ~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~   87 (256)
                      ..|+++|++|..||+...+||||++|++||||+||++||.+|.|.++++|.+|++|||.||..||+++|.++.+|..|++
T Consensus        30 ~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~Na~~yN~~~s~i~~~A~~L~~  109 (129)
T 2grc_A           30 SSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQS  109 (129)
T ss_dssp             TTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHH
T ss_pred             cccCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcc
Q psy1225          88 LMQRKVQEN   96 (256)
Q Consensus        88 ~f~~~~~kl   96 (256)
                      .|...+.++
T Consensus       110 ~f~~~~~~l  118 (129)
T 2grc_A          110 VFTSVRQKI  118 (129)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHc
Confidence            999988876

>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=6.8e-26  Score=173.79  Aligned_cols=95  Identities=27%  Similarity=0.452  Sum_probs=90.7

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+++....++.+++|.+||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++.+
T Consensus        19 ~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~   98 (117)
T 3g0l_A           19 SMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRA   98 (117)
T ss_dssp             HHHHHHHHTSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCSSSHHHHH
T ss_pred             HHHHHHHHhCCCchhhcCcCChhhcCChHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            45778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      |..|++.|++.+.++
T Consensus        99 A~~L~~~f~~~~~~~  113 (117)
T 3g0l_A           99 GHNMRKYFEKKWTDT  113 (117)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999988754

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

Probab=99.93  E-value=5.6e-26  Score=174.00  Aligned_cols=95  Identities=24%  Similarity=0.336  Sum_probs=89.7

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ..+++....++.+.+|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++++
T Consensus        14 ~~il~~L~~~~~~~~F~~PVd~~~~pdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Li~~Na~~yN~~~s~i~~~   93 (117)
T 2i7k_A           14 NQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKA   93 (117)
T ss_dssp             HHHHHHHHTSSGGGTSSSCCCTTTSSSHHHHCSCCCCHHHHHHHHTTTSCCSHHHHHHHHHHHHHHHHHTSCSSSSHHHH
T ss_pred             HHHHHHHHhCcccHHhcCCCCccccCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            45677788899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      |..|++.+.+.+...
T Consensus        94 A~~L~~~f~~~~~~~  108 (117)
T 2i7k_A           94 AKKLLHSGMKILSQE  108 (117)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999887643

>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=5.5e-26  Score=175.15  Aligned_cols=95  Identities=24%  Similarity=0.411  Sum_probs=89.7

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+++....++.+++|.+||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++.+
T Consensus        13 ~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~~~~~   92 (121)
T 2d9e_A           13 RKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRA   92 (121)
T ss_dssp             HHHHHHHHHHCSSCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHH
T ss_pred             HHHHHHHHcCCccHhhCCcCCccccCCHHHHcCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            46777888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      |..|++.+...+.++
T Consensus        93 A~~L~~~~~~~l~~~  107 (121)
T 2d9e_A           93 AVRLREQGGAVLRQA  107 (121)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999998876643

>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=99.92  E-value=1.2e-25  Score=174.61  Aligned_cols=97  Identities=30%  Similarity=0.389  Sum_probs=91.3

Q ss_pred             ccccccccCCccccccccCCCC--CCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAK--RYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~--~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      +.+++....++.|++|.+||+.  ..+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++
T Consensus        27 ~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~  106 (127)
T 2oss_A           27 RVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIV  106 (127)
T ss_dssp             HTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTCHHH
T ss_pred             HHHHHHHHhCccchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            4567788899999999999985  48999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcccc
Q psy1225          80 RDAVKLQKLMQRKVQENPR   98 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~klP~   98 (256)
                      .+|..|++.|.+.+.++|.
T Consensus       107 ~~A~~L~~~f~~~~~~lp~  125 (127)
T 2oss_A          107 LMAEALEKLFLQKINELPT  125 (127)
T ss_dssp             HHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHHHHHCCC
Confidence            9999999999999988753

>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=7.8e-26  Score=173.18  Aligned_cols=94  Identities=28%  Similarity=0.497  Sum_probs=89.8

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ..+++....++.|++|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++.+
T Consensus        22 ~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~  101 (116)
T 3nxb_A           22 YKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKM  101 (116)
T ss_dssp             HHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHHHHHhCCCcHhhcCcCChhhccChHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            45777888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhc
Q psy1225          82 AVKLQKLMQRKVQE   95 (256)
Q Consensus        82 A~~L~~~f~~~~~k   95 (256)
                      |..|++.|...+.+
T Consensus       102 A~~L~~~f~~~~~k  115 (116)
T 3nxb_A          102 SDNLERCFHRAMMK  115 (116)
T ss_dssp             HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhh
Confidence            99999999998765

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

Probab=99.92  E-value=1.1e-25  Score=179.81  Aligned_cols=93  Identities=32%  Similarity=0.608  Sum_probs=89.3

Q ss_pred             ccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHH
Q psy1225           4 QKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAV   83 (256)
Q Consensus         4 ~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~   83 (256)
                      ..++..||+++.+|..||++..+||||++|++||||+||++||++|.|.++++|.+|++|||.||+.||+++|.++.+|.
T Consensus        39 ~~~~~~~~~~~~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~  118 (150)
T 3tlp_A           39 AREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAH  118 (150)
T ss_dssp             CBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHH
T ss_pred             HHhcccCCcccHHhcCCCchhhCcCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence            34466799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcc
Q psy1225          84 KLQKLMQRKVQEN   96 (256)
Q Consensus        84 ~L~~~f~~~~~kl   96 (256)
                      .|+++|.+.+.++
T Consensus       119 ~L~~~f~~~~~~l  131 (150)
T 3tlp_A          119 ILEKLLKEKRKEL  131 (150)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc
Confidence            9999999999877

>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=3.5e-25  Score=171.23  Aligned_cols=96  Identities=29%  Similarity=0.466  Sum_probs=91.3

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCC-CchhHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA-DSRLYR   80 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~-~S~i~~   80 (256)
                      +.+++....++.|++|.+||+...+||||++|++||||+||++||++|.|.++++|..|++|||.||+.||++ +|.++.
T Consensus        16 ~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~~s~i~~   95 (123)
T 3q2e_A           16 KELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYS   95 (123)
T ss_dssp             HHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCCTTSHHHH
T ss_pred             HHHHHHHHhCCCcHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHH
Confidence            4577888899999999999999999999999999999999999999999999999999999999999999996 999999


Q ss_pred             HHHHHHHHHHHHHhccc
Q psy1225          81 DAVKLQKLMQRKVQENP   97 (256)
Q Consensus        81 ~A~~L~~~f~~~~~klP   97 (256)
                      +|..|++.|.+.+.+++
T Consensus        96 ~A~~L~~~f~~~~~~~~  112 (123)
T 3q2e_A           96 MTLRLSALFEEKMKKIS  112 (123)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999988773

>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=99.92  E-value=4.2e-25  Score=176.97  Aligned_cols=97  Identities=26%  Similarity=0.333  Sum_probs=91.8

Q ss_pred             ccccccccCCccccccccCCCCC--CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKR--YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~--~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      +.+++....++.+++|.+||+..  ++||||++|++||||+||++||+++.|.++++|.+|++|||.||..||+++|.++
T Consensus        38 ~~il~~l~~~~~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~i~  117 (154)
T 4alg_A           38 KVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIV  117 (154)
T ss_dssp             HTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHH
T ss_pred             HHHHHHHHhCcCchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            35677888999999999999977  7999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcccc
Q psy1225          80 RDAVKLQKLMQRKVQENPR   98 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~klP~   98 (256)
                      .+|..|+++|...+.++|-
T Consensus       118 ~~A~~L~~~f~~~~~~l~~  136 (154)
T 4alg_A          118 LMAQTLEKIFLQKVASMPQ  136 (154)
T ss_dssp             HHHHHHHHHHHHHHTTSCS
T ss_pred             HHHHHHHHHHHHHHHHCCc
Confidence            9999999999999998843

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

Probab=99.92  E-value=4e-25  Score=170.87  Aligned_cols=95  Identities=21%  Similarity=0.303  Sum_probs=89.9

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+++....++.+++|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++++
T Consensus        19 ~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~   98 (123)
T 3hme_A           19 EHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKL   98 (123)
T ss_dssp             HHHHHHHHTTCTTCSSSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHH
T ss_pred             HHHHHHHHhCCccHhhcCCCChhhccCHHHHCCCCCCHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            45677888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      |..|.+.+.+.+.+.
T Consensus        99 A~~L~~~~~~~~~~~  113 (123)
T 3hme_A           99 AKKILHAGFKMMSKE  113 (123)
T ss_dssp             HHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999887643

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

Probab=99.92  E-value=5.7e-25  Score=176.79  Aligned_cols=102  Identities=25%  Similarity=0.423  Sum_probs=94.9

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      ...+++.|++|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++++|..|.
T Consensus        41 kl~~~~~s~~F~~PVd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~  120 (158)
T 3uv4_A           41 KMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIV  120 (158)
T ss_dssp             TTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHcCCCchhhcCcCChhhcccHHHHcCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccccHHHHHHHhh
Q psy1225          87 KLMQRKVQENPRSLLTIGKTLK  108 (256)
Q Consensus        87 ~~f~~~~~klP~dl~~I~~kl~  108 (256)
                      +.+...+.+++-.+....+.+.
T Consensus       121 ~~~~~~l~e~~~~l~~le~~i~  142 (158)
T 3uv4_A          121 NVCYQTLTEYDEHLTQLEKDIC  142 (158)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999988766666665553

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

Probab=99.91  E-value=4.8e-25  Score=173.16  Aligned_cols=95  Identities=26%  Similarity=0.445  Sum_probs=90.5

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+++....++.+++|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++++
T Consensus        19 ~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~   98 (135)
T 3rcw_A           19 RSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRA   98 (135)
T ss_dssp             HHHHHHHHHTCTTCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHH
T ss_pred             HHHHHHHHhCCcchhhcCCCChhhcCCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            46778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      |..|.+.+...+.+.
T Consensus        99 A~~L~~~~~~~~~~~  113 (135)
T 3rcw_A           99 AVRLRDQGGVVLRQA  113 (135)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999887755

>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=6.2e-25  Score=172.53  Aligned_cols=95  Identities=28%  Similarity=0.470  Sum_probs=90.5

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCC-CchhHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA-DSRLYR   80 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~-~S~i~~   80 (256)
                      ..+++....++.+++|..||+...+||||++|++||||+||++||.+|.|.++++|.+|++|||.||..||++ +|.++.
T Consensus        27 ~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~~s~i~~  106 (135)
T 3mb3_A           27 EELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYS  106 (135)
T ss_dssp             HHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCCTTCHHHH
T ss_pred             HHHHHHHHhCCCChhhcCCCChhhCCCHHHHhCCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHH
Confidence            4567778889999999999999999999999999999999999999999999999999999999999999998 899999


Q ss_pred             HHHHHHHHHHHHHhcc
Q psy1225          81 DAVKLQKLMQRKVQEN   96 (256)
Q Consensus        81 ~A~~L~~~f~~~~~kl   96 (256)
                      +|..|++.|...+.++
T Consensus       107 ~A~~L~~~f~~~~~~~  122 (135)
T 3mb3_A          107 MSLRLSAFFEEHISSV  122 (135)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999988876

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

Probab=99.91  E-value=1.4e-24  Score=169.39  Aligned_cols=95  Identities=28%  Similarity=0.408  Sum_probs=86.5

Q ss_pred             cccccccCCc---cccccccCCCCC--CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCch
Q psy1225           3 PQKNQTEGGN---LSEPFLKLPAKR--YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSR   77 (256)
Q Consensus         3 ~~~~~~~~~~---~s~~F~~~p~~~--~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~   77 (256)
                      ++|+....+.   ++++|..||+..  ++||||++|++||||+||++||.+|.|.++++|.+|++|||.||..||+++|.
T Consensus        29 ~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~  108 (130)
T 2ouo_A           29 GILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHE  108 (130)
T ss_dssp             HHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCH
Confidence            3455554444   589999999865  59999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHhccc
Q psy1225          78 LYRDAVKLQKLMQRKVQENP   97 (256)
Q Consensus        78 i~~~A~~L~~~f~~~~~klP   97 (256)
                      ++.+|..|++.|...+.++|
T Consensus       109 i~~~A~~L~~~f~~~~~~lp  128 (130)
T 2ouo_A          109 VVAMARKLQDVFEMRFAKMP  128 (130)
T ss_dssp             HHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHHHHCC
Confidence            99999999999999998875

>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=7.8e-25  Score=168.59  Aligned_cols=96  Identities=29%  Similarity=0.415  Sum_probs=87.1

Q ss_pred             ccccccCC---ccccccccCCCCCC--CcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchh
Q psy1225           4 QKNQTEGG---NLSEPFLKLPAKRY--NPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRL   78 (256)
Q Consensus         4 ~~~~~~~~---~~s~~F~~~p~~~~--~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i   78 (256)
                      +|+....+   ++|++|..||+...  +||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.+
T Consensus        17 il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~   96 (120)
T 3jvl_A           17 ILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEV   96 (120)
T ss_dssp             HHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHH
T ss_pred             HHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHH
Confidence            44444444   45999999999877  99999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhccccc
Q psy1225          79 YRDAVKLQKLMQRKVQENPRS   99 (256)
Q Consensus        79 ~~~A~~L~~~f~~~~~klP~d   99 (256)
                      +.+|..|++.|...+.++|..
T Consensus        97 ~~~A~~L~~~f~~~~~~~p~~  117 (120)
T 3jvl_A           97 VAMARKLQDVFEMRFAKMPDE  117 (120)
T ss_dssp             HHHHHHHHHHHHHHHTTCCC-
T ss_pred             HHHHHHHHHHHHHHHHHCcCC
Confidence            999999999999999988653

>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=99.91  E-value=7.6e-25  Score=168.40  Aligned_cols=94  Identities=30%  Similarity=0.475  Sum_probs=86.2

Q ss_pred             cccccc-cCCccccccccCCCCC--CCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           3 PQKNQT-EGGNLSEPFLKLPAKR--YNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         3 ~~~~~~-~~~~~s~~F~~~p~~~--~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      .++... ..++.|.+|..||+..  ++||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++
T Consensus        18 ~~l~~l~~~~~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~i~   97 (119)
T 3p1f_A           18 PTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVY   97 (119)
T ss_dssp             HHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHH
T ss_pred             HHHHHHHHhCCCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            344454 3578999999999987  7999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcc
Q psy1225          80 RDAVKLQKLMQRKVQEN   96 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~kl   96 (256)
                      .+|..|++.|++.+.++
T Consensus        98 ~~A~~L~~~f~~~~~~~  114 (119)
T 3p1f_A           98 KFCSKLAEVFEQEIDPV  114 (119)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999987654

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

Probab=99.90  E-value=2.8e-24  Score=168.66  Aligned_cols=94  Identities=29%  Similarity=0.434  Sum_probs=88.4

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKS--GHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~--~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      ..+|+....++.+++|..||+. .+||||++|++||||+||++||++  +.|.++++|.+|++|||.||..||+++|.++
T Consensus        26 ~~il~~L~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmDL~tI~~kL~~~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~  104 (135)
T 2yyn_A           26 ERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVA  104 (135)
T ss_dssp             HHHHHHHHTSGGGGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHHSSSCCCSSHHHHHHHHHHHHHHHHHHSCTTSHHH
T ss_pred             HHHHHHHHhCccchhhcCCCcc-cCCCHHHHcCCCCCHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            4567788899999999998877 799999999999999999999998  5999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcc
Q psy1225          80 RDAVKLQKLMQRKVQEN   96 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~kl   96 (256)
                      .+|..|++.|+..+.++
T Consensus       105 ~~A~~L~~~f~~~~~~~  121 (135)
T 2yyn_A          105 NAGIKLENYFEELLKNL  121 (135)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999999999998776

>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=2.3e-24  Score=176.35  Aligned_cols=95  Identities=26%  Similarity=0.510  Sum_probs=90.9

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+|+....++.+.+|..||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||..||+++|.++++
T Consensus        78 ~~il~~l~~~~~~~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~  157 (174)
T 2ri7_A           78 KRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQC  157 (174)
T ss_dssp             HHHHHHHHTSGGGTTTSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHH
T ss_pred             HHHHHHHHhhhhhhhhhcCCCcccCCchHHHhCCcCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            45777888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      |..|++.|.+.++++
T Consensus       158 A~~L~~~f~~~~~~~  172 (174)
T 2ri7_A          158 AEVLESFFVQKLKGF  172 (174)
T ss_dssp             HHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999998765

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

Probab=99.90  E-value=4.1e-24  Score=173.27  Aligned_cols=98  Identities=23%  Similarity=0.348  Sum_probs=90.0

Q ss_pred             ccccccccCCccccccccCCCC--CCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAK--RYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~--~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      +.+|+....++.+.+|..||+.  ..+||||++|++||||+||++||.+|.|.++++|.+||+|||.||..||+++|.++
T Consensus        27 ~~il~~L~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~  106 (166)
T 3fkm_X           27 NQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLYNTSNSVVA  106 (166)
T ss_dssp             HHHHHHHTTSTTGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHHHSSCTTSHHH
T ss_pred             HHHHHHHHhCCCChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            4577888899999999999874  47999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhccccc
Q psy1225          80 RDAVKLQKLMQRKVQENPRS   99 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~klP~d   99 (256)
                      .+|..|+++|.+.+.+++.+
T Consensus       107 ~~A~~L~~~f~~~l~~~~~~  126 (166)
T 3fkm_X          107 ITGKNIETYFNNQLIVMGYN  126 (166)
T ss_dssp             HHHHHHHHHHHHHHHHTTHH
T ss_pred             HHHHHHHHHHHHHHHHcccc
Confidence            99999999999999988543

>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=99.90  E-value=6.8e-24  Score=165.49  Aligned_cols=93  Identities=20%  Similarity=0.278  Sum_probs=86.0

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchh---
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRL---   78 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i---   78 (256)
                      +.+++...+++.+++|..||+...+||||++|++||||+||++||.+|.|.++++|.+|++|||.||..||+++|++   
T Consensus        16 ~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~   95 (130)
T 3dai_A           16 RNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRL   95 (130)
T ss_dssp             HHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHCCSSSHHHHH
T ss_pred             HHHHHHHHcCCccHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCChhHHH
Confidence            56777888999999999999999999999999999999999999999999999999999999999999999998866   


Q ss_pred             -HHHHHHHHHHHHHHHh
Q psy1225          79 -YRDAVKLQKLMQRKVQ   94 (256)
Q Consensus        79 -~~~A~~L~~~f~~~~~   94 (256)
                       +..|..|++.+...+.
T Consensus        96 i~~~A~~L~~~~~~~i~  112 (130)
T 3dai_A           96 IRHRACALRDTAYAIIK  112 (130)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence             6788888888877764

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

Probab=99.87  E-value=1.8e-22  Score=178.92  Aligned_cols=90  Identities=31%  Similarity=0.583  Sum_probs=86.6

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      ..++|++|++|++||+...+||||++|++||||+||++||++|.|.++++|.+|++|||.||+.||+++|.++.+|..|+
T Consensus       174 ~~~~~~~s~~F~~pvd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~  253 (311)
T 2r0y_A          174 LDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLT  253 (311)
T ss_dssp             CCCSSCTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHH
T ss_pred             cccCCccHHHHhCCCChhhcccHHHHhCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q psy1225          87 KLMQRKVQEN   96 (256)
Q Consensus        87 ~~f~~~~~kl   96 (256)
                      +.|...+++.
T Consensus       254 ~~f~~~~~~~  263 (311)
T 2r0y_A          254 NYFNYLIQKE  263 (311)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHh
Confidence            9999998874

>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=99.87  E-value=4.2e-22  Score=173.18  Aligned_cols=100  Identities=26%  Similarity=0.432  Sum_probs=92.3

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      ...+++.|++|..||+...+||||++|++||||+||++||.+|.|.++++|.+|++|||.||..||+++|.++.+|..|.
T Consensus       148 ~l~~~~~~~~F~~pv~~~~~pdY~~iIk~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~lif~Na~~yN~~~s~~~~~A~~l~  227 (265)
T 3uv5_A          148 KMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIV  227 (265)
T ss_dssp             TTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             HHHhhhhhHHHhCCCChhHhCcHHHHhCCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccccHHHHHHH
Q psy1225          87 KLMQRKVQENPRSLLTIGKT  106 (256)
Q Consensus        87 ~~f~~~~~klP~dl~~I~~k  106 (256)
                      +.+...+.+++-.+..+...
T Consensus       228 ~~~~~~~~~~~~~~~~~e~~  247 (265)
T 3uv5_A          228 NVCYQTLTEYDEHLTQLEKD  247 (265)
T ss_dssp             HHHHHHHHHTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            99999998885555444443

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

Probab=99.87  E-value=3.2e-22  Score=155.94  Aligned_cols=98  Identities=20%  Similarity=0.312  Sum_probs=86.0

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCch----
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSR----   77 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~----   77 (256)
                      +.+++....++.+++|..|     +||||++|++||||+||++||.+|.|.++++|.+|++|||.||..||+++|+    
T Consensus        18 ~~il~~l~~~~~~~~F~~P-----~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s~~~~~   92 (131)
T 2dkw_A           18 RDVTKRLATDKRFNIFSKP-----VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKI   92 (131)
T ss_dssp             HHHHHHHHHSGGGCTTSSC-----CSSCTTSCSSCCCHHHHHHHHHTTCCCSSHHHHHHHHHHHHHHHHSCCCSSTTHHH
T ss_pred             HHHHHHHHhCccchhhcCc-----CccHHhHcCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCChhHHH
Confidence            4567778889999999997     8999999999999999999999999999999999999999999999999996    


Q ss_pred             hHHHHHHHHHHHHHHH-hcccccHHHHH
Q psy1225          78 LYRDAVKLQKLMQRKV-QENPRSLLTIG  104 (256)
Q Consensus        78 i~~~A~~L~~~f~~~~-~klP~dl~~I~  104 (256)
                      ++.+|..|++.+...+ .++...+...-
T Consensus        93 i~~~A~~L~~~~~~~l~~~l~~~f~~~~  120 (131)
T 2dkw_A           93 IRHRACTLKDTAHAIIAAELDPEFNKLC  120 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCTTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999988876 45544544433

>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=99.87  E-value=5.6e-22  Score=155.52  Aligned_cols=87  Identities=28%  Similarity=0.488  Sum_probs=82.7

Q ss_pred             ccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHH
Q psy1225           6 NQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKL   85 (256)
Q Consensus         6 ~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L   85 (256)
                      ++.+||.+|++|+++|+++  |+||.  ++||+|.+|++||.+|.|+++++|..|+.+||.||+.||.++|++|.+|..|
T Consensus        23 ~De~GR~lsd~F~~LPsk~--pdYY~--k~Pi~l~~Ikkri~~~~Y~sld~f~~D~~lmf~NAr~yN~e~S~IyeDAv~L   98 (147)
T 3iu6_A           23 QDDEGRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVEL   98 (147)
T ss_dssp             BCTTSCBGGGGGTTCCSSC--TTSTT--SCCCCHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHH
T ss_pred             cCCCCCcchHHHhHCCCCC--ccccC--CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            3678999999999999998  89998  9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcc
Q psy1225          86 QKLMQRKVQEN   96 (256)
Q Consensus        86 ~~~f~~~~~kl   96 (256)
                      +++|.....++
T Consensus        99 q~~f~~~r~eL  109 (147)
T 3iu6_A           99 QQFFIKIRDEL  109 (147)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999877655

>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=99.87  E-value=1.7e-22  Score=166.58  Aligned_cols=94  Identities=29%  Similarity=0.434  Sum_probs=87.0

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKS--GHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~--~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      +.+|.....++.+.+|..||+. .+|+||++|++||||+||++||++  |.|.++++|.+||+|||.||..||+++|.++
T Consensus        87 ~~il~~l~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmdL~tI~~kl~~~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~v~  165 (184)
T 3o36_A           87 ERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVA  165 (184)
T ss_dssp             HHHHHHHHHSTTCHHHHSCCCT-TSTTHHHHCSSCCCHHHHHHHHHSTTCSCCSHHHHHHHHHHHHHHHHHHSCTTCHHH
T ss_pred             HHHHHHHHhchhhhhhcccccc-CCCchhhhcCCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            3466777788999999999985 489999999999999999999998  7999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcc
Q psy1225          80 RDAVKLQKLMQRKVQEN   96 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~kl   96 (256)
                      ++|..|++.|.+.++++
T Consensus       166 ~~a~~L~~~f~~~~~~~  182 (184)
T 3o36_A          166 NAGIKLENYFEELLKNL  182 (184)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999999999988764

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

Probab=99.86  E-value=5.7e-22  Score=179.24  Aligned_cols=89  Identities=31%  Similarity=0.596  Sum_probs=86.1

Q ss_pred             ccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHH
Q psy1225           8 TEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK   87 (256)
Q Consensus         8 ~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~   87 (256)
                      .++|++|++|++||+...+||||++|++||||+||++||.+|.|.++++|.+||+|||.||..||+++|.++.+|..|++
T Consensus       225 ~~~~~~s~~F~~pvd~~~~PdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~  304 (361)
T 2r10_A          225 DDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTN  304 (361)
T ss_dssp             CCSSCTTGGGSSCCCTTTCTHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHH
T ss_pred             ccCCcchhcccCCCChhhcccHHHHhcCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcc
Q psy1225          88 LMQRKVQEN   96 (256)
Q Consensus        88 ~f~~~~~kl   96 (256)
                      .|...+.+.
T Consensus       305 ~f~~~~~~~  313 (361)
T 2r10_A          305 YFNYLIQKE  313 (361)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHh
Confidence            999998874

>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=99.86  E-value=9.7e-22  Score=172.98  Aligned_cols=98  Identities=26%  Similarity=0.430  Sum_probs=89.8

Q ss_pred             cccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHH
Q psy1225           7 QTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQ   86 (256)
Q Consensus         7 ~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~   86 (256)
                      ...+++.+++|..||+...+||||++|++||||+||++||.+|.|.++++|.+|++|||.||..||+++|.++.+|..|+
T Consensus       181 ~l~~~~~s~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s~i~~~A~~L~  260 (292)
T 3aad_A          181 KMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIV  260 (292)
T ss_dssp             TGGGSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHH
T ss_pred             hhhcCcchhHHHhcccccccccHHHHcCCcCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            35688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccccHHHHH
Q psy1225          87 KLMQRKVQENPRSLLTIG  104 (256)
Q Consensus        87 ~~f~~~~~klP~dl~~I~  104 (256)
                      +.+...+.++.-.+..+.
T Consensus       261 ~~~~~~~~~~~~~l~~le  278 (292)
T 3aad_A          261 NVCYQTLTEYDEHLTQLE  278 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999998887644443333

>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=99.85  E-value=1.1e-21  Score=164.67  Aligned_cols=94  Identities=28%  Similarity=0.426  Sum_probs=87.5

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHhhhCC-----
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKS---GHYSTLNELTGELNLMFENAKKFNP-----   73 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~---~~Y~~~~ef~~D~~li~~Na~~yN~-----   73 (256)
                      +.+|.....++.|.+|.+||+. .+|+||++|++||||+||++||++   |.|.++++|.+|++|||.||+.||+     
T Consensus        87 ~~il~~l~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~v  165 (207)
T 3u5n_A           87 ERLLLYLYCHELSIEFQEPVPA-SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVV  165 (207)
T ss_dssp             HHHHHHHHTSTTCGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccchhhhhccCCh-hhccHhHHhCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHHHHHCCCcchH
Confidence            3577788899999999999886 799999999999999999999997   7999999999999999999999999     


Q ss_pred             ------------CCchhHHHHHHHHHHHHHHHhcc
Q psy1225          74 ------------ADSRLYRDAVKLQKLMQRKVQEN   96 (256)
Q Consensus        74 ------------~~S~i~~~A~~L~~~f~~~~~kl   96 (256)
                                  ++|.++++|..|+..|...++++
T Consensus       166 ~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~~~~~  200 (207)
T 3u5n_A          166 QVYADTQEINLKADSEVAQAGKAVALYFEDKLTEI  200 (207)
T ss_dssp             C----------CCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcccccCHHHHHHHHHHHHHHHHHHHh
Confidence                        99999999999999999988765

>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=1.2e-21  Score=161.95  Aligned_cols=89  Identities=17%  Similarity=0.251  Sum_probs=83.5

Q ss_pred             cccccccCCccccccccCCCCCCCcchhhhcC--CcCcHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHHhhhCCCCch
Q psy1225           3 PQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIK--NPRSLLTIGKTLKSG---HYSTLNELTGELNLMFENAKKFNPADSR   77 (256)
Q Consensus         3 ~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~--~PmdL~tI~~kl~~~---~Y~~~~ef~~D~~li~~Na~~yN~~~S~   77 (256)
                      .+|+....++.|++|.+||+    |+||++|+  +||||+||++||+++   .|.++++|.+||+|||.||++|| +++.
T Consensus        83 ~iL~~l~~~~~s~pF~~pV~----~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~Y~s~~eF~~Dv~Lif~N~~~yN-~~s~  157 (189)
T 2ro1_A           83 RVLLALFCHEPCRPLHQLAT----DSTFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLT-EDKA  157 (189)
T ss_dssp             HHHHHHHHSTTHHHHHSCSC----CTTCSSSCSSCCCCHHHHHHHHHTSSSSCCSCHHHHHHHHHHHHHHHHHHC-CSSC
T ss_pred             HHHhhcccCccchhhcCCCC----hhhhccccCCCcccHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHC-CCCH
Confidence            46777888999999999998    78999998  899999999999999   99999999999999999999999 5889


Q ss_pred             hHHHHHHHHHHHHHHHhcc
Q psy1225          78 LYRDAVKLQKLMQRKVQEN   96 (256)
Q Consensus        78 i~~~A~~L~~~f~~~~~kl   96 (256)
                      ++++|..|++.|++.++++
T Consensus       158 ~~~~a~~L~~~Fe~~~~~~  176 (189)
T 2ro1_A          158 DVQSIIGLQRFFETRMNEA  176 (189)
T ss_dssp             SSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHh
Confidence            9999999999999998876

>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=99.65  E-value=4.8e-16  Score=117.86  Aligned_cols=64  Identities=30%  Similarity=0.408  Sum_probs=60.9

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFS  158 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~  158 (256)
                      +-||||+||++|+++|.|.++++|.+|++|||+||+.||+++|.++.+|..|++.|.+++++++
T Consensus        45 k~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~  108 (112)
T 3d7c_A           45 RFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEGG  108 (112)
T ss_dssp             SSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCcCHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            3399999999999999999999999999999999999999999999999999999999998753

>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=99.65  E-value=9.2e-16  Score=117.84  Aligned_cols=63  Identities=27%  Similarity=0.537  Sum_probs=60.7

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||+||++|+++|.|.++++|.+|++|||+||+.||+++|.++++|..|++.|.++++++
T Consensus        51 k~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~  113 (121)
T 1e6i_A           51 KEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI  113 (121)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            339999999999999999999999999999999999999999999999999999999999876

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

Probab=99.64  E-value=4.8e-16  Score=119.77  Aligned_cols=105  Identities=20%  Similarity=0.358  Sum_probs=78.3

Q ss_pred             CHHHHHHHHHHHHHHHhhhCC----CCchhHHHHHHHHHH-HHHHHhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHH
Q psy1225          53 TLNELTGELNLMFENAKKFNP----ADSRLYRDAVKLQKL-MQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFE  127 (256)
Q Consensus        53 ~~~ef~~D~~li~~Na~~yN~----~~S~i~~~A~~L~~~-f~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~  127 (256)
                      +..++.+-+..|+.....+-.    +-+..+.....-..+ -...+.+-||||+||++|++++.|.++++|.+|++|||.
T Consensus        10 ~~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~   89 (123)
T 2dat_A           10 NPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCH   89 (123)
T ss_dssp             CCHHHHHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCTTTSCHHHHHCSSCCCHHHHHHHHTTTCCCSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhhhcccCCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence            455666777777777665531    123333322211100 011233449999999999999999999999999999999


Q ss_pred             hhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225         128 NAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus       128 Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      ||+.||+++|.+|++|..|++.|+++++++
T Consensus        90 Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~  119 (123)
T 2dat_A           90 NAQTFNLEGSQIYEDSIVLQSVFKSARQSG  119 (123)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999999875

>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=99.63  E-value=1.8e-15  Score=117.64  Aligned_cols=110  Identities=30%  Similarity=0.412  Sum_probs=81.5

Q ss_pred             cCCCCCHHHHHHHHHHHHHHHhhhCCCC----chhHHHHHHHHHH-HHHHHhcccccHHHHHHHhhcCCCCCHHHHHHHH
Q psy1225          48 SGHYSTLNELTGELNLMFENAKKFNPAD----SRLYRDAVKLQKL-MQRKVQENPRSLLTIGKTLKSGHYSTLNELTGEL  122 (256)
Q Consensus        48 ~~~Y~~~~ef~~D~~li~~Na~~yN~~~----S~i~~~A~~L~~~-f~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~  122 (256)
                      ++.+....++...+..++.-...+-...    +..+.....-..+ -...+.+-||||+||++||+++.|.++++|..|+
T Consensus         9 ~~~~~~~~kl~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~~~PdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv   88 (130)
T 3k2j_A            9 SGVDLGTENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDL   88 (130)
T ss_dssp             -CCSCHHHHHHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHH
T ss_pred             CCCccchHHHHHHHHHHHHHHHHHhcccCCCccHhhcCCCChhhCccHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHH
Confidence            3456667777777777777666553321    3333222111100 0112334499999999999999999999999999


Q ss_pred             HHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225         123 NLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus       123 ~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +|||.||+.||+++|.++++|..|++.|.++++++
T Consensus        89 ~Lif~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l  123 (130)
T 3k2j_A           89 NLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKEL  123 (130)
T ss_dssp             HHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999998864

>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=99.63  E-value=8.8e-16  Score=117.29  Aligned_cols=62  Identities=29%  Similarity=0.552  Sum_probs=59.6

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||++|++|++++.|.++++|.+|+.|||.||+.||+++|.++++|..|++.|++++++
T Consensus        51 ~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~  112 (117)
T 3g0l_A           51 KKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTD  112 (117)
T ss_dssp             SSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCSSSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            33999999999999999999999999999999999999999999999999999999999875

>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=99.63  E-value=9e-16  Score=117.74  Aligned_cols=105  Identities=21%  Similarity=0.366  Sum_probs=77.1

Q ss_pred             CHHHHHHHHHHHHHHHhhhCCCC----chhHHHHHHHHHH-HHHHHhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHH
Q psy1225          53 TLNELTGELNLMFENAKKFNPAD----SRLYRDAVKLQKL-MQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFE  127 (256)
Q Consensus        53 ~~~ef~~D~~li~~Na~~yN~~~----S~i~~~A~~L~~~-f~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~  127 (256)
                      +++.+..-++.++.-...+..++    +..+.....-..+ -...+.+-||||++|++|++++.|.++++|..|+.|||.
T Consensus         5 ~p~~l~~~~~~ll~~l~~~~d~~g~~~s~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~   84 (120)
T 3ljw_A            5 SPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAK   84 (120)
T ss_dssp             CHHHHHHHHHHHHHHHHHCBCTTSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHhccCcCCCcccHHhcCCCCcccCCChHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHH
Confidence            45666666777776665543321    2222221110000 011233449999999999999999999999999999999


Q ss_pred             hhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225         128 NAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus       128 Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      ||+.||+++|.++++|..|++.|.++++++
T Consensus        85 Na~~yN~~~s~~~~~A~~L~~~f~~~~~~i  114 (120)
T 3ljw_A           85 NAKTYNEPGSQVFKDANSIKKIFYMKKAEI  114 (120)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999998864

>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=99.63  E-value=7.4e-16  Score=118.90  Aligned_cols=63  Identities=22%  Similarity=0.525  Sum_probs=60.7

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||+||++||+++.|.++++|..|++|||.||+.||+++|.++++|..|++.|.++++++
T Consensus        59 ~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l  121 (124)
T 3mb4_A           59 KKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL  121 (124)
T ss_dssp             SSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            449999999999999999999999999999999999999999999999999999999999875

>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=99.62  E-value=9.1e-16  Score=120.28  Aligned_cols=78  Identities=24%  Similarity=0.432  Sum_probs=70.3

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCChhhhhchhhhhhccch
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTGELSLMFENAK  174 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~~~~~~~d~~~~~~n~~  174 (256)
                      +.||+|++|++|++++.|.++++|..|+.+||+||+.||.+||+||+||..|++.|.+..++     ++.++.....+|.
T Consensus        47 k~Pi~l~~Ikkri~~~~Y~sld~f~~D~~lmf~NAr~yN~e~S~IyeDAv~Lq~~f~~~r~e-----L~~~g~~~~spa~  121 (147)
T 3iu6_A           47 KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDE-----LCKNGEILLSPAL  121 (147)
T ss_dssp             SCCCCHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH-----HHHHTTCCCCGGG
T ss_pred             CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHH-----HhhCCCeecCcch
Confidence            55999999999999999999999999999999999999999999999999999999998864     5666656667777


Q ss_pred             hcC
Q psy1225         175 KFN  177 (256)
Q Consensus       175 ~yn  177 (256)
                      .|.
T Consensus       122 ~~t  124 (147)
T 3iu6_A          122 SYT  124 (147)
T ss_dssp             GSC
T ss_pred             hhh
Confidence            666

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

Probab=99.62  E-value=9.3e-16  Score=119.24  Aligned_cols=65  Identities=28%  Similarity=0.491  Sum_probs=61.6

Q ss_pred             hcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCC
Q psy1225          94 QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFS  158 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~  158 (256)
                      .+-||||+||++||+++.|.++++|.+|++|||.||+.||+++|.++.+|..|++.|+++++++.
T Consensus        64 Ik~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~lp  128 (130)
T 2ouo_A           64 IKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMP  128 (130)
T ss_dssp             CSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHTSC
T ss_pred             cCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            34499999999999999999999999999999999999999999999999999999999998764

>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=99.62  E-value=1.8e-15  Score=115.84  Aligned_cols=104  Identities=26%  Similarity=0.352  Sum_probs=78.8

Q ss_pred             CCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHH---HHHHHHhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHh
Q psy1225          52 STLNELTGELNLMFENAKKFNPADSRLYRDAVKLQK---LMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFEN  128 (256)
Q Consensus        52 ~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~---~f~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~N  128 (256)
                      .+.+++..-+..++......+ +.+..+.....-..   --...+.+-||||+||++|++++.|.++++|.+|+.|||+|
T Consensus         7 ~~~~el~~~l~~~l~~l~~~~-~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~N   85 (119)
T 3p1f_A            7 FKPEELRQALMPTLEALYRQD-PESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNN   85 (119)
T ss_dssp             CCHHHHHHHHHHHHHHHHTCT-TTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhC-CCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            356777777777777654422 33443333222111   01122344599999999999999999999999999999999


Q ss_pred             hhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225         129 AKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus       129 a~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      |+.||+++|.++++|..|++.|++.+++
T Consensus        86 a~~yN~~~s~i~~~A~~L~~~f~~~~~~  113 (119)
T 3p1f_A           86 AWLYNRKTSRVYKFCSKLAEVFEQEIDP  113 (119)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999998874

>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=99.62  E-value=8.4e-16  Score=119.02  Aligned_cols=66  Identities=27%  Similarity=0.389  Sum_probs=62.2

Q ss_pred             HhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCC
Q psy1225          93 VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFS  158 (256)
Q Consensus        93 ~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~  158 (256)
                      +.+-||||+||++|++++.|.++++|.+|+.|||+||+.||+++|.++.+|..|++.|.++++++.
T Consensus        59 iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~lp  124 (127)
T 2oss_A           59 IIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELP  124 (127)
T ss_dssp             HCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            344499999999999999999999999999999999999999999999999999999999998764

>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=99.62  E-value=8.9e-16  Score=117.09  Aligned_cols=62  Identities=37%  Similarity=0.564  Sum_probs=59.7

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||++|++|++++.|.++++|..|++|||.||+.||+++|.++++|..|++.|.+.+++
T Consensus        49 ~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~  110 (116)
T 3iu5_A           49 SQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNE  110 (116)
T ss_dssp             SSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            44999999999999999999999999999999999999999999999999999999998875

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

Probab=99.61  E-value=1.6e-15  Score=115.74  Aligned_cols=61  Identities=25%  Similarity=0.440  Sum_probs=59.0

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      -||||+||++|+++|.|.++++|.+|++|||+||+.||+++|.++++|..|++.|.+.+++
T Consensus        47 ~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~  107 (117)
T 2i7k_A           47 HPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQ  107 (117)
T ss_dssp             CCCCHHHHHHHHTTTSCCSHHHHHHHHHHHHHHHHHTSCSSSSHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3999999999999999999999999999999999999999999999999999999998874

>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=99.61  E-value=1.6e-15  Score=117.31  Aligned_cols=63  Identities=29%  Similarity=0.453  Sum_probs=59.9

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||++|++|++++.|.++++|.+|+.|||.||+.||+++|.+|++|..|++.|.++++++
T Consensus        53 k~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~  115 (126)
T 3mqm_A           53 SDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEA  115 (126)
T ss_dssp             SSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            349999999999999999999999999999999999999999999999999999999988753

>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=99.61  E-value=2.3e-15  Score=114.81  Aligned_cols=62  Identities=24%  Similarity=0.482  Sum_probs=59.3

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||+||++|++++.|.++++|..|+.|||.||+.||+++|.++.+|..|++.|++.++.
T Consensus        54 ~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~k  115 (116)
T 3nxb_A           54 KAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK  115 (116)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            33999999999999999999999999999999999999999999999999999999998864

>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=99.61  E-value=1.6e-15  Score=116.28  Aligned_cols=65  Identities=29%  Similarity=0.496  Sum_probs=61.8

Q ss_pred             hcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCC
Q psy1225          94 QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFS  158 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~  158 (256)
                      .+-||||+||++|++++.|.++++|..|++|||.||+.||+++|.++.+|..|++.|+++++++.
T Consensus        51 I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~p  115 (120)
T 3jvl_A           51 IKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMP  115 (120)
T ss_dssp             CSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHTTCC
T ss_pred             cCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCc
Confidence            34499999999999999999999999999999999999999999999999999999999998764

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

Probab=99.60  E-value=3.8e-15  Score=114.38  Aligned_cols=61  Identities=25%  Similarity=0.512  Sum_probs=58.6

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      -||||++|++|++++.|.++++|.+|++|||.||+.||+++|.+|++|..|++.|.+.+++
T Consensus        46 ~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~~~~~l~~  106 (121)
T 2d9e_A           46 KPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQ  106 (121)
T ss_dssp             SCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3999999999999999999999999999999999999999999999999999999888765

>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=99.60  E-value=1.5e-15  Score=117.99  Aligned_cols=103  Identities=21%  Similarity=0.383  Sum_probs=76.5

Q ss_pred             CHHHHHHHHHHHHHHHhhhCC-----CCchhHHHHHH---HHHHHHHHHhcccccHHHHHHHhhcCCCCCHHHHHHHHHH
Q psy1225          53 TLNELTGELNLMFENAKKFNP-----ADSRLYRDAVK---LQKLMQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNL  124 (256)
Q Consensus        53 ~~~ef~~D~~li~~Na~~yN~-----~~S~i~~~A~~---L~~~f~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~l  124 (256)
                      +..++.+-+..|+.....+-.     +.+..+.....   +-.+  ..+.+-||||+||++||+++.|.++++|.+|+.|
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 NPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEY--YELIRKPVDFKKIKERIRNHKYRSLNDLEKDVML   85 (129)
T ss_dssp             CCHHHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHH--HHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHhcccccccCeeeHHhcCCCCcccCCCH--HHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            345566666666666655421     12233322211   1111  1233449999999999999999999999999999


Q ss_pred             HHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225         125 MFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus       125 mf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      ||+||+.||+++|.+|.+|..|++.|.+.++++
T Consensus        86 i~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l  118 (129)
T 2grc_A           86 LCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKI  118 (129)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999999998865

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

Probab=99.60  E-value=2.9e-15  Score=121.18  Aligned_cols=109  Identities=17%  Similarity=0.254  Sum_probs=79.3

Q ss_pred             HHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHHHHH-HH--HhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhh
Q psy1225          54 LNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ-RK--VQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK  130 (256)
Q Consensus        54 ~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~~f~-~~--~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~  130 (256)
                      ..+|..-+..|+....  ..+.+..+.......+.-. ..  +.+-||||+||++||+++.|.++++|..|++|||.||+
T Consensus        19 ~~~~~~~~~~il~~L~--~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~Na~   96 (166)
T 3fkm_X           19 NKQWYLLANQLILSLS--KYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCS   96 (166)
T ss_dssp             THHHHHHHHHHHHHHT--TSTTGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHH--hCCCChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence            3455555555554433  3344554444332221111 11  12239999999999999999999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHhcCChhhhhc
Q psy1225         131 KFNPADSRLYRDAVKLQKLMQRKVQEFSLNELTG  164 (256)
Q Consensus       131 ~yN~~~s~i~~~a~~L~~~~~~~~~~~~~~~~~~  164 (256)
                      .||+++|.++.+|..|++.|.++++++..+.+..
T Consensus        97 ~yN~~~s~i~~~A~~L~~~f~~~l~~~~~~~~~~  130 (166)
T 3fkm_X           97 LYNTSNSVVAITGKNIETYFNNQLIVMGYNNFIL  130 (166)
T ss_dssp             HSSCTTSHHHHHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHccccccch
Confidence            9999999999999999999999999887666553

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

Probab=99.60  E-value=3.7e-15  Score=119.50  Aligned_cols=62  Identities=24%  Similarity=0.461  Sum_probs=60.2

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      -||||+||++|++++.|.++++|..|+.|||.||+.||+++|.++++|..|++.|.+.++++
T Consensus        69 ~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~~~~~~~l~e~  130 (158)
T 3uv4_A           69 NPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEY  130 (158)
T ss_dssp             SCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            39999999999999999999999999999999999999999999999999999999999876

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

Probab=99.59  E-value=3.6e-15  Score=114.88  Aligned_cols=60  Identities=30%  Similarity=0.621  Sum_probs=58.5

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCC-CCHHHHHHHHHHHHHHHHHhc
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA-DSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~-~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      ||||+||++||+++.|.++++|..|+.|||.||+.||++ +|.+|.+|..|++.|.+++++
T Consensus        50 PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~~s~i~~~A~~L~~~f~~~~~~  110 (123)
T 3q2e_A           50 PMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKK  110 (123)
T ss_dssp             CCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999996 999999999999999999886

>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=99.58  E-value=3e-15  Score=119.60  Aligned_cols=67  Identities=24%  Similarity=0.341  Sum_probs=63.0

Q ss_pred             hcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCChh
Q psy1225          94 QENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFSLN  160 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~~~  160 (256)
                      .+-||||+||++||+++.|.++++|.+|++|||.||+.||+++|.++.+|..|++.|.++++++..+
T Consensus        71 Ik~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~l~~~  137 (154)
T 4alg_A           71 IKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQE  137 (154)
T ss_dssp             CSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHTTSCSS
T ss_pred             cCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCch
Confidence            3449999999999999999999999999999999999999999999999999999999999987544

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

Probab=99.58  E-value=8.5e-15  Score=114.57  Aligned_cols=62  Identities=27%  Similarity=0.632  Sum_probs=59.3

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCC-CCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPA-DSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~-~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||+||++||+++.|.++++|.+|+.|||.||+.||++ +|.+|.+|..|++.|.+++++
T Consensus        59 ~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~~s~i~~~A~~L~~~f~~~~~~  121 (135)
T 3mb3_A           59 DTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISS  121 (135)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCCTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            34999999999999999999999999999999999999997 999999999999999999875

>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=99.57  E-value=4.1e-15  Score=118.40  Aligned_cols=63  Identities=30%  Similarity=0.563  Sum_probs=60.7

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||++|++||+++.|.++++|..|+.|||.||+.||+++|.+|++|..|++.|.++++++
T Consensus        69 k~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l  131 (150)
T 3tlp_A           69 LEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKEL  131 (150)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            349999999999999999999999999999999999999999999999999999999999875

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

Probab=99.57  E-value=7.3e-15  Score=114.90  Aligned_cols=64  Identities=28%  Similarity=0.534  Sum_probs=59.8

Q ss_pred             hcccccHHHHHHHhhc--CCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          94 QENPRSLLTIGKTLKS--GHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~--~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      .+-||||+||++||++  +.|.++++|.+|++|||.||+.||+++|.++++|..|++.|+++++++
T Consensus        56 Ik~PmDL~tI~~kL~~~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~  121 (135)
T 2yyn_A           56 IKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNL  121 (135)
T ss_dssp             CSSCCCHHHHHHHHHSSSCCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            3449999999999998  599999999999999999999999999999999999999999998763

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

Probab=99.55  E-value=8.1e-15  Score=112.87  Aligned_cols=62  Identities=21%  Similarity=0.400  Sum_probs=58.8

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||+||++|++++.|.++++|..|+.|||.||+.||+++|.++++|..|++.|.+.+++
T Consensus        51 k~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~  112 (123)
T 3hme_A           51 KHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSK  112 (123)
T ss_dssp             SSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTCH
T ss_pred             CCCCCHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            44999999999999999999999999999999999999999999999999999999887754

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

Probab=99.54  E-value=1.2e-14  Score=113.72  Aligned_cols=62  Identities=27%  Similarity=0.531  Sum_probs=59.1

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||++|++|++++.|.++++|.+|+.|||.||+.||+++|.+|++|..|++.+.+.+++
T Consensus        51 ~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~  112 (135)
T 3rcw_A           51 KHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQ  112 (135)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            33999999999999999999999999999999999999999999999999999999888875

>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=99.54  E-value=2.1e-14  Score=116.99  Aligned_cols=63  Identities=27%  Similarity=0.576  Sum_probs=60.1

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||+||++||+++.|.++++|.+|+.|||.||+.||+++|.++++|..|++.|.++++++
T Consensus       110 ~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~  172 (174)
T 2ri7_A          110 KEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGF  172 (174)
T ss_dssp             SSCCCHHHHHHHHHTTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCcCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            339999999999999999999999999999999999999999999999999999999998764

>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=99.47  E-value=6.9e-14  Score=114.95  Aligned_cols=63  Identities=29%  Similarity=0.532  Sum_probs=59.6

Q ss_pred             hcccccHHHHHHHhhc--CCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          94 QENPRSLLTIGKTLKS--GHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~--~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      .+-||||+||++||++  +.|.++++|.+||+|||.||+.||+++|.++++|..|++.|++++++
T Consensus       117 Ik~PmdL~tI~~kl~~~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~v~~~a~~L~~~f~~~~~~  181 (184)
T 3o36_A          117 IKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKN  181 (184)
T ss_dssp             CSSCCCHHHHHHHHHSTTCSCCSHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3449999999999998  79999999999999999999999999999999999999999999875

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

Probab=99.47  E-value=2.8e-14  Score=117.70  Aligned_cols=61  Identities=21%  Similarity=0.353  Sum_probs=57.9

Q ss_pred             ccccHHHHHHHhhcC---CCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          96 NPRSLLTIGKTLKSG---HYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        96 lP~dl~~I~~kl~~~---~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      -||||+||++||+++   .|.++++|.+|++|||+||+.|| ++|.++++|..|++.|+++++++
T Consensus       113 ~PMDL~tIk~kL~~~~~~~Y~s~~eF~~Dv~Lif~N~~~yN-~~s~~~~~a~~L~~~Fe~~~~~~  176 (189)
T 2ro1_A          113 GTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLT-EDKADVQSIIGLQRFFETRMNEA  176 (189)
T ss_dssp             CCCCHHHHHHHHHTSSSSCCSCHHHHHHHHHHHHHHHHHHC-CSSCSSHHHHHHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHh
Confidence            399999999999999   99999999999999999999999 68899999999999999999864

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

Probab=99.46  E-value=3.1e-13  Score=105.00  Aligned_cols=59  Identities=20%  Similarity=0.381  Sum_probs=55.8

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCH----HHHHHHHHHHHHHHHHh
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSR----LYRDAVKLQKLMQRKVQ  155 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~----i~~~a~~L~~~~~~~~~  155 (256)
                      ||||+||++|++++.|.++++|..|+.|||.||+.||+++|+    ++.+|..|++.+...++
T Consensus        47 PmDL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s~~~~~i~~~A~~L~~~~~~~l~  109 (131)
T 2dkw_A           47 PMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIA  109 (131)
T ss_dssp             CCCHHHHHHHHHTTCCCSSHHHHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999995    67999999999988774

>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=99.45  E-value=3.9e-13  Score=104.36  Aligned_cols=65  Identities=18%  Similarity=0.310  Sum_probs=58.3

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHH----HHHHHHHHHHHHHHHh-cCCh
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRL----YRDAVKLQKLMQRKVQ-EFSL  159 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i----~~~a~~L~~~~~~~~~-~~~~  159 (256)
                      +-||||+||++|++++.|.++++|..|+.|||.||+.||+++|.+    +.+|..|++.+...++ +++.
T Consensus        48 ~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~s~~~~~i~~~A~~L~~~~~~~i~~el~~  117 (130)
T 3dai_A           48 KQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDE  117 (130)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            339999999999999999999999999999999999999999866    7889999999988886 4433

>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=99.38  E-value=3.3e-13  Score=110.25  Aligned_cols=84  Identities=10%  Similarity=0.245  Sum_probs=73.5

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+|+....+..|.||.+.           .++.||||.+|++||+.|.|.++++|..||.+||.||..+|++.+.+.++
T Consensus        81 ~~vl~~L~~~~~s~~~~~y-----------~~k~PmDL~~i~kKl~~~~Y~s~~eF~~Dv~lIf~n~~~~~~~~~e~~~a  149 (183)
T 3lqh_A           81 KQVLTALLNSRTTSHLLRY-----------RQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKA  149 (183)
T ss_dssp             HHHHHHHHTCHHHHHHHTC-----------CC--CCSHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             HHHHHHHHhccccHhhhhh-----------hhcCCccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhccCCChhhhhh
Confidence            4566667778888888762           25999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      +..|+..|.+.++++
T Consensus       150 g~~l~~~f~~~l~~v  164 (183)
T 3lqh_A          150 NSMVKSFFIRQMERV  164 (183)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHH
Confidence            999999999988765

>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=99.33  E-value=1.1e-12  Score=109.69  Aligned_cols=64  Identities=27%  Similarity=0.513  Sum_probs=59.9

Q ss_pred             hcccccHHHHHHHhhc---CCCCCHHHHHHHHHHHHHhhhhhCC-----------------CCCHHHHHHHHHHHHHHHH
Q psy1225          94 QENPRSLLTIGKTLKS---GHYSTLNELTGELNLMFENAKKFNP-----------------ADSRLYRDAVKLQKLMQRK  153 (256)
Q Consensus        94 ~klP~dl~~I~~kl~~---~~Y~s~~~f~~D~~lmf~Na~~yN~-----------------~~s~i~~~a~~L~~~~~~~  153 (256)
                      .+-||||++|++||++   +.|.++++|.+|++|||.||+.||+                 ++|.++++|..|++.|+++
T Consensus       117 Ik~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~v~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~  196 (207)
T 3u5n_A          117 IKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDK  196 (207)
T ss_dssp             CSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHHHHHHHHHHHHC----------CCCCHHHHHHHHHHHHHHHH
T ss_pred             hCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHHHHHCCCcchHHHHHHHHHhcccccCHHHHHHHHHHHHHHHH
Confidence            4449999999999997   7999999999999999999999999                 9999999999999999999


Q ss_pred             HhcC
Q psy1225         154 VQEF  157 (256)
Q Consensus       154 ~~~~  157 (256)
                      ++++
T Consensus       197 ~~~~  200 (207)
T 3u5n_A          197 LTEI  200 (207)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9864

>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=99.17  E-value=1.2e-10  Score=95.03  Aligned_cols=61  Identities=11%  Similarity=0.341  Sum_probs=58.8

Q ss_pred             ccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          96 NPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        96 lP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      .||||.+|++|++++.|.|+++|+.|+.+||.||..+|+++|++.+++..|+.+|.+++++
T Consensus       103 ~PmDL~~i~kKl~~~~Y~s~~eF~~Dv~lIf~n~~~~~~~~~e~~~ag~~l~~~f~~~l~~  163 (183)
T 3lqh_A          103 QPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMER  163 (183)
T ss_dssp             -CCSHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhccCCChhhhhhhhHHHHHHHHHHHH
Confidence            3999999999999999999999999999999999999999999999999999999999885

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A*

Probab=97.59  E-value=3e-06  Score=87.16  Aligned_cols=76  Identities=13%  Similarity=0.090  Sum_probs=60.2

Q ss_pred             cchhcCCccccccccH--HH---HHHHHHHHHHHhcCCCC-ccceeecccceeEe-----EEeecCcccccccCCCCCCc
Q psy1225         172 NAKKFNPADLRLYRDA--VK---LQKLMQRKVQEVMILDI-ECQVYLISDELTHY-----QVVLTGTAEQVRLSGLPDGD  240 (256)
Q Consensus       172 n~~~yn~~~~~i~~~a--~~---l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-----ev~kt~~~~~~~~~~i~~~~  240 (256)
                      ++..|+.+|.+.....  +.   +.+|.+.|.+.+|..|+ ++|||||++|+|..     |||+|.+..+.|++.|+|+|
T Consensus       466 ~g~~~~vGD~V~v~~~d~~~p~yiarIe~iwe~~dg~~~~~~~WfyRp~ETvlg~~~~~rElFlS~~~d~~~l~~I~gKC  545 (1330)
T 3av4_A          466 DEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYIHSKV  545 (1330)
T ss_dssp             ESSEEETTCEEEECBCCSSCCCEEEEEEEEEEETTCCEEEEEEEEEEGGGSTTGGGSCTTEEEEEEEEEEEEGGGEEEEE
T ss_pred             CCEEEecCCEEEEeCCCCCCCCEEEEEeeeeecCCCCEEEEEEEEEchHHcccccccCCCeEEEecccccCcHHHhccee
Confidence            4556666776654422  21   34577778888898899 68999999998642     99999999999999999999


Q ss_pred             eeeeeec
Q psy1225         241 WLAFTLP  247 (256)
Q Consensus       241 ~v~f~~~  247 (256)
                      .|++..+
T Consensus       546 ~V~~~~~  552 (1330)
T 3av4_A          546 KVIYKAP  552 (1330)
T ss_dssp             CEEECCC
T ss_pred             EEEEecc
Confidence            9999877

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A*

Probab=97.18  E-value=1.4e-05  Score=80.16  Aligned_cols=76  Identities=14%  Similarity=0.085  Sum_probs=59.0

Q ss_pred             cchhcCCccccccc--cHHH---HHHHHHHHHHHhcCCCC-ccceeecccceeEe-----EEeecCcccccccCCCCCCc
Q psy1225         172 NAKKFNPADLRLYR--DAVK---LQKLMQRKVQEVMILDI-ECQVYLISDELTHY-----QVVLTGTAEQVRLSGLPDGD  240 (256)
Q Consensus       172 n~~~yn~~~~~i~~--~a~~---l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h~~-----ev~kt~~~~~~~~~~i~~~~  240 (256)
                      ++..|..+|-++..  +++.   +.+|...|.+.+|.+++ +.|||||++|+|..     |||+|..+.+.+++.|+|+|
T Consensus       155 ~g~~i~VGD~V~v~~~d~~~ppyIarIe~m~ed~~g~k~~~v~Wf~rp~ET~lg~~~~~~ElFlsd~cd~~~l~~I~gkc  234 (1002)
T 3swr_A          155 DAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKV  234 (1002)
T ss_dssp             TTEEEETTCEEEECBSSTTSCCEEEEEEEEEEETTTEEEEEEEEEEEGGGSTTGGGSCTTEEEEEEEEEEEEGGGEEEEE
T ss_pred             CCEEEecCCEEEEecCCCCCCceEEEEEEEeecCCCCeEEEEEEEecchhcccccCCCCCceEeeccccCCcHHHhceee
Confidence            44556666655543  2222   23477778888888888 68999999998874     99999999999999999999


Q ss_pred             eeeeeec
Q psy1225         241 WLAFTLP  247 (256)
Q Consensus       241 ~v~f~~~  247 (256)
                      .|++...
T Consensus       235 ~V~~~~~  241 (1002)
T 3swr_A          235 KVIYKAP  241 (1002)
T ss_dssp             CEEECCC
T ss_pred             EEEEccC
Confidence            9998755

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A*

Probab=97.04  E-value=7e-05  Score=77.13  Aligned_cols=49  Identities=6%  Similarity=0.068  Sum_probs=42.7

Q ss_pred             CCCC-ccceeecccceeE---------eEEeecCcccccccCCCCCCceeeeeeccccc
Q psy1225         203 ILDI-ECQVYLISDELTH---------YQVVLTGTAEQVRLSGLPDGDWLAFTLPVVSG  251 (256)
Q Consensus       203 ~~~~-~c~y~rpeqt~h~---------~ev~kt~~~~~~~~~~i~~~~~v~f~~~~~~g  251 (256)
                      ..++ .+||||||+|.|.         .|||-|.++..+|++.|.|+|+|.|++.+++.
T Consensus       726 ~~~vrV~wFyRPedt~~~~~~~~~~D~nELf~S~~~~~vp~~~I~GKC~V~~~~d~~~~  784 (1330)
T 3av4_A          726 DIKLRLYKFYRPENTHRSYNGSYHTDINMLYWSDEEAVVNFSDVQGRCTVEYGEDLLES  784 (1330)
T ss_dssp             CCEEEEEEEECTTTSTTGGGTTTTSCTTBCEEEEEEEEEEGGGCCEEEEEEESTTCSSC
T ss_pred             ceEEEEEEeeChhhcccccccccccCcceEEeeccceecCHHHcCceEEEEeccccccc
Confidence            3466 5899999999753         19999999999999999999999999988774

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A*

Probab=95.38  E-value=0.0031  Score=63.47  Aligned_cols=44  Identities=5%  Similarity=0.006  Sum_probs=38.3

Q ss_pred             ccceeecccceeE---------eEEeecCcccccccCCCCCCceeeeeecccc
Q psy1225         207 ECQVYLISDELTH---------YQVVLTGTAEQVRLSGLPDGDWLAFTLPVVS  250 (256)
Q Consensus       207 ~c~y~rpeqt~h~---------~ev~kt~~~~~~~~~~i~~~~~v~f~~~~~~  250 (256)
                      ..||||||+|-|.         .|||.|.++..+|++.|.|+|.|+++.-+..
T Consensus       420 v~~fyRPed~~~~~~~~~~~D~~elf~S~~~~~~~~~~i~GkC~V~~~~d~~~  472 (1002)
T 3swr_A          420 VNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPE  472 (1002)
T ss_dssp             EEECBCGGGSTTCGGGGSSSCTTEEEECCCEEEEEGGGCCEEEEEEEGGGCSS
T ss_pred             EEEEECcccccccccccccCCcceEEEecceeccCHHHcceEEEEEEeccccc
Confidence            4899999998541         3999999999999999999999999977653

>4ft4_B DNA (cytosine-5)-methyltransferase 1; chromodomain, BAH domain, DNA methyltransferase domain, H3K9 binding, methylation, transferase; HET: DNA MLY SAH; 2.70A {Zea mays} PDB: 4ft2_A* 4fsx_A*

Probab=94.03  E-value=0.0058  Score=59.98  Aligned_cols=76  Identities=8%  Similarity=-0.021  Sum_probs=53.7

Q ss_pred             cchhcCCccccccccHH----HHHHHHHHHHHHhcCCCC-ccceeeccccee-----------E---eEEeecCcccccc
Q psy1225         172 NAKKFNPADLRLYRDAV----KLQKLMQRKVQEVMILDI-ECQVYLISDELT-----------H---YQVVLTGTAEQVR  232 (256)
Q Consensus       172 n~~~yn~~~~~i~~~a~----~l~~i~~~~~~~~g~~~~-~c~y~rpeqt~h-----------~---~ev~kt~~~~~~~  232 (256)
                      ++..|+.+|-...+...    -+.+|...+...+|..++ +=|+||||+|+-           +   .|||.|+...+.+
T Consensus        54 ~~~~~~~~d~~~v~~~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~r~~d~~~~~~~~~~~~~~~~d~~~~~~s~~~~~~~  133 (784)
T 4ft4_B           54 DNVVYCLGDDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAEDTVINSLVSISVDGHKHDPRRVFLSEEKNDNV  133 (784)
T ss_dssp             TTEEEETTCEEEECCSTTSCCEEEEEEEEEEETTSCEEEEEEEEEEGGGSTTGGGGGCCBTTBCCCTTBEEEEEEEEEEE
T ss_pred             CCEEEeCCCeEEEeCCCCCCCEEEEEEEEEEcCCCCEEEEEEEeeChhhhcccccccccccccccccceEEEeCcEEEec
Confidence            34556655554443211    123444445566788888 469999999962           1   1999999999999


Q ss_pred             cCCCCCCceeeeeec
Q psy1225         233 LSGLPDGDWLAFTLP  247 (256)
Q Consensus       233 ~~~i~~~~~v~f~~~  247 (256)
                      ++.|++||.|++...
T Consensus       134 ~~~i~~k~~v~~~~~  148 (784)
T 4ft4_B          134 LDCIISKVKIVHVDP  148 (784)
T ss_dssp             GGGEEEECCEEECCT
T ss_pred             hHHeeeeEEEEeeCc
Confidence            999999999998654

>4dov_A ORC1, origin recognition complex subunit 1; DNA replication, replication; 1.70A {Mus musculus} PDB: 4dow_A*

Probab=91.42  E-value=0.036  Score=43.64  Aligned_cols=40  Identities=3%  Similarity=-0.030  Sum_probs=32.2

Q ss_pred             ceeecccceeE------e-----EEeecCccc---ccccCCCCCCceeeeeecc
Q psy1225         209 QVYLISDELTH------Y-----QVVLTGTAE---QVRLSGLPDGDWLAFTLPV  248 (256)
Q Consensus       209 ~y~rpeqt~h~------~-----ev~kt~~~~---~~~~~~i~~~~~v~f~~~~  248 (256)
                      ||+||++--++      .     |||.+.+..   +..++-|+|+|-|..+..+
T Consensus        80 Wy~R~~EiP~~k~~l~g~~~~~qEIF~~d~~~~d~~I~aeTIi~~c~V~~~~~~  133 (163)
T 4dov_A           80 WFVRFLEIPVSKRHLLGRSPPAQEIFWYDCSDWDNKINVETIIGPVQVVALAPE  133 (163)
T ss_dssp             EEEEGGGSCTTTGGGGCSCCCTTEEEEECCSCSCCEEEGGGEEEEEEEEECCTT
T ss_pred             eeechhhccccchhhccCCCCCCeEEEecCCCCcccccHHHeeeceEEEEcCCc
Confidence            99999965222      1     999988884   8999999999999887544

---

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	256
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	7e-22
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	3e-12
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	2e-05
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	3e-21
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	1e-11
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	4e-05
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	1e-20
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	4e-12
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	3e-06
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	3e-20
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	3e-11
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	4e-05
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	1e-19
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	2e-11
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	7e-06
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	3e-19
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	2e-11
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	6e-06

>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 = 86.2 bits (213), Expect = 7e-22
 Identities = 22/95 (23%), Positives = 41/95 (43%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PF      +   DYY+II  P  L T+ + ++   Y +  E    L L+ +N+  +N 
Sbjct: 44  TYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNG 103

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLK 108
               L + +  +  L   K++E    L  + K + 
Sbjct: 104 PKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAIN 138

>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 = 60.4 bits (146), Expect = 3e-12
 Identities = 14/66 (21%), Positives = 29/66 (43%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           K+   P  L T+ + ++   Y +  E    L L+ +N+  +N     L + +  +  L  
Sbjct: 61  KIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCD 120

Query: 152 RKVQEF 157
            K++E 
Sbjct: 121 EKLKEK 126

>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 = 41.1 bits (96), Expect = 2e-05
 Identities = 10/43 (23%), Positives = 19/43 (44%)

Query: 158 SLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQE 200
           S  E    L L+ +N+  +N     L + +  +  L   K++E
Sbjct: 83  SREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKE 125

>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 = 83.9 bits (207), Expect = 3e-21
 Identities = 26/97 (26%), Positives = 48/97 (49%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           S PF     K++ PDYY++I NP  L TI K +    Y +      ++NL+  N+ K+N 
Sbjct: 28  SWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNG 87

Query: 74  ADSRLYRDAVKLQKLMQRKVQENPRSLLTIGKTLKSG 110
            +S+  + A ++  +  + + E    L  + K + + 
Sbjct: 88  PESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTA 124

>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 = 58.4 bits (141), Expect = 1e-11
 Identities = 17/66 (25%), Positives = 33/66 (50%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           KV  NP  L TI K +    Y +      ++NL+  N+ K+N  +S+  + A ++  +  
Sbjct: 45  KVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCY 104

Query: 152 RKVQEF 157
           + + E+
Sbjct: 105 QTLTEY 110

>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 = 39.9 bits (93), Expect = 4e-05
 Identities = 6/44 (13%), Positives = 20/44 (45%)

Query: 159 LNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
                 +++L+  N+ K+N  + +  + A ++  +  + + E  
Sbjct: 68  RESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYD 111

>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 = 81.6 bits (201), Expect = 1e-20
 Identities = 27/82 (32%), Positives = 44/82 (53%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PF++   K   PDYY +I+ P  L T+ + L+S +Y T      +L  +  N +++NP
Sbjct: 20  AWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNP 79

Query: 74  ADSRLYRDAVKLQKLMQRKVQE 95
            DS   R A  L+K    K++E
Sbjct: 80  PDSEYCRCASALEKFFYFKLKE 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 = 58.9 bits (142), Expect = 4e-12
 Identities = 20/66 (30%), Positives = 33/66 (50%)

Query: 91  RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLM 150
            +V   P  L T+ + L+S +Y T      +L  +  N +++NP DS   R A  L+K  
Sbjct: 36  YEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFF 95

Query: 151 QRKVQE 156
             K++E
Sbjct: 96  YFKLKE 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 = 42.7 bits (100), Expect = 3e-06
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 130 KKFNPADSRLYRDAVK----LQKLMQRKVQE--FSLNELTGELSLMFENAKKFNPADLRL 183
           +    +++  Y + ++    L+ + +R       +      +L  +  N +++NP D   
Sbjct: 25  EPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEY 84

Query: 184 YRDAVKLQKLMQRKVQE 200
            R A  L+K    K++E
Sbjct: 85  CRCASALEKFFYFKLKE 101

>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 = 80.8 bits (199), Expect = 3e-20
 Identities = 28/84 (33%), Positives = 44/84 (52%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PFL+   K   PDYY  IK P  L T+   L+S  Y  + +   +  L+F N + +N 
Sbjct: 21  AWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNG 80

Query: 74  ADSRLYRDAVKLQKLMQRKVQENP 97
            ++  Y+ A +L+K    KV+E P
Sbjct: 81  ENTSYYKYANRLEKFFNNKVKEIP 104

>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 = 56.9 bits (137), Expect = 3e-11
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 75  DSRLYRDAVKLQKLMQ-RKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFN 133
            +  +   V  +++       + P  L T+   L+S  Y  + +   +  L+F N + +N
Sbjct: 20  AAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYN 79

Query: 134 PADSRLYRDAVKLQKLMQRKVQEF 157
             ++  Y+ A +L+K    KV+E 
Sbjct: 80  GENTSYYKYANRLEKFFNNKVKEI 103

>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 = 39.5 bits (92), Expect = 4e-05
 Identities = 11/42 (26%), Positives = 22/42 (52%)

Query: 160 NELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEV 201
            +   +  L+F N + +N  +   Y+ A +L+K    KV+E+
Sbjct: 62  EDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEI 103

>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 = 79.2 bits (195), Expect = 1e-19
 Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 2/89 (2%)

Query: 14  SEPFLKL--PAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKF 71
           S PF +   P     PDY+ I+KNP  L TI + L +G Y    +   ++ LMF NA  +
Sbjct: 25  SLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLY 84

Query: 72  NPADSRLYRDAVKLQKLMQRKVQENPRSL 100
           N   SR+Y+   KL ++ ++++    +SL
Sbjct: 85  NRKTSRVYKFCSKLAEVFEQEIDPVMQSL 113

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 28/108 (25%), Positives = 48/108 (44%), Gaps = 4/108 (3%)

Query: 53  TLNELTGELNLMFENAKKFNPADSRLYR---DAVKLQKLMQRKVQENPRSLLTIGKTLKS 109
              EL   L    E   + +P +S  +R   D   L       + +NP  L TI + L +
Sbjct: 3   KPEELRQALMPTLEALYRQDP-ESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDT 61

Query: 110 GHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF 157
           G Y    +   ++ LMF NA  +N   SR+Y+   KL ++ ++++   
Sbjct: 62  GQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPV 109

>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 = 41.9 bits (98), Expect = 7e-06
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 147 QKLMQRKVQEFSLNELTGELSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVM 202
           +KL   + QE    +   ++ LMF NA  +N    R+Y+   KL ++ ++++  VM
Sbjct: 57  RKLDTGQYQE--PWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVM 110

>d1wuma1 a.29.2.1 (A:715-832) P300/CAF histone acetyltransferase bromodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 118

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: P300/CAF histone acetyltransferase bromodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.5 bits (193), Expect = 3e-19
 Identities = 25/82 (30%), Positives = 45/82 (54%)

Query: 14  SEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNP 73
           + PF++   +   P YY +I+ P  L T+ + LK+ +Y +      +L  +F N K++NP
Sbjct: 31  AWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNP 90

Query: 74  ADSRLYRDAVKLQKLMQRKVQE 95
            +S  Y+ A  L+K    K++E
Sbjct: 91  PESEYYKCANILEKFFFSKIKE 112

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 21/68 (30%), Positives = 36/68 (52%)

Query: 92  KVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQ 151
           +V   P  L T+ + LK+ +Y +      +L  +F N K++NP +S  Y+ A  L+K   
Sbjct: 48  EVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFF 107

Query: 152 RKVQEFSL 159
            K++E  L
Sbjct: 108 SKIKEAGL 115

>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 = 42.0 bits (98), Expect = 6e-06
 Identities = 13/40 (32%), Positives = 23/40 (57%)

Query: 166 LSLMFENAKKFNPADLRLYRDAVKLQKLMQRKVQEVMILD 205
           L  +F N K++NP +   Y+ A  L+K    K++E  ++D
Sbjct: 78  LQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID 117

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	256
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.94
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.93
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.93
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.92
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.92
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.9
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.64
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.6
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.59
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.58
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.57
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.56
d1m4za_	217	Origin-recognition complex protein 120kDa subunit,	94.46

>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=99.94  E-value=4.1e-27  Score=174.48  Aligned_cols=95  Identities=29%  Similarity=0.462  Sum_probs=90.4

Q ss_pred             CccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHH
Q psy1225           1 MRPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYR   80 (256)
Q Consensus         1 l~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~   80 (256)
                      |+++++....++.|.+|..||+...+||||++|++||||+||++||++|.|.|+++|.+|+++||.||..||+++|.+++
T Consensus         7 l~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~   86 (102)
T d3d7ca1           7 LKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCR   86 (102)
T ss_dssp             HHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHH
T ss_pred             HHHHHHHHHhCCCCCccCCCCChhhCcCHHHHcCCccCHHHHHHHhccCccCCHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            35678888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhc
Q psy1225          81 DAVKLQKLMQRKVQE   95 (256)
Q Consensus        81 ~A~~L~~~f~~~~~k   95 (256)
                      +|..|++.|.+++++
T Consensus        87 ~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          87 CASALEKFFYFKLKE  101 (102)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999988764

>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=99.93  E-value=1.1e-26  Score=174.72  Aligned_cols=96  Identities=29%  Similarity=0.514  Sum_probs=92.6

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ..+|+....++.|+||..||+...+|+||++|++||||+||++||++|.|.|+++|..|++|||.||..||+++|.++.+
T Consensus         9 ~~il~~l~~~~~a~pF~~pvd~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~i~~~   88 (111)
T d1e6ia_           9 QNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKY   88 (111)
T ss_dssp             HHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHH
T ss_pred             HHHHHHHHhCCCChhhcCCCCchhCcCHHHHcCCchhHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            56788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhccc
Q psy1225          82 AVKLQKLMQRKVQENP   97 (256)
Q Consensus        82 A~~L~~~f~~~~~klP   97 (256)
                      |..|++.|.+.++++|
T Consensus        89 A~~l~~~f~~~~~~ip  104 (111)
T d1e6ia_          89 ANRLEKFFNNKVKEIP  104 (111)
T ss_dssp             HHHHHHHHHHHHHTSG
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            9999999999998875

>d1eqfa2 a.29.2.1 (A:1498-1625) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=7.9e-26  Score=174.03  Aligned_cols=103  Identities=25%  Similarity=0.431  Sum_probs=94.0

Q ss_pred             cccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHHHHH
Q psy1225           5 KNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVK   84 (256)
Q Consensus         5 ~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~   84 (256)
                      ++....++.|+||..||+...+||||++|++||||+||++||++|.|.|+++|..|+++||.||..||+++|.++.+|..
T Consensus        19 ~~~~~~~p~a~pF~~pVd~~~~PdY~~vIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~   98 (128)
T d1eqfa2          19 TQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQE   98 (128)
T ss_dssp             HHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHHcCCCCChhcCCCCcccCcCHHHHcCCcccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence            35667889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcccccHHHHHHHh
Q psy1225          85 LQKLMQRKVQENPRSLLTIGKTL  107 (256)
Q Consensus        85 L~~~f~~~~~klP~dl~~I~~kl  107 (256)
                      |.+.+.+.+.+++-.+....+.+
T Consensus        99 L~~~~~~~l~~~~~~~~~le~~i  121 (128)
T d1eqfa2          99 IVNVCYQTLTEYDEHLTQLEKDI  121 (128)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHhHH
Confidence            99999999888765555544443

>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=99.92  E-value=8.8e-26  Score=176.22  Aligned_cols=106  Identities=22%  Similarity=0.354  Sum_probs=98.1

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      ..+++...+++.|++|..||+...+||||++|++||||++|++||++|.|.|+++|.+|++|||.||..||+++|.++.+
T Consensus        32 ~~il~~l~~~~~s~pF~~Pvd~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~  111 (139)
T d1eqfa1          32 ESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQI  111 (139)
T ss_dssp             HHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTTSHHHHH
T ss_pred             HHHHHHHHcCCCchhhhCCCChhhccCHHHHcCChhhHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            45778888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcccccHHHHHHHh
Q psy1225          82 AVKLQKLMQRKVQENPRSLLTIGKTL  107 (256)
Q Consensus        82 A~~L~~~f~~~~~klP~dl~~I~~kl  107 (256)
                      |..|.+.|.+.+++++-.+..+++.+
T Consensus       112 A~~L~~~~~~~~~~~~~~~~~~e~~i  137 (139)
T d1eqfa1         112 SQSMLDLCDEKLKEKEDKLARLEKAI  137 (139)
T ss_dssp             HHHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999988866666665543

>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=99.92  E-value=4e-26  Score=173.39  Aligned_cols=95  Identities=27%  Similarity=0.487  Sum_probs=90.7

Q ss_pred             ccccccccCCccccccccCCCCCCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhHHH
Q psy1225           2 RPQKNQTEGGNLSEPFLKLPAKRYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRD   81 (256)
Q Consensus         2 ~~~~~~~~~~~~s~~F~~~p~~~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~~~   81 (256)
                      +.+++....++.|.+|..||+...+|+||++|++||||++|++||++|.|.++++|.+|+++||.||..||+++|.++.+
T Consensus        19 ~~il~~l~~~~~a~~F~~pv~~~~~pdY~~iI~~PmdL~~I~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yn~~~s~~~~~   98 (118)
T d1wuma1          19 KSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKC   98 (118)
T ss_dssp             HHHHHHHHHSSSCHHHHSCCCSSSSSSCTTTCSSCCCHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHHHSCTTSSHHHH
T ss_pred             HHHHHHHHhCCCcCcccCCCChhhCcCHHHHcCChhhHHHHHHHhcccccCchHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            46777888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcc
Q psy1225          82 AVKLQKLMQRKVQEN   96 (256)
Q Consensus        82 A~~L~~~f~~~~~kl   96 (256)
                      |..|++.|.+.++++
T Consensus        99 A~~l~~~f~~~~~e~  113 (118)
T d1wuma1          99 ANILEKFFFSKIKEA  113 (118)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHc
Confidence            999999999988764

>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=99.90  E-value=2e-24  Score=162.91  Aligned_cols=94  Identities=30%  Similarity=0.451  Sum_probs=85.3

Q ss_pred             cccccccC-CccccccccCCCC--CCCcchhhhcCCcCcHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCchhH
Q psy1225           3 PQKNQTEG-GNLSEPFLKLPAK--RYNPDYYRIIKNPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLY   79 (256)
Q Consensus         3 ~~~~~~~~-~~~s~~F~~~p~~--~~~pdYy~~I~~PmdL~tI~~kl~~~~Y~~~~ef~~D~~li~~Na~~yN~~~S~i~   79 (256)
                      ++++.... ++.|.+|..||+.  .++||||++|++||||++|++||++|.|.|+++|.+|+++||.||+.||+++|.++
T Consensus        13 ~~l~~l~~~~p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~~~   92 (114)
T d3dwya1          13 PTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVY   92 (114)
T ss_dssp             HHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHH
T ss_pred             HHHHHHHhcCcCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCccccHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            45555544 4799999999875  47999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcc
Q psy1225          80 RDAVKLQKLMQRKVQEN   96 (256)
Q Consensus        80 ~~A~~L~~~f~~~~~kl   96 (256)
                      ..|..|++.|.+.+.++
T Consensus        93 ~~A~~L~~~f~~~~~~i  109 (114)
T d3dwya1          93 KFCSKLAEVFEQEIDPV  109 (114)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999887654

>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=99.64  E-value=3.4e-16  Score=114.91  Aligned_cols=62  Identities=31%  Similarity=0.447  Sum_probs=59.5

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      +-||||++|++|++++.|.|+++|.+|+.|||.||+.||+++|.++++|..|++.|.+++++
T Consensus        40 ~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          40 RFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             SSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCHHHHHHHhccCccCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            34999999999999999999999999999999999999999999999999999999998874

>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=99.60  E-value=1.1e-15  Score=114.38  Aligned_cols=102  Identities=27%  Similarity=0.389  Sum_probs=77.0

Q ss_pred             HHHHHHHHHHHHHHHhhhCCCCchhHHHHHHHHHH---HHHHHhcccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhh
Q psy1225          54 LNELTGELNLMFENAKKFNPADSRLYRDAVKLQKL---MQRKVQENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAK  130 (256)
Q Consensus        54 ~~ef~~D~~li~~Na~~yN~~~S~i~~~A~~L~~~---f~~~~~klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~  130 (256)
                      ++++...+.-++.+-.. ..|.+..+.....-...   -...+.+-||||++|++|++++.|.|+++|.+|+.|||.||+
T Consensus         4 p~el~~~l~~~l~~l~~-~~p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~   82 (114)
T d3dwya1           4 PEELRQALMPTLEALYR-QDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAW   82 (114)
T ss_dssp             HHHHHHHHHHHHHHHHT-CTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHh-cCcCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCccccHHHHHHHHHHHHHHHH
Confidence            56666666666665532 23455555443321111   112233449999999999999999999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHhc
Q psy1225         131 KFNPADSRLYRDAVKLQKLMQRKVQE  156 (256)
Q Consensus       131 ~yN~~~s~i~~~a~~L~~~~~~~~~~  156 (256)
                      .||+++|.++..|..|++.|.+++++
T Consensus        83 ~yN~~~s~~~~~A~~L~~~f~~~~~~  108 (114)
T d3dwya1          83 LYNRKTSRVYKFCSKLAEVFEQEIDP  108 (114)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999988764

>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=99.59  E-value=1.6e-15  Score=113.00  Aligned_cols=64  Identities=27%  Similarity=0.531  Sum_probs=61.1

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcCC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEFS  158 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~~  158 (256)
                      +-||||++|++|++++.|.|+++|.+|+.|||.||+.||+++|.++.+|..|++.|.++++++.
T Consensus        41 ~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~i~~~A~~l~~~f~~~~~~ip  104 (111)
T d1e6ia_          41 KEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIP  104 (111)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHTSG
T ss_pred             CCchhHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            4499999999999999999999999999999999999999999999999999999999998763

>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=99.58  E-value=1.8e-15  Score=113.84  Aligned_cols=61  Identities=31%  Similarity=0.517  Sum_probs=59.4

Q ss_pred             cccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          97 PRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        97 P~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      ||||++|++|++++.|.++++|.+|+.|||.||+.||+++|.++.+|..|++.|.++++++
T Consensus        53 PmdL~~I~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yn~~~s~~~~~A~~l~~~f~~~~~e~  113 (118)
T d1wuma1          53 PMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEA  113 (118)
T ss_dssp             CCCHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHHHSCTTSSHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHhcccccCchHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999999999999999999999999999999999999999998863

>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=99.57  E-value=5.1e-15  Score=112.89  Aligned_cols=63  Identities=24%  Similarity=0.443  Sum_probs=60.1

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||++|++|+++|.|.|+++|..|++|||.||+.||+++|.++++|..|++.|.+.++++
T Consensus        48 k~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~L~~~~~~~l~~~  110 (128)
T d1eqfa2          48 VNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEY  110 (128)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCcccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            339999999999999999999999999999999999999999999999999999999988765

>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=99.56  E-value=7.7e-15  Score=113.45  Aligned_cols=63  Identities=21%  Similarity=0.358  Sum_probs=60.4

Q ss_pred             cccccHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q psy1225          95 ENPRSLLTIGKTLKSGHYSTLNELTGELNLMFENAKKFNPADSRLYRDAVKLQKLMQRKVQEF  157 (256)
Q Consensus        95 klP~dl~~I~~kl~~~~Y~s~~~f~~D~~lmf~Na~~yN~~~s~i~~~a~~L~~~~~~~~~~~  157 (256)
                      +-||||.+|++|++++.|.|+++|..|+.|||.||+.||+++|.+++.|..|++.|.++++++
T Consensus        64 ~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~i~~~A~~L~~~~~~~~~~~  126 (139)
T d1eqfa1          64 TRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEK  126 (139)
T ss_dssp             SSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CChhhHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            449999999999999999999999999999999999999999999999999999999999874

>d1m4za_ b.34.12.1 (A:) Origin-recognition complex protein 120kDa subunit, Orc1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: SH3-like barrel
superfamily: BAH domain
family: BAH domain
domain: Origin-recognition complex protein 120kDa subunit, Orc1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.46  E-value=0.00066  Score=54.55  Aligned_cols=53  Identities=6%  Similarity=-0.103  Sum_probs=42.7

Q ss_pred             HHHHHhcCCCC-ccceeecccc--------eeEeEEeecCcccccccCCCCCCceeeeeecc
Q psy1225         196 RKVQEVMILDI-ECQVYLISDE--------LTHYQVVLTGTAEQVRLSGLPDGDWLAFTLPV  248 (256)
Q Consensus       196 ~~~~~~g~~~~-~c~y~rpeqt--------~h~~ev~kt~~~~~~~~~~i~~~~~v~f~~~~  248 (256)
                      .|....++.+. ..|+++|+++        +|..|+|+|-++...|++.|+|+|-|+...-|
T Consensus       100 ~~~~~~~~~~~~~~w~~~p~e~~~~k~r~~~~~~ElflT~~~d~i~~~~I~~k~~V~s~~ef  161 (217)
T d1m4za_         100 NPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKW  161 (217)
T ss_dssp             CHHHHHHHHCHHHHHSCCCHHHHHHHHHHHSCTTEEEEEEEEEEECGGGEEEEEEEECHHHH
T ss_pred             ccchhhhhcccceeeecCchhhhhhccccccCcceeEecCccceeehhheeeeEEEecHHHh
Confidence            34444566677 4799999974        55569999999999999999999999977666