Citrus Sinensis ID: 048123

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200--
Protein Sequence
MAQGQGTRKSSDHKLARKRKTRPVHDLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRNKAISGPLNSHSCNKTTGTITCSMKY
Secondary Structure (PSIPRED)
ccccccccccccHHHHHcccccccccccccHHHHHHccccccccccccccccHHcccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccHHHcccccccccccHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
maqgqgtrkssdhklarkrktrpvhdlvdndveiqvrktgdgdhhtnavdmssiiamPERKMLDLLLDRLKrrdsykifakpvdgteveDYYKVIKHPMDLSKITEklnegsyqtlgDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGrrrnkaisgplnshscnkttgtitcsmky
Flexible Loop (DISEMBL)
maqgqgtrkssdhklarkrktrpvhdlvdndveiqvrktgdgdhhtnavdmssiiampeRKMLDLLLDRLKRRdsykifakpvdgtevedyYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRNkaisgplnshscnkttgtitcsmky
Low Complexity Region (SEG)
MAQGQGTRKSSDHKLARKRKTRPVHDLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMldllldrlkrrdSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRNKAISGPLNSHSCNKTTGTITCSMKY
Disordered region (IsUnstruct)
**************************************************MSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTL********************************************
Disordered Region (DISOPRED)
************************************************************KMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFR**********************************************
Disordered Region (DISEMBL)
**********************PVHDLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRNKAISGPLNSHSCNKTTGTITCSMKY
Disordered Region (DISPRO)
*******************************************************AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLK*******************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAQGQGTRKSSDHKLARKRKTRPVHDLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRNKAISGPLNSHSCNKTTGTITCSMKY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	202	2.2.26 [Sep-21-2011]
Q9ULD4	1205	Bromodomain and PHD finge	yes	no	0.534	0.089	0.388	2e-16
O95696	1058	Bromodomain-containing pr	no	no	0.495	0.094	0.38	2e-15
Q7ZUF2	631	Bromodomain-containing pr	no	no	0.440	0.141	0.393	6e-13
Q6NVM8	596	Bromodomain-containing pr	no	no	0.470	0.159	0.362	9e-13
P55201	1214	Peregrin OS=Homo sapiens	no	no	0.504	0.084	0.343	9e-13
Q6GLP7	527	Bromodomain-containing pr	N/A	no	0.470	0.180	0.362	1e-12
Q93ZB7	620	Transcription factor GTE1	no	no	0.564	0.183	0.325	4e-12
Q9H8M2	597	Bromodomain-containing pr	no	no	0.524	0.177	0.345	5e-12
Q3UQU0	596	Bromodomain-containing pr	no	no	0.440	0.149	0.370	5e-12
O88665	651	Bromodomain-containing pr	no	no	0.509	0.158	0.333	1e-11

>sp|Q9ULD4|BRPF3_HUMAN Bromodomain and PHD finger-containing protein 3 OS=Homo sapiens GN=BRPF3 PE=1 SV=2

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 42/108 (38%), Positives = 63/108 (58%)

Query: 57  MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTL 116
           MP   +L   LD L+ +D   IFA+PV+ +EV DY + I  PMD S +  KL    Y+TL
Sbjct: 592 MPFNVLLRTTLDLLQEKDPAHIFAEPVNLSEVPDYLEFISKPMDFSTMRRKLESHLYRTL 651

Query: 117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPEN 164
            +FE D  L++ N M +NA DT+++R A  +++L   + R  +   EN
Sbjct: 652 EEFEEDFNLIVTNCMKYNAKDTIFHRAAVRLRDLGGAILRHARRQAEN 699

Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity.
Homo sapiens (taxid: 9606)

>sp|O95696|BRD1_HUMAN Bromodomain-containing protein 1 OS=Homo sapiens GN=BRD1 PE=1 SV=1

 Score = 82.0 bits (201), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/100 (38%), Positives = 61/100 (61%)

Query: 62  MLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEH 121
           +L  +LD+L+ +D  +IFA+PV   EV DY   IKHPMD + + ++L    Y+ L +FE 
Sbjct: 570 LLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEE 629

Query: 122 DIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKND 161
           D  L++ N M +NA DTV+YR A  +++    + R  + +
Sbjct: 630 DFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARRE 669

Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity.

Homo sapiens (taxid: 9606)

>sp|Q7ZUF2|BRD9_DANRE Bromodomain-containing protein 9 OS=Danio rerio GN=brd9 PE=2 SV=1

 Score = 74.3 bits (181), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 54/89 (60%)

Query: 56  AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQT 115
           A P +++L+  L  L+R+D++  FA PV       Y  +IKHPMD S + +K+    Y+T
Sbjct: 168 ATPHQQLLEHFLRLLQRKDAHGFFAFPVTDAIAPGYSMIIKHPMDFSTMKDKIAANEYKT 227

Query: 116 LGDFEHDIYLMLKNAMHFNASDTVYYRQA 144
           + +F+ D  LM  NAM +N  +TVYY+ A
Sbjct: 228 ITEFKADFKLMCDNAMVYNRPETVYYKAA 256

Danio rerio (taxid: 7955)

>sp|Q6NVM8|BRD9_XENTR Bromodomain-containing protein 9 OS=Xenopus tropicalis GN=brd9 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 37/102 (36%), Positives = 60/102 (58%), Gaps = 7/102 (6%)

Query: 56  AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQT 115
           + P +++L+  L +L+R+D    FA PV       Y+ +IK+PMD S + EK+++  Y++
Sbjct: 150 STPLQQLLEYFLRQLQRKDPNGFFAFPVTDQIAPGYFMIIKNPMDFSTMKEKISQNEYKS 209

Query: 116 LGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRT 157
           + +F+ D  LM  NAM +N  +TVYY+       LA KL  T
Sbjct: 210 VTEFKADFKLMCDNAMTYNRPETVYYK-------LAKKLLHT 244

Xenopus tropicalis (taxid: 8364)

>sp|P55201|BRPF1_HUMAN Peregrin OS=Homo sapiens GN=BRPF1 PE=1 SV=2

 Score = 73.6 bits (179), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 35/102 (34%), Positives = 56/102 (54%)

Query: 62  MLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEH 121
           +L   L++L+ +D+  IF++PV  +EV DY   IK PMD   + + L    Y    DFE 
Sbjct: 636 LLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEE 695

Query: 122 DIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE 163
           D  L++ N + +NA DT++YR A  ++E    + R  +   E
Sbjct: 696 DFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAE 737

Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. Positively regulates the transcription of RUNX1 and RUNX2.

Homo sapiens (taxid: 9606)

>sp|Q6GLP7|BRD9_XENLA Bromodomain-containing protein 9 OS=Xenopus laevis GN=brd9 PE=2 SV=1

 Score = 73.2 bits (178), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/102 (36%), Positives = 60/102 (58%), Gaps = 7/102 (6%)

Query: 56  AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQT 115
           + P +++L+  L +L+R+D    FA PV       Y+ +IK+PMD S + EK+++  Y++
Sbjct: 80  STPLQQLLEYFLRQLQRKDPNGFFAFPVTDQIAPGYFMIIKNPMDFSTMKEKISQDEYKS 139

Query: 116 LGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRT 157
           + +F+ D  LM  NAM +N  +TVYY+       LA KL  T
Sbjct: 140 VTEFKADFKLMCDNAMTYNRPETVYYK-------LAKKLLHT 174

Xenopus laevis (taxid: 8355)

>sp|Q93ZB7|GTE11_ARATH Transcription factor GTE11 OS=Arabidopsis thaliana GN=GTE11 PE=1 SV=1

 Score = 71.2 bits (173), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 41/126 (32%), Positives = 65/126 (51%), Gaps = 12/126 (9%)

Query: 49  VDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTE--VEDYYKVIKHPMDLSKITE 106
           V  S+++ M   K  + LL RL  +    +F  PVD  +  + DY+ +IKHPMDL  +  
Sbjct: 122 VTTSTMLRM---KQCESLLKRLMSQQHCWLFNTPVDVVKLNIPDYFTIIKHPMDLGTVKS 178

Query: 107 KLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTL-------K 159
           KL  G+Y +  +F  D+ L  +NAM +N SD   YR A  + +     ++T+       K
Sbjct: 179 KLTSGTYSSPSEFSADVRLTFRNAMTYNPSDNNVYRFADTLSKFFEVRWKTIEKKSSGTK 238

Query: 160 NDPENF 165
           ++P N 
Sbjct: 239 SEPSNL 244

Arabidopsis thaliana (taxid: 3702)

>sp|Q9H8M2|BRD9_HUMAN Bromodomain-containing protein 9 OS=Homo sapiens GN=BRD9 PE=1 SV=2

 Score = 70.9 bits (172), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 38/110 (34%), Positives = 62/110 (56%), Gaps = 4/110 (3%)

Query: 56  AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQT 115
           + P +++L+  L +L+R+D +  FA PV       Y  +IKHPMD   + +K+    Y++
Sbjct: 138 STPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKS 197

Query: 116 LGDFEHDIYLMLKNAMHFNASDTVYYRQA----HAMKELANKLFRTLKND 161
           + +F+ D  LM  NAM +N  DTVYY+ A    HA  ++ +K    L N+
Sbjct: 198 VTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKQAALLGNE 247

Homo sapiens (taxid: 9606)

>sp|Q3UQU0|BRD9_MOUSE Bromodomain-containing protein 9 OS=Mus musculus GN=Brd9 PE=2 SV=1

 Score = 70.9 bits (172), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 53/89 (59%)

Query: 56  AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQT 115
           + P +++L+  L +L+R+D +  FA PV       Y  +IKHPMD   + +K+    Y++
Sbjct: 138 STPIQRLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKS 197

Query: 116 LGDFEHDIYLMLKNAMHFNASDTVYYRQA 144
           + +F+ D  LM  NAM +N  DTVYY+ A
Sbjct: 198 VTEFKADFKLMCDNAMTYNRPDTVYYKLA 226

Mus musculus (taxid: 10090)

>sp|O88665|BRD7_MOUSE Bromodomain-containing protein 7 OS=Mus musculus GN=Brd7 PE=1 SV=1

 Score = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 36/108 (33%), Positives = 60/108 (55%), Gaps = 5/108 (4%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           P ++ L+ L+ +L+R+D    F+ PV       Y  +IKHPMD S + EK+    YQ++ 
Sbjct: 135 PLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIE 194

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQA-----HAMKELANKLFRTLKN 160
           + + +  LM  NAM +N  +T+YY+ A       MK L+ +  ++LK 
Sbjct: 195 ELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQ 242

Acts both as coactivator and as corepressor. May play a role in chromatin remodeling. Transcriptional corepressor that down-regulates the expression of target genes. Binds to target promoters, leading to increased histone H3 acetylation at 'Lys-9' (H3K9ac). Binds to the ESR1 promoter. Recruits BRCA1 and POU2F1 to the ESR1 promoter. Coactivator for TP53-mediated activation of transcription of a set of target genes. Required for TP53-mediated cell-cycle arrest in response to oncogene activation. Promotes acetylation of TP53 at 'Lys-382', and thereby promotes efficient recruitment of TP53 to target promoters. Inhibits cell cycle progression from G1 to S phase (By similarity). Activator of the Wnt signaling pathway in a DVL1-dependent manner by negatively regulating the GSK3B phosphotransferase activity. Induces dephosphorylation of GSK3B at 'Tyr-216'. Down-regulates TRIM24-mediated activation of transcriptional activation by AR.

Mus musculus (taxid: 10090)

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	202
296085827	593	unnamed protein product [Vitis vinifera]	0.569	0.193	0.546	1e-33
255582032	707	bromodomain-containing protein [Ricinus	0.559	0.159	0.539	7e-33
147865333	747	hypothetical protein VITISV_004433 [Viti	0.742	0.200	0.394	6e-32
297745735	254	unnamed protein product [Vitis vinifera]	0.653	0.519	0.492	6e-30
115480537	567	Os09g0550000 [Oryza sativa Japonica Grou	0.707	0.252	0.438	1e-29
222642038	1322	hypothetical protein OsJ_30246 [Oryza sa	0.693	0.105	0.424	2e-29
357512687	524	Bromodomain-containing protein [Medicago	0.608	0.234	0.451	8e-29
414590127	535	TPA: hypothetical protein ZEAMMB73_00025	0.707	0.267	0.417	1e-28
224140639	770	bromodomain protein [Populus trichocarpa	0.693	0.181	0.390	1e-28
255559820	767	bromodomain-containing protein [Ricinus	0.836	0.220	0.377	2e-28

>gi|296085827|emb|CBI31151.3| unnamed protein product [Vitis vinifera]

 Score =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 65/119 (54%), Positives = 92/119 (77%), Gaps = 4/119 (3%)

Query: 52  SSIIA----MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEK 107
           SSI++    +PE+ +L+L+LD L+RRD+++IFA+PVD  EVEDYY++IK PMD   +  K
Sbjct: 15  SSIVSSSEWLPEKHILELILDTLQRRDTHEIFAEPVDPEEVEDYYEIIKEPMDFGTMRAK 74

Query: 108 LNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFE 166
           L+EG Y+ L  FEHD++L+  NAMHFN+S T+Y+RQA A++EL+ K+F  LK DP NFE
Sbjct: 75  LHEGMYKNLEQFEHDVFLISSNAMHFNSSATIYFRQARALQELSKKVFHVLKTDPRNFE 133

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582032|ref|XP_002531813.1| bromodomain-containing protein [Ricinus communis] gi|223528547|gb|EEF30570.1| bromodomain-containing protein [Ricinus communis]

 Score =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 61/113 (53%), Positives = 89/113 (78%)

Query: 54  IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSY 113
           +  +P++++L+L+LD L+RRD+++IFA+PV+   VEDYY++IK PMD   +  KL+EG Y
Sbjct: 126 VSWIPKKRILELILDVLQRRDTHEIFAEPVNQEVVEDYYEIIKEPMDFGTMRAKLHEGMY 185

Query: 114 QTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFE 166
            +L  FEHD++L+ +NAMHFN+S T+Y+RQA A+ ELA K+F  LK DPENFE
Sbjct: 186 NSLEQFEHDVFLISRNAMHFNSSSTIYFRQARAIDELAKKVFHVLKTDPENFE 238

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865333|emb|CAN79819.1| hypothetical protein VITISV_004433 [Vitis vinifera]

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 77/195 (39%), Positives = 111/195 (56%), Gaps = 45/195 (23%)

Query: 17  RKRKTRPVHDLVDNDVEI----QVRKTGDGDHHTNAVDMS---------------SIIA- 56
           +KRK RPV D+  + V      + +   D DH  N+  +S               SI++ 
Sbjct: 57  KKRKLRPVQDVAVSSVTTTXNQESKSPVDEDHPINSDQLSVFQAKGSPKREDGQSSIVSS 116

Query: 57  ---MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSY 113
              +PE+ +L+L+LD L+RRD+++IFA+PVD  EVEDYY++IK PMD   +  KL+EG Y
Sbjct: 117 SEWLPEKHILELILDTLQRRDTHEIFAEPVDPEEVEDYYEIIKEPMDFGTMRAKLHEGMY 176

Query: 114 QTLGDFE----------------------HDIYLMLKNAMHFNASDTVYYRQAHAMKELA 151
           + L  FE                      HD++L+  NAMHFN+S T+Y+RQA A++EL+
Sbjct: 177 KNLEQFENTAPPLLVDVQKLTCLIVIFLKHDVFLISSNAMHFNSSATIYFRQARALQELS 236

Query: 152 NKLFRTLKNDPENFE 166
            K+F  LK DP NFE
Sbjct: 237 KKVFHVLKTDPRNFE 251

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745735|emb|CBI15791.3| unnamed protein product [Vitis vinifera]

 Score =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 65/132 (49%), Positives = 86/132 (65%)

Query: 51  MSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE 110
           + S   +PE+  L+ +LD L+RRD+++IFA+PVD  EVE YY VIK PMD   +  KL E
Sbjct: 22  LPSTKPLPEKSRLEFILDILQRRDTHEIFAEPVDADEVEGYYDVIKEPMDFGTMRAKLQE 81

Query: 111 GSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACS 170
           G Y+TL  FEHD++ +  NAM FN+S TVY+RQA A++ELA K+F  LK  PE  E   S
Sbjct: 82  GMYKTLEQFEHDVFQISSNAMLFNSSTTVYFRQARALRELAQKVFDALKTHPETLELEFS 141

Query: 171 MRGRRRNKAISG 182
              RR  +   G
Sbjct: 142 QIRRRPGRKPQG 153

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115480537|ref|NP_001063862.1| Os09g0550000 [Oryza sativa Japonica Group] gi|50725131|dbj|BAD33748.1| unknown protein [Oryza sativa Japonica Group] gi|50726301|dbj|BAD33876.1| unknown protein [Oryza sativa Japonica Group] gi|113632095|dbj|BAF25776.1| Os09g0550000 [Oryza sativa Japonica Group] gi|215695365|dbj|BAG90556.1| unnamed protein product [Oryza sativa Japonica Group] gi|215767367|dbj|BAG99595.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 64/146 (43%), Positives = 95/146 (65%), Gaps = 3/146 (2%)

Query: 17  RKRKTRPVHDLVDNDVEIQ-VRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDS 75
           R++K R V  L D   + +  RK  DG    +  D      +P++K+L  +LDRL+++D+
Sbjct: 77  REKKLRLVMGLPDGSAKGEKTRKATDGSEEPS--DSGPTTPLPDKKLLVFVLDRLQKKDT 134

Query: 76  YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA 135
           Y +F+ PVD  E+ DY+ +IKHPMD S I +KLN+G+Y  L  FE D++L+  NAM +N+
Sbjct: 135 YGVFSDPVDPEELPDYHDIIKHPMDFSTIRKKLNKGAYGNLEQFEDDVFLLTSNAMCYNS 194

Query: 136 SDTVYYRQAHAMKELANKLFRTLKND 161
            DT+YYRQA A++ELA K F  L+ D
Sbjct: 195 PDTIYYRQARAIQELAKKDFENLRQD 220

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222642038|gb|EEE70170.1| hypothetical protein OsJ_30246 [Oryza sativa Japonica Group]

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 62/146 (42%), Positives = 94/146 (64%), Gaps = 6/146 (4%)

Query: 22  RPVHDLVDNDVEIQ----VRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYK 77
           RP +    N+ E++     RK  DG    +  D      +P++K+L  +LDRL+++D+Y 
Sbjct: 817 RPAYFAQRNNNEVEQGEKTRKATDGSEEPS--DSGPTTPLPDKKLLVFVLDRLQKKDTYG 874

Query: 78  IFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD 137
           +F+ PVD  E+ DY+ +IKHPMD S I +KLN+G+Y  L  FE D++L+  NAM +N+ D
Sbjct: 875 VFSDPVDPEELPDYHDIIKHPMDFSTIRKKLNKGAYGNLEQFEDDVFLLTSNAMCYNSPD 934

Query: 138 TVYYRQAHAMKELANKLFRTLKNDPE 163
           T+YYRQA A++ELA K F  L+ D +
Sbjct: 935 TIYYRQARAIQELAKKDFENLRQDSD 960

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357512687|ref|XP_003626632.1| Bromodomain-containing protein [Medicago truncatula] gi|140046893|gb|ABO79399.1| Bromodomain [Medicago truncatula] gi|355520654|gb|AET01108.1| Bromodomain-containing protein [Medicago truncatula]

 Score =  132 bits (332), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 60/133 (45%), Positives = 88/133 (66%), Gaps = 10/133 (7%)

Query: 48  AVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEK 107
           +VD      +PE+++L+L+LD L+R+D+Y+IFA+PVD  EVE+YY ++K PMD   +  K
Sbjct: 67  SVDDQPSTLLPEKQILELVLDTLQRKDTYEIFAEPVDPNEVENYYTIVKQPMDFGTMRAK 126

Query: 108 LNEGSYQTLGDFE----------HDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRT 157
           L+EG Y+TL  FE          HD++L+  NAM+FN   T+Y++QA  + ELA K+F  
Sbjct: 127 LHEGMYKTLQQFEVEVYKHWSCNHDVFLIFNNAMNFNPPGTIYFKQARVIGELAKKVFDV 186

Query: 158 LKNDPENFEAACS 170
           L+ DPE FE   S
Sbjct: 187 LRTDPEKFEIEFS 199

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414590127|tpg|DAA40698.1| TPA: hypothetical protein ZEAMMB73_000257 [Zea mays]

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 61/146 (41%), Positives = 95/146 (65%), Gaps = 3/146 (2%)

Query: 17  RKRKTRPVHDLVDNDVEIQ-VRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDS 75
           R++K R V  L D   +++  RK  DG  H    D      +P +K+L  +LDRL+++D+
Sbjct: 79  REKKLRLVMGLHDGSPKVEKTRKATDG--HEEPSDSGPTTPLPNKKLLLFILDRLQKKDT 136

Query: 76  YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA 135
           Y +F++PVD  E+ DY+ ++KHPMD S I +KL++G+Y  L  FE D++L+  NAM +N+
Sbjct: 137 YGVFSEPVDPEELPDYHDIVKHPMDFSTIRKKLDKGAYSNLEQFEDDVFLISTNAMCYNS 196

Query: 136 SDTVYYRQAHAMKELANKLFRTLKND 161
            DT+YYRQA  ++E+A K F  L+ D
Sbjct: 197 PDTIYYRQARGIQEIAKKDFENLRQD 222

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224140639|ref|XP_002323689.1| bromodomain protein [Populus trichocarpa] gi|222868319|gb|EEF05450.1| bromodomain protein [Populus trichocarpa]

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 66/169 (39%), Positives = 97/169 (57%), Gaps = 29/169 (17%)

Query: 37  RKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTE--------- 87
           ++ G  D             +PE+++L+ ++D L+RRD+++IFA+PVD  E         
Sbjct: 130 KQKGQADSPDQPSSSPCTSWVPEKRILEHIIDVLQRRDTHEIFAEPVDPNEVGIWPEVSF 189

Query: 88  -------------------VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLK 128
                              VE+YY++IK PMD   +  KL+EG Y++L  FEHD++L+  
Sbjct: 190 HTMNLSFLVHFIYGITADKVEEYYEIIKEPMDFGTMRAKLHEGMYKSLEQFEHDVFLISG 249

Query: 129 NAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRN 177
           NAMHFN+S T+Y+RQA A+ ELA K+F  L+ DPENFE    +  RRRN
Sbjct: 250 NAMHFNSSSTIYFRQARAIDELAKKVFHVLRTDPENFELEF-LGTRRRN 297

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559820|ref|XP_002520929.1| bromodomain-containing protein [Ricinus communis] gi|223539895|gb|EEF41474.1| bromodomain-containing protein [Ricinus communis]

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 71/188 (37%), Positives = 109/188 (57%), Gaps = 19/188 (10%)

Query: 15  LARKRKTRPVHDLVDNDVEIQVRKTGD-----GDHHTNAV-DMSSIIAMPERKMLDLLLD 68
           L RKRK   + D         +R+ GD     G + TN V D+     +P+ K+L  +L+
Sbjct: 147 LNRKRKINAIGD-------GSIREKGDNRTVSGANPTNTVQDLGPSTPLPDEKLLLFILE 199

Query: 69  RLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLK 128
           RL+++D+Y +F++PVD  E+ DY++VI+HPMD   + +KL  G Y  L  FE D++L+  
Sbjct: 200 RLQKKDTYGVFSEPVDPDELPDYHEVIEHPMDFGTVRKKLAGGVYANLEQFEKDVFLICS 259

Query: 129 NAMHFNASDTVYYRQAHAMKELANKLFRTLK-----NDPENFEAACSMRGRRRNKAISGP 183
           NAM +NA DT+Y+RQA +++ELA K F  L+     N+PE  E     RGR   K +  P
Sbjct: 260 NAMQYNAPDTIYFRQARSIQELAKKNFENLRQDSDDNEPEP-EPTVVRRGRPPTKNLKKP 318

Query: 184 LNSHSCNK 191
           +   S ++
Sbjct: 319 VGRPSLDR 326

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	202
TAIR|locus:2030422	652	AT1G20670 "AT1G20670" [Arabido	0.643	0.199	0.369	1.1e-21
TAIR|locus:2014594	580	AT1G76380 "AT1G76380" [Arabido	0.698	0.243	0.358	8.1e-21
TAIR|locus:2151948	916	AT5G55040 "AT5G55040" [Arabido	0.712	0.157	0.310	1.2e-17
UNIPROTKB|E1BSE7	1186	E1BSE7 "Uncharacterized protei	0.440	0.075	0.404	3e-15
UNIPROTKB|J9P1E6	1012	BRD1 "Uncharacterized protein"	0.470	0.093	0.381	2.9e-14
ZFIN|ZDB-GENE-081104-468	1222	brpf3 "bromodomain and PHD fin	0.435	0.072	0.397	3.6e-14
UNIPROTKB|E2R0N5	1189	BRD1 "Uncharacterized protein"	0.470	0.079	0.381	4.3e-14
UNIPROTKB|B4E3L9	995	BRD1 "cDNA FLJ61578, highly si	0.470	0.095	0.371	5.7e-14
UNIPROTKB|O95696	1058	BRD1 "Bromodomain-containing p	0.470	0.089	0.371	6.7e-14
RGD|1311855	1189	Brd1 "bromodomain containing 1	0.470	0.079	0.381	7e-14

TAIR|locus:2030422 AT1G20670 "AT1G20670" [Arabidopsis thaliana (taxid:3702)]

 Score = 262 (97.3 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 48/130 (36%), Positives = 80/130 (61%)

Query:    49 VDMSSIIAMPERKMXXXXXXXXXXXXSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKL 108
             V+      +P++K+            +Y +++ PVD  E+ DY+++IK+PMD S +  KL
Sbjct:   166 VESGPTTPLPDKKLLLFILDRLQKKDTYGVYSDPVDPEELPDYFEIIKNPMDFSTLRNKL 225

Query:   109 NEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAA 168
             + G+Y TL  FE D++L+  NAM +N++DTVYYRQA A++ELA K F  L+ D ++ E  
Sbjct:   226 DSGAYSTLEQFERDVFLICTNAMEYNSADTVYYRQARAIQELAKKDFENLRQDSDDEEPQ 285

Query:   169 CSMRGRRRNK 178
                + +++ K
Sbjct:   286 SQQQQQQQPK 295

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2014594 AT1G76380 "AT1G76380" [Arabidopsis thaliana (taxid:3702)]

 Score = 253 (94.1 bits), Expect = 8.1e-21, P = 8.1e-21
 Identities = 53/148 (35%), Positives = 83/148 (56%)

Query:    57 MPERKMXXXXXXXXXXXXSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTL 116
             +P++K+            +Y +++ P D  E+ DYY++IK+PMD + + +KL  G+Y TL
Sbjct:   144 LPDKKLLFFILDRVQKKDTYGVYSDPADPEELPDYYEIIKNPMDFTTLRKKLESGAYTTL 203

Query:   117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFE-AACSM---- 171
               FE D++L+  NAM +N++DTVYYRQA AM ELA K F  L+ + +  E  + S     
Sbjct:   204 EQFEQDVFLICTNAMEYNSADTVYYRQARAMLELAKKDFGNLRQESDGEEPVSLSQQPKV 263

Query:   172 --RGRRRNKAISGPLNSHSCNKTTGTIT 197
               RGR     +   L     ++TT  I+
Sbjct:   264 VKRGRPPGSGLKKQLEQSLIDRTTSDIS 291

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2151948 AT5G55040 "AT5G55040" [Arabidopsis thaliana (taxid:3702)]

 Score = 227 (85.0 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 46/148 (31%), Positives = 83/148 (56%)

Query:     9 KSSDHKLARKRKTRPVH-DLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMXXXXX 67
             +  D+ +  + +    H D  + D + + R++  G+   ++ + + I+   ++K      
Sbjct:   139 EEKDYDVEEEEEEEEGHADSEEEDDKERKRRSASGNQCDHSSETTPIL---DKKSLELIL 195

Query:    68 XXXXXXXSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLML 127
                     Y ++A+PVD  E+ DY+ +I+HPMD S + +KL  GSY TL + E D+ L+ 
Sbjct:   196 DKLQKKDIYGVYAEPVDPEELPDYHDMIEHPMDFSTVRKKLANGSYSTLEELESDVLLIC 255

Query:   128 KNAMHFNASDTVYYRQAHAMKELANKLF 155
              NAM +N+SDTVYY+QA  ++E+  + F
Sbjct:   256 SNAMQYNSSDTVYYKQARTIQEMGKRKF 283

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

UNIPROTKB|E1BSE7 E1BSE7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 189 (71.6 bits), Expect = 3.0e-15, Sum P(2) = 3.0e-15
 Identities = 36/89 (40%), Positives = 55/89 (61%)

Query:    75 SYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN 134
             S +IFA+PV+  EV DY   IKHPMD S + ++L+   Y+ L +FE D  L++ N M +N
Sbjct:   583 SARIFAQPVNLKEVPDYLDHIKHPMDFSTMRKRLDAQGYKNLSEFEEDFNLIIDNCMKYN 642

Query:   135 ASDTVYYRQAHAMKELANKLFRTLKNDPE 163
             A DT++YR A  +++    + R  + D E
Sbjct:   643 AKDTIFYRAAVRLRDQGGVVLRQARRDAE 671

GO:0008270 "zinc ion binding" evidence=IEA

GO:0042393 "histone binding" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0070776 "MOZ/MORF histone acetyltransferase complex" evidence=IEA

UNIPROTKB|J9P1E6 BRD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 177 (67.4 bits), Expect = 2.9e-14, Sum P(2) = 2.9e-14
 Identities = 37/97 (38%), Positives = 56/97 (57%)

Query:    77 KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
             +IFA+PV   EV DY   IKHPMD + + ++L    Y+ L +FE D  L++ N M +NA 
Sbjct:   602 RIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYRHLTEFEEDFNLIVDNCMKYNAK 661

Query:   137 DTVYYRQAHAMKELANKLFRTLKNDPEN--FEAACSM 171
             DTV+YR A  +++    + R  +   ++  FE A  M
Sbjct:   662 DTVFYRAAVRLRDQGGVVLRQARRQADSIGFEEASGM 698

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-081104-468 brpf3 "bromodomain and PHD finger containing, 3" [Danio rerio (taxid:7955)]

 Score = 181 (68.8 bits), Expect = 3.6e-14, Sum P(2) = 3.6e-14
 Identities = 35/88 (39%), Positives = 53/88 (60%)

Query:    77 KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
             KIFA+PV+  EV DY + I HPMD S +  KL    Y+++ D E D  LM+ N + +NA 
Sbjct:   627 KIFAQPVNLKEVPDYLEFITHPMDFSTMQSKLEAHKYRSVTDLEADFNLMISNCLLYNAK 686

Query:   137 DTVYYRQAHAMKELANKLFRTLKNDPEN 164
             DTV+Y+ A  +++L   + R  +   +N
Sbjct:   687 DTVFYQAAIRLRDLGGAILRHAQRQAQN 714

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|E2R0N5 BRD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 177 (67.4 bits), Expect = 4.3e-14, Sum P(2) = 4.3e-14
 Identities = 37/97 (38%), Positives = 56/97 (57%)

Query:    77 KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
             +IFA+PV   EV DY   IKHPMD + + ++L    Y+ L +FE D  L++ N M +NA 
Sbjct:   585 RIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYRHLTEFEEDFNLIVDNCMKYNAK 644

Query:   137 DTVYYRQAHAMKELANKLFRTLKNDPEN--FEAACSM 171
             DTV+YR A  +++    + R  +   ++  FE A  M
Sbjct:   645 DTVFYRAAVRLRDQGGVVLRQARRQADSIGFEEASGM 681

GO:0070776 "MOZ/MORF histone acetyltransferase complex" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0042393 "histone binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|B4E3L9 BRD1 "cDNA FLJ61578, highly similar to Bromodomain-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 173 (66.0 bits), Expect = 5.7e-14, Sum P(2) = 5.7e-14
 Identities = 36/97 (37%), Positives = 56/97 (57%)

Query:    77 KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
             +IFA+PV   EV DY   IKHPMD + + ++L    Y+ L +FE D  L++ N M +NA 
Sbjct:   585 RIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNAR 644

Query:   137 DTVYYRQAHAMKELANKLFRTLKNDPENF--EAACSM 171
             DTV+YR A  +++    + R  + + ++   E A  M
Sbjct:   645 DTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASGM 681

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|O95696 BRD1 "Bromodomain-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 173 (66.0 bits), Expect = 6.7e-14, Sum P(2) = 6.7e-14
 Identities = 36/97 (37%), Positives = 56/97 (57%)

Query:    77 KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
             +IFA+PV   EV DY   IKHPMD + + ++L    Y+ L +FE D  L++ N M +NA 
Sbjct:   585 RIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNAR 644

Query:   137 DTVYYRQAHAMKELANKLFRTLKNDPENF--EAACSM 171
             DTV+YR A  +++    + R  + + ++   E A  M
Sbjct:   645 DTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASGM 681

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA;TAS

GO:0070776 "MOZ/MORF histone acetyltransferase complex" evidence=IDA

GO:0043966 "histone H3 acetylation" evidence=IDA

GO:0042393 "histone binding" evidence=IDA

RGD|1311855 Brd1 "bromodomain containing 1" [Rattus norvegicus (taxid:10116)]

 Score = 173 (66.0 bits), Expect = 7.0e-14, Sum P(2) = 7.0e-14
 Identities = 37/97 (38%), Positives = 55/97 (56%)

Query:    77 KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
             KIFA+PV   EV DY   IKHPMD + + ++L    Y+ L  FE D  L++ N M +NA 
Sbjct:   585 KIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHAFEEDFNLIVDNCMKYNAK 644

Query:   137 DTVYYRQAHAMKELANKLFRTLKNDPENF--EAACSM 171
             DTV+YR A  +++    + R  + + ++   E A  M
Sbjct:   645 DTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASGM 681

GO:0005634 "nucleus" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0042393 "histone binding" evidence=ISO

GO:0043966 "histone H3 acetylation" evidence=ISO

GO:0070776 "MOZ/MORF histone acetyltransferase complex" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: 4347782 bromodomain domain containing protein, expressed (567 aa) (Oryza sativa Japonica)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	202
cd04369	99	cd04369, Bromodomain, Bromodomain	1e-29
smart00297	107	smart00297, BROMO, bromo domain	4e-28
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	1e-27
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	2e-26
pfam00439	84	pfam00439, Bromodomain, Bromodomain	3e-25
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	9e-21
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	6e-19
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	1e-18
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	2e-17
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	2e-16
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	2e-16
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	6e-16
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	3e-15
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	3e-14
COG5076	371	COG5076, COG5076, Transcription factor involved in	1e-13
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	3e-13
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	3e-13
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	6e-13
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	1e-12
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	6e-12
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	1e-11
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	1e-11
cd05517	103	cd05517, Bromo_polybromo_II, Bromodomain, polybrom	5e-11
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	8e-11
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	3e-10
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	1e-09
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	3e-09
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	4e-09
cd05508	99	cd05508, Bromo_RACK7, Bromodomain, RACK7_like subf	1e-08
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	4e-08
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	6e-08
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	1e-07
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	5e-07
cd05501	102	cd05501, Bromo_SP100C_like, Bromodomain, SP100C_li	3e-06
COG5076	371	COG5076, COG5076, Transcription factor involved in	5e-04
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	0.002
cd05492	109	cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like	0.004

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score =  104 bits (262), Expect = 1e-29
 Identities = 43/99 (43%), Positives = 61/99 (61%), Gaps = 2/99 (2%)

Query: 59  ERKMLDLLLDRLKR--RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTL 116
            +K L  LLD LK+  RD  + F +PVD  E  DYY+VIK+PMDLS I +KL  G Y++L
Sbjct: 1   LKKKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSL 60

Query: 117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLF 155
            +FE D+ L+  NA  +N   +  Y+ A  +++L  KL 
Sbjct: 61  EEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 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 =  101 bits (253), Expect = 4e-28
 Identities = 36/98 (36%), Positives = 51/98 (52%)

Query: 61  KMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
           ++L  +LD+L        F KPV   E  DYY +IK PMDL  I +KL  G Y ++ +F 
Sbjct: 10  ELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFV 69

Query: 121 HDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTL 158
            D  LM  NA  +N  D+  Y+ A  +++   K  R L
Sbjct: 70  ADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

Length = 107

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

 Score =  100 bits (250), Expect = 1e-27
 Identities = 38/94 (40%), Positives = 60/94 (63%)

Query: 62  MLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEH 121
           +L   LD+L+ +D+ +IF++PVD +EV DY   IK PMD S + +KL    Y+TL DFE 
Sbjct: 5   LLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEA 64

Query: 122 DIYLMLKNAMHFNASDTVYYRQAHAMKELANKLF 155
           D  L++ N + +NA DT++YR A  +++    + 
Sbjct: 65  DFNLIINNCLAYNAKDTIFYRAAVRLRDQGGAIL 98

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|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily

 Score = 97.2 bits (243), Expect = 2e-26
 Identities = 40/93 (43%), Positives = 53/93 (56%)

Query: 66  LLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYL 125
           +LD LK   S   F +PVD  E  DYY VIK PMDLS + EKL  G Y TL +F  D+ L
Sbjct: 9   VLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKL 68

Query: 126 MLKNAMHFNASDTVYYRQAHAMKELANKLFRTL 158
           +  N   +N  DT YY+ A+ +++   K  + L
Sbjct: 69  IFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL 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|215921 pfam00439, Bromodomain, Bromodomain

 Score = 93.6 bits (233), Expect = 3e-25
 Identities = 33/82 (40%), Positives = 48/82 (58%)

Query: 63  LDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHD 122
              +L+ L      + F +PVD  E  DYY+VIK PMDLS I +KL  G Y++L +F  D
Sbjct: 1   CLEILEDLMEHPLAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKD 60

Query: 123 IYLMLKNAMHFNASDTVYYRQA 144
           + L+  NA+ +N  D+  Y+ A
Sbjct: 61  VELIFSNAITYNGEDSDIYKDA 82

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|99945 cd05513, Bromo_brd7_like, Bromodomain, brd7_like subgroup

 Score = 82.1 bits (203), Expect = 9e-21
 Identities = 36/87 (41%), Positives = 54/87 (62%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           P +K L+ L+ +L+R+D +  FA PV       Y  +IKHPMD S + EK+    YQ++ 
Sbjct: 1   PLQKALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIE 60

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQA 144
           +F+ D  LM +NAM +N  DT+YY+ A
Sbjct: 61  EFKDDFKLMCENAMKYNKPDTIYYKAA 87

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

 Score = 78.1 bits (193), Expect = 6e-19
 Identities = 39/94 (41%), Positives = 62/94 (65%), Gaps = 2/94 (2%)

Query: 62  MLDLLLDRLKR-RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
           +LD +++ LK   DS+  F  PV+  +V DYYK+IK PMDL  I +K+++  YQ+  +F 
Sbjct: 4   ILDEIVNELKNLPDSWP-FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFL 62

Query: 121 HDIYLMLKNAMHFNASDTVYYRQAHAMKELANKL 154
            DI L++ N++ +N  D+VY ++A  M ELA +L
Sbjct: 63  EDIELIVDNSVLYNGPDSVYTKKAKEMLELAEEL 96

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|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score = 76.9 bits (190), Expect = 1e-18
 Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 78  IFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA 135
            F  PVD     + +Y+ +IK PMDL  I++KL  G YQ+  +FE D+ L+ KN   FN 
Sbjct: 23  PFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNP 82

Query: 136 SDTVYYRQAHAMKELANKL 154
             T  Y   H ++E+ N  
Sbjct: 83  EGTDVYMMGHQLEEVFNDK 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|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily

 Score = 74.0 bits (182), Expect = 2e-17
 Identities = 34/79 (43%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 64  DLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDI 123
            LL++ +K +DS+  F +PV   EV DYY +IK PMDL  I EKLN G Y+   +F  DI
Sbjct: 19  QLLVEIVKHKDSWP-FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDI 77

Query: 124 YLMLKNAMHFNASDTVYYR 142
            L+  N   +N   T  Y+
Sbjct: 78  QLVFSNCFLYNPEHTSVYK 96

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

 Score = 71.2 bits (175), Expect = 2e-16
 Identities = 31/87 (35%), Positives = 41/87 (47%), Gaps = 9/87 (10%)

Query: 66  LLDRLKRRDSYKI---FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
           +L  L  +        F KPVD     + DY+ +IKHPMDLS I +KL+   Y    +F 
Sbjct: 8   ILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFA 67

Query: 121 HDIYLMLKNAMHFNASDTVYYRQAHAM 147
            D+ LM  N   +N  D       HAM
Sbjct: 68  ADVRLMFSNCYKYNPPDHP----VHAM 90

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

 Score = 71.2 bits (175), Expect = 2e-16
 Identities = 34/79 (43%), Positives = 44/79 (55%)

Query: 60  RKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDF 119
           R  L  +L RL     +  F KPVD  EV DYY++IK PMDL  I +KL+   Y T  DF
Sbjct: 5   RLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDF 64

Query: 120 EHDIYLMLKNAMHFNASDT 138
             DI L++ NA+ +N    
Sbjct: 65  LKDIDLIVTNALEYNPDRD 83

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

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

 Score = 69.7 bits (171), Expect = 6e-16
 Identities = 32/100 (32%), Positives = 47/100 (47%), Gaps = 6/100 (6%)

Query: 60  RKMLDLLLDRLKRRDSYKIFAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
            K    LL +L +     +F  PVD     + DY+ +IK PMDL  + +KL +G Y +  
Sbjct: 2   MKQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPE 61

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRT 157
           +F  D+ L   NAM +N          H M +   K+F T
Sbjct: 62  EFAADVRLTFANAMRYNPPGN----DVHTMAKELLKIFET 97

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

 Score = 67.8 bits (166), Expect = 3e-15
 Identities = 32/84 (38%), Positives = 45/84 (53%)

Query: 65  LLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIY 124
            +LD ++  +    F +PV+   V  Y K+IK PMD S I EKL  G Y+TL +F  D+ 
Sbjct: 7   TILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVR 66

Query: 125 LMLKNAMHFNASDTVYYRQAHAMK 148
           L+  N   FN  D+   R  H M+
Sbjct: 67  LVFDNCETFNEDDSEVGRAGHNMR 90

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|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 65.5 bits (160), Expect = 3e-14
 Identities = 32/100 (32%), Positives = 53/100 (53%), Gaps = 2/100 (2%)

Query: 63  LDLLLDRLKRRDSYKI-FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEH 121
           LD +L+ LK    +   F   V   E  DYY +IK PMDL  + +KL    Y++  +F  
Sbjct: 12  LDKVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVD 71

Query: 122 DIYLMLKNAMHFNASDTVYYRQ-AHAMKELANKLFRTLKN 160
           D+ L+ KN + +N+  +   R+ A+ MK+ A  L + + +
Sbjct: 72  DLNLIWKNCLLYNSDPSHPLRRHANFMKKKAEHLLKLIPD 111

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

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

 Score = 68.3 bits (167), Expect = 1e-13
 Identities = 36/128 (28%), Positives = 53/128 (41%), Gaps = 3/128 (2%)

Query: 61  KMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
           K    L  R  R  S  IF       E  DYY++IK PMDL  I +KL  G Y++  +F 
Sbjct: 152 KFKKQLFLRDGRFLS-SIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFV 210

Query: 121 HDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFR--TLKNDPENFEAACSMRGRRRNK 178
            D+ LM  N   +N  D+  Y  A  +++   KL      +    + +     R  R + 
Sbjct: 211 SDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLELSIKPGREEREERESV 270

Query: 179 AISGPLNS 186
            I+     
Sbjct: 271 LITNSQAH 278

Length = 371

>gnl|CDD|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 62.7 bits (153), Expect = 3e-13
 Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 70  LKR-RDSYKIFAKPVDGTE--VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLM 126
           LKR +D+   F  PVD  +  +  Y  +IK PMDL  I  KL    Y ++ +F  D  LM
Sbjct: 16  LKRLKDARP-FLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLM 74

Query: 127 LKNAMHFNASDTVYYRQAHAMKE 149
           + N + FN  +    +    ++ 
Sbjct: 75  VDNCLTFNGPEHPVSQMGKRLQA 97

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

>gnl|CDD|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily

 Score = 62.7 bits (153), Expect = 3e-13
 Identities = 28/72 (38%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGS---YQTLGDFEHDIYLMLKNAMHFNA 135
           F +PV    V +YYK+IK PMDLS I +KL   S   Y +  +F  D+ LM KN   FN 
Sbjct: 25  FHEPV-SPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNE 83

Query: 136 SDTVYYRQAHAM 147
            D+   +    +
Sbjct: 84  EDSEVAQAGKEL 95

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

 Score = 62.7 bits (153), Expect = 6e-13
 Identities = 34/129 (26%), Positives = 56/129 (43%), Gaps = 10/129 (7%)

Query: 33  EIQVRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVD-GTEVEDY 91
           E ++   G    H    +    +     K+L  L     + +  + F  PVD      DY
Sbjct: 8   EWELFDPGWEQPH-IRDEERERLISGLDKLLLSL-----QLEIAEYFEYPVDLRAWYPDY 61

Query: 92  YKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELA 151
           +  +  PMDL  I  +L    Y++L    HD+ L+L NA  FN  ++   ++A   K L+
Sbjct: 62  WNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKA---KRLS 118

Query: 152 NKLFRTLKN 160
           + L R L +
Sbjct: 119 DWLLRILSS 127

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|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily

 Score = 61.3 bits (149), Expect = 1e-12
 Identities = 31/94 (32%), Positives = 52/94 (55%), Gaps = 3/94 (3%)

Query: 60  RKMLDLLLDRLKRRDSYKI-FAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTL 116
           R+ L   L++L ++D   + F +PVD     + DY+ ++K+PMDLS I  KL+ G YQ  
Sbjct: 5   RQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDP 64

Query: 117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKEL 150
             +  D++LM  NA  +N   +  Y+    + E+
Sbjct: 65  WQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEV 98

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

 Score = 59.1 bits (143), Expect = 6e-12
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 70  LKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKN 129
           LK R S   F +PV   E EDY KVI +PMDL  +  K + GSY ++ +F  D+ L+  N
Sbjct: 13  LKYRFS-WPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSN 71

Query: 130 AMHFNASDT 138
           A  +  + +
Sbjct: 72  AEKYYENGS 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|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 31/77 (40%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 68  DRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLML 127
           D   RR S  IF +    +E  DYY VIK P+D+ KI  K+    YQ+L D   D  LM 
Sbjct: 17  DGRGRRLSL-IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMF 75

Query: 128 KNAMHFNASDTVYYRQA 144
            NA  +N  D+  Y+ A
Sbjct: 76  DNACKYNEPDSQIYKDA 92

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|99951 cd05520, Bromo_polybromo_III, Bromodomain, polybromo repeat III

 Score = 58.5 bits (142), Expect = 1e-11
 Identities = 24/64 (37%), Positives = 39/64 (60%)

Query: 90  DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKE 149
           DYY+ IK+P+ L +I  KL  G Y+TL + E D+ LM +NA  +N  ++  Y+ A  +++
Sbjct: 38  DYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQK 97

Query: 150 LANK 153
           L   
Sbjct: 98  LMQA 101

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|99948 cd05517, Bromo_polybromo_II, Bromodomain, polybromo repeat II

 Score = 56.7 bits (137), Expect = 5e-11
 Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 12/95 (12%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           P  +++  L  +L  +  Y             DYY VIK P+DL  I +++  G Y+++ 
Sbjct: 18  PSGRLISELFQKLPSKVLYP------------DYYAVIKEPIDLKTIAQRIQSGYYKSIE 65

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELAN 152
           D E D+ LM+KNA  FN   +  Y+ A+A+K++  
Sbjct: 66  DMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFT 100

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

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

 Score = 56.3 bits (136), Expect = 8e-11
 Identities = 19/48 (39%), Positives = 32/48 (66%)

Query: 87  EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN 134
           E+ +YY++I+ P+D  KI E++    Y++L D E D+ L+ +NA  FN
Sbjct: 36  ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83

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

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

 Score = 54.7 bits (132), Expect = 3e-10
 Identities = 28/90 (31%), Positives = 47/90 (52%)

Query: 60  RKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDF 119
           +K + L+   L       +F KPV       Y+ V+  PMDLS I + +  G+ ++  +F
Sbjct: 5   KKAILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEF 64

Query: 120 EHDIYLMLKNAMHFNASDTVYYRQAHAMKE 149
           + D+ LM +NA+ +N+SD   Y  A  M+ 
Sbjct: 65  QRDVLLMFQNAIMYNSSDHDVYLMAVEMQR 94

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

>gnl|CDD|99928 cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat II_like subfamily

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 20/69 (28%), Positives = 35/69 (50%)

Query: 66  LLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYL 125
           L++ +   +  + F +PVD  +  DY  +I  PMDL  + E L  G+Y    +F  D+ L
Sbjct: 13  LVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRL 72

Query: 126 MLKNAMHFN 134
           +  N+  + 
Sbjct: 73  IFSNSKSYT 81

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

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

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 20/61 (32%), Positives = 34/61 (55%)

Query: 90  DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKE 149
           +YY+V+ +P+DL KI +KL    Y  + D   D  L++ NA  +   D+  ++ A  + E
Sbjct: 40  EYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWE 99

Query: 150 L 150
           L
Sbjct: 100 L 100

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Length = 113

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

 Score = 51.7 bits (124), Expect = 4e-09
 Identities = 20/64 (31%), Positives = 33/64 (51%)

Query: 90  DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKE 149
           DYYK+I  P+DL  I   +    Y T  +   D  LM +NA H+N   +  Y  A+ +++
Sbjct: 38  DYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEK 97

Query: 150 LANK 153
           +  +
Sbjct: 98  VLKE 101

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|99940 cd05508, Bromo_RACK7, Bromodomain, RACK7_like subfamily

 Score = 50.1 bits (120), Expect = 1e-08
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 61  KMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
           K+L   L+R+K+  +     KPVD  +  DY + +  PMDLS + + + + +Y +   F 
Sbjct: 6   KLLKFALERMKQPGAEPFL-KPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFL 64

Query: 121 HDIYLMLKNAMHFNASD 137
            D   +L NA+ +N  D
Sbjct: 65  ADAKWILHNAIIYNGGD 81

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

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

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 79  FAKPVDGTEVE--DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN 134
           F +PVD  ++   DY+K+IK PMDL  I ++L    Y +  +   D   M  N   +N
Sbjct: 26  FQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYN 83

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

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 23/76 (30%), Positives = 41/76 (53%)

Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F K  D     +YY+ I +P+ L  I +K+    Y++   F +D+ LM +NA  +N +D+
Sbjct: 28  FEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDS 87

Query: 139 VYYRQAHAMKELANKL 154
             Y+ A  +++ A  L
Sbjct: 88  QEYKDAVLLEKEARLL 103

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

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

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 22/79 (27%), Positives = 41/79 (51%)

Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           ++F +        DYY +IK P+ L +I  ++   +Y++L +F  D +LM  NA  +N  
Sbjct: 25  ELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQE 84

Query: 137 DTVYYRQAHAMKELANKLF 155
            ++ Y  A  M++   K +
Sbjct: 85  GSIVYEDAVEMEKAFKKKY 103

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

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

 Score = 46.2 bits (110), Expect = 5e-07
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 90  DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKE 149
           DYYK+IK+P+ L+ + ++L    Y    +F +D+  +  NA  +N   +V Y+ A  +++
Sbjct: 39  DYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEK 96

Query: 150 LANK 153
             N 
Sbjct: 97  YIND 100

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

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

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 20/50 (40%), Positives = 28/50 (56%)

Query: 88  VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD 137
           + DY + IK PM L+K+ E+LNE  Y T+  F  D+ L+  N   F   D
Sbjct: 30  IRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD 79

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

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

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 29/78 (37%), Positives = 39/78 (50%)

Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PV   EV DYYK I+ PMDLS    KL    Y+    F  D  L   N + +N   T
Sbjct: 284 FLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVT 343

Query: 139 VYYRQAHAMKELANKLFR 156
            YY+ A+ +++   K  R
Sbjct: 344 DYYKNANVLEDFVIKKTR 361

Length = 371

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 16/49 (32%), Positives = 28/49 (57%)

Query: 86  TEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN 134
            +  DYY+ I  P+DLS I +++  G Y+T   F+ D+  + +NA  + 
Sbjct: 36  KKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYY 84

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|99924 cd05492, Bromo_ZMYND11, Bromodomain; ZMYND11_like sub-family

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 17/53 (32%), Positives = 29/53 (54%)

Query: 95  IKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAM 147
           I   +D++ I EK+N   Y +L +F+ D  L+L N   F+ +D+  Y  A  +
Sbjct: 43  IHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWL 95

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. Length = 109

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	202
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.97
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	99.97
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.97
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.97
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.96
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.96
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.96
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.96
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.96
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.96
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.96
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.96
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.96
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.96
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.95
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.95
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.95
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.95
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.95
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.95
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.95
KOG1474	640	consensus Transcription initiation factor TFIID, s	99.95
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.95
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.94
smart00297	107	BROMO bromo domain.	99.94
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.94
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.94
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.94
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.94
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.94
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.93
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.93
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.92
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.92
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.91
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.91
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.85
COG5076	371	Transcription factor involved in chromatin remodel	99.8
KOG1245	1404	consensus Chromatin remodeling complex WSTF-ISWI,	99.78
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	99.63
KOG0955	1051	consensus PHD finger protein BR140/LIN-49 [General	99.49
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	99.33
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.33
KOG0008	1563	consensus Transcription initiation factor TFIID, s	99.27
KOG1827	629	consensus Chromatin remodeling complex RSC, subuni	99.22
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	99.16
KOG0008	1563	consensus Transcription initiation factor TFIID, s	99.14
KOG1472	720	consensus Histone acetyltransferase SAGA/ADA, cata	98.95
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	98.84
KOG1828	418	consensus IRF-2-binding protein CELTIX-1, contains	98.71
KOG1474	640	consensus Transcription initiation factor TFIID, s	98.5
COG5076	371	Transcription factor involved in chromatin remodel	97.67
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	97.39
KOG0644	1113	consensus Uncharacterized conserved protein, conta	94.74
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	94.41
KOG1827	629	consensus Chromatin remodeling complex RSC, subuni	82.73

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

Probab=99.97  E-value=2.4e-30  Score=186.06  Aligned_cols=95  Identities=26%  Similarity=0.412  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCH
Q 048123           60 RKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTV  139 (202)
Q Consensus        60 ~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~  139 (202)
                      .+.|..||+.|++++.+++|..||++..+||||++|++||||+||++||+++.|.|+++|..||.|||.||+.||+++|.
T Consensus         2 ~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~   81 (97)
T cd05505           2 LQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSY   81 (97)
T ss_pred             HHHHHHHHHHHHhCCCcccccCCCChhhcccHHHHcCCcCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q 048123          140 YYRQAHAMKELANKL  154 (202)
Q Consensus       140 ~~~~A~~L~~~~~~~  154 (202)
                      ++..|..|++.|.++
T Consensus        82 i~~~a~~le~~f~~~   96 (97)
T cd05505          82 VLSCMRKTEQCCVNL   96 (97)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999999875

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.

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=99.97  E-value=3.4e-30  Score=191.48  Aligned_cols=107  Identities=22%  Similarity=0.378  Sum_probs=101.3

Q ss_pred             cHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           57 MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      ..|.+.|..||+.|++++.+++|..||++..+|||+++|++||||+||++||.++.|.++.+|..||+|||.||+.||++
T Consensus         4 ~~w~~~c~~il~~l~~~~~s~~F~~PVd~~~~pdY~~iIk~PmDL~tIk~kL~~~~Y~~~~ef~~D~~lif~Na~~yN~~   83 (119)
T cd05496           4 SDWKKQCKELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPN   83 (119)
T ss_pred             HHHHHHHHHHHHHHHhCCccccccCCCChhhcCcHHHHhCCcccHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999985


Q ss_pred             -CCHHHHHHHHHHHHHHHHHHHhhCCCc
Q 048123          137 -DTVYYRQAHAMKELANKLFRTLKNDPE  163 (202)
Q Consensus       137 -~s~~~~~A~~L~~~~~~~~~~~~~~~~  163 (202)
                       +|.+|.+|..|+..|++.+..+.....
T Consensus        84 ~~s~i~~~a~~L~~~F~~~~~~l~~~~~  111 (119)
T cd05496          84 KRSRIYSMTLRLSALFEEHIKKIISDWK  111 (119)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             899999999999999999999865443

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

>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I

Probab=99.97  E-value=6.1e-30  Score=187.14  Aligned_cols=100  Identities=25%  Similarity=0.395  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHHHHcCCCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           59 ERKMLDLLLDRLKRRDSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      +.-++..||+.|.+++.+++|..|||+.  .+||||++|++||||++|++||+++.|.++++|..||+|||.||+.||++
T Consensus         6 ~~~~~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~   85 (107)
T cd05497           6 LQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKP   85 (107)
T ss_pred             HHHHHHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            4556789999999999999999999986  69999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Q 048123          137 DTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      +|.++.+|..|+..|++.++++
T Consensus        86 ~s~i~~~A~~l~~~f~~~l~~~  107 (107)
T cd05497          86 GDDVVLMAQTLEKLFLQKLAQM  107 (107)
T ss_pred             CCHHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999988753

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

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.97  E-value=1.7e-29  Score=185.09  Aligned_cols=102  Identities=29%  Similarity=0.524  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHHHHcC-CCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           58 PERKMLDLLLDRLKRR-DSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~-~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      .+++.|..++++|.++ +.+++|..||++.  .+||||++|++||||+||++||++|.|.++.+|..||+|||.||+.||
T Consensus         3 ~l~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN   82 (108)
T cd05495           3 ELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYN   82 (108)
T ss_pred             HHHHHHHHHHHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            4678999999999999 9999999999987  699999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          135 ASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      +++|.++.+|..|+..|++.++.+.
T Consensus        83 ~~~s~i~~~a~~l~~~F~~~~~~~~  107 (108)
T cd05495          83 RKTSRVYKYCTKLAEVFEQEIDPVM  107 (108)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999988763

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.96  E-value=2.3e-29  Score=186.35  Aligned_cols=105  Identities=33%  Similarity=0.511  Sum_probs=100.8

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      .....+...|..||+.|..++.+++|..||+...+|+||++|++||||++|++||+++.|.|+++|..||.|||+||+.|
T Consensus         8 ~~~~~~~~~c~~il~~l~~~~~s~~F~~pvd~~~~pdY~~vI~~PmDL~tI~~kL~~~~Y~s~~~f~~Dv~LI~~Na~~y   87 (115)
T cd05504           8 HHGPLNLSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLY   87 (115)
T ss_pred             CCCHHHHHHHHHHHHHHHhCCCchhhcCCCCccccccHHHHhcCcccHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHH
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHh
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      |+++|.++.+|..|+..|++.++++
T Consensus        88 N~~~s~i~~~A~~l~~~f~~~~~~~  112 (115)
T cd05504          88 NPEHTSVYKAGTRLQRFFIKRCRKL  112 (115)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999886

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=99.96  E-value=1.5e-29  Score=182.07  Aligned_cols=96  Identities=34%  Similarity=0.589  Sum_probs=93.4

Q ss_pred             HHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCH
Q 048123           60 RKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTV  139 (202)
Q Consensus        60 ~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~  139 (202)
                      ...|..||+.|..++.+++|..||++..+|+|+++|++||||++|++||+++.|.|+++|..||.|||.||+.||+++|.
T Consensus         2 ~~~c~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~   81 (97)
T cd05503           2 LALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE   81 (97)
T ss_pred             HHHHHHHHHHHHcCCCchhhcCCCCccccCCHHHHhCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 048123          140 YYRQAHAMKELANKLF  155 (202)
Q Consensus       140 ~~~~A~~L~~~~~~~~  155 (202)
                      ++.+|..|++.|++.|
T Consensus        82 i~~~a~~l~~~f~~~~   97 (97)
T cd05503          82 VGRAGHNMRKFFEKRW   97 (97)
T ss_pred             HHHHHHHHHHHHHHhC
Confidence            9999999999999875

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=99.96  E-value=2.8e-29  Score=182.90  Aligned_cols=102  Identities=28%  Similarity=0.457  Sum_probs=97.3

Q ss_pred             cHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           57 MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      ..|++.|..|++.|..++.+++|..||+...+|+|+++|++||||++|++||+++.|.++++|..||.|||+||..||++
T Consensus         2 ~~~~~~~~~il~~l~~~~~a~~F~~pV~~~~~p~Y~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~   81 (104)
T cd05507           2 RAWKKAILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSS   81 (104)
T ss_pred             hHHHHHHHHHHHHHHcCCCCHhhcCCCCccccCCHHHHhCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Q 048123          137 DTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      ++.++.+|..|+..+.+.+..+
T Consensus        82 ~s~v~~~A~~l~~~~~~~~~~~  103 (104)
T cd05507          82 DHDVYLMAVEMQREVMSQIQQL  103 (104)
T ss_pred             CCHHHHHHHHHHHHHHHHhhcc
Confidence            9999999999999988877653

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

>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily

Probab=99.96  E-value=2.5e-29  Score=182.23  Aligned_cols=101  Identities=42%  Similarity=0.647  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      |+...|..|++.|.+++.+++|..||++..+|+|+++|++||||++|++||.++.|.|+++|..||+|||+||+.||+++
T Consensus         1 ~~~~~~~~il~~l~~~~~a~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~   80 (101)
T cd05509           1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD   80 (101)
T ss_pred             ChHHHHHHHHHHHHhCCCchhhcCCCChhhcCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHh
Q 048123          138 TVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      |.++.+|..|+..|+++++++
T Consensus        81 s~~~~~a~~l~~~f~~~~~~~  101 (101)
T cd05509          81 TEYYKCANKLEKFFWKKLKEL  101 (101)
T ss_pred             CHHHHHHHHHHHHHHHHHhhC
Confidence            999999999999999998864

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

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.96  E-value=3.2e-29  Score=180.71  Aligned_cols=95  Identities=28%  Similarity=0.480  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      .+..+|..+++.|. ++.+++|..||++..+|||+.+|++||||+||++||++|.|.++++|..||+|||.||+.||+++
T Consensus         3 ~l~~~L~~~~~~~~-~~~s~~F~~PV~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~Na~~YN~~~   81 (99)
T cd05508           3 QLSKLLKFALERMK-QPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGD   81 (99)
T ss_pred             HHHHHHHHHHHHHh-CcCcchhcCCCChhhCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            35778999999999 99999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHH
Q 048123          138 TVYYRQAHAMKELANK  153 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~  153 (202)
                      |.++.+|..|.+.|+.
T Consensus        82 s~i~~~A~~l~~~~~~   97 (99)
T cd05508          82 HKLTQAAKAIVKICEQ   97 (99)
T ss_pred             CHHHHHHHHHHHHHHh
Confidence            9999999999988865

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.

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.96  E-value=4.2e-29  Score=179.78  Aligned_cols=96  Identities=39%  Similarity=0.681  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      |+...|..|++.|+.++.+++|..||+...+|+|+++|++||||+||++||+++.|.|+++|..||+|||.||+.||+++
T Consensus         1 ~l~~~l~~il~~l~~~~~~~~F~~PV~~~~~pdY~~vIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~   80 (98)
T cd05513           1 PLQKALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPD   80 (98)
T ss_pred             CHHHHHHHHHHHHHcCCccccccCcCCccccccHHHHHcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHH
Q 048123          138 TVYYRQAHAMKELANK  153 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~  153 (202)
                      |.+|++|..|.....+
T Consensus        81 s~~~~~A~~L~~~~~~   96 (98)
T cd05513          81 TIYYKAAKKLLHSGMK   96 (98)
T ss_pred             CHHHHHHHHHHHhhhh
Confidence            9999999999776543

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.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.96  E-value=7.5e-29  Score=182.58  Aligned_cols=104  Identities=31%  Similarity=0.492  Sum_probs=98.2

Q ss_pred             CcHHHHHHHHHHHHHHcC-CCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           56 AMPERKMLDLLLDRLKRR-DSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        56 ~~~~~~~~~~il~~l~~~-~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      ..++.+.|..||+.|+.+ +.+++|..||++..+|+||++|++||||++|++||+++.|.|+++|.+||.|||.||+.||
T Consensus         5 ~~~~~~~~~~il~~l~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~Li~~N~~~yN   84 (112)
T cd05510           5 QEEFYESLDKVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN   84 (112)
T ss_pred             HHHHHHHHHHHHHHHHhcCccccchhcCCChhhcCCHHHHhcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            456788999999999999 8999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC-HHHHHHHHHHHHHHHHHHHhh
Q 048123          135 ASDT-VYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       135 ~~~s-~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      ++++ .++++|..|++.|++++..+.
T Consensus        85 ~~~s~~~~~~A~~l~~~~~~~~~~~~  110 (112)
T cd05510          85 SDPSHPLRRHANFMKKKAEHLLKLIP  110 (112)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence            9866 688999999999999998873

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.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.96  E-value=4.7e-29  Score=179.68  Aligned_cols=96  Identities=41%  Similarity=0.730  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      |+..+|+.+|++|..++.+++|..||+...+|+|+++|++||||+||++||.++.|.|+++|..||+|||.||+.||+++
T Consensus         1 p~~~~l~~il~~l~~~~~~~~F~~pVd~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~   80 (98)
T cd05512           1 PLEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD   80 (98)
T ss_pred             CHHHHHHHHHHHHHhCCCchhhcCCCCccccCCHHHHhcCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHH
Q 048123          138 TVYYRQAHAMKELANK  153 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~  153 (202)
                      |.+|++|..|+.....
T Consensus        81 s~~~~~A~~l~~~~~~   96 (98)
T cd05512          81 TIFYRAAVRLRDQGGA   96 (98)
T ss_pred             CHHHHHHHHHHHhhcc
Confidence            9999999999886543

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.96  E-value=2.3e-28  Score=179.58  Aligned_cols=101  Identities=30%  Similarity=0.471  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhC---CCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE---GSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~---~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      .+++.|..||.+|++++.+++|..||++ .+|+|+++|++||||++|++||++   +.|.++++|..||+|||+||..||
T Consensus         4 ~~~~~c~~il~~l~~~~~s~~F~~pv~~-~~p~Y~~iI~~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~~yN   82 (109)
T cd05502           4 IDQRKCERLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFN   82 (109)
T ss_pred             HHHHHHHHHHHHHHhCCCChhhcCCCCC-CCCCHHHHCCCCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            3578999999999999999999999999 899999999999999999999998   599999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          135 ASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      +++|.++.+|..|+..|++++.++.
T Consensus        83 ~~~s~i~~~a~~l~~~f~~~~~~~~  107 (109)
T cd05502          83 EEDSEVAQAGKELELFFEEQLKEIL  107 (109)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHC
Confidence            9999999999999999999998874

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.

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.96  E-value=1.4e-28  Score=181.46  Aligned_cols=108  Identities=35%  Similarity=0.589  Sum_probs=101.8

Q ss_pred             HHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCH
Q 048123           60 RKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTV  139 (202)
Q Consensus        60 ~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~  139 (202)
                      ..+++.|+++|+.++.+++|..||++..+|+||++|++||||++|++||.++.|.++++|..||+|||+||..||+++|.
T Consensus         2 ~~~l~~ii~~l~~~~~s~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~   81 (112)
T cd05511           2 SFILDEIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSV   81 (112)
T ss_pred             HHHHHHHHHHHHhCCCchhhcCCCChhhcccHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCchHHH
Q 048123          140 YYRQAHAMKELANKLFRTLKNDPENFEA  167 (202)
Q Consensus       140 ~~~~A~~L~~~~~~~~~~~~~~~~~~~~  167 (202)
                      ++.+|..|...|.++++++.......+.
T Consensus        82 i~~~A~~l~~~~~~~~~~~~~~~~~~~~  109 (112)
T cd05511          82 YTKKAKEMLELAEELLAEREEKLTQLEK  109 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            9999999999999999999776655543

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.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.95  E-value=3.6e-28  Score=176.49  Aligned_cols=96  Identities=34%  Similarity=0.608  Sum_probs=91.3

Q ss_pred             HHHHHHHHHHHHcC---CCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           60 RKMLDLLLDRLKRR---DSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        60 ~~~~~~il~~l~~~---~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      .+.|..||+.|++.   +.+++|..||++.  .+|+||++|++||||++|++||+++.|.++++|..||+|||.||+.||
T Consensus         2 ~~~c~~Il~~l~~~~~~~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I~~kl~~~~Y~s~~ef~~D~~li~~N~~~yn   81 (102)
T cd05499           2 LKFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFN   81 (102)
T ss_pred             hHHHHHHHHHHHcccCCcccchhcCCCCccccCCCCHHHHhcCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            46899999999984   5689999999998  899999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q 048123          135 ASDTVYYRQAHAMKELANKLF  155 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~  155 (202)
                      +++|.++.+|..|+..|++.|
T Consensus        82 ~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          82 PEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999875

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

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.95  E-value=8.3e-28  Score=173.46  Aligned_cols=98  Identities=27%  Similarity=0.364  Sum_probs=91.9

Q ss_pred             HHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCC
Q 048123           59 ERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT  138 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s  138 (202)
                      ....|+.||..|..++.+++|..+  +..+||||++|++||||+||++||.++.|.|+++|.+||+|||.||+.||+++ 
T Consensus         3 ~l~~ce~il~~l~~~~~s~~f~~~--p~~~pdY~~iIk~PMDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~N~~~yN~~~-   79 (102)
T cd05501           3 ELLKCEFLLLKVYCMSKSGFFISK--PYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-   79 (102)
T ss_pred             HHHHHHHHHHHHHhCcccccccCC--CCCCCchHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHcCCC-
Confidence            356799999999999999999763  45899999999999999999999999999999999999999999999999999 


Q ss_pred             HHHHHHHHHHHHHHHHHHHhh
Q 048123          139 VYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       139 ~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      .++.+|..|+..|++.++.+.
T Consensus        80 ~~~~~a~~L~~~Fek~~~~~f  100 (102)
T cd05501          80 DFGQVGITLEKKFEKNFKEVF  100 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999998764

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.95  E-value=5e-28  Score=174.79  Aligned_cols=96  Identities=29%  Similarity=0.503  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHHHcCCCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           60 RKMLDLLLDRLKRRDSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        60 ~~~~~~il~~l~~~~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      .+.|..||+.|++++.+++|..||++.  .+|+|+++|++||||++|++||+++.|.++++|..||.+||.||+.||+++
T Consensus         2 ~~~c~~il~~l~~~~~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yn~~~   81 (99)
T cd05506           2 MKQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPG   81 (99)
T ss_pred             HHHHHHHHHHHHhCCCCccccCCCCccccCCCCHHHHHcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            467999999999999999999999976  699999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHH
Q 048123          138 TVYYRQAHAMKELANKLF  155 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~~~  155 (202)
                      |.++.+|..|+..|++.|
T Consensus        82 s~i~~~a~~l~~~fe~~w   99 (99)
T cd05506          82 NDVHTMAKELLKIFETRW   99 (99)
T ss_pred             CHHHHHHHHHHHHHHHhC
Confidence            999999999999999875

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.95  E-value=5e-28  Score=175.72  Aligned_cols=96  Identities=31%  Similarity=0.488  Sum_probs=91.9

Q ss_pred             HHHHHHHHHHHHcC---CCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           60 RKMLDLLLDRLKRR---DSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        60 ~~~~~~il~~l~~~---~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      .+.|..||+.|+++   +.+++|..||++.  .+|+|+++|++||||++|+++|+++.|.|+++|..||+|||+||+.||
T Consensus         2 ~~~c~~il~~l~~~~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~yn   81 (102)
T cd05498           2 LKFCSGILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYN   81 (102)
T ss_pred             hhHHHHHHHHHHhCCCccccCcccCcCCccccCCCcHHHHccCCCcHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            56899999999999   8899999999986  599999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q 048123          135 ASDTVYYRQAHAMKELANKLF  155 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~  155 (202)
                      +++|.++.+|..|+..|+++|
T Consensus        82 ~~~s~i~~~a~~l~~~fe~~~  102 (102)
T cd05498          82 PPDHPVHAMARKLQDVFEDRW  102 (102)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999875

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.

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

Probab=99.95  E-value=1e-27  Score=175.49  Aligned_cols=99  Identities=23%  Similarity=0.501  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHHHHcCCC------cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhh
Q 048123           59 ERKMLDLLLDRLKRRDS------YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMH  132 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~------~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  132 (202)
                      +.+.|..||+.|..+..      +++|..||+...+||||++|++||||++|++||.+|.|.++++|..||.|||.||+.
T Consensus         2 l~~~~~~il~~v~~~~d~~g~~~s~~F~~~p~~~~~pdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~   81 (107)
T cd05516           2 LTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQT   81 (107)
T ss_pred             HHHHHHHHHHHHHhhhCcCCCEeeHHhhcCCCcccCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHH
Confidence            45678888888887766      799999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHH
Q 048123          133 FNASDTVYYRQAHAMKELANKLFRT  157 (202)
Q Consensus       133 yN~~~s~~~~~A~~L~~~~~~~~~~  157 (202)
                      ||+++|.+|.+|..|+..|++.++.
T Consensus        82 yN~~~s~i~~~a~~l~~~f~~~~~~  106 (107)
T cd05516          82 FNLEGSLIYEDSIVLQSVFKSARQK  106 (107)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999998865

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

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

Probab=99.95  E-value=1.6e-27  Score=175.64  Aligned_cols=101  Identities=35%  Similarity=0.582  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC-
Q 048123           59 ERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD-  137 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~-  137 (202)
                      ++..|..|+++|+.++.+++|..||++..+||||++|++||||++|++||+++.|.|+++|..||+|||.||+.||+++ 
T Consensus         4 lr~~L~~il~~l~~~~~~~~F~~pv~~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s   83 (112)
T cd05528           4 LRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRD   83 (112)
T ss_pred             HHHHHHHHHHHHHhCCCchhhcCCCCccccCcHHHHHcCCCCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            4667899999999999999999999999999999999999999999999999999999999999999999999999995 


Q ss_pred             ---CHHHHHHHHHHHHHHHHHHHhh
Q 048123          138 ---TVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       138 ---s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                         +.++..|..|++.|.++++...
T Consensus        84 ~~~s~i~~~A~~L~~~~~~~~~~~~  108 (112)
T cd05528          84 PADKLIRSRACELRDEVHAMIEAEL  108 (112)
T ss_pred             ccccHHHHHHHHHHHHHHHHHHhcC
Confidence               6999999999999999988753

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

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.95  E-value=1.6e-27  Score=173.41  Aligned_cols=96  Identities=29%  Similarity=0.482  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHHHHcCCCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           59 ERKMLDLLLDRLKRRDSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      +.+.|..||+.|++++.+++|..||++.  .+|+|+++|++||||++|++||.++.|.++.+|..||+|||+||+.||++
T Consensus         5 ~~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~   84 (103)
T cd05500           5 QHKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGP   84 (103)
T ss_pred             HHHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            5788999999999999999999999976  69999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHH
Q 048123          137 DTVYYRQAHAMKELANKL  154 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~  154 (202)
                      +|.++.+|..|+..|++.
T Consensus        85 ~s~~~~~A~~l~~~fe~~  102 (103)
T cd05500          85 EHPVSQMGKRLQAAFEKH  102 (103)
T ss_pred             CCHHHHHHHHHHHHHHHh
Confidence            999999999999999875

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.

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

Probab=99.95  E-value=3e-27  Score=219.03  Aligned_cols=118  Identities=30%  Similarity=0.475  Sum_probs=107.8

Q ss_pred             CCCcCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCC--ccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 048123           51 MSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTE--VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLK  128 (202)
Q Consensus        51 ~~~~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~--~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~  128 (202)
                      ........+.+.|..||..|+.|.++|+|..|||+..  +||||+||++||||+||+.||.++.|.++.+|..||+|||.
T Consensus       215 ~~~~~~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~Y~~~~eF~~DVRL~F~  294 (640)
T KOG1474|consen  215 PKSKLTVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGEYKSAEEFAADVRLTFD  294 (640)
T ss_pred             ccccccHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccccCCHHHHHHHHHHHHH
Confidence            3456667788999999999999999999999999975  89999999999999999999999999999999999999999


Q ss_pred             HHhhhcCCCCHHHHHHHHHHHHHHHHHHHhhCCCchHHHH
Q 048123          129 NAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAA  168 (202)
Q Consensus       129 Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~  168 (202)
                      ||++||+++++||.+|..|+.+|+..|..+...++.....
T Consensus       295 Ncm~YNp~g~dV~~Ma~~L~~~Fe~rw~~~~~~~~~~~~~  334 (640)
T KOG1474|consen  295 NCMTYNPEGSDVYAMAKKLQEVFEERWASMPLEIEESESA  334 (640)
T ss_pred             HHHhcCCCCCHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            9999999999999999999999999999976655544433

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.95  E-value=7e-27  Score=172.53  Aligned_cols=102  Identities=24%  Similarity=0.361  Sum_probs=94.9

Q ss_pred             HHHHHHHHHHHHc------CCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           60 RKMLDLLLDRLKR------RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        60 ~~~~~~il~~l~~------~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      .+.|..|++.|.+      ++.+.+|..+|+...+|+||++|++||||++|++||.++.|.|+++|..||.|||.||+.|
T Consensus         4 ~~~c~~il~~l~~~~~~~g~~l~~~F~~~p~~~~~PdYy~iI~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~y   83 (113)
T cd05524           4 IAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAY   83 (113)
T ss_pred             HHHHHHHHHHHHhhcccCCCchhHHHhcCCCcccCCCHHHHhCCccCHHHHHHHhCcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            5679999999986      4445789999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      |+++|.++.+|..|+..|++.++++...
T Consensus        84 N~~~s~~~~~A~~L~~~f~~~~~~~~~~  111 (113)
T cd05524          84 YKPDSPEHKDACKLWELFLSARNEVLSG  111 (113)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999999888643

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

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

Probab=99.94  E-value=4.7e-27  Score=170.94  Aligned_cols=96  Identities=25%  Similarity=0.469  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHH------cCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           60 RKMLDLLLDRLK------RRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        60 ~~~~~~il~~l~------~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ++.|..|++.|.      .++.+++|..||+...+|+||++|++||||++|++||+++.|.|+.+|..||+|||.||+.|
T Consensus         2 ~~~~~~i~~~v~~~~~~~~~~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~y   81 (103)
T cd05519           2 KAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTY   81 (103)
T ss_pred             HHHHHHHHHHHHHhcCcCCCchhHHhcCCCCCCCCcCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHH
Confidence            567888888888      45568999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHH
Q 048123          134 NASDTVYYRQAHAMKELANKLF  155 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~  155 (202)
                      |+++|.++.+|..|+..|++++
T Consensus        82 n~~~s~i~~~A~~l~~~f~~~~  103 (103)
T cd05519          82 NQEGSIVYEDAVEMEKAFKKKY  103 (103)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhC
Confidence            9999999999999999998763

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

>smart00297 BROMO bromo domain

Probab=99.94  E-value=2.8e-26  Score=167.34  Aligned_cols=102  Identities=37%  Similarity=0.642  Sum_probs=97.7

Q ss_pred             cHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           57 MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      ..+..+|..|++.+.+++.+++|..||++..+|+|+++|++||||++|++||+++.|.|+.+|..||.+||.||+.||++
T Consensus         6 ~~~~~~~~~i~~~~~~~~~~~~F~~~~~~~~~p~Y~~~i~~P~dl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~~n~~   85 (107)
T smart00297        6 KKLQSLLKAVLDKLDSHRLSWPFLKPVDRKEAPDYYDIIKKPMDLSTIKKKLENGKYSSVEEFVADVQLMFSNAKTYNGP   85 (107)
T ss_pred             HHHHHHHHHHHHHHHhCccchhhccCCChhhccCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Q 048123          137 DTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      ++.++.+|..|...|++.++++
T Consensus        86 ~s~~~~~a~~l~~~f~~~~~~~  107 (107)
T smart00297       86 DSEVYKDAKKLEKFFEKKLREL  107 (107)
T ss_pred             CCHHHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999998763

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.94  E-value=2.4e-26  Score=167.66  Aligned_cols=96  Identities=33%  Similarity=0.531  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHHc------CCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           61 KMLDLLLDRLKR------RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        61 ~~~~~il~~l~~------~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      +.|..|++.|..      ++.+++|..||+...+|+||++|++||||++|++||.++.|.++++|..||.|||.||+.||
T Consensus         3 ~~~~~~~~~i~~~~d~~~~~~a~~F~~~p~~~~~pdYy~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~~yN   82 (105)
T cd05515           3 QKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYN   82 (105)
T ss_pred             HHHHHHHHHHHHhhCcCCCcccHHhccCCCcccCCcHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            457777777755      45578999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHH
Q 048123          135 ASDTVYYRQAHAMKELANKLFR  156 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~~  156 (202)
                      +++|.++.+|..|+..|.+..+
T Consensus        83 ~~~s~i~~~A~~L~~~~~~~~~  104 (105)
T cd05515          83 EPDSQIYKDALTLQKVLLETKR  104 (105)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999887643

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=99.94  E-value=2.9e-26  Score=166.64  Aligned_cols=98  Identities=29%  Similarity=0.494  Sum_probs=86.1

Q ss_pred             cHHHHHHHHHHHHHH--cCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           57 MPERKMLDLLLDRLK--RRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        57 ~~~~~~~~~il~~l~--~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      .|+..++..|....-  .++.+++|..||+...+|+||++|++||||++|++||+++.|.++.+|+.||+|||.||+.||
T Consensus         3 ~~~~~l~~~i~~~~~~~g~~~s~pF~~~p~~~~~PdYy~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN   82 (103)
T cd05520           3 NPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYN   82 (103)
T ss_pred             chHHHHHHHHHhhcCCCCCCccHhhhcCCCcccCCCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            355555555554332  235678999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHH
Q 048123          135 ASDTVYYRQAHAMKELANKL  154 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~  154 (202)
                      +++|.++.+|..|+..|++.
T Consensus        83 ~~~s~i~~~A~~L~~~f~~~  102 (103)
T cd05520          83 VPNSRIYKDAEKLQKLMQAK  102 (103)
T ss_pred             CCCCHHHHHHHHHHHHHHHh
Confidence            99999999999999999763

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

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.94  E-value=7e-26  Score=170.70  Aligned_cols=103  Identities=29%  Similarity=0.449  Sum_probs=95.8

Q ss_pred             CCcHHHHHHHHHHHHHH---cCCCcccccCCCCcC-CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Q 048123           55 IAMPERKMLDLLLDRLK---RRDSYKIFAKPVDGT-EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNA  130 (202)
Q Consensus        55 ~~~~~~~~~~~il~~l~---~~~~~~~F~~pv~~~-~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  130 (202)
                      ....+...|..++.+|.   .++.+++|..||+.. .+|+||++|++||||++|++||+++.|.++++|..||+|||.||
T Consensus        21 ~~~~~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~~~p~Y~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~Na  100 (128)
T cd05529          21 IRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNA  100 (128)
T ss_pred             CCHHHHHHHHHHHHHHHhcccCcccccccCCCCccccCCcHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence            34445677888888898   899999999999999 99999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHH
Q 048123          131 MHFNASDTVYYRQAHAMKELANKLFRT  157 (202)
Q Consensus       131 ~~yN~~~s~~~~~A~~L~~~~~~~~~~  157 (202)
                      +.||+++|.++..|..|+..|.+++..
T Consensus       101 ~~yN~~~s~i~~~A~~l~~~~~~~l~~  127 (128)
T cd05529         101 ETFNEPNSEIAKKAKRLSDWLLRILSS  127 (128)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHhcc
Confidence            999999999999999999999988753

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.

>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family

Probab=99.94  E-value=6e-26  Score=165.66  Aligned_cols=96  Identities=21%  Similarity=0.323  Sum_probs=86.5

Q ss_pred             HHHHHHHHHHHHHcC------CCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhh
Q 048123           59 ERKMLDLLLDRLKRR------DSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMH  132 (202)
Q Consensus        59 ~~~~~~~il~~l~~~------~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  132 (202)
                      +...|..|++.|...      ..+++|..+|+...+|+||++|++||||++|++||.++.|.|+++|..||.|||.||..
T Consensus         3 l~~~l~~i~~~i~~~kd~~g~~~s~~F~~lp~k~~~pdYy~~I~~P~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f~Na~~   82 (106)
T cd05525           3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEK   82 (106)
T ss_pred             HHHHHHHHHHHHHHhhccCCCcccHhhccCCCcccCCchhhhCCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            345566666666553      44689999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHH
Q 048123          133 FNASDTVYYRQAHAMKELANKL  154 (202)
Q Consensus       133 yN~~~s~~~~~A~~L~~~~~~~  154 (202)
                      ||+++|.++.+|..|+..|++.
T Consensus        83 yn~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          83 YYGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHc
Confidence            9999999999999999999763

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

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.94  E-value=4.9e-26  Score=165.39  Aligned_cols=94  Identities=33%  Similarity=0.592  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHHHcC------CCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           60 RKMLDLLLDRLKRR------DSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        60 ~~~~~~il~~l~~~------~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ++.|..|++.|..+      +.+++|..+|+...+|+||++|++||||++|++||.++.|.++.+|..||.|||.||+.|
T Consensus         2 ~~~~~~l~~~i~~~~d~~gr~~~~~F~~lp~~~~~pdYy~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~y   81 (103)
T cd05517           2 KQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTF   81 (103)
T ss_pred             hHHHHHHHHHHHHhhCcCCCChhHHHhcCCCCCCCCCHHHHcCCCcCHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            45677777777664      346899999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHH
Q 048123          134 NASDTVYYRQAHAMKELANK  153 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~  153 (202)
                      |+++|.++.+|..|+..|..
T Consensus        82 N~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          82 NEPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             CCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999874

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=5.4e-26  Score=165.11  Aligned_cols=82  Identities=27%  Similarity=0.535  Sum_probs=78.5

Q ss_pred             cCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHHHH
Q 048123           72 RRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELA  151 (202)
Q Consensus        72 ~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~~  151 (202)
                      .+..+.+|..+|+...+||||++|++||||++|+.+|.++.|.|+++|..||.|||.||+.||+++|.++.+|..|+..|
T Consensus        20 gr~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le~~~   99 (103)
T cd05518          20 GRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVL   99 (103)
T ss_pred             CCcccHHHhcCCCcccCccHHHHcCCCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            44667899999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HH
Q 048123          152 NK  153 (202)
Q Consensus       152 ~~  153 (202)
                      ++
T Consensus       100 ~~  101 (103)
T cd05518         100 KE  101 (103)
T ss_pred             Hh
Confidence            75

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

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

Probab=99.93  E-value=1.2e-25  Score=163.73  Aligned_cols=96  Identities=27%  Similarity=0.455  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHHHHc------CCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhh
Q 048123           59 ERKMLDLLLDRLKR------RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMH  132 (202)
Q Consensus        59 ~~~~~~~il~~l~~------~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  132 (202)
                      ....+..|++.|.+      ++.+++|..+|+...+|+||++|++||||++|++||.++.|.++++|..||.|||.||+.
T Consensus         2 ~~~~~~~i~~~v~~~~d~~g~~l~~~F~~~p~~~~~pdYy~~I~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~   81 (104)
T cd05522           2 YEARIKNILKGLRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKL   81 (104)
T ss_pred             HHHHHHHHHHHHHHHhCcCCCcccHHHhcCCCccccCcHHHHhCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHH
Confidence            45566777777755      467899999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHH
Q 048123          133 FNASDTVYYRQAHAMKELANKL  154 (202)
Q Consensus       133 yN~~~s~~~~~A~~L~~~~~~~  154 (202)
                      ||+++|.++.+|..|+..|+++
T Consensus        82 yn~~~s~i~~~A~~l~~~f~~l  103 (104)
T cd05522          82 YNENDSQEYKDAVLLEKEARLL  103 (104)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999875

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

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

Probab=99.92  E-value=8.6e-25  Score=152.77  Aligned_cols=84  Identities=39%  Similarity=0.717  Sum_probs=79.9

Q ss_pred             HHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHH
Q 048123           63 LDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYR  142 (202)
Q Consensus        63 ~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~  142 (202)
                      |..||+.|.+++.+++|..||+...+|+|+++|++||||.+|++||++|.|.++.+|..||++||.||+.||+++|.++.
T Consensus         1 C~~il~~l~~~~~~~~F~~~~~~~~~p~y~~~i~~P~dL~~I~~kl~~~~Y~s~~~f~~Dv~~i~~Na~~yn~~~s~~~~   80 (84)
T PF00439_consen    1 CREILEELMKHPISSPFSKPVDPKEYPDYYEIIKNPMDLSTIRKKLENGKYKSIEEFEADVRLIFQNARRYNPPDSPIYK   80 (84)
T ss_dssp             HHHHHHHHHTSTTGGGGSSSTHTTTSTTHHHHSSSS--HHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHHHSCTTSHHHH
T ss_pred             CHHHHHHHHcCCCchhhcCCCChhhCCCHHHHHhhccchhhhhHHhhccchhhHHHHHHHHHHHHHHHHHHCCCcCHHHH
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHH
Q 048123          143 QAHA  146 (202)
Q Consensus       143 ~A~~  146 (202)
                      +|.+
T Consensus        81 ~A~~   84 (84)
T PF00439_consen   81 AAEK   84 (84)
T ss_dssp             HHHH
T ss_pred             HhcC
Confidence            9964

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 ....

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

Probab=99.92  E-value=2.2e-24  Score=157.32  Aligned_cols=94  Identities=27%  Similarity=0.435  Sum_probs=85.5

Q ss_pred             HHHHHHHHHHHHcCCC------cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           60 RKMLDLLLDRLKRRDS------YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        60 ~~~~~~il~~l~~~~~------~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      .+.|..+++.|.....      +.+|..+|+...+||||++|++||||++|++||++  |.++++|..||.|||.||..|
T Consensus         3 ~~~~~~l~~~i~~~~~~~g~~~~~~F~~lp~~~~~pdYy~iI~~PmdL~tI~~kl~~--Y~s~~ef~~D~~li~~Na~~y   80 (106)
T cd05521           3 SKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLY   80 (106)
T ss_pred             HHHHHHHHHHHHhhcCcCCCCchHhhhcCCccccCccHHHHhcCCCCHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHHH
Confidence            4567778887766444      46999999999999999999999999999999998  999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHH
Q 048123          134 NASDTVYYRQAHAMKELANKLF  155 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~  155 (202)
                      |+++|.++.+|..|+..|.+++
T Consensus        81 N~~~s~i~~~A~~le~~~~~~~  102 (106)
T cd05521          81 NTKGSVIYKYALILEKYINDVI  102 (106)
T ss_pred             cCCCCHHHHHHHHHHHHHHHhh
Confidence            9999999999999999998765

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

>cd04369 Bromodomain Bromodomain

Probab=99.91  E-value=4.2e-24  Score=152.26  Aligned_cols=95  Identities=44%  Similarity=0.738  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHHHcC--CCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           60 RKMLDLLLDRLKRR--DSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        60 ~~~~~~il~~l~~~--~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      ...|..+++.|..+  +.+++|..||++..+|+|+++|++||||.+|+.||.++.|.++.+|..||.+||.||+.||+++
T Consensus         2 ~~~~~~i~~~l~~~~~~~~~~F~~~~~~~~~~~Y~~~i~~P~~l~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~~n~~~   81 (99)
T cd04369           2 KKKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPG   81 (99)
T ss_pred             HHHHHHHHHHHHhhcccccHHHhcCCChhcCCCHHHHHhCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            35788999999999  9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHH
Q 048123          138 TVYYRQAHAMKELANKL  154 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~~  154 (202)
                      +.++.+|..|+..|++.
T Consensus        82 ~~~~~~a~~l~~~~~~~   98 (99)
T cd04369          82 SPIYKDAKKLEKLFEKL   98 (99)
T ss_pred             CHHHHHHHHHHHHHHHh
Confidence            99999999999998875

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

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.91  E-value=1e-23  Score=154.07  Aligned_cols=99  Identities=23%  Similarity=0.367  Sum_probs=90.3

Q ss_pred             HHHHHHHHHHHc-CCCcccccCCCCc---C--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           61 KMLDLLLDRLKR-RDSYKIFAKPVDG---T--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        61 ~~~~~il~~l~~-~~~~~~F~~pv~~---~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      .+|..++..+++ .+.+.+|..||.+   .  .+|+|+.+|++||||+||++||+++.|.++++|..||.|||+||..||
T Consensus         3 ~~L~f~~~~~k~~lp~~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~N~~~yN   82 (109)
T cd05492           3 CLLKFIVSRMKSWLPPDTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFH   82 (109)
T ss_pred             hhHHHHHHHHHhcCcccccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            467788888888 7778999999963   2  499999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          135 ASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      +++|.++.+|..|...+..-+.++.
T Consensus        83 g~~s~~~~~A~~l~~d~~~el~Ei~  107 (109)
T cd05492          83 GADSEQYDAARWLYRDTCHDLRELR  107 (109)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999888888774

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

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.85  E-value=1e-20  Score=138.09  Aligned_cols=99  Identities=20%  Similarity=0.329  Sum_probs=89.8

Q ss_pred             HHHHHHHHHHHHHcCCC------cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhh
Q 048123           59 ERKMLDLLLDRLKRRDS------YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMH  132 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~------~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  132 (202)
                      .+.++..|+..|+++..      +.+|.+.|+  ..|+|+.+|+.||||++|+.||.+|.|.++++|..||.+||.||+.
T Consensus         4 vq~~l~~l~~~V~~~~D~~Gr~~s~~f~~LP~--~~~~~~~~ik~Pi~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NAr~   81 (110)
T cd05526           4 VQELLATLFVSVMNHQDEEGRCYSDSLAELPE--LAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARR   81 (110)
T ss_pred             HHHHHHHHHHHHHhccCCCCCCchHHHHHCCC--cccCchhhhcCCccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHHHH
Confidence            46778888888887653      579999887  4577789999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          133 FNASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       133 yN~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      ||.++|.+|.+|..|+..|.+..+++.
T Consensus        82 yN~~~S~iy~dA~eLq~~f~~~rd~~~  108 (110)
T cd05526          82 LSRTDSEIYEDAVELQQFFIKIRDELC  108 (110)
T ss_pred             hCcccCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999888874

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

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

Probab=99.80  E-value=5e-19  Score=155.30  Aligned_cols=91  Identities=32%  Similarity=0.524  Sum_probs=85.2

Q ss_pred             CCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHH
Q 048123           73 RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELAN  152 (202)
Q Consensus        73 ~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~~~  152 (202)
                      .....+|..+|+...+|+||.+|+.||||.+|+++|+++.|.++++|..|+.|||.||..||++++.++.+|..|+..|.
T Consensus       163 ~~~s~~F~~~p~k~~~PdYy~iIk~Pm~L~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~~~  242 (371)
T COG5076         163 RFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFL  242 (371)
T ss_pred             cccccccccCCccccCCChheeecchhhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHHHHHH
Confidence            34468999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhCCCc
Q 048123          153 KLFRTLKNDPE  163 (202)
Q Consensus       153 ~~~~~~~~~~~  163 (202)
                      .++..+.....
T Consensus       243 ~~i~~~~~~~~  253 (371)
T COG5076         243 KLIEEIPEEML  253 (371)
T ss_pred             HHHHhccccch
Confidence            99997755433

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

Probab=99.78  E-value=2.2e-19  Score=176.49  Aligned_cols=95  Identities=34%  Similarity=0.546  Sum_probs=92.4

Q ss_pred             HHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHH
Q 048123           63 LDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYR  142 (202)
Q Consensus        63 ~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~  142 (202)
                      |..||..|..|+.+|||+.||++..+|+||+||++||||.||+.++..|.|.++++|..||.|||.||..||.+ |.+++
T Consensus      1306 ~e~il~e~~~~~~awPFlepVn~~~vp~Y~~IIk~Pmdl~tir~k~~~~~Y~~~eef~~Di~lvf~Nc~~yN~~-s~i~~ 1384 (1404)
T KOG1245|consen 1306 CEDILHELVVHKAAWPFLEPVNPKEVPDYYDIIKKPMDLSTIREKLSKGIYPSPEEFATDIELVFDNCETYNED-SEIGR 1384 (1404)
T ss_pred             HHHHHHHHHHhhhcchhhccCChhhcccHHHHhcChhHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHhccc-hhhhh
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHHHHHHh
Q 048123          143 QAHAMKELANKLFRTL  158 (202)
Q Consensus       143 ~A~~L~~~~~~~~~~~  158 (202)
                      ++..|..+|++.|+..
T Consensus      1385 ag~~l~~ff~~~~~~~ 1400 (1404)
T KOG1245|consen 1385 AGTCLRRFFHKRWRKK 1400 (1404)
T ss_pred             hcchHHHHHHHHHHhh
Confidence            9999999999977654

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

Probab=99.63  E-value=2.5e-16  Score=145.15  Aligned_cols=102  Identities=33%  Similarity=0.528  Sum_probs=96.5

Q ss_pred             cHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           57 MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      -.....+..+|+.|..|..+|+|.+||+..++||||.+|.+||||.||+.+|.++.|..+..|+.|+.+||.||+.||+.
T Consensus       605 ~~~~s~~~~il~~l~~h~~awPf~~Pv~~~e~pdyy~~I~~pmDl~tM~~~l~~~~y~~~~~f~ad~~~vf~ncr~yn~~  684 (720)
T KOG1472|consen  605 GKLFSAIQNILDQLQNHGDAWPFLKPVNKKEVPDYYDVIKHPMDLRTMQNRLKDNQYTEVELFMADVVRVFANCRMYNGS  684 (720)
T ss_pred             chhhHHHHhHHhhhhcCCccCCccCccccccCCcHHHHhcccccHHHHhhhccccchhhHHHHHHHHHHHHhhhhccCCc
Confidence            34566788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Q 048123          137 DTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      ++..++.|..|+..|...+.+.
T Consensus       685 ~~~y~k~~~~le~~~~~k~~~~  706 (720)
T KOG1472|consen  685 DTQYYKCAQALEKFFLFKLNEL  706 (720)
T ss_pred             cchheecccchhhhhcchhhhh
Confidence            9999999999999998877765

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

Probab=99.49  E-value=6.6e-14  Score=134.08  Aligned_cols=113  Identities=44%  Similarity=0.750  Sum_probs=107.5

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ....|...+|+.++..|...+...+|..||++.++|||.++|++||||.+|+.+++++.|.++++|..|+.+|+.||+.|
T Consensus       561 ~~l~p~~kLl~~~l~~lq~kD~~gif~~pvd~~e~pdy~~iik~pmd~~t~~~kl~s~~y~tle~ieed~~l~~~nc~~y  640 (1051)
T KOG0955|consen  561 LGLNPFKKLLQKSLDKLQKKDSYGIFAEPVDPSELPDYIDIIKKPMDFFTMRLKLESGAYSTLEPIEEDVNLIVSNCMEY  640 (1051)
T ss_pred             ccCchHHHHHHHHHHHhhcccccCceeeccChhhcccHHHHhcCccchhhhhhhccccchhhhhHHHHhHhHhHhHHHHh
Confidence            35668889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhhCCCchHH
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTLKNDPENFE  166 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~  166 (202)
                      |..++.+|.+|..+.+...+.+...+.+++...
T Consensus       641 n~~dtv~~r~av~~~e~~~~~~~~arke~e~~~  673 (1051)
T KOG0955|consen  641 NAKDTVYYRAAVRLRELIKKDFRNARKEPESEG  673 (1051)
T ss_pred             hccCeehHhhhHHHHhhhhhHHHhcccchhhhc
Confidence            999999999999999999999998888777665

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=99.33  E-value=2.3e-12  Score=94.66  Aligned_cols=44  Identities=32%  Similarity=0.419  Sum_probs=41.5

Q ss_pred             cCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCC
Q 048123           95 IKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT  138 (202)
Q Consensus        95 I~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s  138 (202)
                      +-.||||+||++||.+|.|.++.+|+.||+|||.||..||.++.
T Consensus        61 ~~y~MDL~tIe~RL~ng~Y~tp~~F~~DiklI~~Nc~~ynd~dr  104 (119)
T cd05491          61 KFYNMDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKTIGDRER  104 (119)
T ss_pred             eEeccCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCHHH
Confidence            45689999999999999999999999999999999999999865

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=99.33  E-value=6.2e-13  Score=98.22  Aligned_cols=78  Identities=21%  Similarity=0.152  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHHcCCCcccccCCCCc--CCccchHhhcCCCCCHHHHHHHHhCCC-------CCCHHHHHHHHHHHHHHH
Q 048123           60 RKMLDLLLDRLKRRDSYKIFAKPVDG--TEVEDYYKVIKHPMDLSKITEKLNEGS-------YQTLGDFEHDIYLMLKNA  130 (202)
Q Consensus        60 ~~~~~~il~~l~~~~~~~~F~~pv~~--~~~p~Y~~iI~~PmdL~~I~~kl~~~~-------Y~s~~~f~~Dv~li~~Na  130 (202)
                      ...|..+|..+..++.+++|..||++  ..+|||+++|++||||+||+.+|.++.       |..-..+.+++..++.||
T Consensus         5 ~~~~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (114)
T cd05494           5 LERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGRR   84 (114)
T ss_pred             HHHHHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHcccccccccccccccccccccccccccc
Confidence            34566666777777799999999999  789999999999999999999999863       444445556666677777


Q ss_pred             hhhcCCC
Q 048123          131 MHFNASD  137 (202)
Q Consensus       131 ~~yN~~~  137 (202)
                      ..+|..+
T Consensus        85 ~~~~~~~   91 (114)
T cd05494          85 SPSNIYA   91 (114)
T ss_pred             Ccccccc
Confidence            6666643

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

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

Probab=99.27  E-value=4.5e-12  Score=122.00  Aligned_cols=95  Identities=28%  Similarity=0.531  Sum_probs=86.1

Q ss_pred             HHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHH
Q 048123           62 MLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYY  141 (202)
Q Consensus        62 ~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~  141 (202)
                      ++..++.+++.-+.+|+|..||++..+|+||.+|++||||.+|.+++..+.|.+.++|..||++|+.|+..||+.++.+.
T Consensus      1386 ~~d~~vs~~~~ipes~~f~~~v~~k~~~~yy~kik~pmdl~~i~~n~~~~~y~s~~e~l~dv~~i~~n~~~~ng~e~~y~ 1465 (1563)
T KOG0008|consen 1386 ILDNIVSQMKEIPESWPFHEPVNKKRVPDYYKKIKNPMDLETILKNIPPHKYDSRSEFLDDVNLIYVNSVEYNGAESAYT 1465 (1563)
T ss_pred             hhhhHHHHHHhcchhcccccccchhhchHHHHHhcChhhHHHHhhcCCccccccHHHHhhhhHhhcccceeecCcccccc
Confidence            46677778888899999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             HHHHHHHHHHHHHHH
Q 048123          142 RQAHAMKELANKLFR  156 (202)
Q Consensus       142 ~~A~~L~~~~~~~~~  156 (202)
                      .-|..+-.+....+-
T Consensus      1466 ~k~~k~~ev~~~~~~ 1480 (1563)
T KOG0008|consen 1466 KKARKIGEVGLANLL 1480 (1563)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            888877666655544

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

Probab=99.22  E-value=3.2e-11  Score=110.21  Aligned_cols=107  Identities=27%  Similarity=0.452  Sum_probs=93.6

Q ss_pred             CCCcCCcHHHHHHHHHHHHHHcCCC------cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHH
Q 048123           51 MSSIIAMPERKMLDLLLDRLKRRDS------YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIY  124 (202)
Q Consensus        51 ~~~~~~~~~~~~~~~il~~l~~~~~------~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~  124 (202)
                      .+.....+....+..||..+.....      ...|.+.++....|+||.+|..||+|..|+.|+..+.|.+.+.|+.|+.
T Consensus        45 d~p~i~~~~~~~f~~il~~~~~~~d~~gk~~~d~feklp~~~~~p~yy~~i~~pisl~~ik~kv~k~~y~~~~~f~~D~~  124 (629)
T KOG1827|consen   45 DSPVIDPPLIPKFKTILASLLDLKDDEGKQLFDKFEKLPSRKEFPEYYYVIQQPISLDQIKRKVKKGRYKRLSFFQLDFL  124 (629)
T ss_pred             CccccChHHHHHHHHHHHHHHhhccccCcccchhHhhccccccCCCcceeecCcccHHHHHHHHHhcccccHHHHHHHHH
Confidence            3445566677777777777765433      4689999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHH
Q 048123          125 LMLKNAMHFNASDTVYYRQAHAMKELANKLFRT  157 (202)
Q Consensus       125 li~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~  157 (202)
                      +|+.||..||.+++.++++|..|+..|..+..+
T Consensus       125 lm~ena~~~n~~ds~~~~~s~~l~~~~~~~~~~  157 (629)
T KOG1827|consen  125 LMTENARLYNRPDSLIYKDSGELEKYFISLEDE  157 (629)
T ss_pred             HHHHHHHHhcCcchhhhhhhhhhhcchhhhhcc
Confidence            999999999999999999999999999876653

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

Probab=99.16  E-value=6.5e-11  Score=111.90  Aligned_cols=103  Identities=23%  Similarity=0.435  Sum_probs=92.3

Q ss_pred             HHHHHHHHHHH------cCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           61 KMLDLLLDRLK------RRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        61 ~~~~~il~~l~------~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      ..+..|+....      .+..+..|...++...+||||++|+.||++..|.++|.++.|.+..+...||.++|.||++||
T Consensus      1027 ~~~~~i~~~~~~~~~~~~r~~~~~~~~~~s~k~~~d~~~~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~na~~~~ 1106 (1157)
T KOG0386|consen 1027 KQALKIASTSIKYKDSAGRELSEVFLKLPSRKEYPDYYEIIKKPVAIDKIKKRIENHKYNSLKELEKDFMLLFNNARTYN 1106 (1157)
T ss_pred             HHHHHHHHHHHhcccccccccchhcccCcccccccchHHHhcchhhHHHHhhhccccccchHHHHHHHHHhhcchhhhhc
Confidence            45666666665      345568999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhCCCc
Q 048123          135 ASDTVYYRQAHAMKELANKLFRTLKNDPE  163 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~~~~~~~~~  163 (202)
                      ..+|.+|.+|..|..+|.....++..+.+
T Consensus      1107 ~egs~~y~d~~~l~~~~~~~~~~~~~~~~ 1135 (1157)
T KOG0386|consen 1107 EEGSRVYEDAIVLQSVFKSARQEISKEDE 1135 (1157)
T ss_pred             cCCceechhHHHHHHHHhhhHHHHhcccc
Confidence            99999999999999999999988875433

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

Probab=99.14  E-value=1.4e-10  Score=112.04  Aligned_cols=100  Identities=24%  Similarity=0.454  Sum_probs=90.7

Q ss_pred             CcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcC
Q 048123           56 AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA  135 (202)
Q Consensus        56 ~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~  135 (202)
                      .+.+.-++..|++++...+...+|..||+...+++||.||..||||.++++.+....|.+-++|+.|+.||+.|..+||+
T Consensus      1259 ~V~~ss~l~~i~n~~~~~~~t~~f~~Pv~~k~v~dyy~vi~~P~~lq~~kk~v~kr~y~~r~~fle~~~~~~~ns~~yng 1338 (1563)
T KOG0008|consen 1259 SVSLSSILETIINQARSSPNTYPFPTPVNAKEVKDYYRVITPPMDLQTQKKLVRKRLYESREHFLEELPLIVSNSTKYNG 1338 (1563)
T ss_pred             eeecccchHHHHHHHhcCCCCcCCCCccchhhccchhhccCCCcchHHHHHHHHHHHHHHHHHHHHHhHHHhhchhhhcC
Confidence            34456688999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHH
Q 048123          136 SDTVYYRQAHAMKELANKLF  155 (202)
Q Consensus       136 ~~s~~~~~A~~L~~~~~~~~  155 (202)
                      +.+.+...|..+...+-..|
T Consensus      1339 ~~~~~t~~~q~mls~~~~~~ 1358 (1563)
T KOG0008|consen 1339 PLASLTRQQQSMLSLCFEKL 1358 (1563)
T ss_pred             chHHHHHHHHHHHHHHHHhh
Confidence            99998888887766654433

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

Probab=98.95  E-value=1.8e-09  Score=100.37  Aligned_cols=68  Identities=31%  Similarity=0.600  Sum_probs=64.6

Q ss_pred             cCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCH
Q 048123           72 RRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTV  139 (202)
Q Consensus        72 ~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~  139 (202)
                      .+.++++|..+|+...+|+||.+|+.||||.++.+++..+.|.+.++|+.|+.+||.||..||...+.
T Consensus       300 ~~~~s~~~~~kvs~~~a~~y~~i~k~pmdl~t~~~k~~~~~y~~~~~fv~d~~~~~~n~~~~n~ee~~  367 (720)
T KOG1472|consen  300 RTEHSTPFLEKVSKEDAPNYYQIIKAPMDLSTELKKLKSGPYCSKEEFVNDLMLIWRNCEKYNSEESH  367 (720)
T ss_pred             ccccccccccCCChhhCcchHHhhhcchHHHHHHHHhccccccchhHHHHHHHHHHhcchhhccccch
Confidence            37789999999999999999999999999999999999999999999999999999999999998653

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

Probab=98.84  E-value=4.4e-10  Score=96.79  Aligned_cols=97  Identities=25%  Similarity=0.332  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      |.....+.++.++-+.+....|..||.....|+|.++|+.|||+.+++.+++.+.|.+..+|..|.+++..||..||..+
T Consensus        19 p~~~~~ehhlrkl~sKdp~q~fafplt~~map~y~~iis~Pmd~~t~r~kidd~~yl~L~~m~~d~kl~~~na~~yn~~~   98 (418)
T KOG1828|consen   19 PDSGDAEHHLRKLPSKDPKQKFAFPLTDKMAPNYLEIISEPMDRITKRSKIDDTRYLVLSQMEFDRKLPDGNATLYNLHP   98 (418)
T ss_pred             cchhhHHHHHHhccccChhhhhccccchhhccchHhhhhcccccccccccCCCccceechhhhhhhcccccchhhhhcCC
Confidence            34456777888888889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHH
Q 048123          138 TVYYRQAHAMKELANKL  154 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~~  154 (202)
                      +.++..|+.|..+-...
T Consensus        99 Tv~~~aaKrL~~v~~~~  115 (418)
T KOG1828|consen   99 TVPIVAAKRLCPVRLGM  115 (418)
T ss_pred             ccccccccccchhhcch
Confidence            99999999887655433

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

Probab=98.71  E-value=9.2e-09  Score=88.77  Aligned_cols=95  Identities=17%  Similarity=0.186  Sum_probs=85.5

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ....+...++.....++...+....|..+|....+|.|..+|++|+++.|++.+..++.|.| -+|..|+.+|+.||++|
T Consensus       204 ~lqtg~~~l~~~q~~kl~~~~p~~~lnyg~tas~aP~YSm~Ik~~~~~~Tygdk~~andy~S-~~f~~D~kl~~l~amT~  282 (418)
T KOG1828|consen  204 DLQTGGQQLQTLQEDKLNRVDPVAYLNYGPTASFAPGYSMTITEVEPPGTYGDKSSANDYES-LSFTQDRKLIALKAVTN  282 (418)
T ss_pred             hhccccHHHHHHHHHHhcccCchhhhcccchhhhcccccccccccCCCcchhhhhhhhhhhh-hhhhcccchhhHHHHhc
Confidence            33444456677778888888899999999999999999999999999999999999999999 89999999999999999


Q ss_pred             cCCCCHHHHHHHHHHH
Q 048123          134 NASDTVYYRQAHAMKE  149 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~  149 (202)
                      |.++..+|.+|+.+.-
T Consensus       283 gehsk~yyelank~lh  298 (418)
T KOG1828|consen  283 GEHSKSYYELANKQLH  298 (418)
T ss_pred             CCcchHHHHHHHhhhh
Confidence            9999999999987655

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

Probab=98.50  E-value=2.3e-08  Score=93.50  Aligned_cols=92  Identities=25%  Similarity=0.445  Sum_probs=82.5

Q ss_pred             HHcCCCcccccCCCCcCC--ccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHH
Q 048123           70 LKRRDSYKIFAKPVDGTE--VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAM  147 (202)
Q Consensus        70 l~~~~~~~~F~~pv~~~~--~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L  147 (202)
                      +..+.++|+|..||+...  .|+||.+|.+|||+++|..+++++.|.+..+..+|+..+|.||..||.+.-.+...+..+
T Consensus         4 ~~~~~~~~~f~~~v~~v~l~~~~~~~~~~~~~d~~~~~~~~e~n~~~~~~~~~~~f~~~~sn~~~~~~~~~~v~~~~~~~   83 (640)
T KOG1474|consen    4 ARKHKLAWPFLEPVDAVALNLPAYYEIIKRPMDIGTIEKRVENNYYFSASECIADFKTKFSNCYLFNDSGDDVVRMKQSL   83 (640)
T ss_pred             cccccccccccCccchhhccchhhhcccCCCCCchhhhhhhccCccccHhhhhhhccccccchhcccCCccchhhccccc
Confidence            456788999999999654  899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhCC
Q 048123          148 KELANKLFRTLKND  161 (202)
Q Consensus       148 ~~~~~~~~~~~~~~  161 (202)
                      +..|.+........
T Consensus        84 ~~~~~~~~~~~~~~   97 (640)
T KOG1474|consen   84 EKLFPKKLRSMPSD   97 (640)
T ss_pred             hhhccccccccccc
Confidence            99887766655433

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

Probab=97.67  E-value=1.3e-05  Score=70.72  Aligned_cols=96  Identities=31%  Similarity=0.505  Sum_probs=86.6

Q ss_pred             HHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHH
Q 048123           67 LDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHA  146 (202)
Q Consensus        67 l~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~  146 (202)
                      +.....+..+|+|..+++....|+|+++|..+|++.+.+.++..+.|...+.|..|..++++||..||+....++..+..
T Consensus       272 i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  351 (371)
T COG5076         272 ITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANV  351 (371)
T ss_pred             ccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhccc
Confidence            33445667789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhCCC
Q 048123          147 MKELANKLFRTLKNDP  162 (202)
Q Consensus       147 L~~~~~~~~~~~~~~~  162 (202)
                      +...+....+......
T Consensus       352 ~~~~~~~~~~~~~~~~  367 (371)
T COG5076         352 LEDFVIKKTRLIREYP  367 (371)
T ss_pred             hhhhHhhhhhhhhccc
Confidence            9999888877665443

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

Probab=97.39  E-value=0.00039  Score=52.27  Aligned_cols=61  Identities=25%  Similarity=0.439  Sum_probs=51.0

Q ss_pred             CCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHh
Q 048123           98 PMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus        98 PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      |-||..|++||++|.|.|+.+|.+||-.|+.-++.=.+...++-++-..+..+|-++++.+
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~v  119 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESV  119 (131)
T ss_pred             cccHHHHHHHHhccceehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHh
Confidence            8899999999999999999999999999999988776655555555556677777777765

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

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

Probab=94.74  E-value=0.015  Score=55.47  Aligned_cols=60  Identities=20%  Similarity=0.326  Sum_probs=49.4

Q ss_pred             hcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHH
Q 048123           94 VIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANK  153 (202)
Q Consensus        94 iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~~~~  153 (202)
                      --.-|..|..|..+|++.+|.+.+.|..|+..|..||.+|.+-+.-+-..+..|...|..
T Consensus      1049 ~fpvpls~evi~~rlEn~yYrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~ 1108 (1113)
T KOG0644|consen 1049 RFPVPLSLEVIRSRLENNYYRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDR 1108 (1113)
T ss_pred             CCCCcccHHHHHHHHHhhhhhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhh
Confidence            356789999999999999999999999999999999999999876555555555554443

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

Probab=94.41  E-value=0.066  Score=52.78  Aligned_cols=96  Identities=18%  Similarity=0.253  Sum_probs=76.5

Q ss_pred             cccccCCCCcCC-----ccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHH--HHHHHHHHHhhhcCCC--------CHH
Q 048123           76 YKIFAKPVDGTE-----VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEH--DIYLMLKNAMHFNASD--------TVY  140 (202)
Q Consensus        76 ~~~F~~pv~~~~-----~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~--Dv~li~~Na~~yN~~~--------s~~  140 (202)
                      ...|..|++...     +++|-.+|+.+||+...-.++..+.|.++-+|..  ++.|||.|++.||+..        ..|
T Consensus       533 ~~~~s~Pl~~~~~~ll~~~~~~~~iq~~~~va~~~~k~~e~~~~~v~~~e~~~~i~lic~~~lli~~~~~~g~~~lg~aI  612 (1080)
T KOG0732|consen  533 SVIFSRPLSTYLKPLLPFQDALEDIQGLMDVASSMAKIEEHLKLLVRSFESNFAIRLICRPRLLINGGKGSGQDYLGPAI  612 (1080)
T ss_pred             ccCCCCCCCcceecccchHHHHHHhhcchhHHhhhhhHHHHhHHHHHhhhcccchhhhcCcHHhcCCCcccccCcccHHH
Confidence            567888887643     5689999999999999999999999999999999  9999999999999975        245


Q ss_pred             HHHHHHHHHHHHHHHHHhhCC-CchHHHHhhh
Q 048123          141 YRQAHAMKELANKLFRTLKND-PENFEAACSM  171 (202)
Q Consensus       141 ~~~A~~L~~~~~~~~~~~~~~-~~~~~~~~~~  171 (202)
                      ...+..+......+...+... ....+.++..
T Consensus       613 lh~~~~~~v~s~~issll~d~~~~~~~~~iv~  644 (1080)
T KOG0732|consen  613 LHRLEGLPVQSLDISSLLSDEGTEDLEEEIVH  644 (1080)
T ss_pred             HHHHhccchHHHHHHHHHhccccccHHHHHHH
Confidence            556666666666666655544 6666777663

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

Probab=82.73  E-value=0.14  Score=47.87  Aligned_cols=76  Identities=9%  Similarity=0.022  Sum_probs=69.0

Q ss_pred             cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHHHH
Q 048123           76 YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELA  151 (202)
Q Consensus        76 ~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~~  151 (202)
                      ...|+..++...+|+||.+++-||.++...+++..+.|.....|..|+.+.|.|+-.|+.....++..+..|.+..
T Consensus       213 Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~q~l~g~c~v~~~~~yi~~~p~~ls~~d  288 (629)
T KOG1827|consen  213 IERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLVQRLLGKCYVMKPTEYISGDPENLSEED  288 (629)
T ss_pred             ecccccCcccccccceeEeeCCccCccccccchhcccceecccccccHHHHhhcceEEeehhHhhhcCcccccccc
Confidence            3568888889999999999999999999999999999999999999999999999999999998888888765543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	202
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		2e-13
3dai_A	130	Crystal Structure Of The Bromodomain Of The Human A		2e-11
3lxj_A	136	Crystal Structure Of The Bromodomain Of Human Aaa D		2e-11
2d9e_A	121	Solution Structure Of The Bromodomain Of Peregrin L		2e-11
1e6i_A	121	Bromodomain From Gcn5 Complexed With Acetylated H4		1e-10
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		2e-09
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		2e-09
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		3e-09
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		3e-09
3hme_A	123	Crystal Structure Of Human Bromodomain Containing 9		5e-09
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		5e-09
3i3j_A	124	Crystal Structure Of The Bromodomain Of Human Ep300		1e-08
2dkw_A	131	Solution Structure Of The Bromodomain Of Human Prot		1e-08
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		1e-08
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		2e-08
3g0l_A	117	Crystal Structure Of Human Bromodomain Adjacent To		2e-08
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		2e-08
3dwy_A	119	Crystal Structure Of The Bromodomain Of Human Crebb		2e-08
2i7k_A	117	Solution Structure Of The Bromodomain Of Human Brd7		2e-08
1jsp_B	121	Nmr Structure Of Cbp Bromodomain In Complex With P5		3e-08
2e7o_A	112	Solution Structure Of The Bromodomain From Human Br		3e-08
3uv4_A	158	Crystal Structure Of The Second Bromodomain Of Huma		3e-08
2f6j_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		5e-08
3jvl_A	120	Crystal Structure Of Bromodomain 2 Of Mouse Brd4 Le		6e-08
1f68_A	103	Nmr Solution Structure Of The Bromodomain From Huma		6e-08
3d7c_A	112	Crystal Structure Of The Bromodomain Of Human Gcn5,		6e-08
2h60_A	128	Solution Structure Of Human Brg1 Bromodomain Length		1e-07
3o33_A	184	Crystal Structure Of Trim24 Phd-Bromo In The Free S		1e-07
3nxb_A	116	Crystal Structure Of The Bromodomain Of Human Cecr2		1e-07
2dat_A	123	Solution Structure Of The Bromodomain Of Human SwiS		2e-07
3uvd_A	124	Crystal Structure Of The Bromodomain Of Human Trans		2e-07
2grc_A	129	1.5 A Structure Of Bromodomain From Human Brg1 Prot		2e-07
2ktb_B	121	Solution Structure Of The Second Bromodomain Of Hum		2e-07
2yyn_A	135	Crystal Sturcture Of Human Bromodomain Protein Leng		2e-07
3ljw_A	120	Crystal Structure Of The Second Bromodomain Of Huma		3e-07
3oni_A	114	Crystal Structure Of The Second Bromodomain Of Huma		5e-07
2oo1_A	113	Crystal Structure Of The Bromo Domain 2 Of Human Br		5e-07
2g4a_A	116	Solution Structure Of A Bromodomain From Ring3 Prot		5e-07
2dvv_A	112	Crystal Structure Of The Second Bromodomain Of The		6e-07
2e7n_A	117	Solution Structure Of The Second Bromodomain From H		6e-07
3hmf_A	116	Crystal Structure Of The Second Bromodomain Of Huma		6e-07
3hmh_A	155	Crystal Structure Of The Second Bromodomain Of Huma		7e-07
2ouo_A	130	Crystal Structure Of The Bromo Domain 2 In Human Br		1e-06
2lsp_B	128	Solution Structures Of Brd4 Second Bromodomain With		2e-06
2r10_A	361	Structure Of An Acetylated Rsc4 Tandem Bromodomain		2e-06
3g0j_A	124	Crystal Structure Of The Fifth Bromodomain Of Human		2e-06
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		2e-06
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		2e-06
2r0v_A	346	Structure Of The Rsc4 Tandem Bromodomain Acetylated		2e-06
2i8n_A	114	Solution Structure Of The Second Bromodomain Of Brd		2e-06
3u5m_A	207	Crystal Structure Of Trim33 Phd-Bromo In The Free S		4e-06
3k2j_A	130	Crystal Structure Of The 3rd Bromodomain Of Human P		7e-06
2yqd_A	120	Solution Structure Of The Fifth Bromodomain From Mo		8e-06
3tlp_A	150	Crystal Structure Of The Fourth Bromodomain Of Huma		2e-05
2wp1_A	126	Structure Of Brdt Bromodomain 2 Bound To An Acetyla		2e-05
2r0y_A	311	Structure Of The Rsc4 Tandem Bromodomain In Complex		3e-05
2r0s_A	285	Crystal Structure Of The Rsc4 Tandem Bromodomain Le		3e-05
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		3e-05
3fkm_X	166	Plasmodium Falciparum Bromodomain-Containing Protei		5e-05
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		1e-04
2dww_A	114	Crystal Structure Of Bromodomain-Containing Protein		1e-04
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		2e-04
2wp2_A	120	Structure Of Brdt Bromodomain Bd1 Bound To A Diacet		3e-04
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		4e-04
3jvj_A	131	Crystal Structure Of The Bromodomain 1 In Mouse Brd		5e-04
2oss_A	127	Crystal Structure Of The Bromo Domain 1 In Human Br		5e-04
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		6e-04
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		6e-04
3iu5_A	116	Crystal Structure Of The First Bromodomain Of Human		7e-04

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 54/97 (55%), Gaps = 2/97 (2%)
Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           +IFA+PV   EV DY   IKHPMD + + ++L    Y+ L +FE D  L++ N M +NA 
Sbjct: 32  RIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNAR 91
Query: 137 DTVYYRQAHAMKELANKLFRTLKN--DPENFEAACSM 171
           DTV+YR A  +++    + R  +   D    E A  M
Sbjct: 92  DTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASGM 128

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 55/99 (55%), Gaps = 6/99 (6%)
Query: 76  YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA 135
           +++F KPVD  EV DY  VIK PMDLS +  K++   Y T+ D+  DI L+  NA+ +N 
Sbjct: 28  FRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 87
Query: 136 S----DTVYYRQAHAMKELANKLFRTLKNDPENFEAACS 170
                D +   +A A+++ A  + +   +  E+FE  C 
Sbjct: 88  DRDPGDRLIRHRACALRDTAYAIIKEELD--EDFEQLCE 124

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 38/99 (38%), Positives = 56/99 (56%), Gaps = 6/99 (6%)
Query: 76  YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA 135
           + IF+KPVD  EV DY +VIK PMDLS +  K+++ +Y T  DF  DI L+  NA+ +N 
Sbjct: 30  FNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 89
Query: 136 S----DTVYYRQAHAMKELANKLFRTLKNDPENFEAACS 170
                D +   +A  +K+ A+ +    + DPE F   C 
Sbjct: 90  DKDPGDKIIRHRACTLKDTAHAIIAA-ELDPE-FNKLCE 126

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 48/93 (51%)
Query: 78  IFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD 137
           IF++PV  +EV DY   IK PMD   + + L    Y    DFE D  L++ N + +NA D
Sbjct: 27  IFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKD 86
Query: 138 TVYYRQAHAMKELANKLFRTLKNDPENFEAACS 170
           T++YR A  ++E    + R  +   E   +  S
Sbjct: 87  TIFYRAAVRLREQGGAVLRQARRQAEKMGSGPS 119

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 43/74 (58%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PV+  EV DYY  IK PMDLS +  KL    YQ + DF +D  L+  N   +N  +T
Sbjct: 34  FLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENT 93
Query: 139 VYYRQAHAMKELAN 152
            YY+ A+ +++  N
Sbjct: 94  SYYKYANRLEKFFN 107

>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 = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 45/81 (55%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PVD  +  DYY VIK PMDL+ + E++    Y+ L +F  D+  +  N  ++N SD+
Sbjct: 93  FLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDS 152
Query: 139 VYYRQAHAMKELANKLFRTLK 159
            +Y+ A  ++    +  +  K
Sbjct: 153 PFYQCAEVLESFFVQKLKGFK 173

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 45/81 (55%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PVD  +  DYY VIK PMDL+ + E++    Y+ L +F  D+  +  N  ++N SD+
Sbjct: 93  FLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDS 152
Query: 139 VYYRQAHAMKELANKLFRTLK 159
            +Y+ A  ++    +  +  K
Sbjct: 153 PFYQCAEVLESFFVQKLKGFK 173

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PVD  +  DYY VIK PMDL+ + E++    Y+ L +F  D+  +  N  ++N SD+
Sbjct: 34  FLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTAIFDNCRYYNPSDS 93
Query: 139 VYYRQAHAMKEL 150
            +Y+ A  ++  
Sbjct: 94  PFYQCAEVLESF 105

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PVD  +  DYY VIK PMDL+ + E++    Y+ L +F  D+  +  N  ++N SD+
Sbjct: 41  FLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDS 100
Query: 139 VYYRQAHAMKEL 150
            +Y+ A  ++  
Sbjct: 101 PFYQCAEVLESF 112

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 38/67 (56%)
Query: 78  IFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD 137
            FA PV       Y  +IKHPMD   + +K+    Y+++ +F+ D  LM  NAM +N  D
Sbjct: 33  FFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPD 92
Query: 138 TVYYRQA 144
           TVYY+ A
Sbjct: 93  TVYYKLA 99

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PVD  +  DYY VIK PMDL+ + E++    Y+ L +F  D+  +  N  ++N SD+
Sbjct: 34  FLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDS 93
Query: 139 VYYRQAHAMKEL 150
            +Y+ A  ++  
Sbjct: 94  PFYQCAEVLESF 105

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 79  FAKPVDG--TEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD     + DY+ ++K PMDLS I  KL+ G YQ    +  DI+LM  NA  +N  
Sbjct: 38  FRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRK 97
Query: 137 DTVYYRQAHAMKEL 150
            +  Y+    + E+
Sbjct: 98  TSRVYKYCSKLSEV 111

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/98 (35%), Positives = 53/98 (54%), Gaps = 11/98 (11%)
Query: 76  YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN- 134
           + IF+KPV      DY +VIK PMDLS +  K+++ +Y T  DF  DI L+  NA+ +N 
Sbjct: 30  FNIFSKPV-----SDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 84
Query: 135 ---ASDTVYYRQAHAMKELANKLFRTLKNDPENFEAAC 169
                D +   +A  +K+ A+ +    + DPE F   C
Sbjct: 85  DKDPGDKIIRHRACTLKDTAHAIIAA-ELDPE-FNKLC 120

>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 = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F  PV+   V DYYKVI +PMDL  I + +++  YQ+   F  D+ L+L N++ +N  ++
Sbjct: 191 FHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPES 250
Query: 139 VYYRQAHAMKELANKLFRTL 158
            Y + A   +E+ N  ++TL
Sbjct: 251 QYTKTA---QEIVNVCYQTL 267

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F  PV+   V DYYKVI +PMDL  I + +++  YQ+   F  D+ L+L N++ +N  ++
Sbjct: 170 FHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPES 229
Query: 139 VYYRQAHAMKELANKLFRTL 158
            Y + A   +E+ N  ++TL
Sbjct: 230 QYTKTA---QEIVNVCYQTL 246

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 38/75 (50%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F  PV+   V  Y KVIK PMD S I EKL+ G Y  L  F  D+ L+  N   FN  D+
Sbjct: 34  FLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDS 93
Query: 139 VYYRQAHAMKELANK 153
              R  H M++   K
Sbjct: 94  DIGRAGHNMRKYFEK 108

>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 = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F  PV+   V DYYKVI +PMDL  I + +++  YQ+   F  D+ L+L N++ +N  ++
Sbjct: 158 FHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPES 217
Query: 139 VYYRQAHAMKELANKLFRTL 158
            Y + A   +E+ N  ++TL
Sbjct: 218 QYTKTA---QEIVNVCYQTL 234

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 79  FAKPVDG--TEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD     + DY+ ++K+PMDLS I  KL+ G YQ    +  D++LM  NA  +N  
Sbjct: 33  FRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRK 92
Query: 137 DTVYYRQAHAMKEL 150
            +  Y+    + E+
Sbjct: 93  TSRVYKFCSKLAEV 106

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 39/70 (55%)
Query: 78  IFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD 137
            F+ PV       Y  +IKHPMD S + EK+    YQ++ + + +  LM  NAM +N  +
Sbjct: 28  FFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPE 87
Query: 138 TVYYRQAHAM 147
           T+YY+ A  +
Sbjct: 88  TIYYKAAKKL 97

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 79  FAKPVDG--TEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD     + DY+ ++K+PMDLS I  KL+ G YQ    +  D++LM  NA  +N  
Sbjct: 35  FRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRK 94
Query: 137 DTVYYRQAHAMKEL 150
            +  Y+    + E+
Sbjct: 95  TSRVYKFCSKLAEV 108

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 38/75 (50%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F  PV+   V  Y KVIK PMD S I EKL+ G Y  L  F  D+ L+  N   FN  D+
Sbjct: 31  FLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDDS 90
Query: 139 VYYRQAHAMKELANK 153
              R  H M++   K
Sbjct: 91  DIGRAGHNMRKYFEK 105

>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 = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F  PV+   V DYYKVI +PMDL  I + +++  YQ+   F  D+ L+L N++ +N  ++
Sbjct: 51  FHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPES 110
Query: 139 VYYRQAHAMKELANKLFRTL 158
            Y + A   +E+ N  ++TL
Sbjct: 111 QYTKTA---QEIVNVCYQTL 127

>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 = 54.3 bits (129), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 42/81 (51%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PVD  +  DYY VIK P DL+   E++    Y+ L +F  D   +  N  ++N SD+
Sbjct: 93  FLEPVDPNDAPDYYGVIKEPXDLATXEERVQRRYYEKLTEFVADXTKIFDNCRYYNPSDS 152
Query: 139 VYYRQAHAMKELANKLFRTLK 159
            +Y+ A  ++    +  +  K
Sbjct: 153 PFYQCAEVLESFFVQKLKGFK 173

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 2/88 (2%)
Query: 79  FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD     + DY  +IKHPMD+S I  KL    Y+   +F  D+ LM  N   +N  
Sbjct: 33  FYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPP 92
Query: 137 DTVYYRQAHAMKELANKLFRTLKNDPEN 164
           D      A  ++++    F  + ++PE 
Sbjct: 93  DHEVVAMARKLQDVFEMRFAKMPDEPEE 120

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 41/72 (56%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PV  +E  DYY+VI+ P+DL  +TE+L    Y T   F  D+  ++ N   +N  D+
Sbjct: 24  FMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDS 83
Query: 139 VYYRQAHAMKEL 150
            Y R A A+++ 
Sbjct: 84  EYCRCASALEKF 95

>pdb|3D7C|A Chain A, Crystal Structure Of The Bromodomain Of Human Gcn5, The General Control Of Amino-Acid Synthesis Protein 5-Like 2 Length = 112

Iteration: 1
 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 41/72 (56%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PV  +E  DYY+VI+ P+DL  +TE+L    Y T   F  D+  ++ N   +N  D+
Sbjct: 28  FMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDS 87
Query: 139 VYYRQAHAMKEL 150
            Y R A A+++ 
Sbjct: 88  EYCRCASALEKF 99

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/90 (24%), Positives = 51/90 (56%)
Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           ++F +     E+ +YY++I+ P+D  KI E++    Y++L D E D+ L+ +NA  FN  
Sbjct: 33  EVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLE 92
Query: 137 DTVYYRQAHAMKELANKLFRTLKNDPENFE 166
            ++ Y  +  ++ +   + + ++ + ++ E
Sbjct: 93  GSLIYEDSIVLQSVFTSVRQKIEKEDDSLE 122

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE--GSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F  PV  T V DYYK+IK+PMDLS I ++L E    Y    DF  D  L+ +N   FN  
Sbjct: 102 FQDPVPLT-VPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEP 160
Query: 137 DTVYYRQAHAMKELANKLFRTLKN 160
           D+     A+A  +L N     LKN
Sbjct: 161 DS---EVANAGIKLENYFEELLKN 181

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 38/62 (61%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PVD +   +YY++IK PMD+S + +KLN G Y T  +F +D+  M +N   +N   +
Sbjct: 37  FLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESS 96
Query: 139 VY 140
            Y
Sbjct: 97  EY 98

>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 = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 42/74 (56%)
Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           ++F +     E+ +YY++I+ P+D  KI E++    Y++LGD E D+ L+  NA  FN  
Sbjct: 38  EVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLE 97
Query: 137 DTVYYRQAHAMKEL 150
            +  Y  +  ++ +
Sbjct: 98  GSQIYEDSIVLQSV 111

>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 = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 42/72 (58%)
Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           ++F +     E+ +YY++I+ P+D  KI E++    Y++L D E D+ L+ +NA  FN  
Sbjct: 38  EVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLE 97
Query: 137 DTVYYRQAHAMK 148
            ++ Y  +  ++
Sbjct: 98  GSLIYEDSIVLQ 109

>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 = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 42/72 (58%)
Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           ++F +     E+ +YY++I+ P+D  KI E++    Y++L D E D+ L+ +NA  FN  
Sbjct: 37  EVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLE 96
Query: 137 DTVYYRQAHAMK 148
            ++ Y  +  ++
Sbjct: 97  GSLIYEDSIVLQ 108

>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 = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 51/92 (55%), Gaps = 4/92 (4%)
Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           ++F K     +  DYY +IK P+DL  I +++  GSY+++     DI L+ KNA  +N  
Sbjct: 34  ELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEP 93
Query: 137 DTVYYRQAHAMKELANKLFRTLKNDPENFEAA 168
            +  ++ A+++K    K+F   K + E+ E A
Sbjct: 94  GSQVFKDANSIK----KIFYMKKAEIEHHEMA 121

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE--GSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F  PV  T V DYYK+IK+PMDLS I ++L E    Y    DF  D  L+ +N   FN  
Sbjct: 41  FQDPVPLT-VPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEP 99
Query: 137 DTVYYRQAHAMKELANKLFRTLKN 160
           D+     A+A  +L N     LKN
Sbjct: 100 DS---EVANAGIKLENYFEELLKN 120

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 51/92 (55%), Gaps = 4/92 (4%)
Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           ++F K     +  DYY +IK P+DL  I +++  GSY+++     DI L+ KNA  +N  
Sbjct: 33  ELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEP 92
Query: 137 DTVYYRQAHAMKELANKLFRTLKNDPENFEAA 168
            +  ++ A+++K    K+F   K + E+ E A
Sbjct: 93  GSQVFKDANSIK----KIFYMKKAEIEHHEMA 120

>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 = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD + +   DY+ +IKHPMDLS +  K+    Y+   +F  D+ LM  N   +N  
Sbjct: 31  FYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPP 90
Query: 137 D 137
           D
Sbjct: 91  D 91

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 79  FAKPVDG--TEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD    E+ DY+ +IKHPMDLS +  K++   Y     F  D+ LM  N   +N  
Sbjct: 31  FYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPP 90
Query: 137 D 137
           D
Sbjct: 91  D 91

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD + +   DY+ +IKHPMDLS +  K+    Y+   +F  D+ LM  N   +N  
Sbjct: 25  FYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPP 84
Query: 137 D 137
           D
Sbjct: 85  D 85

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD + +   DY+ +IKHPMDLS +  K+    Y+   +F  D+ LM  N   +N  
Sbjct: 29  FYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPP 88
Query: 137 D 137
           D
Sbjct: 89  D 89

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 79  FAKPVDG--TEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD    E+ DY+ +IKHPMDLS +  K++   Y     F  D+ LM  N   +N  
Sbjct: 36  FYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPP 95
Query: 137 D 137
           D
Sbjct: 96  D 96

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 77  KIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           ++F K     +  DYY +IK P+DL  I +++  GSY+++     DI L+ KNA  +N  
Sbjct: 31  ELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEP 90
Query: 137 DTVYYRQAHAMKEL 150
            +  ++ A+++K++
Sbjct: 91  GSQVFKDANSIKKI 104

>pdb|3HMH|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Tbp-Associated Factor Rna Polymerase 1-Like (Taf1l) Length = 155

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F  PV+   V DYYK+I +P+DL  I + +++  YQ+   F  D+ L+L N++ +N  ++
Sbjct: 48  FHHPVNKKFVPDYYKMIVNPVDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPES 107
Query: 139 VYYRQAHAMKELANKLFRTL 158
            Y + A   +E+ N  ++T+
Sbjct: 108 QYTKTA---QEIVNICYQTI 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 = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 2/85 (2%)
Query: 79  FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD     + DY  +IKHPMD+S I  KL    Y+   +F  D+ LM  N   +N  
Sbjct: 46  FYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPP 105
Query: 137 DTVYYRQAHAMKELANKLFRTLKND 161
           D      A  ++++    F  + ++
Sbjct: 106 DHEVVAMARKLQDVFEMRFAKMPDE 130

>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 = 27/85 (31%), Positives = 41/85 (48%), Gaps = 2/85 (2%)
Query: 79  FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD     + DY  +IKHPMD+S I  KL    Y+   +F  D+ LM  N   +N  
Sbjct: 44  FYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPP 103
Query: 137 DTVYYRQAHAMKELANKLFRTLKND 161
           D      A  ++++    F  + ++
Sbjct: 104 DHEVVAMARKLQDVFEMRFAKMPDE 128

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 41/78 (52%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F + VD  E+ +YY+++  PM LS + + L  G Y  + DF  D+ L+ +NA  FN    
Sbjct: 234 FMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSA 293
Query: 139 VYYRQAHAMKELANKLFR 156
           + Y+ A  +    N L +
Sbjct: 294 LIYKDATTLTNYFNYLIQ 311

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 42/84 (50%)
Query: 78  IFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD 137
           IF +    +E+ DYY  IK PMD+ KI   +    YQ +     D  +M  NA  +N  +
Sbjct: 41  IFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPE 100
Query: 138 TVYYRQAHAMKELANKLFRTLKND 161
           ++ Y+ A  + ++  +  R L+ D
Sbjct: 101 SLIYKDALVLHKVLLETRRDLEGD 124

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PV  TE   YY+VI+ PMDL  ++E+L    Y +   F  D+  +  N   +N  ++
Sbjct: 36  FMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPES 95
Query: 139 VYYRQAHAMKEL 150
            YY+ A+ +++ 
Sbjct: 96  EYYKCANILEKF 107

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F +PV  TE   YY+VI+ PMDL  ++E+L    Y +   F  D+  +  N   +N  ++
Sbjct: 34  FMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPES 93
Query: 139 VYYRQAHAMKEL 150
            YY+ A+ +++ 
Sbjct: 94  EYYKCANILEKF 105

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 41/78 (52%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F + VD  E+ +YY+++  PM LS + + L  G Y  + DF  D+ L+ +NA  FN    
Sbjct: 219 FMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSA 278
Query: 139 VYYRQAHAMKELANKLFR 156
           + Y+ A  +    N L +
Sbjct: 279 LIYKDATTLTNYFNYLIQ 296

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 79  FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD     + DY  +IKHPMD+S I  KL    Y+   +F  D+ LM  N   +N  
Sbjct: 25  FYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPP 84
Query: 137 D 137
           D
Sbjct: 85  D 85

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 35/59 (59%), Gaps = 4/59 (6%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE---GSYQTLGDFEHDIYLMLKNAMHFN 134
           F +PV  + + +YYK+IK PMDLS + +KL +     YQ   DF  D+ L+ KN   FN
Sbjct: 102 FQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFN 159

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 36/61 (59%)
Query: 90  DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKE 149
           DYY+ IK P+ L +I  KL    Y+TL   E D+ LM +NA  +N  ++  Y++   +++
Sbjct: 55  DYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQ 114
Query: 150 L 150
           +
Sbjct: 115 V 115

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 35/70 (50%)
Query: 78  IFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD 137
           IF +    +E+ DYY  IK PMD+ KI   +    YQ +     D  +M  NA  +N  +
Sbjct: 41  IFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPE 100
Query: 138 TVYYRQAHAM 147
           ++ Y+ A  +
Sbjct: 101 SLIYKDALVL 110

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 39/80 (48%)
Query: 90  DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKE 149
           DYYK+I  PMDL  I   +    Y        D+ LM +NA H+N   +  Y  AH +++
Sbjct: 63  DYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEK 122
Query: 150 LANKLFRTLKNDPENFEAAC 169
           L  +  + L   P++ + A 
Sbjct: 123 LLKEKRKELGPLPDDDDMAS 142

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F  PVD   +   +YY V+K+PMDL  I  K++   Y+   +F  D+ LM  N   +N  
Sbjct: 38  FYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPP 97
Query: 137 DTVYYRQAHAMKELANKLFRTLKNDP 162
           D      A  ++++    F  + ++P
Sbjct: 98  DHEVVAMARTLQDVFELHFAKIPDEP 123

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 39/78 (50%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F + VD  E+ +YY+++  P  LS + + L  G Y  + DF  D  L+ +NA  FN    
Sbjct: 184 FXELVDKDELPEYYEIVHSPXALSIVKQNLEIGQYSKIYDFIIDXLLVFQNAHIFNDPSA 243
Query: 139 VYYRQAHAMKELANKLFR 156
           + Y+ A  +    N L +
Sbjct: 244 LIYKDATTLTNYFNYLIQ 261

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 39/78 (50%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT 138
           F + VD  E+ +YY+++  P  LS + + L  G Y  + DF  D  L+ +NA  FN    
Sbjct: 178 FXELVDKDELPEYYEIVHSPXALSIVKQNLEIGQYSKIYDFIIDXLLVFQNAHIFNDPSA 237
Query: 139 VYYRQAHAMKELANKLFR 156
           + Y+ A  +    N L +
Sbjct: 238 LIYKDATTLTNYFNYLIQ 255

>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 = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 29/52 (55%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNA 130
           F +PVD  E  DY  +I  PMD   + E L+ G+Y +  +F  DI L+  NA
Sbjct: 31  FRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNA 82

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 78  IFAKPVDGTE--VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA 135
           IF K VD  +    DYY VIK+P   S I  KL +G Y    +F  D+ L+  N   +N 
Sbjct: 41  IFEKLVDAKKQNCPDYYDVIKNPXSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLYNT 100
Query: 136 SDTV 139
           S++V
Sbjct: 101 SNSV 104

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 79  FAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD  E  DY  +I  PMD + + E L  G+Y++  +   D+ L+  N+  +  S
Sbjct: 42  FRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPS 99

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 79  FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F KPVD     + DY  +IKHP D S I  KL    Y+   +F  D+ L   N   +N  
Sbjct: 31  FYKPVDVEALGLHDYCDIIKHPXDXSTIKSKLESREYRDAQEFGADVRLXFSNCYKYNPP 90
Query: 137 D 137
           D
Sbjct: 91  D 91

>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 = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 79  FAKPVDGTEVE--DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD  +++  DYY +IK+PMDL+ I ++L    Y    +   D   M  N   +N  
Sbjct: 34  FQRPVDAVKLQLPDYYTIIKNPMDLNTIKKRLENKYYAKASECIEDFNTMFSNCYLYNKP 93
Query: 137 DTVYYRQAHAMKEL 150
                  A A+++L
Sbjct: 94  GDDIVLMAQALEKL 107

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 79  FAKPVDGTEVE--DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD  +++  DYY +IK PMDL+ I ++L    Y+   +   D   M  N   +N +
Sbjct: 35  FQQPVDAVKLKLPDYYTIIKTPMDLNTIKKRLENKYYEKASECIEDFNTMFSNCYLYNKT 94
Query: 137 DTVYYRQAHAMKEL 150
                  A A+++L
Sbjct: 95  GDDIVVMAQALEKL 108

>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 = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/112 (25%), Positives = 46/112 (41%), Gaps = 17/112 (15%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN-A 135
           F +PVD  ++   DY+K+IK PMD+  I  +L    Y    +   D   M  N   +N  
Sbjct: 53  FRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKP 112
Query: 136 SDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRNKAISGPLNSH 187
           +D +       M +   K+F          +   SM    +   ++ P NSH
Sbjct: 113 TDDIV-----LMAQTLEKIF---------LQKVASMPQEEQELVVTIPKNSH 150

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD  ++   DYYK+IK PMD+  I ++L    Y    +   D   M  N   +N  
Sbjct: 46  FQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKP 105
Query: 137 DTVYYRQAHAMKEL 150
                  A A+++L
Sbjct: 106 GDDIVLMAEALEKL 119

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD  ++   DYYK+IK PMD+  I ++L    Y    +   D   M  N   +N  
Sbjct: 42  FQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKP 101
Query: 137 DTVYYRQAHAMKEL 150
                  A A+++L
Sbjct: 102 GDDIVLMAEALEKL 115

>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 = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD  ++   DYYK+IK PMD+  I ++L    Y    +   D   M  N   +N  
Sbjct: 62  FQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKP 121
Query: 137 DTVYYRQAHAMKEL 150
                  A A+++L
Sbjct: 122 GDDIVLMAEALEKL 135

>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 = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 79  FAKPVDGTEV--EDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS 136
           F +PVD  ++   DYYK+IK PMD+  I ++L    Y    +   D   M  N   +N  
Sbjct: 42  FQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKP 101
Query: 137 DTVYYRQAHAMKEL 150
                  A A+++L
Sbjct: 102 GDDIVLMAEALEKL 115

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 31/61 (50%)
Query: 90  DYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKE 149
           DYY+V+  P+DL KI +KL    Y  +     D  L+  NA  +   D+  Y+ A  + +
Sbjct: 43  DYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWD 102
Query: 150 L 150
           L
Sbjct: 103 L 103

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	202
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	9e-40
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	2e-39
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	2e-38
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	5e-37
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	7e-34
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	9e-34
2grc_A	129	Probable global transcription activator SNF2L4; br	1e-33
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	7e-33
3d7c_A	112	General control of amino acid synthesis protein 5;	8e-32
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	1e-31
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	2e-30
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	3e-24
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	2e-30
3uv4_A	158	Second bromodomain of human transcription initiat	3e-30
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	7e-30
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	1e-29
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	2e-23
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-29
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	4e-29
2dat_A	123	Possible global transcription activator SNF2L2; br	8e-29
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	1e-28
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-28
3p1f_A	119	CREB-binding protein; structural genomics consorti	5e-28
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	6e-28
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	1e-27
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-27
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	2e-27
4alg_A	154	Bromodomain-containing protein 2; signaling protei	7e-27
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	1e-26
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	7e-21
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	1e-26
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	2e-26
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	2e-26
2r10_A	361	Chromatin structure-remodeling complex protein RSC	6e-26
2r10_A	361	Chromatin structure-remodeling complex protein RSC	1e-17
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	8e-26
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	4e-25
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	2e-23
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-18
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	9e-15
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	2e-12
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	3e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05

>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 =  131 bits (331), Expect = 9e-40
 Identities = 35/110 (31%), Positives = 57/110 (51%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
               +L   L++L+ +D+  IF++PV  +EV DY   IK PMD   + + L    Y    
Sbjct: 7   GFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFD 66

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEA 167
           DFE D  L++ N + +NA DT++YR A  ++E    + R  +   E   +
Sbjct: 67  DFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMGS 116

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

 Score =  131 bits (330), Expect = 2e-39
 Identities = 39/109 (35%), Positives = 64/109 (58%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           P   +L  +LD+L+ +D  +IFA+PV   EV DY   IKHPMD + + ++L    Y+ L 
Sbjct: 13  PLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLH 72

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFE 166
           +FE D  L++ N M +NA DTV+YR A  +++    + R  + + ++  
Sbjct: 73  EFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVDSIG 121

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

 Score =  127 bits (321), Expect = 2e-38
 Identities = 33/114 (28%), Positives = 59/114 (51%)

Query: 51  MSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE 110
           M  +   P ++ L+ L+ +L+R+D    F+ PV       Y  +IKHPMD S + EK+  
Sbjct: 1   MEEVEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKN 60

Query: 111 GSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPEN 164
             YQ++ + + +  LM  NAM +N  +T+YY+ A  +     K+    + +  +
Sbjct: 61  NDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERLEHHH 114

>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 =  124 bits (312), Expect = 5e-37
 Identities = 34/102 (33%), Positives = 56/102 (54%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           P +++L+  L +L+R+D +  FA PV       Y  +IKHPMD   + +K+    Y+++ 
Sbjct: 13  PIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVT 72

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLK 159
           +F+ D  LM  NAM +N  DTVYY+ A  +     K+    +
Sbjct: 73  EFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKER 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 =  116 bits (292), Expect = 7e-34
 Identities = 33/109 (30%), Positives = 53/109 (48%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           P    +  +L  L+   +   F +PV+  EV DYY  IK PMDLS +  KL    YQ + 
Sbjct: 13  PHDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKME 72

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFE 166
           DF +D  L+  N   +N  +T YY+ A+ +++  N   + +       +
Sbjct: 73  DFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPEYSHLID 121

>3dai_A ATPase family AAA domain-containing protein 2; ancca, AAA+ nuclear coregulator cancer-associated Pro2000 protein, two AAA DOMA containing protein; 1.95A {Homo sapiens} PDB: 3lxj_A Length = 130

 Score =  115 bits (291), Expect = 9e-34
 Identities = 40/123 (32%), Positives = 61/123 (49%), Gaps = 6/123 (4%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
             R  L  +  RL     +++F KPVD  EV DY  VIK PMDLS +  K++   Y T+ 
Sbjct: 10  ELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVK 69

Query: 118 DFEHDIYLMLKNAMHFNAS----DTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRG 173
           D+  DI L+  NA+ +N      D +   +A A+++ A  + +  +   E+FE  C    
Sbjct: 70  DYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIK--EELDEDFEQLCEEIQ 127

Query: 174 RRR 176
             R
Sbjct: 128 ESR 130

>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 =  115 bits (290), Expect = 1e-33
 Identities = 23/99 (23%), Positives = 52/99 (52%)

Query: 66  LLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYL 125
             D    R   ++F +     E+ +YY++I+ P+D  KI E++    Y++L D E D+ L
Sbjct: 26  YKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVML 85

Query: 126 MLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPEN 164
           + +NA  FN   ++ Y  +  ++ +   + + ++ + ++
Sbjct: 86  LCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDS 124

>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 =  113 bits (285), Expect = 7e-33
 Identities = 32/101 (31%), Positives = 47/101 (46%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
            +  +  ++L  ++  +    F  PV+   V  Y KVIK PMD S I EKL+ G Y  L 
Sbjct: 13  KDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLE 72

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTL 158
            F  D+ L+  N   FN  D+   R  H M++   K +   
Sbjct: 73  TFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDT 113

>3d7c_A General control of amino acid synthesis protein 5; GCN5, bromodomain, structural genomics consortium, SGC, HOST-virus interaction, nucleus; 2.06A {Homo sapiens} SCOP: a.29.2.1 PDB: 1f68_A 1jm4_B* 1n72_A 1wug_A* 1wum_A* 1zs5_A* 2rnw_A* 2rnx_A* 3gg3_A Length = 112

 Score =  110 bits (277), Expect = 8e-32
 Identities = 31/99 (31%), Positives = 49/99 (49%)

Query: 61  KMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
             L  LL ++K   S   F +PV  +E  DYY+VI+ P+DL  +TE+L    Y T   F 
Sbjct: 10  TTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFV 69

Query: 121 HDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLK 159
            D+  ++ N   +N  D+ Y R A A+++      +   
Sbjct: 70  ADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEGG 108

>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 =  112 bits (281), Expect = 1e-31
 Identities = 29/103 (28%), Positives = 52/103 (50%)

Query: 57  MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTL 116
             + + L  +L  L+       F +PVD  +  DYY VIK PMDL+ + E++    Y+ L
Sbjct: 71  EKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKL 130

Query: 117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLK 159
            +F  D+  +  N  ++N SD+ +Y+ A  ++    +  +  K
Sbjct: 131 TEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 173

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A Length = 265

 Score =  111 bits (279), Expect = 2e-30
 Identities = 33/171 (19%), Positives = 67/171 (39%), Gaps = 5/171 (2%)

Query: 9   KSSDHKLARKRKTRPVHDLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLD 68
           K S  ++++        DL D  ++ +  K    +   N +            + +++  
Sbjct: 93  KHSLTQISQSM-----LDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQ 147

Query: 69  RLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLK 128
           ++        F  PV+   V DYYKVI +PMDL  I + +++  YQ+   F  D+ L+L 
Sbjct: 148 KMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILA 207

Query: 129 NAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRNKA 179
           N++ +N  ++ Y + A  +  +  +            E           + 
Sbjct: 208 NSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEE 258

>3uv5_A Transcription initiation factor TFIID subunit 1; tandem bromodomain, TAF1, cell cycle gene 1 protein, TBP-ASS factor 250 kDa; 2.03A {Homo sapiens} PDB: 1eqf_A Length = 265

 Score = 95.4 bits (237), Expect = 3e-24
 Identities = 23/105 (21%), Positives = 53/105 (50%)

Query: 61  KMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
            +L+ +++ ++   +   F  PV+   V+DYYK+I  PMDL  + E + +  Y +  +F 
Sbjct: 17  SILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFR 76

Query: 121 HDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENF 165
             + L++KN+  +N       + + +M +L ++  +  ++     
Sbjct: 77  EHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARL 121

>3nxb_A CAT eye syndrome critical region protein 2; structural genomics consortium, SGC, CECR2, CAT eye syndrome chromosome region candidate 2, bromodomain; 1.83A {Homo sapiens} Length = 116

 Score =  107 bits (268), Expect = 2e-30
 Identities = 27/99 (27%), Positives = 51/99 (51%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
            +   +  +LD +K       F +PVD +   +YY++IK PMD+S + +KLN G Y T  
Sbjct: 16  DDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKE 75

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFR 156
           +F +D+  M +N   +N   + Y + +  ++   ++   
Sbjct: 76  EFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMM 114

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

 Score =  108 bits (270), Expect = 3e-30
 Identities = 30/149 (20%), Positives = 60/149 (40%), Gaps = 10/149 (6%)

Query: 41  DGDHHTNAVDMSSIIAMPERK----------MLDLLLDRLKRRDSYKIFAKPVDGTEVED 90
              HH++ VD+ +     +            + +++  ++        F  PV+   V D
Sbjct: 3   HHHHHSSGVDLGTENLYFQSMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPD 62

Query: 91  YYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKEL 150
           YYKVI +PMDL  I + +++  YQ+   F  D+ L+L N++ +N  ++ Y + A  +  +
Sbjct: 63  YYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNV 122

Query: 151 ANKLFRTLKNDPENFEAACSMRGRRRNKA 179
             +            E           + 
Sbjct: 123 CYQTLTEYDEHLTQLEKDICTAKEAALEE 151

>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 =  105 bits (265), Expect = 7e-30
 Identities = 26/111 (23%), Positives = 50/111 (45%), Gaps = 4/111 (3%)

Query: 59  ERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGD 118
            +K    L++ + + +  + F +PVD  E  DY  +I  PMD   + E L+ G+Y +  +
Sbjct: 11  WKKQCKELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLE 70

Query: 119 FEHDIYLMLKNAMHFNASD-TVYYRQAHAMKELANKLFRTLKNDPENFEAA 168
           F  DI L+  NA  +  +  +  Y     +  L  +  + +     +F+  
Sbjct: 71  FCKDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKI---SSDFKIG 118

>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 (276), Expect = 1e-29
 Identities = 27/135 (20%), Positives = 53/135 (39%)

Query: 44  HHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSK 103
              N +            + +++  ++        F  PV+   V DYYKVI +PMDL  
Sbjct: 156 KAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLET 215

Query: 104 ITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE 163
           I + +++  YQ+   F  D+ L+L N++ +N  ++ Y + A  +  +  +          
Sbjct: 216 IRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLT 275

Query: 164 NFEAACSMRGRRRNK 178
             E           +
Sbjct: 276 QLEKDICTAKEAALE 290

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

 Score = 93.9 bits (233), Expect = 2e-23
 Identities = 23/105 (21%), Positives = 53/105 (50%)

Query: 61  KMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
            +L+ +++ ++   +   F  PV+   V+DYYK+I  PMDL  + E + +  Y +  +F 
Sbjct: 50  SILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFR 109

Query: 121 HDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENF 165
             + L++KN+  +N       + + +M +L ++  +  ++     
Sbjct: 110 EHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARL 154

>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 =  104 bits (262), Expect = 2e-29
 Identities = 29/110 (26%), Positives = 52/110 (47%), Gaps = 6/110 (5%)

Query: 58  PERKMLDLLLDRLKR------RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEG 111
           P ++ L+ + + +K       R    IF +    +E+ DYY  IK PMD+ KI   +   
Sbjct: 15  PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMAN 74

Query: 112 SYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKND 161
            YQ +     D  +M  NA  +N  +++ Y+ A  + ++  +  R L+ D
Sbjct: 75  KYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLEGD 124

>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 =  104 bits (261), Expect = 4e-29
 Identities = 24/107 (22%), Positives = 51/107 (47%), Gaps = 1/107 (0%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
             +K  + LL+ + + +  + F +PVD  E  DY  +I  PMD + + E L  G+Y++  
Sbjct: 21  AWKKQCEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPM 80

Query: 118 DFEHDIYLMLKNAMHFNASD-TVYYRQAHAMKELANKLFRTLKNDPE 163
           +   D+ L+  N+  +  S  +  Y  +  +     +   ++ +D +
Sbjct: 81  ELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSDYK 127

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

 Score =  103 bits (258), Expect = 8e-29
 Identities = 25/107 (23%), Positives = 53/107 (49%), Gaps = 5/107 (4%)

Query: 60  RKMLDLLLDRLKRRDSYK-----IFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQ 114
           ++M  ++   +  +DS       +F +     E+ +YY++I+ P+D  KI E++    Y+
Sbjct: 16  KQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYR 75

Query: 115 TLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKND 161
           +LGD E D+ L+  NA  FN   +  Y  +  ++ +     ++  + 
Sbjct: 76  SLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQSGPSS 122

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

 Score =  102 bits (257), Expect = 1e-28
 Identities = 33/124 (26%), Positives = 50/124 (40%), Gaps = 7/124 (5%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
             R  L  +  RL     + IF+KPV      DY +VIK PMDLS +  K+++ +Y T  
Sbjct: 12  ELRLFLRDVTKRLATDKRFNIFSKPVS-----DYLEVIKEPMDLSTVITKIDKHNYLTAK 66

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAM-KELANKLFRTLKNDP-ENFEAACSMRGRR 175
           DF  DI L+  NA+ +N       +        L +     +  +    F   C      
Sbjct: 67  DFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKES 126

Query: 176 RNKA 179
              +
Sbjct: 127 GPSS 130

>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 =  103 bits (258), Expect = 2e-28
 Identities = 26/107 (24%), Positives = 48/107 (44%), Gaps = 3/107 (2%)

Query: 60  RKMLDLLLDRLKRRDSYK---IFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTL 116
           + + +++L+  +     +   +F       +  DYYK+I  PMDL  I   +    Y   
Sbjct: 30  KILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGE 89

Query: 117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE 163
                D+ LM +NA H+N   +  Y  AH +++L  +  + L   P+
Sbjct: 90  EGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKELGPLPD 136

>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 =  101 bits (253), Expect = 5e-28
 Identities = 32/105 (30%), Positives = 53/105 (50%), Gaps = 3/105 (2%)

Query: 58  PERKMLDLLLDRLKRRDSYKI-FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQ 114
             R+ L   L+ L R+D   + F +PVD     + DY+ ++K+PMDLS I  KL+ G YQ
Sbjct: 11  ELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQ 70

Query: 115 TLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLK 159
               +  D++LM  NA  +N   +  Y+    + E+  +    + 
Sbjct: 71  EPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVM 115

>3iu5_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo0ID, PBRM1, BRG associated factor 180, structural genomics, SGC; 1.63A {Homo sapiens} Length = 116

 Score =  100 bits (252), Expect = 6e-28
 Identities = 24/109 (22%), Positives = 43/109 (39%), Gaps = 6/109 (5%)

Query: 61  KMLDLLLDRLKR------RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQ 114
            +   L + ++       R   ++F +        DYY+V+  P+DL KI +KL    Y 
Sbjct: 8   AVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYD 67

Query: 115 TLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE 163
            +     D  L+  NA  +   D+  Y+ A  + +L  +         E
Sbjct: 68  DVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQKGE 116

>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 =  100 bits (250), Expect = 1e-27
 Identities = 31/111 (27%), Positives = 49/111 (44%), Gaps = 5/111 (4%)

Query: 58  PERKMLDLLLDRLKRRDSYKI---FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGS 112
            + K    +L  +  +        F KPVD     + DY  +IKHPMD+S I  KL    
Sbjct: 9   EQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESRE 68

Query: 113 YQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE 163
           Y+   +F  D+ LM  N   +N  D      A  ++++    F  + ++PE
Sbjct: 69  YRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPE 119

>3k2j_A Protein polybromo-1; PB1, polybromo 1 isoform 1, BAF180, polybromo01D, PBRM1, BRG associated factor 180, structural genomics consortium, SGC; 2.20A {Homo sapiens} Length = 130

 Score = 99.8 bits (249), Expect = 2e-27
 Identities = 29/127 (22%), Positives = 55/127 (43%), Gaps = 9/127 (7%)

Query: 43  DHHTNAVDMSSIIAMPERKMLDLLLDRLKR------RDSYKIFAKPVDGTEVEDYYKVIK 96
            HH++ VD+ +            L D ++       +   + F       +  DYY+ IK
Sbjct: 5   HHHSSGVDLGT---ENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIK 61

Query: 97  HPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFR 156
            P+ L +I  KL    Y+TL   E D+ LM +NA  +N  ++  Y++   ++++     +
Sbjct: 62  MPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKK 121

Query: 157 TLKNDPE 163
            L    +
Sbjct: 122 ELARRDD 128

>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 = 99.7 bits (249), Expect = 2e-27
 Identities = 27/104 (25%), Positives = 45/104 (43%), Gaps = 2/104 (1%)

Query: 60  RKMLDLLLDRLKRRDSYKIFAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           + +L ++L  L +      F +PVD     + DYYK+IK PMD+  I ++L    Y    
Sbjct: 23  QYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQ 82

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKND 161
           +   D   M  N   +N         A A+++L  +    L  +
Sbjct: 83  ECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTE 126

>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 = 99.0 bits (247), Expect = 7e-27
 Identities = 21/119 (17%), Positives = 46/119 (38%), Gaps = 2/119 (1%)

Query: 60  RKMLDLLLDRLKRRDSYKIFAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           + +  +++  L +      F +PVD     + DY+K+IK PMD+  I  +L    Y    
Sbjct: 34  QYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAAS 93

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRR 176
           +   D   M  N   +N         A  ++++  +   ++  + +           ++
Sbjct: 94  ECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQELVVTIPKNSHKK 152

>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 =  102 bits (255), Expect = 1e-26
 Identities = 31/150 (20%), Positives = 58/150 (38%)

Query: 7   TRKSSDHKLARKRKTRPVHDLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMLDLL 66
            + S    +  + +     +L  N +     K     +    VD +              
Sbjct: 112 VKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSP 171

Query: 67  LDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLM 126
            +   +    + F + VD  E+ +YY+++  PM LS + + L  G Y  + DF  D+ L+
Sbjct: 172 KNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLV 231

Query: 127 LKNAMHFNASDTVYYRQAHAMKELANKLFR 156
            +NA  FN    + Y+ A  +    N L +
Sbjct: 232 FQNAHIFNDPSALIYKDATTLTNYFNYLIQ 261

>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 = 87.1 bits (215), Expect = 7e-21
 Identities = 25/120 (20%), Positives = 48/120 (40%), Gaps = 3/120 (2%)

Query: 60  RKMLDLLLDRLKR--RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
            + +   LD L    +D +K F K         YY  I+ PM +++I  +  E       
Sbjct: 30  NRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYE-YEDGPS 88

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRN 177
           +F  D+ L+ KN   +N  D++  + +  +  L        KN   N+     ++ +  +
Sbjct: 89  NFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLH 148

>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 = 97.4 bits (243), Expect = 1e-26
 Identities = 33/115 (28%), Positives = 61/115 (53%), Gaps = 10/115 (8%)

Query: 60  RKMLDLLLDRLKR------RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSY 113
           +++L+ LL+ +        R   ++F K     +  DYY +IK P+DL  I +++  GSY
Sbjct: 10  KEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSY 69

Query: 114 QTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAA 168
           +++     DI L+ KNA  +N   +  ++ A+++K    K+F   K + E+ E A
Sbjct: 70  KSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIK----KIFYMKKAEIEHHEMA 120

>2ouo_A HUNK1 protein, bromodomain-containing protein 4; BRD4, structural genomics consortium, SGC, signaling protein; 1.89A {Homo sapiens} PDB: 2yem_A* Length = 130

 Score = 97.4 bits (243), Expect = 2e-26
 Identities = 29/109 (26%), Positives = 47/109 (43%), Gaps = 5/109 (4%)

Query: 58  PERKMLDLLLDRLKRRDSYKI---FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGS 112
            + K    +L  +  +        F KPVD     + DY  +IKHPMD+S I  KL    
Sbjct: 22  EQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE 81

Query: 113 YQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKND 161
           Y+   +F  D+ LM  N   +N  D      A  ++++    F  + ++
Sbjct: 82  YRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE 130

>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 = 97.0 bits (242), Expect = 2e-26
 Identities = 18/106 (16%), Positives = 42/106 (39%), Gaps = 2/106 (1%)

Query: 60  RKMLDLLLDR--LKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           +++ D ++      R+             +  DYY+ I  P+DL  I +++  G Y+T+ 
Sbjct: 15  KEICDGIISYKDSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVE 74

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE 163
            F+ D+  + +NA  +    +   R    +++             +
Sbjct: 75  AFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQID 120

>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 =  101 bits (252), Expect = 6e-26
 Identities = 30/132 (22%), Positives = 53/132 (40%)

Query: 25  HDLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVD 84
            +L  N +     K     +    VD +               +   +    + F + VD
Sbjct: 180 KNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVD 239

Query: 85  GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQA 144
             E+ +YY+++  PM LS + + L  G Y  + DF  D+ L+ +NA  FN    + Y+ A
Sbjct: 240 KDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDA 299

Query: 145 HAMKELANKLFR 156
             +    N L +
Sbjct: 300 TTLTNYFNYLIQ 311

>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 = 78.7 bits (193), Expect = 1e-17
 Identities = 25/120 (20%), Positives = 48/120 (40%), Gaps = 3/120 (2%)

Query: 60  RKMLDLLLDRLKR--RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
            + +   LD L    +D +K F K         YY  I+ PM +++I  +  E       
Sbjct: 80  NRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEY-EDGPS 138

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRRN 177
           +F  D+ L+ KN   +N  D++  + +  +  L        KN   N+     ++ +  +
Sbjct: 139 NFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLH 198

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

 Score = 95.9 bits (239), Expect = 8e-26
 Identities = 31/107 (28%), Positives = 49/107 (45%), Gaps = 3/107 (2%)

Query: 59  ERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKL--NEGSYQTL 116
           +++  + LL  L   +    F  PV    V DYYK+IK+PMDLS I ++L  +   Y   
Sbjct: 21  DKRKCERLLLFLYCHEMSLAFQDPVP-LTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKP 79

Query: 117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE 163
            DF  D  L+ +N   FN  D+        ++    +L + L  +  
Sbjct: 80  EDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPEKR 126

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

 Score = 94.9 bits (236), Expect = 4e-25
 Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 2/105 (1%)

Query: 59  ERKMLDLLLDRLKRRDSYKIFAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTL 116
              + + L+  L + +   IF K VD       DYY VIK+PM  S I  KL +G Y   
Sbjct: 22  WYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYP 81

Query: 117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKND 161
            +F  D+ L+  N   +N S++V       ++   N     +  +
Sbjct: 82  SEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFNNQLIVMGYN 126

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A Length = 184

 Score = 91.2 bits (226), Expect = 2e-23
 Identities = 31/147 (21%), Positives = 52/147 (35%), Gaps = 3/147 (2%)

Query: 14  KLARKRKTRPVHDLVDNDVEIQVRKTGDGDHHTNAVDMSSIIAMPERKMLDLLLDRLKRR 73
                         +              +      +    +   +++  + LL  L   
Sbjct: 37  NFPSGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCH 96

Query: 74  DSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKL--NEGSYQTLGDFEHDIYLMLKNAM 131
           +    F  PV    V DYYK+IK+PMDLS I ++L  +   Y    DF  D  L+ +N  
Sbjct: 97  EMSLAFQDPVP-LTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCA 155

Query: 132 HFNASDTVYYRQAHAMKELANKLFRTL 158
            FN  D+        ++    +L + L
Sbjct: 156 EFNEPDSEVANAGIKLENYFEELLKNL 182

>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 = 78.0 bits (192), Expect = 1e-18
 Identities = 18/115 (15%), Positives = 47/115 (40%), Gaps = 2/115 (1%)

Query: 55  IAMPERKMLDLLLDRLK--RRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGS 112
           + +  ++++  L   +   + D  + ++  +      D     K P+    I + +    
Sbjct: 4   VTLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPNFPNKPPLTFDIIRKNVENNR 63

Query: 113 YQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEA 167
           Y+ L  F+  ++ +L+ A   N +D+  Y  A  +++   K+   L  + E   +
Sbjct: 64  YRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCKNGEILLS 118

>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 = 68.8 bits (167), Expect = 9e-15
 Identities = 28/87 (32%), Positives = 39/87 (44%), Gaps = 4/87 (4%)

Query: 70  LKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE---GSYQTLGDFEHDIYLM 126
           L   +    F +PV    + +YYK+IK PMDLS + +KL +     YQ   DF  D+ L+
Sbjct: 93  LYCHELSIEFQEPVP-ASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLI 151

Query: 127 LKNAMHFNASDTVYYRQAHAMKELANK 153
            KN   FN    V    A   +     
Sbjct: 152 FKNCERFNEMMKVVQVYADTQEINLKA 178

>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 = 62.3 bits (150), Expect = 2e-12
 Identities = 11/64 (17%), Positives = 30/64 (46%)

Query: 91  YYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKEL 150
                + P+DL  +  K+++G+Y ++ +F  DI  +++ A++ +       +    +K  
Sbjct: 97  LRYRQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSF 156

Query: 151 ANKL 154
             + 
Sbjct: 157 FIRQ 160

>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 = 56.0 bits (134), Expect = 3e-10
 Identities = 13/119 (10%), Positives = 36/119 (30%), Gaps = 6/119 (5%)

Query: 43  DHHTNAVDMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLS 102
               ++  + + ++   ++  + +L  L   +  +   +    T+           +DL+
Sbjct: 61  LDGADSTGVVAKLSPANQRKCERVLLALFCHEPCRPLHQLA--TDSTFSLDQPGGTLDLT 118

Query: 103 KITEKLNE---GSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTL 158
            I  +L E     Y +  +F  D+  M K             +    ++          
Sbjct: 119 LIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLTEDKAD-VQSIIGLQRFFETRMNEA 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 = 41.8 bits (97), Expect = 9e-05
 Identities = 29/187 (15%), Positives = 61/187 (32%), Gaps = 61/187 (32%)

Query: 8   RKSSDHKLARKRKTRPVHDL-------VDNDVEI--------QVRKTGDGD--------- 43
            K S  +   K  T  +  +       ++N+  +         + KT D D         
Sbjct: 412 HKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471

Query: 44  -------HHTNAVDMSSIIAMPERKMLDL-LLDRLKRRDSYKIFAKPVDGTEVED--YYK 93
                  HH   ++    + +     LD   L++  R DS    A       ++   +YK
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYK 531

Query: 94  VIKHPMDLSKITEKLNEGSYQ----TLGDF----EHDIYL-----MLKNAMHFNASDTVY 140
              +      I +  N+  Y+     + DF    E ++       +L+ A+     + ++
Sbjct: 532 --PY------ICD--NDPKYERLVNAILDFLPKIEENLICSKYTDLLRIAL-MAEDEAIF 580

Query: 141 ---YRQA 144
              ++Q 
Sbjct: 581 EEAHKQV 587

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	202
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	99.97
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	99.97
3d7c_A	112	General control of amino acid synthesis protein 5;	99.97
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.97
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.97
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.97
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.97
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.97
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	99.97
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.97
2dat_A	123	Possible global transcription activator SNF2L2; br	99.97
2grc_A	129	Probable global transcription activator SNF2L4; br	99.97
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.97
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.97
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	99.97
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	99.97
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.96
3uv4_A	158	Second bromodomain of human transcription initiat	99.96
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.96
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.96
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.96
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.96
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.96
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.96
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.96
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.96
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	99.95
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.95
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.95
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.94
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.94
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.94
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.93
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.93
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.93
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.93
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.9
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.9
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.89
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.87
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.84
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	99.68

>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=99.97  E-value=3.1e-31  Score=196.08  Aligned_cols=107  Identities=30%  Similarity=0.436  Sum_probs=102.2

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      .....+...|..||+.|..++.+++|..||++..+||||++|++||||++|++||+++.|.++++|..||+|||.||+.|
T Consensus         9 ~~~~~~~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~y   88 (117)
T 3g0l_A            9 RDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETF   88 (117)
T ss_dssp             CCCTTHHHHHHHHHHHHHTSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhCCCchhhcCcCChhhcCChHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            44455789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhhC
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTLKN  160 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~~~  160 (202)
                      |+++|.++.+|..|+..|++.|+++..
T Consensus        89 N~~~s~~~~~A~~L~~~f~~~~~~~~~  115 (117)
T 3g0l_A           89 NEDDSDIGRAGHNMRKYFEKKWTDTFK  115 (117)
T ss_dssp             SCSSSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999998864

>2d9e_A Peregrin; four-helix bundle, transcription activator, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.97  E-value=3.7e-31  Score=196.76  Aligned_cols=108  Identities=31%  Similarity=0.548  Sum_probs=103.4

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ....|+...|..||+.|.+++.+++|..||++..+|+||++|++||||++|++||+++.|.++++|..||+|||.||+.|
T Consensus         3 ~~~~pl~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~y   82 (121)
T 2d9e_A            3 SGSSGFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKY   82 (121)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHCSSCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHcCCccHhhCCcCCccccCCHHHHcCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            44678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      |+++|.++.+|..|+..|++++++++..
T Consensus        83 N~~~s~~~~~A~~L~~~~~~~l~~~~~~  110 (121)
T 2d9e_A           83 NAKDTIFYRAAVRLREQGGAVLRQARRQ  110 (121)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999988653

>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=99.97  E-value=5e-31  Score=193.53  Aligned_cols=104  Identities=30%  Similarity=0.418  Sum_probs=100.3

Q ss_pred             CcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcC
Q 048123           56 AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA  135 (202)
Q Consensus        56 ~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~  135 (202)
                      ...+...|..||+.|.+++.+++|..||++..+|+||++|++||||+||++||++|.|.++++|..||+|||.||+.||+
T Consensus         5 ~~~l~~~~~~il~~l~~~~~~~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~   84 (112)
T 3d7c_A            5 PDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNP   84 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHcCCCchhhcCCCCcccccCHHHHccCCcCHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHHHCC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          136 SDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       136 ~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      ++|.++.+|..|+..|++.++++.
T Consensus        85 ~~s~~~~~A~~L~~~f~~~~~~~~  108 (112)
T 3d7c_A           85 PDSEYCRCASALEKFFYFKLKEGG  108 (112)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCC
Confidence            999999999999999999999874

>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=99.97  E-value=2.5e-31  Score=205.36  Aligned_cols=118  Identities=18%  Similarity=0.316  Sum_probs=107.0

Q ss_pred             cCCCcCCcHHHHHHHHHHHHHHcCCCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 048123           50 DMSSIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLML  127 (202)
Q Consensus        50 ~~~~~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~  127 (202)
                      ..+......+..+|..||+.|.+++.+++|..||++.  .+|+||++|++||||++|++||+++.|.++++|+.||+|||
T Consensus        24 ~~~~r~t~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif  103 (154)
T 4alg_A           24 KKPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMF  103 (154)
T ss_dssp             --CCCCBHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHHHHHHHHhCcCchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence            3444555667888999999999999999999999988  69999999999999999999999999999999999999999


Q ss_pred             HHHhhhcCCCCHHHHHHHHHHHHHHHHHHHhhCCCchHHH
Q 048123          128 KNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEA  167 (202)
Q Consensus       128 ~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~~  167 (202)
                      .||++||++++.++.+|..|+..|++.|+++..+......
T Consensus       104 ~Na~~YN~~~s~i~~~A~~L~~~f~~~~~~l~~~~~e~~~  143 (154)
T 4alg_A          104 TNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQELVV  143 (154)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHTTSCSSCCBCCC
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCchhccccC
Confidence            9999999999999999999999999999999776655443

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

Probab=99.97  E-value=6.8e-31  Score=194.16  Aligned_cols=107  Identities=30%  Similarity=0.559  Sum_probs=102.1

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ....++...|..||+.|.+++.+++|..||++..+|+||++|++||||++|++||++|.|.++++|..||+|||.||+.|
T Consensus         4 ~~~~~l~~~l~~il~~L~~~~~~~~F~~PVd~~~~pdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Li~~Na~~y   83 (117)
T 2i7k_A            4 VEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIY   83 (117)
T ss_dssp             TTHHHHHHHHHHHHHHHHTSSGGGTSSSCCCTTTSSSHHHHCSCCCCHHHHHHHHTTTSCCSHHHHHHHHHHHHHHHHHT
T ss_pred             cchHHHHHHHHHHHHHHHhCcccHHhcCCCCccccCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            34568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhhC
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTLKN  160 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~~~  160 (202)
                      |+++|.++.+|..|+..|++++..+.-
T Consensus        84 N~~~s~i~~~A~~L~~~f~~~~~~~~~  110 (117)
T 2i7k_A           84 NKPETIYYKAAKKLLHSGMKILSQERL  110 (117)
T ss_dssp             SCSSSSHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999987743

>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=99.97  E-value=1.7e-30  Score=194.00  Aligned_cols=109  Identities=28%  Similarity=0.492  Sum_probs=102.8

Q ss_pred             CcCCcHHHHHHHHHHHHHHc------CCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 048123           53 SIIAMPERKMLDLLLDRLKR------RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLM  126 (202)
Q Consensus        53 ~~~~~~~~~~~~~il~~l~~------~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li  126 (202)
                      +....++.+.|..||+.|..      ++.+++|..||+...+|+||++|++||||++|++||+++.|.++++|..||+||
T Consensus        10 ~k~~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li   89 (124)
T 3mb4_A           10 SKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMM   89 (124)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHH
T ss_pred             cccChHHHHHHHHHHHHHHhHhcccCCcccHHhhcCCCccccCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            35577899999999999998      566799999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          127 LKNAMHFNASDTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       127 ~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      |.||+.||+++|.++.+|..|+..|++.|+++..+
T Consensus        90 ~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~d  124 (124)
T 3mb4_A           90 FNNACTYNEPESLIYKDALVLHKVLLETRRDLEGD  124 (124)
T ss_dssp             HHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999998653

>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=99.97  E-value=2.9e-30  Score=193.42  Aligned_cols=107  Identities=25%  Similarity=0.377  Sum_probs=100.5

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAM  131 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~  131 (202)
                      .....++.+|..||+.|.+++.+++|..||++.  .+||||++|++||||++|++||+++.|.++++|..||+|||+||+
T Consensus        17 r~~~~l~~~~~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~   96 (127)
T 2oss_A           17 RQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCY   96 (127)
T ss_dssp             CCCHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHhCccchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence            445567888999999999999999999999975  799999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHHHhhC
Q 048123          132 HFNASDTVYYRQAHAMKELANKLFRTLKN  160 (202)
Q Consensus       132 ~yN~~~s~~~~~A~~L~~~~~~~~~~~~~  160 (202)
                      +||+++|.++.+|..|+..|++.++++..
T Consensus        97 ~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  125 (127)
T 2oss_A           97 IYNKPGDDIVLMAEALEKLFLQKINELPT  125 (127)
T ss_dssp             HHSCTTCHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            99999999999999999999999988754

>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=99.97  E-value=1.3e-30  Score=193.82  Aligned_cols=102  Identities=32%  Similarity=0.574  Sum_probs=98.7

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      +....|..||+.|..++.+++|..||++..+|+||++|++||||++|++||+++.|.++++|..||+|||.||+.||+++
T Consensus        13 ~~~~~~~~il~~l~~~~~a~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~   92 (121)
T 1e6i_A           13 PHDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGEN   92 (121)
T ss_dssp             TTHHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHHHcCCCchhhCCCCChhhCcCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHhh
Q 048123          138 TVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      |.++.+|..|+..|++.++++.
T Consensus        93 s~i~~~A~~L~~~f~~~~~~~p  114 (121)
T 1e6i_A           93 TSYYKYANRLEKFFNNKVKEIP  114 (121)
T ss_dssp             SHHHHHHHHHHHHHHHHHHTSG
T ss_pred             CHHHHHHHHHHHHHHHHHHHcc
Confidence            9999999999999999998874

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

Probab=99.97  E-value=2.1e-30  Score=196.19  Aligned_cols=114  Identities=34%  Similarity=0.646  Sum_probs=107.2

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ....++...|..||+.|..++.+++|..||++..+||||++|++||||++|++||+++.|.++++|..||+|||.||+.|
T Consensus         9 ~~~~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~y   88 (135)
T 3rcw_A            9 LRLTPLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKY   88 (135)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCTTCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             hcchHHHHHHHHHHHHHHhCCcchhhcCCCChhhcCCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhhCCCchHHH
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTLKNDPENFEA  167 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~~  167 (202)
                      |+++|.+|++|..|+..|+++++++....+....
T Consensus        89 N~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~~  122 (135)
T 3rcw_A           89 NARDTVFYRAAVRLRDQGGVVLRQARREVDSIGL  122 (135)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence            9999999999999999999999999776655444

>3hme_A Bromodomain-containing protein 9; BRD9, bromodomain containing 9 isoform 1, LAVS3040, rhabdomyosarcoma antigen MU-RMS-40.8; 2.23A {Homo sapiens}

Probab=99.97  E-value=2.7e-30  Score=192.59  Aligned_cols=105  Identities=32%  Similarity=0.575  Sum_probs=99.8

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ....|+...|..||+.|..++.+++|..||++..+||||++|++||||++|++||+++.|.++++|..||+|||.||+.|
T Consensus         9 ~~~~p~~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~y   88 (123)
T 3hme_A            9 NESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTY   88 (123)
T ss_dssp             --CCHHHHHHHHHHHHHHTTCTTCSSSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHhCCccHhhcCCCChhhccCHHHHCCCCCCHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHH
Confidence            34568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHh
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      |+++|.++++|..|+..|.+.+.+.
T Consensus        89 N~~~s~~~~~A~~L~~~~~~~~~~~  113 (123)
T 3hme_A           89 NRPDTVYYKLAKKILHAGFKMMSKE  113 (123)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHTCHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999988755

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

Probab=99.97  E-value=4e-30  Score=191.71  Aligned_cols=106  Identities=23%  Similarity=0.440  Sum_probs=99.7

Q ss_pred             cCCcHHHHHHHHHHHHHHcCC------CcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 048123           54 IIAMPERKMLDLLLDRLKRRD------SYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLML  127 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~------~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~  127 (202)
                      .....+.+.|..||+.|..+.      .+++|..||+...+|+||++|++||||++|++||+++.|.++++|..||+|||
T Consensus         9 ~~~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~   88 (123)
T 2dat_A            9 PNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLC   88 (123)
T ss_dssp             CCCHHHHHHHHHHHHHHHHCBCSSSCBSGGGGTSCCCTTTSCHHHHHCSSCCCHHHHHHHHTTTCCCSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhhhcccCCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence            345667899999999999875      58999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          128 KNAMHFNASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       128 ~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      .||+.||+++|.++.+|..|+..|++.++++.
T Consensus        89 ~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~p  120 (123)
T 2dat_A           89 HNAQTFNLEGSQIYEDSIVLQSVFKSARQSGP  120 (123)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHSSS
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHcC
Confidence            99999999999999999999999999998764

>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=99.97  E-value=3.1e-30  Score=193.75  Aligned_cols=113  Identities=20%  Similarity=0.435  Sum_probs=102.8

Q ss_pred             cCCcHHHHHHHHHHHHHHcCC-------CcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 048123           54 IIAMPERKMLDLLLDRLKRRD-------SYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLM  126 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~-------~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li  126 (202)
                      .....+.+.|..||+.|.++.       .+++|..||+...+|+||++|++||||+||++||.++.|.++++|..||+||
T Consensus         7 ~~~~~l~~~~~~il~~l~~~~d~~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li   86 (129)
T 2grc_A            7 PNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLL   86 (129)
T ss_dssp             CCCHHHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHhcccccccCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            445667899999999999875       5799999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHhhCCCchHH
Q 048123          127 LKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFE  166 (202)
Q Consensus       127 ~~Na~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~  166 (202)
                      |.||++||+++|.++.+|..|+..|++.++++....+..+
T Consensus        87 ~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~~~~~~  126 (129)
T 2grc_A           87 CQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSEG  126 (129)
T ss_dssp             HHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHHTC---
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccCCCcccc
Confidence            9999999999999999999999999999999976655433

>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=99.97  E-value=4.3e-30  Score=189.66  Aligned_cols=101  Identities=27%  Similarity=0.465  Sum_probs=97.1

Q ss_pred             cHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           57 MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      .++.+.|..||+.|..++.+++|..||++..+|+||++|++||||++|++||+++.|.++++|..||+|||.||+.||++
T Consensus        15 ~~~~~~~~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~   94 (116)
T 3nxb_A           15 DDDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGE   94 (116)
T ss_dssp             CCHHHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHhCCCcHhhcCcCChhhccChHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            34688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q 048123          137 DTVYYRQAHAMKELANKLFRT  157 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~  157 (202)
                      +|.++.+|..|+..|++.|.+
T Consensus        95 ~s~~~~~A~~L~~~f~~~~~k  115 (116)
T 3nxb_A           95 SSEYTKMSDNLERCFHRAMMK  115 (116)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999998863

>3q2e_A Bromodomain and WD repeat-containing protein 1; structural genomics consortium, SGC, cell cycle progression, signal transduction, apoptosis; 1.74A {Homo sapiens}

Probab=99.97  E-value=5.1e-30  Score=191.12  Aligned_cols=107  Identities=24%  Similarity=0.435  Sum_probs=100.5

Q ss_pred             CCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           55 IAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        55 ~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      ....+++.|..||+.|..++.+++|..||++..+|+||++|++||||++|++||+++.|.++++|..||+|||.||+.||
T Consensus         7 ~~~~~~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN   86 (123)
T 3q2e_A            7 VESNWKKQCKELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYT   86 (123)
T ss_dssp             ---CHHHHHHHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHHHHhCCCcHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC-CCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          135 AS-DTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       135 ~~-~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      ++ +|.++.+|..|+..|++.++++..+
T Consensus        87 ~~~~s~i~~~A~~L~~~f~~~~~~~~~~  114 (123)
T 3q2e_A           87 PNKRSKIYSMTLRLSALFEEKMKKISSD  114 (123)
T ss_dssp             CCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            96 9999999999999999999988644

>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=99.97  E-value=2.7e-30  Score=191.79  Aligned_cols=109  Identities=28%  Similarity=0.470  Sum_probs=101.0

Q ss_pred             CCcHHHHHHHHHHHHHHcCCC---cccccCCCCcCC--ccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Q 048123           55 IAMPERKMLDLLLDRLKRRDS---YKIFAKPVDGTE--VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKN  129 (202)
Q Consensus        55 ~~~~~~~~~~~il~~l~~~~~---~~~F~~pv~~~~--~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  129 (202)
                      ....+.+.|..||..|..++.   +++|..||++..  +|+||++|++||||++|++||+++.|.++++|..||+|||.|
T Consensus         6 ~~~~~l~~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~N   85 (120)
T 3jvl_A            6 KISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSN   85 (120)
T ss_dssp             SSCHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHH
Confidence            445678999999999999887   899999999988  999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCCCHHHHHHHHHHHHHHHHHHHhhCCCc
Q 048123          130 AMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE  163 (202)
Q Consensus       130 a~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~~~  163 (202)
                      |++||+++|.++.+|..|+..|++.|+++..+++
T Consensus        86 a~~yN~~~s~~~~~A~~L~~~f~~~~~~~p~~~~  119 (120)
T 3jvl_A           86 CYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPE  119 (120)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHTTCCC---
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            9999999999999999999999999999876543

>3mb3_A PH-interacting protein; PHIP, pleckstrin homology domain interacting protein, DCAF14 DDB1 and CUL4 associated factor 14, SGC; 2.25A {Homo sapiens}

Probab=99.97  E-value=8.8e-30  Score=192.73  Aligned_cols=107  Identities=22%  Similarity=0.389  Sum_probs=101.8

Q ss_pred             CCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           55 IAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        55 ~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      ....+.+.|..||+.|..++.+++|..||++..+||||++|++||||++|++||+++.|.++++|..||+|||.||+.||
T Consensus        18 ~~~~l~~~~~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN   97 (135)
T 3mb3_A           18 DIQAWKKQCEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYT   97 (135)
T ss_dssp             CSSTHHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHHHHhCCCChhhcCCCChhhCCCHHHHhCCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC-CCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          135 AS-DTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       135 ~~-~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      ++ +|.++.+|..|+..|++.+..+..+
T Consensus        98 ~~~~s~i~~~A~~L~~~f~~~~~~~~~~  125 (135)
T 3mb3_A           98 PSKRSRIYSMSLRLSAFFEEHISSVLSD  125 (135)
T ss_dssp             CCTTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            98 8999999999999999999987443

>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=99.96  E-value=1.4e-29  Score=186.89  Aligned_cols=105  Identities=21%  Similarity=0.357  Sum_probs=98.9

Q ss_pred             cHHHHHHHHHHHHHHcC------CCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Q 048123           57 MPERKMLDLLLDRLKRR------DSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNA  130 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~------~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  130 (202)
                      ....+.|..|++.|..+      +.+++|..||+...+|+||++|++||||++|++||+++.|.++++|..||+|||.||
T Consensus         4 ~~~~~~c~~il~~l~~~~d~~g~~~s~~F~~p~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na   83 (116)
T 3iu5_A            4 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNA   83 (116)
T ss_dssp             CCHHHHHHHHHHHHHHCBCTTCCBGGGGGSSCCCGGGCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhccCCCeeeHHhcCCCCcccCCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            34578899999999887      458999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          131 MHFNASDTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       131 ~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      +.||+++|.++.+|..|+..|++.++++.+.
T Consensus        84 ~~yN~~~s~~~~~A~~L~~~f~~~~~~l~~~  114 (116)
T 3iu5_A           84 KSYYKPDSPEYKAACKLWDLYLRTRNEFVQK  114 (116)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999998663

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

Probab=99.96  E-value=8e-30  Score=197.57  Aligned_cols=121  Identities=23%  Similarity=0.403  Sum_probs=106.9

Q ss_pred             CcHHHHHHHHHHHH-HHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           56 AMPERKMLDLLLDR-LKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        56 ~~~~~~~~~~il~~-l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      ...+..+|..|+.. |..++.+++|..||++..+|+||++|++||||+||++||+++.|.++++|..||+|||.||++||
T Consensus        27 ~~~l~~iL~~i~~~kl~~~~~s~~F~~PVd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~yN  106 (158)
T 3uv4_A           27 QVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYN  106 (158)
T ss_dssp             HHHHHHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCchhhcCcCChhhcccHHHHcCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            33445566666654 77789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhCCCchHHHHhhhhcccC
Q 048123          135 ASDTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMRGRRR  176 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  176 (202)
                      +++|.++.+|..|...|.+.++++.......+..+.+...+.
T Consensus       107 ~~~s~i~~~A~~L~~~~~~~l~e~~~~l~~le~~i~~~~e~a  148 (158)
T 3uv4_A          107 GPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAA  148 (158)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHCC--
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999888877777777664443

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

Probab=99.96  E-value=1.3e-29  Score=190.63  Aligned_cols=104  Identities=28%  Similarity=0.457  Sum_probs=97.3

Q ss_pred             cHHHHHHHHHHHHHHcCCC---cccccCCCCcCC--ccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHh
Q 048123           57 MPERKMLDLLLDRLKRRDS---YKIFAKPVDGTE--VEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAM  131 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~---~~~F~~pv~~~~--~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~  131 (202)
                      ....+.|..||..|..++.   +++|..||++..  +|+||++|++||||+||++||+++.|.++++|..||+|||.||+
T Consensus        21 ~~~l~~c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~  100 (130)
T 2ouo_A           21 SEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCY  100 (130)
T ss_dssp             HHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence            3457889999999998875   789999999874  99999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHHHhhC
Q 048123          132 HFNASDTVYYRQAHAMKELANKLFRTLKN  160 (202)
Q Consensus       132 ~yN~~~s~~~~~A~~L~~~~~~~~~~~~~  160 (202)
                      +||+++|.++.+|..|+..|++.|.++..
T Consensus       101 ~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  129 (130)
T 2ouo_A          101 KYNPPDHEVVAMARKLQDVFEMRFAKMPD  129 (130)
T ss_dssp             HHSCTTSHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            99999999999999999999999998754

>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=99.96  E-value=1.6e-29  Score=187.59  Aligned_cols=104  Identities=25%  Similarity=0.486  Sum_probs=98.6

Q ss_pred             CcHHHHHHHHHHHHHHcCCC------cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Q 048123           56 AMPERKMLDLLLDRLKRRDS------YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKN  129 (202)
Q Consensus        56 ~~~~~~~~~~il~~l~~~~~------~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  129 (202)
                      ...+...|..+++.|.....      +++|..||+...+|+||++|++||||++|++||.++.|.++++|..||+|||.|
T Consensus         6 p~~l~~~~~~ll~~l~~~~d~~g~~~s~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~N   85 (120)
T 3ljw_A            6 PAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKN   85 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHCBCTTSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccCcCCCcccHHhcCCCCcccCCChHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHH
Confidence            34568899999999988766      899999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          130 AMHFNASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       130 a~~yN~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      |+.||+++|.++.+|..|+..|++.|+++.
T Consensus        86 a~~yN~~~s~~~~~A~~L~~~f~~~~~~i~  115 (120)
T 3ljw_A           86 AKTYNEPGSQVFKDANSIKKIFYMKKAEIE  115 (120)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999999885

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

Probab=99.96  E-value=3.6e-29  Score=189.35  Aligned_cols=103  Identities=31%  Similarity=0.491  Sum_probs=98.1

Q ss_pred             HHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhC--CCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           59 ERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE--GSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~--~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      ..+.|..||..|+.++.+++|..||+. .+|+||++|++||||++|++||++  +.|.++++|..||+|||.||++||++
T Consensus        21 ~~~~c~~il~~L~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmDL~tI~~kL~~~~~~Y~s~~ef~~Dv~Lif~Na~~yN~~   99 (135)
T 2yyn_A           21 DKRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEP   99 (135)
T ss_dssp             HHHHHHHHHHHHHTSGGGGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHHSSSCCCSSHHHHHHHHHHHHHHHHHHSCT
T ss_pred             HHHHHHHHHHHHHhCccchhhcCCCcc-cCCCHHHHcCCCCCHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            468899999999999999999999988 799999999999999999999998  58999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhCCC
Q 048123          137 DTVYYRQAHAMKELANKLFRTLKNDP  162 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~~~~~~  162 (202)
                      +|.++.+|..|+..|+++++++..+.
T Consensus       100 ~s~i~~~A~~L~~~f~~~~~~~~~~~  125 (135)
T 2yyn_A          100 DSEVANAGIKLENYFEELLKNLYPEK  125 (135)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhcccc
Confidence            99999999999999999999986554

>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=99.96  E-value=3.1e-29  Score=185.85  Aligned_cols=103  Identities=30%  Similarity=0.501  Sum_probs=97.3

Q ss_pred             cHHHHHHHHHHHHHHc-CCCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhh
Q 048123           57 MPERKMLDLLLDRLKR-RDSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHF  133 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~-~~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  133 (202)
                      ..+.+.|..+|..|.. ++.+++|..||++.  .+|+||++|++||||++|++||+++.|.++++|..||+|||+||+.|
T Consensus        10 ~el~~~l~~~l~~l~~~~~~s~~F~~pv~~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~y   89 (119)
T 3p1f_A           10 EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLY   89 (119)
T ss_dssp             HHHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCCchhcCCCCchhccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            3467889999999887 67999999999988  79999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          134 NASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       134 N~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      |+++|.++.+|..|+..|++.++.+.
T Consensus        90 N~~~s~i~~~A~~L~~~f~~~~~~~~  115 (119)
T 3p1f_A           90 NRKTSRVYKFCSKLAEVFEQEIDPVM  115 (119)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999998874

>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=99.96  E-value=1.2e-29  Score=189.83  Aligned_cols=109  Identities=16%  Similarity=0.255  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHHHHcCC------CcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHh
Q 048123           58 PERKMLDLLLDRLKRRD------SYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAM  131 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~------~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~  131 (202)
                      .+.+.|..|++.|..+.      .+++|..||+...+||||++|++||||++|++||+++.|.++++|..||+|||.||+
T Consensus         9 ~l~~~~~~i~~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~   88 (126)
T 3mqm_A            9 RLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAE   88 (126)
T ss_dssp             HHHHHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGGGCTTHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCcCCCChhHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence            46788999999998764      389999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHHHhhCCCchHH
Q 048123          132 HFNASDTVYYRQAHAMKELANKLFRTLKNDPENFE  166 (202)
Q Consensus       132 ~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~  166 (202)
                      .||+++|.++.+|..|+..|++.+.++....+.+.
T Consensus        89 ~yN~~~s~~~~~A~~L~~~f~~~~~~~~~~l~~i~  123 (126)
T 3mqm_A           89 KYYGRKSPVGRDVCRLRKAYYNARHEASAQIDEIV  123 (126)
T ss_dssp             HHHCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999877665544

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

Probab=99.96  E-value=4e-29  Score=195.20  Aligned_cols=107  Identities=27%  Similarity=0.392  Sum_probs=99.1

Q ss_pred             CcCCcHHHHHHHHHHHHHHcCCCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Q 048123           53 SIIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNA  130 (202)
Q Consensus        53 ~~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  130 (202)
                      ......|...|..||..|+.++.+++|..||++.  .+|+||++|++||||+||++||.++.|.++++|..||+|||.||
T Consensus        16 ~p~~~~~~~~~~~il~~L~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~Na   95 (166)
T 3fkm_X           16 FQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSFSCIKTKLKKGQYAYPSEFVKDVQLIFDNC   95 (166)
T ss_dssp             -CTTHHHHHHHHHHHHHHTTSTTGGGGSSCCC-----CCCGGGCCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHHhCCCChhhcCCCChhhccCCCHHHhcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Confidence            3456678899999999999999999999999976  59999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          131 MHFNASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       131 ~~yN~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      ++||+++|.++.+|..|+..|++.|.++.
T Consensus        96 ~~yN~~~s~i~~~A~~L~~~f~~~l~~~~  124 (166)
T 3fkm_X           96 SLYNTSNSVVAITGKNIETYFNNQLIVMG  124 (166)
T ss_dssp             HHSSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            99999999999999999999999998874

>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=99.96  E-value=5.5e-29  Score=187.11  Aligned_cols=103  Identities=24%  Similarity=0.393  Sum_probs=96.2

Q ss_pred             HHHHHHHHHHHHHcCCC------cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhh
Q 048123           59 ERKMLDLLLDRLKRRDS------YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMH  132 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~------~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  132 (202)
                      +...|..+++.|.....      +++|..||+...+|+||++|++||||++|++||+++.|.++++|..||+|||.||+.
T Consensus        18 l~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~~~PdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~Na~~   97 (130)
T 3k2j_A           18 LYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKR   97 (130)
T ss_dssp             HHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccCCCccHhhcCCCChhhCccHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            45678888888877644      899999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          133 FNASDTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       133 yN~~~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      ||+++|.++++|..|+..|++.|+++...
T Consensus        98 yN~~~s~i~~~A~~L~~~f~~~~~~l~~~  126 (130)
T 3k2j_A           98 YNVPNSAIYKRVLKLQQVMQAKKKELARR  126 (130)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999998644

>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=99.96  E-value=1.2e-28  Score=185.38  Aligned_cols=112  Identities=33%  Similarity=0.509  Sum_probs=99.8

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      .+..+|..+++.|..++.+++|..||++..+||||++|++||||+||++||.++.|.++++|..||+|||.||+.||+++
T Consensus        10 ~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~   89 (130)
T 3dai_A           10 ELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDR   89 (130)
T ss_dssp             HHHHHHHHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHCCSS
T ss_pred             HHHHHHHHHHHHHHcCCccHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            45778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHH----HHHHHHHHHHHHHHHH-HhhCCCchHHHHh
Q 048123          138 TVY----YRQAHAMKELANKLFR-TLKNDPENFEAAC  169 (202)
Q Consensus       138 s~~----~~~A~~L~~~~~~~~~-~~~~~~~~~~~~~  169 (202)
                      |++    +..|..|++.+..+++ ++..+......+.
T Consensus        90 s~~~~~i~~~A~~L~~~~~~~i~~el~~~~~~~ce~i  126 (130)
T 3dai_A           90 DPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEI  126 (130)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            866    7888999999999986 5555444443333

>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=99.95  E-value=2e-28  Score=192.49  Aligned_cols=105  Identities=28%  Similarity=0.498  Sum_probs=99.7

Q ss_pred             CCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           55 IAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        55 ~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      ....+...|..||..|..++.+++|..||++..+|+||++|++||||++|++||+++.|.++++|..||+|||+||++||
T Consensus        69 l~~~~~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN  148 (174)
T 2ri7_A           69 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYN  148 (174)
T ss_dssp             CCHHHHHHHHHHHHHHHTSGGGTTTSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCBHHHHHHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHHHHhhhhhhhhhcCCCcccCCchHHHhCCcCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            34456788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          135 ASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      +++|.++.+|..|+..|++.+++++
T Consensus       149 ~~~s~~~~~A~~L~~~f~~~~~~~~  173 (174)
T 2ri7_A          149 PSDSPFYQCAEVLESFFVQKLKGFK  173 (174)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHhcc
Confidence            9999999999999999999988764

>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=99.95  E-value=8.3e-28  Score=184.91  Aligned_cols=107  Identities=24%  Similarity=0.463  Sum_probs=96.0

Q ss_pred             HHHHHHHHHHHHcCCC-------cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhh
Q 048123           60 RKMLDLLLDRLKRRDS-------YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMH  132 (202)
Q Consensus        60 ~~~~~~il~~l~~~~~-------~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  132 (202)
                      ...|..|+..|.+...       +++|..||+...+|+||++|++||||++|++||+++.|.++++|..||+|||.||+.
T Consensus        26 ~~~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~  105 (150)
T 3tlp_A           26 KQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARH  105 (150)
T ss_dssp             HHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccCCcccHHhcCCCchhhCcCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            5678888888876544       899999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHHhhCCCchHH
Q 048123          133 FNASDTVYYRQAHAMKELANKLFRTLKNDPENFE  166 (202)
Q Consensus       133 yN~~~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~  166 (202)
                      ||+++|.+|.+|..|+..|++.|+++...++...
T Consensus       106 yN~~~s~i~~~A~~L~~~f~~~~~~l~~~pd~d~  139 (150)
T 3tlp_A          106 YNEEGSQVYNDAHILEKLLKEKRKELGPLPDDDD  139 (150)
T ss_dssp             HSCTTSHHHHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHccCCCChhh
Confidence            9999999999999999999999999987766543

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

Probab=99.95  E-value=7.8e-28  Score=180.97  Aligned_cols=117  Identities=30%  Similarity=0.464  Sum_probs=105.5

Q ss_pred             CCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           55 IAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        55 ~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      ....+..+|..||+.|..++.+++|..|     +||||++|++||||+||++||.++.|.++++|..||+|||.||+.||
T Consensus         9 ~~~~L~~~~~~il~~l~~~~~~~~F~~P-----~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN   83 (131)
T 2dkw_A            9 TLRELRLFLRDVTKRLATDKRFNIFSKP-----VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN   83 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHSGGGCTTSSC-----CSSCTTSCSSCCCHHHHHHHHHTTCCCSSHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHhCccchhhcCc-----CccHHhHcCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            3345678999999999999999999998     89999999999999999999999999999999999999999999999


Q ss_pred             CCCCH----HHHHHHHHHHHHHHHH-HHhhCCCchHHHHhhhhcccC
Q 048123          135 ASDTV----YYRQAHAMKELANKLF-RTLKNDPENFEAACSMRGRRR  176 (202)
Q Consensus       135 ~~~s~----~~~~A~~L~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  176 (202)
                      +++|+    ++..|..|++.|..++ .++....+....+..+.++.+
T Consensus        84 ~~~s~~~~~i~~~A~~L~~~~~~~l~~~l~~~f~~~~~~i~~~~~~r  130 (131)
T 2dkw_A           84 PDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKESGPSS  130 (131)
T ss_dssp             CCSSTTHHHHHHHHHHHHHHHHHHHHHHSCTTTHHHHHHHHTTSCCC
T ss_pred             CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            99985    6799999999999988 688888887777777776554

>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=99.94  E-value=6.9e-27  Score=185.39  Aligned_cols=105  Identities=31%  Similarity=0.475  Sum_probs=98.3

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhC--CCCCCHHHHHHHHHHHHHHHh
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE--GSYQTLGDFEHDIYLMLKNAM  131 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~--~~Y~s~~~f~~Dv~li~~Na~  131 (202)
                      .....+++.|+.||..|..++.+++|..||+.. +|+||++|++||||++|++||++  +.|.++++|..||+|||+||+
T Consensus        77 ~l~~~~~~~c~~il~~l~~~~~s~~F~~Pv~~~-~pdY~~iIk~PmdL~tI~~kl~~~~~~Y~s~~ef~~Dv~li~~Na~  155 (184)
T 3o36_A           77 KLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLT-VPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCA  155 (184)
T ss_dssp             CCCHHHHHHHHHHHHHHHHSTTCHHHHSCCCTT-STTHHHHCSSCCCHHHHHHHHHSTTCSCCSHHHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHhchhhhhhccccccC-CCchhhhcCCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHH
Confidence            344566789999999999999999999999864 89999999999999999999998  789999999999999999999


Q ss_pred             hhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          132 HFNASDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       132 ~yN~~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      +||+++|.++++|..|+..|+++++++.
T Consensus       156 ~yN~~~s~v~~~a~~L~~~f~~~~~~~~  183 (184)
T 3o36_A          156 EFNEPDSEVANAGIKLENYFEELLKNLY  183 (184)
T ss_dssp             HHSCTTCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999998873

>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=99.94  E-value=8.2e-27  Score=194.72  Aligned_cols=106  Identities=22%  Similarity=0.476  Sum_probs=101.1

Q ss_pred             CcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcC
Q 048123           56 AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA  135 (202)
Q Consensus        56 ~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~  135 (202)
                      ...+...|..||+.|..++.+++|..||++..+|+||++|++||||+||++||+++.|.++++|..||+|||+||+.||+
T Consensus        12 ~~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   91 (265)
T 3uv5_A           12 MVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNG   91 (265)
T ss_dssp             HHHHHHHHHHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHcCCCchhhhCCCChhhcCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhhhcCC
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          136 SDTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       136 ~~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      ++|.++.+|..|+..|++.++++...
T Consensus        92 ~~s~i~~~A~~l~~~~~~~~~~~~~~  117 (265)
T 3uv5_A           92 PKHSLTQISQSMLDLCDEKLKEKEDK  117 (265)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             CCChHHHHHHHHHHHHHHHHHHHhhh
Confidence            99999999999999999999887543

>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=99.94  E-value=3.3e-26  Score=191.03  Aligned_cols=115  Identities=24%  Similarity=0.425  Sum_probs=103.0

Q ss_pred             HHHHHHHHHHHH-HHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           58 PERKMLDLLLDR-LKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        58 ~~~~~~~~il~~-l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      .+..+|..++.. |..++.+++|..||++..+|+||++|++||||+||++||.+|.|.++++|..||+|||.||+.||++
T Consensus       136 ~~~~il~~i~~~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~lif~Na~~yN~~  215 (265)
T 3uv5_A          136 AFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGP  215 (265)
T ss_dssp             HHHHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCT
T ss_pred             HHHHHHHHHHHHHHHhhhhhHHHhCCCChhHhCcHHHHhCCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            345566666644 7889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhCCCchHHHHhhhh
Q 048123          137 DTVYYRQAHAMKELANKLFRTLKNDPENFEAACSMR  172 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~  172 (202)
                      +|.++.+|..|+..|.+.++++.......+.++...
T Consensus       216 ~s~~~~~A~~l~~~~~~~~~~~~~~~~~~e~~i~~~  251 (265)
T 3uv5_A          216 ESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTA  251 (265)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence            999999999999999999999987776666655433

>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=99.93  E-value=9.4e-26  Score=181.98  Aligned_cols=107  Identities=29%  Similarity=0.447  Sum_probs=100.2

Q ss_pred             cCCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhC---CCCCCHHHHHHHHHHHHHHH
Q 048123           54 IIAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNE---GSYQTLGDFEHDIYLMLKNA  130 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~---~~Y~s~~~f~~Dv~li~~Na  130 (202)
                      .....+++.|+.||..|..++.+++|..||+. .+|+||++|++||||++|++||++   +.|.++++|..||+|||+||
T Consensus        77 ~ls~~~~~~c~~il~~l~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li~~Na  155 (207)
T 3u5n_A           77 GLSPVDQRKCERLLLYLYCHELSIEFQEPVPA-SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNC  155 (207)
T ss_dssp             SSCHHHHHHHHHHHHHHHTSTTCGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhccchhhhhccCCh-hhccHhHHhCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHH
Confidence            44455678999999999999999999999987 799999999999999999999997   79999999999999999999


Q ss_pred             hhhcC-----------------CCCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          131 MHFNA-----------------SDTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       131 ~~yN~-----------------~~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      ++||+                 +++.++++|..|+..|+++++++..+
T Consensus       156 ~~yN~~~s~v~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~~~~~~p~  203 (207)
T 3u5n_A          156 ERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSD  203 (207)
T ss_dssp             HHHHHHHHHHC----------CCCCHHHHHHHHHHHHHHHHHHHHSTT
T ss_pred             HHHCCCcchHHHHHHHHHhcccccCHHHHHHHHHHHHHHHHHHHhCCC
Confidence            99999                 99999999999999999999998654

>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=99.93  E-value=2.9e-26  Score=193.77  Aligned_cols=102  Identities=23%  Similarity=0.485  Sum_probs=97.2

Q ss_pred             cHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           57 MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      ..+..+|..||+.|..++.+++|..||++..+|+||++|++||||+||++||+++.|.++.+|..||+|||+||++||++
T Consensus        46 ~~l~~~~~~il~~l~~~~~a~~F~~pV~~~~~pdY~~iIk~PmDL~tIk~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~  125 (292)
T 3aad_A           46 VTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGP  125 (292)
T ss_dssp             HHHHHHHHHHHHHHSSSTTCGGGSSSCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHHHhCCcchhhcCCCCchhcccHHHHcCCcCCHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHHHcCC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Q 048123          137 DTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      +|.++.+|..|+..|++.++++
T Consensus       126 ~s~i~~~A~~L~~~~~~~~~~~  147 (292)
T 3aad_A          126 KHSLTQISQSMLDLCDEKLKEK  147 (292)
T ss_dssp             SSHHHHHHTHHHHTTTTTGGGS
T ss_pred             chHHHHHHHHHHHHHHhhhhcc
Confidence            9999999999999998877654

>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=99.93  E-value=1e-25  Score=190.42  Aligned_cols=114  Identities=25%  Similarity=0.439  Sum_probs=102.7

Q ss_pred             HHHHHHHHH-HHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCC
Q 048123           60 RKMLDLLLD-RLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT  138 (202)
Q Consensus        60 ~~~~~~il~-~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s  138 (202)
                      ..++..++. .|+.++.+++|..||++..+||||++|++||||++|++||.++.|.++++|..||+|||.||+.||+++|
T Consensus       171 ~~~l~~i~~~~l~~~~~s~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s  250 (292)
T 3aad_A          171 SFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPES  250 (292)
T ss_dssp             HHHHHHHHHHTGGGSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTS
T ss_pred             HHHHHHHhhhhhhcCcchhHHHhcccccccccHHHHcCCcCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            344555443 4788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCchHHHHhhhhc
Q 048123          139 VYYRQAHAMKELANKLFRTLKNDPENFEAACSMRG  173 (202)
Q Consensus       139 ~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (202)
                      .+|.+|..|+..|++.++++......++.++...+
T Consensus       251 ~i~~~A~~L~~~~~~~~~~~~~~l~~le~~i~~~~  285 (292)
T 3aad_A          251 QYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAK  285 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999887777777766543

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

Probab=99.93  E-value=7.1e-26  Score=180.25  Aligned_cols=103  Identities=14%  Similarity=0.232  Sum_probs=94.6

Q ss_pred             CCcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcC--CCCCHHHHHHHHhCC---CCCCHHHHHHHHHHHHHH
Q 048123           55 IAMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIK--HPMDLSKITEKLNEG---SYQTLGDFEHDIYLMLKN  129 (202)
Q Consensus        55 ~~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~--~PmdL~~I~~kl~~~---~Y~s~~~f~~Dv~li~~N  129 (202)
                      .....+..|..||..|..++.+++|.+||+    |+||.+|+  +||||+||++||+++   .|.++++|++||+|||+|
T Consensus        73 m~~~~~~~c~~iL~~l~~~~~s~pF~~pV~----~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~Y~s~~eF~~Dv~Lif~N  148 (189)
T 2ro1_A           73 LSPANQRKCERVLLALFCHEPCRPLHQLAT----DSTFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQ  148 (189)
T ss_dssp             SCHHHHHHHHHHHHHHHHSTTHHHHHSCSC----CTTCSSSCSSCCCCHHHHHHHHHTSSSSCCSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhhcccCccchhhcCCCC----hhhhccccCCCcccHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHH
Confidence            344457789999999999999999999998    67999998  899999999999999   999999999999999999


Q ss_pred             HhhhcCCCCHHHHHHHHHHHHHHHHHHHhhCCC
Q 048123          130 AMHFNASDTVYYRQAHAMKELANKLFRTLKNDP  162 (202)
Q Consensus       130 a~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~~  162 (202)
                      |++|| +++.++.+|..|+..|++.|+++..+.
T Consensus       149 ~~~yN-~~s~~~~~a~~L~~~Fe~~~~~~~~~~  180 (189)
T 2ro1_A          149 FNKLT-EDKADVQSIIGLQRFFETRMNEAFGDT  180 (189)
T ss_dssp             HHHHC-CSSCSSHHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHC-CCCHHHHHHHHHHHHHHHHHHHhcCcc
Confidence            99999 578889999999999999999986553

>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=99.90  E-value=4.1e-24  Score=181.94  Aligned_cols=87  Identities=29%  Similarity=0.523  Sum_probs=83.9

Q ss_pred             cCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHHHH
Q 048123           72 RRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELA  151 (202)
Q Consensus        72 ~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~~  151 (202)
                      .++.+++|..||++..+|+||++|++||||+||++||+++.|.++++|..||+|||+||++||+++|.+|.+|..|+..|
T Consensus       177 ~~~~s~~F~~pvd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f  256 (311)
T 2r0y_A          177 KVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYF  256 (311)
T ss_dssp             SSCTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHH
T ss_pred             CCccHHHHhCCCChhhcccHHHHhCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHh
Q 048123          152 NKLFRTL  158 (202)
Q Consensus       152 ~~~~~~~  158 (202)
                      ++++++.
T Consensus       257 ~~~~~~~  263 (311)
T 2r0y_A          257 NYLIQKE  263 (311)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHh
Confidence            9999874

>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=99.90  E-value=7.2e-24  Score=183.89  Aligned_cols=86  Identities=29%  Similarity=0.519  Sum_probs=83.4

Q ss_pred             CCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHH
Q 048123           73 RDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELAN  152 (202)
Q Consensus        73 ~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~A~~L~~~~~  152 (202)
                      ++.+++|..||+...+||||++|++||||++|++||+++.|.++++|..||+|||+||+.||+++|.+|.+|..|+..|+
T Consensus       228 ~~~s~~F~~pvd~~~~PdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f~  307 (361)
T 2r10_A          228 VKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFN  307 (361)
T ss_dssp             SCTTGGGSSCCCTTTCTHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHH
T ss_pred             CcchhcccCCCChhhcccHHHHhcCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHh
Q 048123          153 KLFRTL  158 (202)
Q Consensus       153 ~~~~~~  158 (202)
                      +++++.
T Consensus       308 ~~~~~~  313 (361)
T 2r10_A          308 YLIQKE  313 (361)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            999874

>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=99.89  E-value=3.5e-23  Score=179.59  Aligned_cols=101  Identities=22%  Similarity=0.298  Sum_probs=90.5

Q ss_pred             CcHHHHHHHHHHHHHHcC--CCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHhh
Q 048123           56 AMPERKMLDLLLDRLKRR--DSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQ-TLGDFEHDIYLMLKNAMH  132 (202)
Q Consensus        56 ~~~~~~~~~~il~~l~~~--~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~-s~~~f~~Dv~li~~Na~~  132 (202)
                      ...+..+|..+|+.+...  ..+++|..||+...+||||++|++||||+||++||  +.|. ++++|..||+|||.||+.
T Consensus        76 ~~~~~~~~~~~l~~l~~~~~~~~~~F~~p~~~~~~PdY~~iIk~Pmdl~tI~~kl--~~y~~~~~~f~~D~~li~~Na~~  153 (361)
T 2r10_A           76 IPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQA  153 (361)
T ss_dssp             CTTHHHHHHHHHHHHHHHTHHHHGGGSSCCCTTTCTTHHHHCSSCCCHHHHHTSC--CCSTTHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHcCCcccHHhcCCCCcccCCChHhhcCCCcCHHHHHHHh--hccCCCHHHHHHHHHHHHHHHhh
Confidence            445678899999988653  44799999999999999999999999999999998  5555 899999999999999999


Q ss_pred             hcCCCCHHHHHHHHHHHHHHHHHHHh
Q 048123          133 FNASDTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       133 yN~~~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      ||+++|.++.+|..|+.+|.+.|.+.
T Consensus       154 yN~~~s~i~~~a~~l~~~~~~~~~k~  179 (361)
T 2r10_A          154 YNEYDSLIVKNSMQVVMLIEFEVLKA  179 (361)
T ss_dssp             HBCSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999877655

>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=3.8e-22  Score=169.78  Aligned_cols=103  Identities=21%  Similarity=0.280  Sum_probs=90.4

Q ss_pred             cCCcHHHHHHHHHHHHHHcC--CCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHH
Q 048123           54 IIAMPERKMLDLLLDRLKRR--DSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQ-TLGDFEHDIYLMLKNA  130 (202)
Q Consensus        54 ~~~~~~~~~~~~il~~l~~~--~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~-s~~~f~~Dv~li~~Na  130 (202)
                      .....+..++..+|..+...  ..+++|..||+...+|+||++|++||||+||++||  +.|. ++++|..||+|||.||
T Consensus        24 ~~~p~~~~~~~~~L~~~~~~~r~~~~~F~~p~~~~~~PdY~~iIk~PmDL~tI~~kl--~~y~~s~~~f~~D~~li~~Na  101 (311)
T 2r0y_A           24 WHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNC  101 (311)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHSHHHHGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHSC--CCSTTHHHHHHHHHHHHHHHH
T ss_pred             hhchHHHHHHHHHHHHHHHcCCchhHHhcCCCCcccCCChHHHcCCCCCHHHHHHHH--hcccCCHHHHHHHHHHHHHHH
Confidence            33456677777777777653  35789999999999999999999999999999999  5555 8999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHh
Q 048123          131 MHFNASDTVYYRQAHAMKELANKLFRTL  158 (202)
Q Consensus       131 ~~yN~~~s~~~~~A~~L~~~~~~~~~~~  158 (202)
                      ++||+++|.++.+|..|+..|.+.|.+.
T Consensus       102 ~~yN~~~s~i~~~A~~l~~~~~~~~~k~  129 (311)
T 2r0y_A          102 QAYNEYDSLIVKNSMQVVMLIEFEVLKA  129 (311)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHccCCCCHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999887765

>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=99.84  E-value=2.1e-20  Score=141.68  Aligned_cols=101  Identities=16%  Similarity=0.301  Sum_probs=92.4

Q ss_pred             cHHHHHHHHHHHHHHcCCC------cccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Q 048123           57 MPERKMLDLLLDRLKRRDS------YKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNA  130 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~------~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  130 (202)
                      ...+.++..|++.|..+..      +.+|...|+..  |+||.  +.||+|.+|++||..+.|.++++|..||.+||+||
T Consensus         6 ~~lq~~l~~l~~~v~~~~De~GR~lsd~F~~LPsk~--pdYY~--k~Pi~l~~Ikkri~~~~Y~sld~f~~D~~lmf~NA   81 (147)
T 3iu6_A            6 LLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERA   81 (147)
T ss_dssp             CHHHHHHHHHHHHHHTCBCTTSCBGGGGGTTCCSSC--TTSTT--SCCCCHHHHHHHHHTTCCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhcCCCCCcchHHHhHCCCCC--ccccC--CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence            4467888999999988643      57999999887  89998  99999999999999999999999999999999999


Q ss_pred             hhhcCCCCHHHHHHHHHHHHHHHHHHHhhCC
Q 048123          131 MHFNASDTVYYRQAHAMKELANKLFRTLKND  161 (202)
Q Consensus       131 ~~yN~~~s~~~~~A~~L~~~~~~~~~~~~~~  161 (202)
                      ++||.++|.||.+|..|+..|.+..+++...
T Consensus        82 r~yN~e~S~IyeDAv~Lq~~f~~~r~eL~~~  112 (147)
T 3iu6_A           82 RRMNRTDSEIYEDAVELQQFFIKIRDELCKN  112 (147)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999999999998655

>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=99.68  E-value=1.3e-16  Score=125.82  Aligned_cols=93  Identities=15%  Similarity=0.243  Sum_probs=83.2

Q ss_pred             HHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCC
Q 048123           59 ERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT  138 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s  138 (202)
                      +...+..||..|..++.+++|....           ++.||||.+|++||+++.|.|+.+|+.||.|||+||..||.+++
T Consensus        76 l~~~l~~vl~~L~~~~~s~~~~~y~-----------~k~PmDL~~i~kKl~~~~Y~s~~eF~~Dv~lIf~n~~~~~~~~~  144 (183)
T 3lqh_A           76 LQISLKQVLTALLNSRTTSHLLRYR-----------QQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQP  144 (183)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHTCC-----------C--CCSHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSCCCH
T ss_pred             HHHHHHHHHHHHHhccccHhhhhhh-----------hcCCccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhccCCCh
Confidence            3456889999999999999998732           59999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCC
Q 048123          139 VYYRQAHAMKELANKLFRTLKNDP  162 (202)
Q Consensus       139 ~~~~~A~~L~~~~~~~~~~~~~~~  162 (202)
                      ++.+++..|+.+|.++++++..-.
T Consensus       145 e~~~ag~~l~~~f~~~l~~vfpwf  168 (183)
T 3lqh_A          145 EIKKANSMVKSFFIRQMERVFPWF  168 (183)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTS
T ss_pred             hhhhhhhHHHHHHHHHHHHHCCCC
Confidence            999999999999999999986543

---

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	202
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	3e-25
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	3e-24
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	1e-22
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	3e-22
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	3e-21
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	4e-20

>d1eqfa1 a.29.2.1 (A:1359-1497) TAFII250 double bromodomain module {Human (Homo sapiens) [TaxId: 9606]} Length = 139

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: TAFII250 double bromodomain module
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 93.5 bits (232), Expect = 3e-25
 Identities = 25/109 (22%), Positives = 55/109 (50%)

Query: 60  RKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDF 119
             +L+ +++ ++   +   F  PV+   V+DYYK+I  PMDL  + E + +  Y +  +F
Sbjct: 28  SSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEF 87

Query: 120 EHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFEAA 168
              + L++KN+  +N       + + +M +L ++  +  ++     E A
Sbjct: 88  REHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKA 136

>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 = 90.0 bits (223), Expect = 3e-24
 Identities = 33/106 (31%), Positives = 52/106 (49%)

Query: 58  PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLG 117
           P    +  +L  L+   +   F +PV+  EV DYY  IK PMDLS +  KL    YQ + 
Sbjct: 3   PHDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKME 62

Query: 118 DFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPE 163
           DF +D  L+  N   +N  +T YY+ A+ +++  N   + +     
Sbjct: 63  DFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPEYSH 108

>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 = 86.2 bits (213), Expect = 1e-22
 Identities = 26/103 (25%), Positives = 49/103 (47%)

Query: 64  DLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDI 123
           +++  ++        F  PV+   V DYYKVI +PMDL  I + +++  YQ+   F  D+
Sbjct: 16  NIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDV 75

Query: 124 YLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLKNDPENFE 166
            L+L N++ +N  ++ Y + A  +  +  +            E
Sbjct: 76  NLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 118

>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 = 85.0 bits (210), Expect = 3e-22
 Identities = 32/103 (31%), Positives = 53/103 (51%), Gaps = 3/103 (2%)

Query: 60  RKMLDLLLDRLKRRDSYKI-FAKPVD--GTEVEDYYKVIKHPMDLSKITEKLNEGSYQTL 116
           R+ L   L+ L R+D   + F +PVD     + DY+ ++K+PMDLS I  KL+ G YQ  
Sbjct: 8   RQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEP 67

Query: 117 GDFEHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLK 159
             +  D++LM  NA  +N   +  Y+    + E+  +    + 
Sbjct: 68  WQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVM 110

>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 = 82.0 bits (202), Expect = 3e-21
 Identities = 31/96 (32%), Positives = 49/96 (51%)

Query: 61  KMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFE 120
             L  LL ++K   S   F +PV  +E  DYY+VI+ P+DL  +TE+L    Y T   F 
Sbjct: 5   TTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFV 64

Query: 121 HDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFR 156
            D+  ++ N   +N  D+ Y R A A+++      +
Sbjct: 65  ADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLK 100

>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 = 79.7 bits (196), Expect = 4e-20
 Identities = 27/100 (27%), Positives = 48/100 (48%)

Query: 60  RKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDF 119
              L  +L ++K   S   F +PV  TE   YY+VI+ PMDL  ++E+L    Y +   F
Sbjct: 15  YSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLF 74

Query: 120 EHDIYLMLKNAMHFNASDTVYYRQAHAMKELANKLFRTLK 159
             D+  +  N   +N  ++ YY+ A+ +++      +   
Sbjct: 75  MADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAG 114

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	202
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.97
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	99.97
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.97
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.96
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.96
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.96

>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=99.97  E-value=1.3e-31  Score=194.64  Aligned_cols=106  Identities=31%  Similarity=0.537  Sum_probs=101.1

Q ss_pred             cHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCC
Q 048123           57 MPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNAS  136 (202)
Q Consensus        57 ~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~  136 (202)
                      .|+.+.|..||+.|.+++.+++|..||++..+|+|+++|++||||++|++||+++.|.|+.+|..||+|||.||+.||++
T Consensus         2 ~p~~~~l~~il~~l~~~~~a~pF~~pvd~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~   81 (111)
T d1e6ia_           2 GPHDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGE   81 (111)
T ss_dssp             CTTHHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCT
T ss_pred             ChHHHHHHHHHHHHHhCCCChhhcCCCCchhCcCHHHHcCCchhHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHCCC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHhhCCC
Q 048123          137 DTVYYRQAHAMKELANKLFRTLKNDP  162 (202)
Q Consensus       137 ~s~~~~~A~~L~~~~~~~~~~~~~~~  162 (202)
                      +|.++.+|..|+..|++.++++.+..
T Consensus        82 ~s~i~~~A~~l~~~f~~~~~~ipe~~  107 (111)
T d1e6ia_          82 NTSYYKYANRLEKFFNNKVKEIPEYS  107 (111)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHTSGGGG
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhccc
Confidence            99999999999999999998885443

>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=99.97  E-value=7.4e-31  Score=187.88  Aligned_cols=99  Identities=31%  Similarity=0.467  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCC
Q 048123           59 ERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT  138 (202)
Q Consensus        59 ~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s  138 (202)
                      +...|..||..|.+++.+++|..||++..+|+|+++|++||||++|++||+++.|.|+++|..||+|||.||+.||+++|
T Consensus         3 L~~~l~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s   82 (102)
T d3d7ca1           3 LYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDS   82 (102)
T ss_dssp             HHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTTS
T ss_pred             HHHHHHHHHHHHHhCCCCCccCCCCChhhCcCHHHHcCCccCHHHHHHHhccCccCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            57789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 048123          139 VYYRQAHAMKELANKLFRT  157 (202)
Q Consensus       139 ~~~~~A~~L~~~~~~~~~~  157 (202)
                      .++.+|..|++.|.+.+++
T Consensus        83 ~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          83 EYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhc
Confidence            9999999999999988765

>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=99.97  E-value=2.3e-30  Score=195.02  Aligned_cols=109  Identities=22%  Similarity=0.472  Sum_probs=102.4

Q ss_pred             HHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCC
Q 048123           58 PERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASD  137 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~  137 (202)
                      .+..+|..||+.|..++.+++|..||++..+|+||++|++||||.+|++||+++.|.|+++|..||.|||.||+.||+++
T Consensus        26 ~l~~~l~~il~~l~~~~~s~pF~~Pvd~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~  105 (139)
T d1eqfa1          26 TLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPK  105 (139)
T ss_dssp             HHHHHHHHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTT
T ss_pred             HHHHHHHHHHHHHHcCCCchhhhCCCChhhccCHHHHcCChhhHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHhhCCCchHH
Q 048123          138 TVYYRQAHAMKELANKLFRTLKNDPENFE  166 (202)
Q Consensus       138 s~~~~~A~~L~~~~~~~~~~~~~~~~~~~  166 (202)
                      |.++.+|..|+..|++.|+++.......+
T Consensus       106 s~i~~~A~~L~~~~~~~~~~~~~~~~~~e  134 (139)
T d1eqfa1         106 HSLTQISQSMLDLCDEKLKEKEDKLARLE  134 (139)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998865544433

>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=99.96  E-value=3.1e-30  Score=189.20  Aligned_cols=104  Identities=26%  Similarity=0.435  Sum_probs=99.7

Q ss_pred             CcHHHHHHHHHHHHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcC
Q 048123           56 AMPERKMLDLLLDRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNA  135 (202)
Q Consensus        56 ~~~~~~~~~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~  135 (202)
                      ...+...|..||..|++++.+++|..||++..+|+||++|++||||++|++||+++.|.++++|+.||+|||.||+.||+
T Consensus        11 ~~~l~~~l~~il~~l~~~~~a~~F~~pv~~~~~pdY~~iI~~PmdL~~I~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yn~   90 (118)
T d1wuma1          11 PDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNP   90 (118)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCHHHHSCCCSSSSSSCTTTCSSCCCHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHhCCCcCcccCCCChhhCcCHHHHcCChhhHHHHHHHhcccccCchHHHHHHHHHHHHHHHHHCC
Confidence            34568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHhh
Q 048123          136 SDTVYYRQAHAMKELANKLFRTLK  159 (202)
Q Consensus       136 ~~s~~~~~A~~L~~~~~~~~~~~~  159 (202)
                      ++|.++.+|..|+..|.+.++++.
T Consensus        91 ~~s~~~~~A~~l~~~f~~~~~e~~  114 (118)
T d1wuma1          91 PESEYYKCANILEKFFFSKIKEAG  114 (118)
T ss_dssp             TTSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcc
Confidence            999999999999999999998863

>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=99.96  E-value=4.8e-30  Score=190.65  Aligned_cols=110  Identities=25%  Similarity=0.465  Sum_probs=97.3

Q ss_pred             HHHHHHHH-HHHHcCCCcccccCCCCcCCccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhcCCCC
Q 048123           60 RKMLDLLL-DRLKRRDSYKIFAKPVDGTEVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFNASDT  138 (202)
Q Consensus        60 ~~~~~~il-~~l~~~~~~~~F~~pv~~~~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s  138 (202)
                      ..++..|+ +++..++.+|||..||++..+|+||++|++||||++|++||++|.|.|+.+|..||+|||+||+.||+++|
T Consensus        11 ~~il~~l~~~~~~~~p~a~pF~~pVd~~~~PdY~~vIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s   90 (128)
T d1eqfa2          11 SFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPES   90 (128)
T ss_dssp             HHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHHcCCCCChhcCCCCcccCcCHHHHcCCcccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHCCCCC
Confidence            44455543 56677889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCchHHHHh
Q 048123          139 VYYRQAHAMKELANKLFRTLKNDPENFEAAC  169 (202)
Q Consensus       139 ~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~  169 (202)
                      .++..|..|+..|.+.+.++.......+.+.
T Consensus        91 ~i~~~A~~L~~~~~~~l~~~~~~~~~le~~i  121 (128)
T d1eqfa2          91 QYTKTAQEIVNVCYQTLTEYDEHLTQLEKDI  121 (128)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHhHH
Confidence            9999999999999999998866554444443

>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=99.96  E-value=3.6e-29  Score=182.45  Aligned_cols=103  Identities=30%  Similarity=0.516  Sum_probs=96.5

Q ss_pred             HHHHHHHHHHHHHHcC-CCcccccCCCCcC--CccchHhhcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHhhhc
Q 048123           58 PERKMLDLLLDRLKRR-DSYKIFAKPVDGT--EVEDYYKVIKHPMDLSKITEKLNEGSYQTLGDFEHDIYLMLKNAMHFN  134 (202)
Q Consensus        58 ~~~~~~~~il~~l~~~-~~~~~F~~pv~~~--~~p~Y~~iI~~PmdL~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN  134 (202)
                      .+++.|..+|+.|+.+ +.+++|..||++.  .+|||+++|++||||++|++||+++.|.|+++|..||+|||+||+.||
T Consensus         6 el~~~l~~~l~~l~~~~p~a~pF~~pvd~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN   85 (114)
T d3dwya1           6 ELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYN   85 (114)
T ss_dssp             HHHHHHHHHHHHHHTCTTTTGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHhcCcCCCccCCCCChhhccCCCHHHHcCCCCCHHHHHHHHHcCccccHHHHHHHHHHHHHHHHHHC
Confidence            3578899999999876 5899999999976  689999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhC
Q 048123          135 ASDTVYYRQAHAMKELANKLFRTLKN  160 (202)
Q Consensus       135 ~~~s~~~~~A~~L~~~~~~~~~~~~~  160 (202)
                      +++|.++.+|..|+..|++.++.+.+
T Consensus        86 ~~~s~~~~~A~~L~~~f~~~~~~i~~  111 (114)
T d3dwya1          86 RKTSRVYKFCSKLAEVFEQEIDPVMQ  111 (114)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999988753