Psyllid ID: psy5115

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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-
Protein Sequence
MKFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK
Secondary Structure (PSIPRED)
cccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHccccccHHHHHHHHHHHHcHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEcEEEEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccHHHcccccccccccHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccHHHHHHHH
Coil and Loop (DISEMBL)
mkfhtlaviepkfyiccdtcqdwfhgrcvgilqseadnideyicpncnnsssnlanmknltprDFESLRKLMKQIQAHksawpfmepvdpheapdyynvvkepmdlKTIELRIAQQRYKKLSEFIGDMTkifdncryynprespffkhaHQLEMFFVQKVKILREKLVELK
Flexible Loop (DISEMBL)
MKFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK
Low Complexity Region (SEG)
MKFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK
Disordered region (IsUnstruct)
**FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN**************************IQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL****
Disordered Region (DISOPRED)
****TLAVIEPKFYICCDTCQDWFHGRCVGI***********************************SLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLV***
Disordered Region (DISEMBL)
MKFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK
Disordered Region (DISPRO)
*KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSS**ANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK
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	171	2.2.26 [Sep-21-2011]
Q9W0T1	2669	Nucleosome-remodeling fac	yes	N/A	0.935	0.059	0.677	3e-65
Q12830	3046	Nucleosome-remodeling fac	no	N/A	0.888	0.049	0.611	7e-58
Q6BER5	2194	Nucleosome-remodeling fac	no	N/A	0.918	0.071	0.345	5e-26
Q6CXW4	516	Histone acetyltransferase	yes	N/A	0.590	0.195	0.445	5e-23
Q03330	439	Histone acetyltransferase	yes	N/A	0.649	0.252	0.410	1e-22
Q756G9	452	Histone acetyltransferase	yes	N/A	0.590	0.223	0.435	1e-22
Q92831	832	Histone acetyltransferase	no	N/A	0.608	0.125	0.444	3e-22
Q6FTW5	546	Histone acetyltransferase	yes	N/A	0.590	0.184	0.425	2e-21
Q9UUK2	454	Histone acetyltransferase	yes	N/A	0.567	0.213	0.453	2e-21
Q8WZM0	464	Histone acetyltransferase	yes	N/A	0.567	0.209	0.443	5e-21

>sp|Q9W0T1|NU301_DROME Nucleosome-remodeling factor subunit NURF301 OS=Drosophila melanogaster GN=E(bx) PE=1 SV=2

 Score =  247 bits (630), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 109/161 (67%), Positives = 128/161 (79%), Gaps = 1/161 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEA+ IDEY+CP C   + +N ANMK LT  D E L
Sbjct: 2506 ESQFYICCDKCQDWFHGRCVGILQSEAEFIDEYVCPECQRKNDANAANMKKLTSNDVEEL 2565

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            + L+KQ+Q HKSAWPFMEPVDP EAPDYY V+KEPMDLK +E+++    Y KLSEFIGDM
Sbjct: 2566 KNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDM 2625

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVE 169
            TKIFDNCRYYNP+ES F+K A  LE +FVQK+K  RE + +
Sbjct: 2626 TKIFDNCRYYNPKESSFYKCAEALESYFVQKIKNFRENVFD 2666

Histone-binding component of NURF (nucleosome remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. Required for homeotic gene expression, proper larval blood cell development, normal male X chromosome morphology, ecdysteroid signaling and metamorphosis.
Drosophila melanogaster (taxid: 7227)

>sp|Q12830|BPTF_HUMAN Nucleosome-remodeling factor subunit BPTF OS=Homo sapiens GN=BPTF PE=1 SV=3

 Score =  222 bits (566), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 93/152 (61%), Positives = 124/152 (81%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
            E KFYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct: 2878 ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 2937

Query: 70   KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
            ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+KL+EF+ DMT
Sbjct: 2938 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMT 2997

Query: 130  KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
            KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct: 2998 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 3029

Histone-binding component of NURF (nucleosome-remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. May also regulate transcription through direct binding to DNA or transcription factors.

Homo sapiens (taxid: 9606)

>sp|Q6BER5|NU301_CAEEL Nucleosome-remodeling factor subunit NURF301-like OS=Caenorhabditis elegans GN=nurf-1 PE=1 SV=2

 Score =  117 bits (292), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 58/168 (34%), Positives = 99/168 (58%), Gaps = 11/168 (6%)

Query: 12   KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-------NSSSNLANMK----NL 60
            KFY+ CD+CQ WFH  CVG  ++EA+   +Y CP C        + +S+++        L
Sbjct: 1972 KFYVGCDSCQGWFHPECVGTTRAEAEQAADYNCPACTREAEGYESEASDVSGSSRVSVQL 2031

Query: 61   TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKK 120
            T  D+  + +L++ +  H+ + PF  PVD +E PDY   +K+PMDL TI  ++ +  Y  
Sbjct: 2032 TRADYTHVFELLELLLEHRMSTPFRNPVDLNEFPDYEKFIKKPMDLSTITKKVERTEYLY 2091

Query: 121  LSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLV 168
            LS+F+ D+ ++F+N + YNP+ +  FK A  ++  F +K+  +RE++ 
Sbjct: 2092 LSQFVNDVNQMFENAKTYNPKGNAVFKCAETMQEVFDKKLIDVREQMT 2139

Histone-binding component of a NURF-like (nucleosome remodeling factor-like) complex, which would catalyze ATP-dependent nucleosome sliding and facilitate transcription of chromatin (Probable). Involved in vulval cell fates.

Caenorhabditis elegans (taxid: 6239)

>sp|Q6CXW4|GCN5_KLULA Histone acetyltransferase GCN5 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=GCN5 PE=3 SV=1

 Score =  107 bits (266), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 45/101 (44%), Positives = 71/101 (70%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           + +++ L+ ++Q H +AWPF++PV+  E PDYY  +KEPMDL ++E+++   RY+K+  F
Sbjct: 410 YAAMQNLLTELQNHAAAWPFLQPVNKEEVPDYYEFIKEPMDLSSMEMKLNGNRYEKMENF 469

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
           I D   IF+NCR YN   + +FK+A++LE FF  KVK + E
Sbjct: 470 IYDARLIFNNCRAYNGENTSYFKYANRLEKFFNSKVKEIPE 510

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q03330|GCN5_YEAST Histone acetyltransferase GCN5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GCN5 PE=1 SV=1

 Score =  105 bits (263), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 46/112 (41%), Positives = 76/112 (67%), Gaps = 1/112 (0%)

Query: 54  LANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRI 113
           LA      P D  +++ ++ ++Q H +AWPF++PV+  E PDYY+ +KEPMDL T+E+++
Sbjct: 323 LAQRPKRGPHD-AAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKL 381

Query: 114 AQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
              +Y+K+ +FI D   +F+NCR YN   + ++K+A++LE FF  KVK + E
Sbjct: 382 ESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPE 433

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac and H3K36ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation. Operates in concert with certain DNA-binding transcriptional activators such as GCN4 or HAP2/3/4. Its acetylteransferase activity seems to be dependent on the association in different multisubunit complexes. Functions as histone acetyltransferase component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and ADA. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. The ADA histone acetyltransferase complex preferentially acetylates nucleosomal histones H3 (to form H3K14ac and H3K18ac) and H2B, leading to transcription regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.

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

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q756G9|GCN5_ASHGO Histone acetyltransferase GCN5 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=GCN5 PE=3 SV=1

 Score =  105 bits (262), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 44/101 (43%), Positives = 72/101 (71%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           + +++ ++ ++Q H +AWPF++PV+  E PDYY  +KEPMDL T+E+++   RY+K+ +F
Sbjct: 346 YATMQNVLTELQNHAAAWPFLQPVNRDEVPDYYEFIKEPMDLSTMEIKLENNRYEKMEDF 405

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
           I D   IF+NCR YN   + +FK+A++LE FF  K+K + E
Sbjct: 406 IYDARLIFNNCRAYNGENTSYFKYANRLEKFFNTKMKEIPE 446

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q92831|KAT2B_HUMAN Histone acetyltransferase KAT2B OS=Homo sapiens GN=KAT2B PE=1 SV=3

 Score =  104 bits (259), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 48/108 (44%), Positives = 73/108 (67%), Gaps = 4/108 (3%)

Query: 58  KNLTPRD----FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRI 113
           K+  PRD    + +L+ +++Q+++H+SAWPFMEPV   EAP YY V++ PMDLKT+  R+
Sbjct: 718 KSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERL 777

Query: 114 AQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             + Y     F+ D+ ++F NC+ YNP ES ++K A+ LE FF  K+K
Sbjct: 778 KNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIK 825

Functions as a histone acetyltransferase (HAT) to promote transcriptional activation. Has significant histone acetyltransferase activity with core histones (H3 and H4), and also with nucleosome core particles. Inhibits cell-cycle progression and counteracts the mitogenic activity of the adenoviral oncoprotein E1A. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q6FTW5|GCN5_CANGA Histone acetyltransferase GCN5 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=GCN5 PE=3 SV=1

 Score =  102 bits (253), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 43/101 (42%), Positives = 70/101 (69%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           + +++ ++ ++Q H +AWPF+ PV+  E PDYY  +KEPMDL T+EL++   +Y+K+ EF
Sbjct: 440 YAAIQNILVELQNHAAAWPFLRPVNKEEVPDYYEFIKEPMDLSTMELKLENNKYEKMEEF 499

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
           I D   + +NCR YN   + ++K+A++LE FF  KVK + E
Sbjct: 500 IYDARLVCNNCRLYNGENTSYYKYANRLEKFFNNKVKEIPE 540

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q9UUK2|GCN5_SCHPO Histone acetyltransferase gcn5 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=gcn5 PE=1 SV=1

 Score =  102 bits (253), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 44/97 (45%), Positives = 64/97 (65%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           F  L  L  ++Q H S+WPFM+PV   + PDYY V++ PMDL T+E R+   +Y+ + EF
Sbjct: 349 FAVLEMLFTEMQNHPSSWPFMQPVSKEDVPDYYEVIEHPMDLSTMEFRLRNNQYESVEEF 408

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           I D   IFDNCR YN   + ++K+A +LE FF +K++
Sbjct: 409 IRDAKYIFDNCRSYNDSNTTYYKNADRLEKFFQKKLR 445

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, and with a lower preference histone H4 to form H4K8ac and H4K16ac. Acetylation of histones gives a specific tag for epigenetic transcription activation.

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

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q8WZM0|GCN5_YARLI Histone acetyltransferase GCN5 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=GCN5 PE=3 SV=1

 Score =  100 bits (249), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 43/97 (44%), Positives = 65/97 (67%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           F  ++ ++ ++Q H SAWPF + V+  E PDYY V+KEPMDL T+E R+    YK + EF
Sbjct: 358 FAVMQHVLSELQNHASAWPFAQAVNRDEVPDYYEVIKEPMDLSTMEQRLEADSYKTMEEF 417

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           + D   +F+NCR YN   + ++K+A++LE F V K+K
Sbjct: 418 VYDARLVFNNCRAYNNETTTYYKNANKLEKFMVAKIK 454

Acetylates histone H2B to form H2BK11ac and H2BK16ac, histone H3 to form H3K14ac, with a lower preference histone H4 to form H4K8ac and H4K16ac, and contributes to H2A.Z acetylation. Acetylation of histones gives a specific tag for epigenetic transcription activation.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

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	171
332027303	2702	Nucleosome-remodeling factor subunit [Ac	0.947	0.059	0.785	2e-74
383857078	2734	PREDICTED: LOW QUALITY PROTEIN: nucleoso	0.947	0.059	0.785	4e-74
322790016	2261	hypothetical protein SINV_12870 [Solenop	0.947	0.071	0.779	5e-74
340712317	2081	PREDICTED: nucleosome-remodeling factor	0.947	0.077	0.779	8e-74
307206270	3705	Nucleosome-remodeling factor subunit NUR	0.947	0.043	0.779	1e-73
307180228	3651	Nucleosome-remodeling factor subunit NUR	0.935	0.043	0.782	1e-73
328788592	2735	PREDICTED: nucleosome-remodeling factor	0.947	0.059	0.779	1e-73
380014032	2734	PREDICTED: LOW QUALITY PROTEIN: nucleoso	0.947	0.059	0.779	2e-73
340712315	2733	PREDICTED: nucleosome-remodeling factor	0.947	0.059	0.779	2e-73
350417610	2733	PREDICTED: nucleosome-remodeling factor	0.947	0.059	0.779	3e-73

>gi|332027303|gb|EGI67387.1| Nucleosome-remodeling factor subunit [Acromyrmex echinatior]

 Score =  283 bits (723), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 128/163 (78%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E KFYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2540 ETKFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNAKDLDLL 2599

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2600 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2659

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2660 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSEGK 2702

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857078|ref|XP_003704033.1| PREDICTED: LOW QUALITY PROTEIN: nucleosome-remodeling factor subunit NURF301-like [Megachile rotundata]

 Score =  282 bits (721), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 128/163 (78%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2572 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNSKDLDLL 2631

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2632 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2691

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNPRESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2692 TKIFDNCRYYNPRESPFFKCAESLETYFVHKIKSLREKFSEGK 2734

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322790016|gb|EFZ15092.1| hypothetical protein SINV_12870 [Solenopsis invicta]

 Score =  281 bits (720), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 127/163 (77%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2099 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNAKDLDLL 2158

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2159 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2218

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2219 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSEGK 2261

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340712317|ref|XP_003394708.1| PREDICTED: nucleosome-remodeling factor subunit NURF301-like isoform 2 [Bombus terrestris]

 Score =  281 bits (718), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 127/163 (77%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 1919 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNAKDLDLL 1978

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 1979 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2038

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2039 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSEGK 2081

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307206270|gb|EFN84335.1| Nucleosome-remodeling factor subunit NURF301 [Harpegnathos saltator]

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 127/163 (77%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2629 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNTKDLDLL 2688

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2689 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2748

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2749 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSEGK 2791

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307180228|gb|EFN68261.1| Nucleosome-remodeling factor subunit NURF301 [Camponotus floridanus]

 Score =  280 bits (717), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 126/161 (78%), Positives = 139/161 (86%), Gaps = 1/161 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2583 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNAKDLDLL 2642

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2643 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2702

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVE 169
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E
Sbjct: 2703 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSE 2743

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328788592|ref|XP_395718.4| PREDICTED: nucleosome-remodeling factor subunit NURF301-like isoform 1 [Apis mellifera]

 Score =  280 bits (716), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 127/163 (77%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2573 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNAKDLDLL 2632

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2633 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2692

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2693 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSEGK 2735

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380014032|ref|XP_003691048.1| PREDICTED: LOW QUALITY PROTEIN: nucleosome-remodeling factor subunit NURF301-like [Apis florea]

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 127/163 (77%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2572 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNAKDLDLL 2631

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2632 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2691

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2692 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSEGK 2734

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340712315|ref|XP_003394707.1| PREDICTED: nucleosome-remodeling factor subunit NURF301-like isoform 1 [Bombus terrestris]

 Score =  279 bits (714), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 127/163 (77%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2571 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNAKDLDLL 2630

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2631 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2690

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2691 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSEGK 2733

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350417610|ref|XP_003491506.1| PREDICTED: nucleosome-remodeling factor subunit NURF301-like [Bombus impatiens]

 Score =  279 bits (713), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 127/163 (77%), Positives = 140/163 (85%), Gaps = 1/163 (0%)

Query: 10   EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN-NSSSNLANMKNLTPRDFESL 68
            E +FYICCD CQDWFHGRCVGILQSEADNIDEY+CPNC  NSS N ANMKNL  +D + L
Sbjct: 2571 ESQFYICCDKCQDWFHGRCVGILQSEADNIDEYVCPNCQRNSSVNFANMKNLNAKDLDLL 2630

Query: 69   RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
            +KL+KQIQAHKSAWPFMEPVDP+EAPDYY V+KEPMDL+TIELRI  + YKKLSEFIGDM
Sbjct: 2631 KKLIKQIQAHKSAWPFMEPVDPNEAPDYYKVIKEPMDLQTIELRINDRSYKKLSEFIGDM 2690

Query: 129  TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            TKIFDNCRYYNP+ESPFFK A  LE +FV K+K LREK  E K
Sbjct: 2691 TKIFDNCRYYNPKESPFFKCAESLETYFVHKIKSLREKFSEGK 2733

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	171
FB|FBgn0000541	2669	E(bx) "Enhancer of bithorax" [	0.935	0.059	0.677	8.1e-59
UNIPROTKB|E9PE19	650	BPTF "Nucleosome-remodeling fa	0.888	0.233	0.605	8.9e-54
UNIPROTKB|J3QQQ8	420	BPTF "Nucleosome-remodeling fa	0.888	0.361	0.605	8.9e-54
UNIPROTKB|E1C5C7	2789	BPTF "Uncharacterized protein"	0.888	0.054	0.631	1.8e-53
UNIPROTKB|E1C5C8	2802	BPTF "Uncharacterized protein"	0.888	0.054	0.631	1.8e-53
UNIPROTKB|F1LX76	2894	F1LX76 "Uncharacterized protei	0.888	0.052	0.625	8.1e-53
UNIPROTKB|F1M1V5	2952	F1M1V5 "Uncharacterized protei	0.888	0.051	0.625	8.3e-53
UNIPROTKB|F1M1V4	3013	F1M1V4 "Uncharacterized protei	0.888	0.050	0.625	8.5e-53
UNIPROTKB|F1PFZ4	2716	BPTF "Uncharacterized protein"	0.888	0.055	0.611	2e-52
UNIPROTKB|E7ETD6	2764	BPTF "Nucleosome-remodeling fa	0.888	0.054	0.611	2e-52

FB|FBgn0000541 E(bx) "Enhancer of bithorax" [Drosophila melanogaster (taxid:7227)]

 Score = 620 (223.3 bits), Expect = 8.1e-59, P = 8.1e-59
 Identities = 109/161 (67%), Positives = 128/161 (79%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSS-SNLANMKNLTPRDFESL 68
             E +FYICCD CQDWFHGRCVGILQSEA+ IDEY+CP C   + +N ANMK LT  D E L
Sbjct:  2506 ESQFYICCDKCQDWFHGRCVGILQSEAEFIDEYVCPECQRKNDANAANMKKLTSNDVEEL 2565

Query:    69 RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
             + L+KQ+Q HKSAWPFMEPVDP EAPDYY V+KEPMDLK +E+++    Y KLSEFIGDM
Sbjct:  2566 KNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDM 2625

Query:   129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVE 169
             TKIFDNCRYYNP+ES F+K A  LE +FVQK+K  RE + +
Sbjct:  2626 TKIFDNCRYYNPKESSFYKCAEALESYFVQKIKNFRENVFD 2666

GO:0042766 "nucleosome mobilization" evidence=IDA;TAS

GO:0006351 "transcription, DNA-dependent" evidence=IMP;IDA

GO:0016589 "NURF complex" evidence=NAS;IDA;TAS

GO:0006334 "nucleosome assembly" evidence=NAS

GO:0030097 "hemopoiesis" evidence=IMP

GO:0006338 "chromatin remodeling" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0035076 "ecdysone receptor-mediated signaling pathway" evidence=IGI

GO:0035073 "pupariation" evidence=IMP

GO:0016922 "ligand-dependent nuclear receptor binding" evidence=IPI

GO:0048813 "dendrite morphogenesis" evidence=IMP

GO:0006325 "chromatin organization" evidence=IMP

GO:0045747 "positive regulation of Notch signaling pathway" evidence=IGI;IMP

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

GO:0046331 "lateral inhibition" evidence=IMP

UNIPROTKB|E9PE19 BPTF "Nucleosome-remodeling factor subunit BPTF" [Homo sapiens (taxid:9606)]

 Score = 556 (200.8 bits), Expect = 8.9e-54, P = 8.9e-54
 Identities = 92/152 (60%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E +FYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct:   482 ESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 541

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+KL+EF+ DMT
Sbjct:   542 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMT 601

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:   602 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 633

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|J3QQQ8 BPTF "Nucleosome-remodeling factor subunit BPTF" [Homo sapiens (taxid:9606)]

 Score = 556 (200.8 bits), Expect = 8.9e-54, P = 8.9e-54
 Identities = 92/152 (60%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E +FYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct:   262 ESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 321

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+KL+EF+ DMT
Sbjct:   322 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMT 381

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:   382 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 413

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E1C5C7 BPTF "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 570 (205.7 bits), Expect = 1.8e-53, P = 1.8e-53
 Identities = 96/152 (63%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E KFYI CD CQ+W+HGRCVGILQSEAD IDEY+CP C ++   +  +  LT +D+E LR
Sbjct:  2621 ESKFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQCQSTEDAMTVLSPLTDKDYEGLR 2680

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E RI ++ YKK++EF+ DMT
Sbjct:  2681 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERILKRYYKKVTEFVADMT 2740

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:  2741 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 2772

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E1C5C8 BPTF "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 570 (205.7 bits), Expect = 1.8e-53, P = 1.8e-53
 Identities = 96/152 (63%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E KFYI CD CQ+W+HGRCVGILQSEAD IDEY+CP C ++   +  +  LT +D+E LR
Sbjct:  2634 ESKFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQCQSTEDAMTVLSPLTDKDYEGLR 2693

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E RI ++ YKK++EF+ DMT
Sbjct:  2694 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERILKRYYKKVTEFVADMT 2753

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:  2754 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 2785

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0001892 "embryonic placenta development" evidence=IEA

GO:0006338 "chromatin remodeling" evidence=IEA

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

GO:0007420 "brain development" evidence=IEA

GO:0007492 "endoderm development" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0016589 "NURF complex" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

UNIPROTKB|F1LX76 F1LX76 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 564 (203.6 bits), Expect = 8.1e-53, P = 8.1e-53
 Identities = 95/152 (62%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E KFYI CD CQ+WFHGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct:  2726 ESKFYIGCDRCQNWFHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 2785

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E RI ++ Y+KL+EF+ DMT
Sbjct:  2786 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMT 2845

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:  2846 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 2877

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1M1V5 F1M1V5 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 564 (203.6 bits), Expect = 8.3e-53, P = 8.3e-53
 Identities = 95/152 (62%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E KFYI CD CQ+WFHGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct:  2784 ESKFYIGCDRCQNWFHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 2843

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E RI ++ Y+KL+EF+ DMT
Sbjct:  2844 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMT 2903

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:  2904 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 2935

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1M1V4 F1M1V4 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 564 (203.6 bits), Expect = 8.5e-53, P = 8.5e-53
 Identities = 95/152 (62%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E KFYI CD CQ+WFHGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct:  2845 ESKFYIGCDRCQNWFHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 2904

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E RI ++ Y+KL+EF+ DMT
Sbjct:  2905 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMT 2964

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:  2965 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 2996

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1PFZ4 BPTF "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 560 (202.2 bits), Expect = 2.0e-52, P = 2.0e-52
 Identities = 93/152 (61%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E KFYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct:  2548 ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 2607

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+KL+EF+ DMT
Sbjct:  2608 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMT 2667

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:  2668 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 2699

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E7ETD6 BPTF "Nucleosome-remodeling factor subunit BPTF" [Homo sapiens (taxid:9606)]

 Score = 560 (202.2 bits), Expect = 2.0e-52, P = 2.0e-52
 Identities = 93/152 (61%), Positives = 124/152 (81%)

Query:    10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
             E KFYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct:  2596 ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 2655

Query:    70 KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
             ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+KL+EF+ DMT
Sbjct:  2656 RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMT 2715

Query:   130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             KIFDNCRYYNP +SPF++ A  LE FFVQK+K
Sbjct:  2716 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLK 2747

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9W0T1	NU301_DROME	No assigned EC number	0.6770	0.9356	0.0599	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	171
cd05509	101	cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like s	9e-46
smart00297	107	smart00297, BROMO, bromo domain	8e-31
cd04369	99	cd04369, Bromodomain, Bromodomain	2e-29
cd05504	115	cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like o	2e-25
cd05503	97	cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BA	1e-23
cd05511	112	cd05511, Bromo_TFIID, Bromodomain, TFIID-like subf	3e-22
pfam00439	84	pfam00439, Bromodomain, Bromodomain	3e-22
cd05506	99	cd05506, Bromo_plant1, Bromodomain, uncharacterize	1e-21
cd05498	102	cd05498, Bromo_Brdt_II_like, Bromodomain, Brdt_lik	8e-21
cd05497	107	cd05497, Bromo_Brdt_I_like, Bromodomain, Brdt_like	2e-20
cd05499	102	cd05499, Bromo_BDF1_2_II, Bromodomain	6e-20
cd05500	103	cd05500, Bromo_BDF1_2_I, Bromodomain	7e-19
COG5076	371	COG5076, COG5076, Transcription factor involved in	7e-19
cd05512	98	cd05512, Bromo_brd1_like, Bromodomain; brd1_like s	1e-18
cd05518	103	cd05518, Bromo_polybromo_IV, Bromodomain, polybrom	2e-18
cd05510	112	cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like s	3e-18
cd05495	108	cd05495, Bromo_cbp_like, Bromodomain, cbp_like sub	9e-16
cd05502	109	cd05502, Bromo_tif1_like, Bromodomain; tif1_like s	2e-15
cd05505	97	cd05505, Bromo_WSTF_like, Bromodomain; Williams sy	2e-15
cd05528	112	cd05528, Bromo_AAA, Bromodomain; sub-family co-occ	3e-14
cd05515	105	cd05515, Bromo_polybromo_V, Bromodomain, polybromo	2e-13
cd05529	128	cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repe	3e-11
cd05496	119	cd05496, Bromo_WDR9_II, Bromodomain; WDR9 repeat I	2e-10
cd05521	106	cd05521, Bromo_Rsc1_2_I, Bromodomain, repeat I in	4e-10
cd05507	104	cd05507, Bromo_brd8_like, Bromodomain, brd8_like s	6e-10
cd05522	104	cd05522, Bromo_Rsc1_2_II, Bromodomain, repeat II i	1e-09
cd05516	107	cd05516, Bromo_SNF2L2, Bromodomain, SNF2L2-like su	1e-09
cd05513	98	cd05513, Bromo_brd7_like, Bromodomain, brd7_like s	1e-09
COG5076	371	COG5076, COG5076, Transcription factor involved in	3e-09
cd05519	103	cd05519, Bromo_SNF2, Bromodomain, SNF2-like subfam	6e-09
cd05520	103	cd05520, Bromo_polybromo_III, Bromodomain, polybro	2e-08
cd05517	103	cd05517, Bromo_polybromo_II, Bromodomain, polybrom	3e-08
cd05525	106	cd05525, Bromo_ASH1, Bromodomain; ASH1_like sub-fa	8e-08
smart00249	47	smart00249, PHD, PHD zinc finger	2e-07
cd05508	99	cd05508, Bromo_RACK7, Bromodomain, RACK7_like subf	3e-07
cd05524	113	cd05524, Bromo_polybromo_I, Bromodomain, polybromo	3e-07
cd05494	114	cd05494, Bromodomain_1, Bromodomain; uncharacteriz	8e-07
cd05501	102	cd05501, Bromo_SP100C_like, Bromodomain, SP100C_li	6e-06
pfam00628	51	pfam00628, PHD, PHD-finger	9e-06
cd05526	110	cd05526, Bromo_polybromo_VI, Bromodomain, polybrom	0.001

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

 Score =  145 bits (367), Expect = 9e-46
 Identities = 48/98 (48%), Positives = 71/98 (72%)

Query: 64  DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
            +  L+K++  ++ HKSAWPF+EPVD  EAPDYY+V+K+PMDL T+E ++    Y  L E
Sbjct: 2   LYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEE 61

Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           F+ D+  IFDNCR YN  ++ ++K A++LE FF +K+K
Sbjct: 62  FVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLK 99

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|197636 smart00297, BROMO, bromo domain

 Score =  107 bits (269), Expect = 8e-31
 Identities = 40/98 (40%), Positives = 66/98 (67%)

Query: 66  ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           E L+ ++ ++ +H  +WPF++PV   EAPDYY+++K+PMDLKTI+ ++   +Y  + EF+
Sbjct: 10  ELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFV 69

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
            D   +F N R YN  +S  +K A +LE FF +K++ L
Sbjct: 70  ADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107

Length = 107

>gnl|CDD|99922 cd04369, Bromodomain, Bromodomain

 Score =  103 bits (259), Expect = 2e-29
 Identities = 42/97 (43%), Positives = 58/97 (59%), Gaps = 2/97 (2%)

Query: 66  ESLRKLMKQIQAH--KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
           + LR L+  ++      + PF+EPVDP EAPDYY V+K PMDL TI+ ++    YK L E
Sbjct: 3   KKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEE 62

Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
           F  D+  IF N + YN   SP +K A +LE  F + +
Sbjct: 63  FEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFEKLL 99

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

>gnl|CDD|99936 cd05504, Bromo_Acf1_like, Bromodomain; Acf1_like or BAZ1A_like subfamily

 Score = 94.0 bits (234), Expect = 2e-25
 Identities = 38/96 (39%), Positives = 61/96 (63%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           L +L+ +I  HK +WPF+ PV   E PDYY+++K+PMDL TI+ ++    YK   EF+ D
Sbjct: 17  LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSD 76

Query: 128 MTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
           +  +F NC  YNP  +  +K   +L+ FF+++ + L
Sbjct: 77  IQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112

Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 115

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

 Score = 88.6 bits (220), Expect = 1e-23
 Identities = 33/93 (35%), Positives = 53/93 (56%)

Query: 64  DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
           D      ++ +++AH+ AWPF+EPV+    P Y  ++K+PMD  TI  ++   +YK L E
Sbjct: 1   DLALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEE 60

Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
           F  D+  +FDNC  +N  +S   +  H +  FF
Sbjct: 61  FAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF 93

Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 97

>gnl|CDD|99943 cd05511, Bromo_TFIID, Bromodomain, TFIID-like subfamily

 Score = 85.4 bits (212), Expect = 3e-22
 Identities = 33/90 (36%), Positives = 53/90 (58%)

Query: 81  AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP 140
           +WPF  PV+  + PDYY ++K PMDL+TI  +I++ +Y+   EF+ D+  I DN   YN 
Sbjct: 18  SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNG 77

Query: 141 RESPFFKHAHQLEMFFVQKVKILREKLVEL 170
            +S + K A ++     + +    EKL +L
Sbjct: 78  PDSVYTKKAKEMLELAEELLAEREEKLTQL 107

Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 112

>gnl|CDD|215921 pfam00439, Bromodomain, Bromodomain

 Score = 84.8 bits (210), Expect = 3e-22
 Identities = 37/84 (44%), Positives = 53/84 (63%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
             ++++ +  H  A PF+EPVDP E PDYY V+KEPMDL TI  ++   +YK L+EF+ D
Sbjct: 1   CLEILEDLMEHPLAEPFLEPVDPEEYPDYYEVIKEPMDLSTIRQKLKSGKYKSLAEFLKD 60

Query: 128 MTKIFDNCRYYNPRESPFFKHAHQ 151
           +  IF N   YN  +S  +K A +
Sbjct: 61  VELIFSNAITYNGEDSDIYKDAKK 84

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

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

 Score = 83.5 bits (207), Expect = 1e-21
 Identities = 34/92 (36%), Positives = 49/92 (53%), Gaps = 7/92 (7%)

Query: 67  SLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
            LRKLMK    HK  W F  PVD      PDY++++K+PMDL T++ ++ +  Y    EF
Sbjct: 8   LLRKLMK----HKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEF 63

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQL-EMF 155
             D+   F N   YNP  +     A +L ++F
Sbjct: 64  AADVRLTFANAMRYNPPGNDVHTMAKELLKIF 95

Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 99

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

 Score = 81.6 bits (202), Expect = 8e-21
 Identities = 35/95 (36%), Positives = 54/95 (56%), Gaps = 5/95 (5%)

Query: 68  LRKLMKQIQAHKS-AWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           L++L  +   HK+ AWPF +PVDP      DY++++K PMDL TI+ ++  + Y    EF
Sbjct: 9   LKELFSK--KHKAYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEF 66

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQK 159
             D+  +F NC  YNP + P    A +L+  F  +
Sbjct: 67  AADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101

Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 102

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

 Score = 80.5 bits (199), Expect = 2e-20
 Identities = 38/96 (39%), Positives = 51/96 (53%), Gaps = 2/96 (2%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           L+ ++K +  HK AWPF +PVD      PDY+ ++K PMDL TI+ R+    Y   SE I
Sbjct: 10  LKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECI 69

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
            D   +F NC  YN         A  LE  F+QK+ 
Sbjct: 70  QDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLA 105

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

>gnl|CDD|99931 cd05499, Bromo_BDF1_2_II, Bromodomain

 Score = 79.3 bits (196), Expect = 6e-20
 Identities = 36/93 (38%), Positives = 55/93 (59%), Gaps = 3/93 (3%)

Query: 66  ESLRKLMKQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
           E L++LMK  +     WPF++PVDP     P+Y++++K+PMDL TI  ++   +Y+   E
Sbjct: 7   EVLKELMKP-KHSAYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKE 65

Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
           F  D+  IF NC  +NP  +  +   HQLE  F
Sbjct: 66  FERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVF 98

BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 102

>gnl|CDD|99932 cd05500, Bromo_BDF1_2_I, Bromodomain

 Score = 76.6 bits (189), Expect = 7e-19
 Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 73  KQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
           + ++  K A PF+ PVDP     P Y  ++K+PMDL TIE ++    Y  + EF  D   
Sbjct: 14  RSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNL 73

Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFF 156
           + DNC  +N  E P  +   +L+  F
Sbjct: 74  MVDNCLTFNGPEHPVSQMGKRLQAAF 99

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

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

 Score = 81.8 bits (202), Expect = 7e-19
 Identities = 38/115 (33%), Positives = 64/115 (55%), Gaps = 3/115 (2%)

Query: 59  NLTPRDFESLRKLMKQ---IQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ 115
            L   D +++ K  KQ         +  F+      E PDYY ++K PMDL TI+ ++  
Sbjct: 141 ELLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKN 200

Query: 116 QRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
            RYK   EF+ D+  +FDNC+ YN  +S  +  A +LE +F++ ++ + E+++EL
Sbjct: 201 GRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLEL 255

Length = 371

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

 Score = 76.3 bits (188), Expect = 1e-18
 Identities = 34/86 (39%), Positives = 52/86 (60%)

Query: 67  SLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIG 126
            LRK + Q+Q   +A  F EPVD  E PDY + +K+PMD  T+  ++  QRY+ L +F  
Sbjct: 5   LLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEA 64

Query: 127 DMTKIFDNCRYYNPRESPFFKHAHQL 152
           D   I +NC  YN +++ F++ A +L
Sbjct: 65  DFNLIINNCLAYNAKDTIFYRAAVRL 90

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|99949 cd05518, Bromo_polybromo_IV, Bromodomain, polybromo repeat IV

 Score = 75.2 bits (185), Expect = 2e-18
 Identities = 32/84 (38%), Positives = 45/84 (53%), Gaps = 7/84 (8%)

Query: 84  FMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES 143
           FME     + PDYY ++ EP+DLKTIE  I   +Y    E + D   +F N R+YN   S
Sbjct: 27  FMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGS 86

Query: 144 PFFKHAHQLEMFFVQKVKILREKL 167
             ++ A+ LE       K+L+EK 
Sbjct: 87  QVYEDANILE-------KVLKEKR 103

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

>gnl|CDD|99942 cd05510, Bromo_SPT7_like, Bromodomain; SPT7_like subfamily

 Score = 75.2 bits (185), Expect = 3e-18
 Identities = 33/91 (36%), Positives = 59/91 (64%), Gaps = 2/91 (2%)

Query: 65  FESLRKLMKQIQAH-KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
           +ESL K++ +++ + + + PF+  V   EAPDYY+++K+PMDL T+  ++   +YK  +E
Sbjct: 9   YESLDKVLNELKTYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAE 68

Query: 124 FIGDMTKIFDNCRYYNPRES-PFFKHAHQLE 153
           F+ D+  I+ NC  YN   S P  +HA+ ++
Sbjct: 69  FVDDLNLIWKNCLLYNSDPSHPLRRHANFMK 99

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|99927 cd05495, Bromo_cbp_like, Bromodomain, cbp_like subfamily

 Score = 68.6 bits (168), Expect = 9e-16
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 5/95 (5%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           L KL KQ      + PF +PVDP     PDY+++VK PMDL TI  ++   +Y+   +++
Sbjct: 12  LEKLYKQ---DPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYV 68

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
            D+  +FDN   YN + S  +K+  +L   F Q++
Sbjct: 69  DDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQEI 103

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

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

 Score = 67.7 bits (166), Expect = 2e-15
 Identities = 35/105 (33%), Positives = 59/105 (56%), Gaps = 4/105 (3%)

Query: 60  LTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRI---AQQ 116
           L+P D     +L+ ++  H+ + PF EPV P   P+YY ++K PMDL  I  ++   + Q
Sbjct: 1   LSPIDQRKCERLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQ 59

Query: 117 RYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
            Y    EF+ D+  +F NC  +N  +S   +   +LE+FF +++K
Sbjct: 60  HYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLK 104

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

 Score = 67.6 bits (165), Expect = 2e-15
 Identities = 26/80 (32%), Positives = 44/80 (55%)

Query: 64  DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
           + +   +++ +I  ++ +WPF EPV   EA DY  V+  PMDL+T++ + +   Y  + E
Sbjct: 1   ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQE 60

Query: 124 FIGDMTKIFDNCRYYNPRES 143
           F+ DM  +F N   Y    S
Sbjct: 61  FLDDMKLVFSNAEKYYENGS 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|99957 cd05528, Bromo_AAA, Bromodomain; sub-family co-occurring with AAA domains

 Score = 64.7 bits (158), Expect = 3e-14
 Identities = 29/77 (37%), Positives = 45/77 (58%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           LR ++K++ + K    F +PVD  E PDYY ++K+PMDL+TI  ++   +Y    +F+ D
Sbjct: 8   LRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKD 67

Query: 128 MTKIFDNCRYYNPRESP 144
           +  I  N   YNP   P
Sbjct: 68  IDLIVTNALEYNPDRDP 84

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|99946 cd05515, Bromo_polybromo_V, Bromodomain, polybromo repeat V

 Score = 62.3 bits (152), Expect = 2e-13
 Identities = 25/82 (30%), Positives = 44/82 (53%)

Query: 78  HKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRY 137
            + +  FM      E PDYY+V+K+P+D++ I  +I   +Y+ L + + D   +FDN   
Sbjct: 21  RRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

Query: 138 YNPRESPFFKHAHQLEMFFVQK 159
           YN  +S  +K A  L+   ++ 
Sbjct: 81  YNEPDSQIYKDALTLQKVLLET 102

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

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

 Score = 57.3 bits (139), Expect = 3e-11
 Identities = 31/94 (32%), Positives = 42/94 (44%), Gaps = 2/94 (2%)

Query: 61  TPRDFESLRKLMKQIQAHKSAWPFMEPVD-PHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
             R    L KL+  +Q   +   F  PVD     PDY+N V  PMDL+TI  R+  + Y+
Sbjct: 26  RERLISGLDKLLLSLQLEIAE-YFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYR 84

Query: 120 KLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLE 153
            L     D+  I  N   +N   S   K A +L 
Sbjct: 85  SLEALRHDVRLILSNAETFNEPNSEIAKKAKRLS 118

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

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

 Score = 54.8 bits (132), Expect = 2e-10
 Identities = 27/94 (28%), Positives = 48/94 (51%), Gaps = 1/94 (1%)

Query: 69  RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           ++L+  +   + + PF +PVD  + PDY +++  PMDL T++  +    Y    EF  D+
Sbjct: 11  KELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDV 70

Query: 129 TKIFDNCRYYNP-RESPFFKHAHQLEMFFVQKVK 161
             IF N + Y P + S  +    +L   F + +K
Sbjct: 71  RLIFSNSKSYTPNKRSRIYSMTLRLSALFEEHIK 104

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

 Score = 53.9 bits (130), Expect = 4e-10
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 92  EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQ 151
           + PDYY ++K P+ L T++ R+    Y    EF+ D+ +I  N R YN + S  +K+A  
Sbjct: 36  DYPDYYKIIKNPLSLNTVKKRL--PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALI 93

Query: 152 LEMFFVQKV 160
           LE +    +
Sbjct: 94  LEKYINDVI 102

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

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

 Score = 53.5 bits (129), Expect = 6e-10
 Identities = 24/73 (32%), Positives = 40/73 (54%)

Query: 67  SLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIG 126
           ++  + + + +H+ A  F++PV    AP Y++VV  PMDL TI+  I     +  +EF  
Sbjct: 7   AILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQR 66

Query: 127 DMTKIFDNCRYYN 139
           D+  +F N   YN
Sbjct: 67  DVLLMFQNAIMYN 79

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

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 20/65 (30%), Positives = 37/65 (56%)

Query: 89  DPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKH 148
           D    P+YY  +  P+ L  I+ ++ +++YK   +F+ D+  +F+N + YN  +S  +K 
Sbjct: 33  DKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKD 92

Query: 149 AHQLE 153
           A  LE
Sbjct: 93  AVLLE 97

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

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

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 22/98 (22%), Positives = 48/98 (48%), Gaps = 6/98 (6%)

Query: 66  ESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
           + + K++  +  +K       A  F++     E P+YY ++++P+D K I+ RI   +Y+
Sbjct: 4   KKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYR 63

Query: 120 KLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFV 157
            L +   D+  +  N + +N   S  ++ +  L+  F 
Sbjct: 64  SLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFK 101

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|99945 cd05513, Bromo_brd7_like, Bromodomain, brd7_like subgroup

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 26/87 (29%), Positives = 47/87 (54%)

Query: 66  ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           ++L +L++Q+Q       F  PV    AP Y +++K PMD  T++ +I    Y+ + EF 
Sbjct: 4   KALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFK 63

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQL 152
            D   + +N   YN  ++ ++K A +L
Sbjct: 64  DDFKLMCENAMKYNKPDTIYYKAAKKL 90

The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 98

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

 Score = 54.4 bits (131), Expect = 3e-09
 Identities = 32/91 (35%), Positives = 43/91 (47%), Gaps = 1/91 (1%)

Query: 50  SSSNLANMKNLTPRDFESLRKLMKQ-IQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKT 108
               L         + E    ++    QAH  AWPF+ PV   E PDYY  +++PMDL T
Sbjct: 249 PEEMLELSIKPGREEREERESVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLST 308

Query: 109 IELRIAQQRYKKLSEFIGDMTKIFDNCRYYN 139
            EL++    Y+    F+ D    FDNC  YN
Sbjct: 309 KELKLRNNYYRPEETFVRDAKLFFDNCVMYN 339

Length = 371

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

 Score = 50.8 bits (122), Expect = 6e-09
 Identities = 28/76 (36%), Positives = 41/76 (53%)

Query: 84  FMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES 143
           F+E       PDYY ++K P+ L  I+ RI  + YK L EF+ D   +F N R YN   S
Sbjct: 27  FLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGS 86

Query: 144 PFFKHAHQLEMFFVQK 159
             ++ A ++E  F +K
Sbjct: 87  IVYEDAVEMEKAFKKK 102

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

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

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 22/71 (30%), Positives = 38/71 (53%)

Query: 83  PFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE 142
           PF++     + PDYY  +K P+ L+ I  ++    Y+ L E   D+  +F+N + YN   
Sbjct: 26  PFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPN 85

Query: 143 SPFFKHAHQLE 153
           S  +K A +L+
Sbjct: 86  SRIYKDAEKLQ 96

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 = 48.6 bits (116), Expect = 3e-08
 Identities = 25/66 (37%), Positives = 37/66 (56%)

Query: 94  PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLE 153
           PDYY V+KEP+DLKTI  RI    YK + +   D+  +  N + +N   S  +K A+ ++
Sbjct: 37  PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIK 96

Query: 154 MFFVQK 159
             F  K
Sbjct: 97  KIFTAK 102

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

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

 Score = 47.8 bits (114), Expect = 8e-08
 Identities = 25/65 (38%), Positives = 34/65 (52%)

Query: 94  PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLE 153
           PDYY  + +P+DL TIE +I    YK    F  DM K+F N   Y  R+SP  +   +L 
Sbjct: 39  PDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLR 98

Query: 154 MFFVQ 158
             + Q
Sbjct: 99  KAYYQ 103

ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. Length = 106

>gnl|CDD|214584 smart00249, PHD, PHD zinc finger

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 15 ICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
          + CD C  W+H  C+G    E +   ++ CP C
Sbjct: 15 LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. Length = 47

>gnl|CDD|99940 cd05508, Bromo_RACK7, Bromodomain, RACK7_like subfamily

 Score = 46.2 bits (110), Expect = 3e-07
 Identities = 26/68 (38%), Positives = 35/68 (51%), Gaps = 4/68 (5%)

Query: 72  MKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKI 131
           MKQ  A     PF++PVD  + PDY   V +PMDL T+E  + ++ Y     F+ D   I
Sbjct: 15  MKQPGAE----PFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWI 70

Query: 132 FDNCRYYN 139
             N   YN
Sbjct: 71  LHNAIIYN 78

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|99954 cd05524, Bromo_polybromo_I, Bromodomain, polybromo repeat I

 Score = 46.2 bits (110), Expect = 3e-07
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 94  PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQL- 152
           P+YY VV  P+DL  I+ ++  + Y  + +   D   + +N + Y   +SP  K A +L 
Sbjct: 39  PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLW 98

Query: 153 EMFFVQKVKIL 163
           E+F   + ++L
Sbjct: 99  ELFLSARNEVL 109

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

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

 Score = 45.5 bits (108), Expect = 8e-07
 Identities = 18/41 (43%), Positives = 27/41 (65%), Gaps = 2/41 (4%)

Query: 71  LMKQIQAHKSAWPFMEPVDPHE--APDYYNVVKEPMDLKTI 109
            +K+ + ++ AWPF+EPV+P    APDY +V+K PM   T 
Sbjct: 11  ELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTK 51

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

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

 Score = 42.8 bits (101), Expect = 6e-06
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 89  DPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKH 148
            P+   DY   +KEPM L  ++ R+ ++ Y  +  F+ DM  IF N + +  ++  F + 
Sbjct: 26  KPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFY-KDDDFGQV 84

Query: 149 AHQLEMFF 156
              LE  F
Sbjct: 85  GITLEKKF 92

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

>gnl|CDD|201356 pfam00628, PHD, PHD-finger

 Score = 40.9 bits (96), Expect = 9e-06
 Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)

Query: 10 EPKFYICCDTCQDWFHGRCVGI-LQSEADNIDEYICPNC 47
          +    + CD C  WFH  C+G  L+ E     E+ CP C
Sbjct: 10 DDGELLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPEC 48

PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3. Length = 51

>gnl|CDD|99956 cd05526, Bromo_polybromo_VI, Bromodomain, polybromo repeat VI

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 19/70 (27%), Positives = 37/70 (52%)

Query: 90  PHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHA 149
           P  A D     K P+ L  I+  + + RY++L +F  DM ++ +  R  +  +S  ++ A
Sbjct: 34  PELAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTDSEIYEDA 93

Query: 150 HQLEMFFVQK 159
            +L+ FF++ 
Sbjct: 94  VELQQFFIKI 103

Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. Length = 110

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	171
cd05496	119	Bromo_WDR9_II Bromodomain; WDR9 repeat II_like sub	100.0
cd05497	107	Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily	99.98
cd05505	97	Bromo_WSTF_like Bromodomain; Williams syndrome tra	99.98
cd05495	108	Bromo_cbp_like Bromodomain, cbp_like subfamily. Cb	99.98
cd05502	109	Bromo_tif1_like Bromodomain; tif1_like subfamily.	99.97
cd05504	115	Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_li	99.97
cd05503	97	Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like s	99.97
cd05508	99	Bromo_RACK7 Bromodomain, RACK7_like subfamily. RAC	99.97
cd05511	112	Bromo_TFIID Bromodomain, TFIID-like subfamily. Hum	99.97
cd05507	104	Bromo_brd8_like Bromodomain, brd8_like subgroup. I	99.97
cd05509	101	Bromo_gcn5_like Bromodomain; Gcn5_like subfamily.	99.97
cd05500	103	Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfami	99.97
cd05510	112	Bromo_SPT7_like Bromodomain; SPT7_like subfamily.	99.97
cd05501	102	Bromo_SP100C_like Bromodomain, SP100C_like subfami	99.97
cd05499	102	Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfam	99.96
cd05506	99	Bromo_plant1 Bromodomain, uncharacterized subfamil	99.96
cd05516	107	Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, s	99.96
cd05498	102	Bromo_Brdt_II_like Bromodomain, Brdt_like subfamil	99.96
cd05528	112	Bromo_AAA Bromodomain; sub-family co-occurring wit	99.96
cd05513	98	Bromo_brd7_like Bromodomain, brd7_like subgroup. T	99.96
cd05512	98	Bromo_brd1_like Bromodomain; brd1_like subfamily.	99.96
cd05529	128	Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like	99.96
cd05524	113	Bromo_polybromo_I Bromodomain, polybromo repeat I.	99.96
KOG1474|consensus	640		99.95
cd05519	103	Bromo_SNF2 Bromodomain, SNF2-like subfamily, speci	99.95
cd05525	106	Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1	99.95
cd05515	105	Bromo_polybromo_V Bromodomain, polybromo repeat V.	99.95
cd05520	103	Bromo_polybromo_III Bromodomain, polybromo repeat	99.95
smart00297	107	BROMO bromo domain.	99.95
cd05517	103	Bromo_polybromo_II Bromodomain, polybromo repeat I	99.95
cd05518	103	Bromo_polybromo_IV Bromodomain, polybromo repeat I	99.95
cd05522	104	Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_l	99.94
PF00439	84	Bromodomain: Bromodomain; InterPro: IPR001487 Brom	99.93
cd05521	106	Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_lik	99.93
cd05492	109	Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family	99.93
cd04369	99	Bromodomain Bromodomain. Bromodomains are found in	99.92
KOG1245|consensus	1404		99.91
cd05526	110	Bromo_polybromo_VI Bromodomain, polybromo repeat V	99.88
COG5076	371	Transcription factor involved in chromatin remodel	99.82
KOG1472|consensus	720		99.66
cd05494	114	Bromodomain_1 Bromodomain; uncharacterized subfami	99.45
KOG0955|consensus	1051		99.44
cd05491	119	Bromo_TBP7_like Bromodomain; TBP7_like subfamily,	99.41
KOG0008|consensus	1563		99.33
KOG1827|consensus	629		99.3
KOG0008|consensus	1563		99.17
KOG0386|consensus	1157		99.13
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	99.05
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	98.98
KOG1472|consensus	720		98.96
KOG1828|consensus	418		98.66
KOG1828|consensus	418		98.65
KOG1474|consensus	640		98.52
cd05493	131	Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-	98.21
KOG4299|consensus	613		97.94
KOG1632|consensus	345		97.82
KOG4323|consensus	464		97.7
KOG3612|consensus	588		97.64
PF13831	36	PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.	97.46
COG5076	371	Transcription factor involved in chromatin remodel	97.44
KOG0383|consensus	696		97.36
KOG1512|consensus	381		97.19
KOG0644|consensus	1113		97.09
KOG0825|consensus	1134		96.84
KOG1844|consensus	508		96.53
KOG0954|consensus	893		96.37
KOG2752|consensus	345		96.24
cd04718	148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	95.84
KOG0955|consensus	1051		95.69
KOG0957|consensus	707		95.35
KOG1473|consensus	1414		95.27
PF07496	50	zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zi	94.3
KOG1632|consensus	345		93.7
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	93.42
KOG0732|consensus	1080		92.83
PF15446	175	zf-PHD-like: PHD/FYVE-zinc-finger like domain	92.75
PF00301	47	Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubred	92.23
PF13832	110	zf-HC5HC2H_2: PHD-zinc-finger like domain	92.07
PF07227	446	DUF1423: Protein of unknown function (DUF1423); In	91.97
COG5141	669	PHD zinc finger-containing protein [General functi	91.72
cd00730	50	rubredoxin Rubredoxin; nonheme iron binding domain	91.2
KOG0956|consensus	900		90.89
COG1773	55	Rubredoxin [Energy production and conversion]	89.36
KOG0957|consensus	707		89.34
PF07649	30	C1_3: C1-like domain; InterPro: IPR011424 This sho	89.2
TIGR02606	69	antidote_CC2985 putative addiction module antidote	88.74
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	88.1
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	87.46
KOG0644|consensus	1113		87.42
PF10497	105	zf-4CXXC_R1: Zinc-finger domain of monoamine-oxida	86.47
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	85.38
KOG1512|consensus	381		85.01
PF13771	90	zf-HC5HC2H: PHD-like zinc-binding domain	85.0
KOG1827|consensus	629		84.86
PF03693	80	RHH_2: Uncharacterised protein family (UPF0156); I	84.13
PF14372	101	DUF4413: Domain of unknown function (DUF4413)	82.8
KOG4443|consensus	694		82.22
PF13913	25	zf-C2HC_2: zinc-finger of a C2HC-type	81.4

>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily

Probab=100.00  E-value=4.2e-32  Score=183.66  Aligned_cols=107  Identities=25%  Similarity=0.450  Sum_probs=102.5

Q ss_pred             hhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCC
Q psy5115          62 PRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPR  141 (171)
Q Consensus        62 ~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~  141 (171)
                      +++.+.|..+++.|++++.+++|..||++..+|+|+++|++||||+||++||++|.|.++.+|.+||+|||.||..||++
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            46788999999999999999999999999999999999999999999999999999999999999999999999999985


Q ss_pred             -CCHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy5115         142 -ESPFFKHAHQLEMFFVQKVKILREKLV  168 (171)
Q Consensus       142 -~s~~~~~a~~l~~~f~~~~~~~~~~~~  168 (171)
                       +|.++.+|..|++.|++.++++.+.+.
T Consensus        84 ~~s~i~~~a~~L~~~F~~~~~~l~~~~~  111 (119)
T cd05496          84 KRSRIYSMTLRLSALFEEHIKKIISDWK  111 (119)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             899999999999999999999988774

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=99.98  E-value=6e-32  Score=180.29  Aligned_cols=103  Identities=38%  Similarity=0.619  Sum_probs=95.8

Q ss_pred             ChhHHHHHHHHHHHHHhCcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          61 TPRDFESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      +.+..-.+..+|+.|.+++.+++|..||++.  .+|+|+++|++||||++|++||++|.|.|+++|.+||+|||.||..|
T Consensus         3 ~~q~~~~~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~y   82 (107)
T cd05497           3 TNQLQYLLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIY   82 (107)
T ss_pred             cHHHHHHHHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            3444555678899999999999999999987  69999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      |+++|.++.+|..|++.|++.++++
T Consensus        83 N~~~s~i~~~A~~l~~~f~~~l~~~  107 (107)
T cd05497          83 NKPGDDVVLMAQTLEKLFLQKLAQM  107 (107)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999998764

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

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

Probab=99.98  E-value=4.3e-32  Score=177.83  Aligned_cols=96  Identities=29%  Similarity=0.556  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCC
Q psy5115          64 DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES  143 (171)
Q Consensus        64 ~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s  143 (171)
                      +++.|.++++.|++++.+++|..||++..+|+|+++|++||||+||++||++|.|.|+++|.+||+|||+||..||+++|
T Consensus         1 ~~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s   80 (97)
T cd05505           1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS   80 (97)
T ss_pred             CHHHHHHHHHHHHhCCCcccccCCCChhhcccHHHHcCCcCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q psy5115         144 PFFKHAHQLEMFFVQK  159 (171)
Q Consensus       144 ~~~~~a~~l~~~f~~~  159 (171)
                      .++..|..|++.|.+.
T Consensus        81 ~i~~~a~~le~~f~~~   96 (97)
T cd05505          81 YVLSCMRKTEQCCVNL   96 (97)
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999875

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.

>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily

Probab=99.98  E-value=1.8e-31  Score=178.32  Aligned_cols=102  Identities=29%  Similarity=0.581  Sum_probs=98.0

Q ss_pred             hhHHHHHHHHHHHHHhC-cCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          62 PRDFESLRKLMKQIQAH-KSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        62 ~~~~~~~~~~l~~l~~~-~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      +++++.|..+++.|.++ +.+++|..||++.  ++|+|+++|++||||+||++||++|.|.++.+|.+||++||+||..|
T Consensus         2 ~~l~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~y   81 (108)
T cd05495           2 EELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLY   81 (108)
T ss_pred             HHHHHHHHHHHHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHH
Confidence            46788999999999999 9999999999987  69999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      |+++|.++++|..|++.|++.++.+
T Consensus        82 N~~~s~i~~~a~~l~~~F~~~~~~~  106 (108)
T cd05495          82 NRKTSRVYKYCTKLAEVFEQEIDPV  106 (108)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999998865

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.

>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily

Probab=99.97  E-value=7.4e-31  Score=176.12  Aligned_cols=104  Identities=34%  Similarity=0.702  Sum_probs=100.3

Q ss_pred             CChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHh
Q psy5115          60 LTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ---QRYKKLSEFIGDMTKIFDNCR  136 (171)
Q Consensus        60 l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~---~~Y~s~~~f~~Dv~li~~Na~  136 (171)
                      |++.+++.|.+++..|++++.+++|..||++ .+|+|+++|++||||++|++||++   |.|.++++|.+||++||+||.
T Consensus         1 ~~~~~~~~c~~il~~l~~~~~s~~F~~pv~~-~~p~Y~~iI~~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~   79 (109)
T cd05502           1 LSPIDQRKCERLLLELYCHELSLPFHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCY   79 (109)
T ss_pred             CCHHHHHHHHHHHHHHHhCCCChhhcCCCCC-CCCCHHHHCCCCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Confidence            5788999999999999999999999999999 799999999999999999999998   699999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         137 YYNPRESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       137 ~yn~~~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      .||+++|.++.+|..|++.|++.++++.
T Consensus        80 ~yN~~~s~i~~~a~~l~~~f~~~~~~~~  107 (109)
T cd05502          80 KFNEEDSEVAQAGKELELFFEEQLKEIL  107 (109)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHC
Confidence            9999999999999999999999998864

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.

>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily

Probab=99.97  E-value=7.3e-31  Score=177.22  Aligned_cols=105  Identities=37%  Similarity=0.820  Sum_probs=101.2

Q ss_pred             CCChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          59 NLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        59 ~l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      .-.+.++..|..+|..|+.++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|.+||+|||+||..|
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            44678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      |+++|.++.+|..|++.|++.++++
T Consensus        88 N~~~s~i~~~A~~l~~~f~~~~~~~  112 (115)
T cd05504          88 NPEHTSVYKAGTRLQRFFIKRCRKL  112 (115)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999876

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

>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily

Probab=99.97  E-value=2.9e-31  Score=174.46  Aligned_cols=97  Identities=34%  Similarity=0.747  Sum_probs=93.9

Q ss_pred             HHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCC
Q psy5115          64 DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES  143 (171)
Q Consensus        64 ~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s  143 (171)
                      ++..|.+++..|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|..||++||+||..||+++|
T Consensus         1 ~~~~c~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s   80 (97)
T cd05503           1 DLALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDS   80 (97)
T ss_pred             CHHHHHHHHHHHHcCCCchhhcCCCCccccCCHHHHhCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q psy5115         144 PFFKHAHQLEMFFVQKV  160 (171)
Q Consensus       144 ~~~~~a~~l~~~f~~~~  160 (171)
                      .++++|..|++.|++.|
T Consensus        81 ~i~~~a~~l~~~f~~~~   97 (97)
T cd05503          81 EVGRAGHNMRKFFEKRW   97 (97)
T ss_pred             HHHHHHHHHHHHHHHhC
Confidence            99999999999999875

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.

>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily

Probab=99.97  E-value=7.7e-31  Score=172.27  Aligned_cols=96  Identities=27%  Similarity=0.446  Sum_probs=90.3

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      +....|..++..+. ++.+++|..||++..+|+|+.+|++||||+||++||++|.|.|+++|.+||+|||+||..||+++
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            45566777888888 99999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQK  159 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~  159 (171)
                      |.++.+|+.|.+.+++.
T Consensus        82 s~i~~~A~~l~~~~~~e   98 (99)
T cd05508          82 HKLTQAAKAIVKICEQE   98 (99)
T ss_pred             CHHHHHHHHHHHHHHhh
Confidence            99999999999998865

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.

>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily

Probab=99.97  E-value=9.8e-31  Score=175.91  Aligned_cols=106  Identities=32%  Similarity=0.626  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHH
Q psy5115          66 ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPF  145 (171)
Q Consensus        66 ~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~  145 (171)
                      -.+..+++.|++++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|.+||++||+||..||+++|.+
T Consensus         3 ~~l~~ii~~l~~~~~s~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i   82 (112)
T cd05511           3 FILDEIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVY   82 (112)
T ss_pred             HHHHHHHHHHHhCCCchhhcCCCChhhcccHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHH
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhcC
Q psy5115         146 FKHAHQLEMFFVQKVKILREKLVELK  171 (171)
Q Consensus       146 ~~~a~~l~~~f~~~~~~~~~~~~~~~  171 (171)
                      +.+|..|++.|++.++++++++++++
T Consensus        83 ~~~A~~l~~~~~~~~~~~~~~~~~~~  108 (112)
T cd05511          83 TKKAKEMLELAEELLAEREEKLTQLE  108 (112)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            99999999999999999999998763

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.

>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup

Probab=99.97  E-value=1.2e-30  Score=173.50  Aligned_cols=100  Identities=25%  Similarity=0.407  Sum_probs=96.2

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      .+++.|..+++.|..++.+++|..||++..+|+|+++|++||||+||++||++|.|.|+++|.+||.|||+||..||+++
T Consensus         3 ~~~~~~~~il~~l~~~~~a~~F~~pV~~~~~p~Y~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~   82 (104)
T cd05507           3 AWKKAILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSD   82 (104)
T ss_pred             HHHHHHHHHHHHHHcCCCCHhhcCCCCccccCCHHHHhCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            46788999999999999999999999998999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKI  162 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~  162 (171)
                      |.++.+|..|++.+.+.+..
T Consensus        83 s~v~~~A~~l~~~~~~~~~~  102 (104)
T cd05507          83 HDVYLMAVEMQREVMSQIQQ  102 (104)
T ss_pred             CHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999988765

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=99.97  E-value=1.9e-30  Score=172.10  Aligned_cols=100  Identities=49%  Similarity=0.953  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCC
Q psy5115          64 DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES  143 (171)
Q Consensus        64 ~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s  143 (171)
                      ++..|..+++.+.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|..||++||+||..||+++|
T Consensus         2 ~~~~~~~il~~l~~~~~a~~F~~pv~~~~~p~Y~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s   81 (101)
T cd05509           2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDT   81 (101)
T ss_pred             hHHHHHHHHHHHHhCCCchhhcCCCChhhcCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy5115         144 PFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       144 ~~~~~a~~l~~~f~~~~~~~  163 (171)
                      .++++|..|++.|++.++++
T Consensus        82 ~~~~~a~~l~~~f~~~~~~~  101 (101)
T cd05509          82 EYYKCANKLEKFFWKKLKEL  101 (101)
T ss_pred             HHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999998763

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.

>cd05500 Bromo_BDF1_2_I Bromodomain

Probab=99.97  E-value=3.4e-30  Score=171.25  Aligned_cols=101  Identities=32%  Similarity=0.598  Sum_probs=97.0

Q ss_pred             CChhHHHHHHHHHHHHHhCcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhh
Q psy5115          60 LTPRDFESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRY  137 (171)
Q Consensus        60 l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  137 (171)
                      |++.+++.|.+++..|.+++.+++|..||++.  .+|+|+++|++||||++|++||++|.|.++.+|..||++||+||..
T Consensus         1 ~t~~~~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~   80 (103)
T cd05500           1 MTKHQHKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLT   80 (103)
T ss_pred             CCHHHHHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            57889999999999999999999999999986  6999999999999999999999999999999999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHH
Q psy5115         138 YNPRESPFFKHAHQLEMFFVQKV  160 (171)
Q Consensus       138 yn~~~s~~~~~a~~l~~~f~~~~  160 (171)
                      ||+++|.++.+|..|++.|++.+
T Consensus        81 yN~~~s~~~~~A~~l~~~fe~~~  103 (103)
T cd05500          81 FNGPEHPVSQMGKRLQAAFEKHL  103 (103)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999853

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.

>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily

Probab=99.97  E-value=3.9e-30  Score=172.57  Aligned_cols=104  Identities=33%  Similarity=0.637  Sum_probs=98.1

Q ss_pred             ChhHHHHHHHHHHHHHhC-cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhC
Q psy5115          61 TPRDFESLRKLMKQIQAH-KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYN  139 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~-~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn  139 (171)
                      .++..+.|..+++.|.++ +.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|.+|++|||+||..||
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            467788999999999999 8999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC-HHHHHHHHHHHHHHHHHHHHH
Q psy5115         140 PRES-PFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       140 ~~~s-~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      +++| .++++|..|++.|++.+..++
T Consensus        85 ~~~s~~~~~~A~~l~~~~~~~~~~~~  110 (112)
T cd05510          85 SDPSHPLRRHANFMKKKAEHLLKLIP  110 (112)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence            9766 688999999999999998764

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

>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily

Probab=99.97  E-value=1.3e-29  Score=166.20  Aligned_cols=99  Identities=23%  Similarity=0.355  Sum_probs=93.0

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      +++..|..|+..|..++.+++|..+  +..+|+|+++|++||||+||++||.+|.|.|+++|.+||+|||.||.+||+++
T Consensus         2 ~~l~~ce~il~~l~~~~~s~~f~~~--p~~~pdY~~iIk~PMDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~N~~~yN~~~   79 (102)
T cd05501           2 EELLKCEFLLLKVYCMSKSGFFISK--PYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD   79 (102)
T ss_pred             HHHHHHHHHHHHHHhCcccccccCC--CCCCCchHHHcCCCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence            5678899999999999999999774  45789999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                       .++.+|..|++.|++.++++-
T Consensus        80 -~~~~~a~~L~~~Fek~~~~~f  100 (102)
T cd05501          80 -DFGQVGITLEKKFEKNFKEVF  100 (102)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHh
Confidence             999999999999999998763

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.

>cd05499 Bromo_BDF1_2_II Bromodomain

Probab=99.96  E-value=1.2e-29  Score=168.49  Aligned_cols=96  Identities=34%  Similarity=0.733  Sum_probs=91.3

Q ss_pred             HHHHHHHHHHHHhC---cCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhC
Q psy5115          65 FESLRKLMKQIQAH---KSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYN  139 (171)
Q Consensus        65 ~~~~~~~l~~l~~~---~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn  139 (171)
                      ++.|.++|+.|++.   +.+++|..||++.  .+|+|+++|++||||++|++||++|.|.|+++|.+|+++||+||..||
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            57899999999984   5689999999998  899999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q psy5115         140 PRESPFFKHAHQLEMFFVQKV  160 (171)
Q Consensus       140 ~~~s~~~~~a~~l~~~f~~~~  160 (171)
                      +++|.++.+|..|++.|++.|
T Consensus        82 ~~~s~~~~~a~~l~~~fe~~~  102 (102)
T cd05499          82 PEGTDVYMMGHQLEEVFNDKW  102 (102)
T ss_pred             CCCCHHHHHHHHHHHHHHHhC
Confidence            999999999999999999865

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.

>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants

Probab=99.96  E-value=1.9e-29  Score=166.78  Aligned_cols=96  Identities=30%  Similarity=0.589  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHHHhCcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          65 FESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      ++.|..+|+.|++++.+++|..||++.  .+|+|+++|++||||++|++||++|.|.|+++|.+|+++||.||..||+++
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            578999999999999999999999976  689999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKV  160 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~  160 (171)
                      |.++.+|..|++.|++.|
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.

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

Probab=99.96  E-value=1.7e-29  Score=168.66  Aligned_cols=99  Identities=22%  Similarity=0.429  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHHhCcC------CCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhh
Q psy5115          64 DFESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRY  137 (171)
Q Consensus        64 ~~~~~~~~l~~l~~~~~------~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  137 (171)
                      ..+.+..+++.+.+++.      +++|..||+...+|+||++|++||||++|++||++|.|.++++|..||.|||.||..
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            45678888888887765      899999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHH
Q psy5115         138 YNPRESPFFKHAHQLEMFFVQKVKI  162 (171)
Q Consensus       138 yn~~~s~~~~~a~~l~~~f~~~~~~  162 (171)
                      ||+++|.++.+|..|++.|++.+++
T Consensus        82 yN~~~s~i~~~a~~l~~~f~~~~~~  106 (107)
T cd05516          82 FNLEGSLIYEDSIVLQSVFKSARQK  106 (107)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999998875

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.

>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II

Probab=99.96  E-value=2.3e-29  Score=167.16  Aligned_cols=96  Identities=33%  Similarity=0.693  Sum_probs=91.9

Q ss_pred             HHHHHHHHHHHHhC---cCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhC
Q psy5115          65 FESLRKLMKQIQAH---KSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYN  139 (171)
Q Consensus        65 ~~~~~~~l~~l~~~---~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn  139 (171)
                      ++.|..||+.|+.+   +.+++|..||++.  .+|+|+++|++||||++|++||++|.|.|+++|..||++||+||..||
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            57899999999999   8899999999986  599999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q psy5115         140 PRESPFFKHAHQLEMFFVQKV  160 (171)
Q Consensus       140 ~~~s~~~~~a~~l~~~f~~~~  160 (171)
                      +++|.++.+|..|++.|++.|
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.

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

Probab=99.96  E-value=5.7e-29  Score=167.01  Aligned_cols=102  Identities=29%  Similarity=0.465  Sum_probs=96.5

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      +.+..|..+++.|++++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|.+||++||+||..||+++
T Consensus         3 ~lr~~L~~il~~l~~~~~~~~F~~pv~~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~   82 (112)
T cd05528           3 ELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDR   82 (112)
T ss_pred             HHHHHHHHHHHHHHhCCCchhhcCCCCccccCcHHHHHcCCCCHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            56677899999999999999999999999999999999999999999999999999999999999999999999999994


Q ss_pred             ----CHHHHHHHHHHHHHHHHHHHHH
Q psy5115         143 ----SPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       143 ----s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                          |.++.+|..|++.|.+.+.+..
T Consensus        83 s~~~s~i~~~A~~L~~~~~~~~~~~~  108 (112)
T cd05528          83 DPADKLIRSRACELRDEVHAMIEAEL  108 (112)
T ss_pred             CccccHHHHHHHHHHHHHHHHHHhcC
Confidence                6999999999999999988653

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

>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup

Probab=99.96  E-value=4.1e-29  Score=163.82  Aligned_cols=94  Identities=28%  Similarity=0.481  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCH
Q psy5115          65 FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESP  144 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~  144 (171)
                      ...+..+++.|++++.+++|..||++..+|+|+++|++||||+||++||++|.|.|+++|.+||++||.||..||+++|.
T Consensus         3 ~~~l~~il~~l~~~~~~~~F~~PV~~~~~pdY~~vIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~   82 (98)
T cd05513           3 QKALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTI   82 (98)
T ss_pred             HHHHHHHHHHHHcCCccccccCcCCccccccHHHHHcCccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            56788999999999999999999999899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q psy5115         145 FFKHAHQLEMFFVQ  158 (171)
Q Consensus       145 ~~~~a~~l~~~f~~  158 (171)
                      ++++|..|.....+
T Consensus        83 ~~~~A~~L~~~~~~   96 (98)
T cd05513          83 YYKAAKKLLHSGMK   96 (98)
T ss_pred             HHHHHHHHHHhhhh
Confidence            99999999776543

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.

>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily

Probab=99.96  E-value=7.6e-29  Score=162.85  Aligned_cols=93  Identities=37%  Similarity=0.607  Sum_probs=88.7

Q ss_pred             HHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCH
Q psy5115          65 FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESP  144 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~  144 (171)
                      ...|..+++.|..++.+++|..||++..+|+|+++|++||||+||++||++|.|.|+++|..||++||+||..||+++|.
T Consensus         3 ~~~l~~il~~l~~~~~~~~F~~pVd~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~s~   82 (98)
T cd05512           3 EVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTI   82 (98)
T ss_pred             HHHHHHHHHHHHhCCCchhhcCCCCccccCCHHHHhcCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q psy5115         145 FFKHAHQLEMFFV  157 (171)
Q Consensus       145 ~~~~a~~l~~~f~  157 (171)
                      ++++|..|++.-.
T Consensus        83 ~~~~A~~l~~~~~   95 (98)
T cd05512          83 FYRAAVRLRDQGG   95 (98)
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999987643

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

>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily

Probab=99.96  E-value=7.9e-28  Score=165.34  Aligned_cols=105  Identities=28%  Similarity=0.395  Sum_probs=100.0

Q ss_pred             cCCChhHHHHHHHHHHHHH---hCcCCCCCccCCCCC-CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Q psy5115          58 KNLTPRDFESLRKLMKQIQ---AHKSAWPFMEPVDPH-EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFD  133 (171)
Q Consensus        58 ~~l~~~~~~~~~~~l~~l~---~~~~~~~F~~pv~~~-~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~  133 (171)
                      ..+..+....+..++.+|.   .++.+++|..||++. .+|+|+++|++||||++|++||++|.|.++++|..||+|||+
T Consensus        19 ~~~~~~~~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~~~p~Y~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~Li~~   98 (128)
T cd05529          19 PHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILS   98 (128)
T ss_pred             CCCCHHHHHHHHHHHHHHHhcccCcccccccCCCCccccCCcHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence            4577888999999999999   889999999999999 999999999999999999999999999999999999999999


Q ss_pred             HHhhhCCCCCHHHHHHHHHHHHHHHHHHH
Q psy5115         134 NCRYYNPRESPFFKHAHQLEMFFVQKVKI  162 (171)
Q Consensus       134 Na~~yn~~~s~~~~~a~~l~~~f~~~~~~  162 (171)
                      ||..||+++|.++.+|..|++.|.+.+..
T Consensus        99 Na~~yN~~~s~i~~~A~~l~~~~~~~l~~  127 (128)
T cd05529          99 NAETFNEPNSEIAKKAKRLSDWLLRILSS  127 (128)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999999999999988763

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

>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I

Probab=99.96  E-value=3.3e-28  Score=163.76  Aligned_cols=102  Identities=23%  Similarity=0.425  Sum_probs=94.3

Q ss_pred             HHHHHHHHHHHHhCc------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          65 FESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      .+.|..+++.|.+.+      .+.+|.++|+...+|+||++|++||||++|++||++|.|.|+++|.+||++||+||..|
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            567889999998643      45689999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESPFFKHAHQLEMFFVQKVKILREK  166 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~~~~~~~~  166 (171)
                      |+++|.++++|..|++.|++.++++.+.
T Consensus        84 N~~~s~~~~~A~~L~~~f~~~~~~~~~~  111 (113)
T cd05524          84 YKPDSPEHKDACKLWELFLSARNEVLSG  111 (113)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999999887653

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.

>KOG1474|consensus

Probab=99.95  E-value=1.5e-28  Score=207.56  Aligned_cols=111  Identities=35%  Similarity=0.636  Sum_probs=105.1

Q ss_pred             cCCChhHHHHHHHHHHHHHhCcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Q psy5115          58 KNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNC  135 (171)
Q Consensus        58 ~~l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  135 (171)
                      .....++++.|..||..|+.++.+|+|..|||+.  .+|+|+++|++||||+||+.||.+|.|.++.+|..||+|||.||
T Consensus       217 ~~~~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTIK~kL~~~~Y~~~~eF~~DVRL~F~Nc  296 (640)
T KOG1474|consen  217 SKLTVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTIKKKLEKGEYKSAEEFAADVRLTFDNC  296 (640)
T ss_pred             ccccHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHHHhhhcccccCCHHHHHHHHHHHHHHH
Confidence            3577889999999999999999999999999997  69999999999999999999999999999999999999999999


Q ss_pred             hhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy5115         136 RYYNPRESPFFKHAHQLEMFFVQKVKILREKLV  168 (171)
Q Consensus       136 ~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~~~  168 (171)
                      ++||++++.|+.+|+.|++.|+..|+.+...+.
T Consensus       297 m~YNp~g~dV~~Ma~~L~~~Fe~rw~~~~~~~~  329 (640)
T KOG1474|consen  297 MTYNPEGSDVYAMAKKLQEVFEERWASMPLEIE  329 (640)
T ss_pred             HhcCCCCCHHHHHHHHHHHHHHHHHhhcccccc
Confidence            999999999999999999999999998765543

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

Probab=99.95  E-value=6.6e-28  Score=160.21  Aligned_cols=95  Identities=31%  Similarity=0.514  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHHHhC------cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          65 FESLRKLMKQIQAH------KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        65 ~~~~~~~l~~l~~~------~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      ++.|..+++.+...      +.+++|..||+...+|+|+++|++||||++|++||++|.|.|+.+|..||++||.||..|
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            46788888888844      458899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESPFFKHAHQLEMFFVQK  159 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~  159 (171)
                      |+++|.++.+|..|++.|++.
T Consensus        82 n~~~s~i~~~A~~l~~~f~~~  102 (103)
T cd05519          82 NQEGSIVYEDAVEMEKAFKKK  102 (103)
T ss_pred             CCCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999999875

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.

>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family

Probab=99.95  E-value=1.7e-27  Score=158.44  Aligned_cols=95  Identities=33%  Similarity=0.523  Sum_probs=86.3

Q ss_pred             HHHHHHHHHHHHhCc------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          65 FESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      ...|..+++.+...+      .+++|.++|+...+|+||++|++||||++|++||++|.|.|+++|..|+.+||+||..|
T Consensus         4 ~~~l~~i~~~i~~~kd~~g~~~s~~F~~lp~k~~~pdYy~~I~~P~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f~Na~~y   83 (106)
T cd05525           4 AQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKY   83 (106)
T ss_pred             HHHHHHHHHHHHHhhccCCCcccHhhccCCCcccCCchhhhCCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            345666666666543      46899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESPFFKHAHQLEMFFVQK  159 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~  159 (171)
                      |+++|.++++|..|++.|++.
T Consensus        84 n~~~S~i~~~A~~L~~~f~~~  104 (106)
T cd05525          84 YGRKSPIGRDVCRLRKAYYQA  104 (106)
T ss_pred             CCCCCHHHHHHHHHHHHHHHc
Confidence            999999999999999999874

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.

>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V

Probab=99.95  E-value=1.6e-27  Score=158.74  Aligned_cols=97  Identities=28%  Similarity=0.560  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHHHhC------cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          65 FESLRKLMKQIQAH------KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        65 ~~~~~~~l~~l~~~------~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      .++|..+++.+...      +.+++|..||+..++|+|+++|++||||++|++||++|.|.|+++|..||.+||.||..|
T Consensus         2 ~~~~~~~~~~i~~~~d~~~~~~a~~F~~~p~~~~~pdYy~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~~y   81 (105)
T cd05515           2 QQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKY   81 (105)
T ss_pred             hHHHHHHHHHHHHhhCcCCCcccHHhccCCCcccCCcHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHH
Confidence            35677777777654      457899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESPFFKHAHQLEMFFVQKVK  161 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~~~  161 (171)
                      |+++|.++.+|..|++.|.+..+
T Consensus        82 N~~~s~i~~~A~~L~~~~~~~~~  104 (105)
T cd05515          82 NEPDSQIYKDALTLQKVLLETKR  104 (105)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999987653

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=99.95  E-value=1.5e-27  Score=158.01  Aligned_cols=81  Identities=30%  Similarity=0.580  Sum_probs=78.0

Q ss_pred             cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q psy5115          79 KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQ  158 (171)
Q Consensus        79 ~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~~  158 (171)
                      +.+++|.++|+...+|+||++|++||||++|++||++|.|.++.+|.+||++||.||..||+++|.++.+|..|++.|++
T Consensus        22 ~~s~pF~~~p~~~~~PdYy~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~L~~~f~~  101 (103)
T cd05520          22 LLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKLMQA  101 (103)
T ss_pred             CccHhhhcCCCcccCCCHHHHcCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             H
Q psy5115         159 K  159 (171)
Q Consensus       159 ~  159 (171)
                      .
T Consensus       102 ~  102 (103)
T cd05520         102 K  102 (103)
T ss_pred             h
Confidence            4

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

>smart00297 BROMO bromo domain

Probab=99.95  E-value=3.3e-27  Score=158.15  Aligned_cols=102  Identities=36%  Similarity=0.795  Sum_probs=96.9

Q ss_pred             ChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCC
Q psy5115          61 TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP  140 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~  140 (171)
                      .......|..++..+..++.+++|..||++..+|+|+.+|++||||++|++||++|.|.|+++|.+||++||.||..||+
T Consensus         5 ~~~~~~~~~~i~~~~~~~~~~~~F~~~~~~~~~p~Y~~~i~~P~dl~~I~~kl~~~~Y~s~~ef~~D~~li~~Na~~~n~   84 (107)
T smart00297        5 QKKLQSLLKAVLDKLDSHRLSWPFLKPVDRKEAPDYYDIIKKPMDLSTIKKKLENGKYSSVEEFVADVQLMFSNAKTYNG   84 (107)
T ss_pred             HHHHHHHHHHHHHHHHhCccchhhccCCChhhccCHHHHhcCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            44566788889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q psy5115         141 RESPFFKHAHQLEMFFVQKVKI  162 (171)
Q Consensus       141 ~~s~~~~~a~~l~~~f~~~~~~  162 (171)
                      ++|.++.+|..|++.|++.+++
T Consensus        85 ~~s~~~~~a~~l~~~f~~~~~~  106 (107)
T smart00297       85 PDSEVYKDAKKLEKFFEKKLRE  106 (107)
T ss_pred             CCCHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999876

>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II

Probab=99.95  E-value=2.7e-27  Score=156.86  Aligned_cols=93  Identities=29%  Similarity=0.494  Sum_probs=85.8

Q ss_pred             HHHHHHHHHHHhCc------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhC
Q psy5115          66 ESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYN  139 (171)
Q Consensus        66 ~~~~~~l~~l~~~~------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn  139 (171)
                      +.+..+++.+.+..      .+++|.++|+...+|+||++|++||||++|++||++|.|.++.+|..||++||.||..||
T Consensus         3 ~~~~~l~~~i~~~~d~~gr~~~~~F~~lp~~~~~pdYy~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN   82 (103)
T cd05517           3 QILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN   82 (103)
T ss_pred             HHHHHHHHHHHHhhCcCCCChhHHHhcCCCCCCCCCHHHHcCCCcCHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            46677777777654      468999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q psy5115         140 PRESPFFKHAHQLEMFFVQ  158 (171)
Q Consensus       140 ~~~s~~~~~a~~l~~~f~~  158 (171)
                      +++|.++.+|..|++.|+.
T Consensus        83 ~~~s~i~~~A~~l~~~f~~  101 (103)
T cd05517          83 EPGSQVYKDANAIKKIFTA  101 (103)
T ss_pred             CCCCHHHHHHHHHHHHHHh
Confidence            9999999999999999975

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=99.95  E-value=2.7e-27  Score=156.73  Aligned_cols=93  Identities=32%  Similarity=0.544  Sum_probs=83.8

Q ss_pred             HHHHHHHHHHh------CcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCC
Q psy5115          67 SLRKLMKQIQA------HKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP  140 (171)
Q Consensus        67 ~~~~~l~~l~~------~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~  140 (171)
                      ++..+++.+.+      ++.+.+|..+|+...+|+||++|++||||++|++||++|.|.|+++|.+||++||.||..||+
T Consensus         4 ~~~~l~~~v~~~~d~~gr~~~~~F~~~p~~~~~pdYy~iIk~Pmdl~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~   83 (103)
T cd05518           4 RMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNE   83 (103)
T ss_pred             HHHHHHHHHHHhhccCCCcccHHHhcCCCcccCccHHHHcCCCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            45555555544      356889999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHH
Q psy5115         141 RESPFFKHAHQLEMFFVQK  159 (171)
Q Consensus       141 ~~s~~~~~a~~l~~~f~~~  159 (171)
                      ++|.++.+|..|++.|++.
T Consensus        84 ~~s~i~~~A~~le~~~~~~  102 (103)
T cd05518          84 EGSQVYEDANILEKVLKEK  102 (103)
T ss_pred             CCCHHHHHHHHHHHHHHhc
Confidence            9999999999999998763

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=99.94  E-value=5.1e-26  Score=151.15  Aligned_cols=94  Identities=23%  Similarity=0.503  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHHh------CcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhC
Q psy5115          66 ESLRKLMKQIQA------HKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYN  139 (171)
Q Consensus        66 ~~~~~~l~~l~~------~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn  139 (171)
                      .++..+++.+.+      ++.+++|.++|+....|+||++|++||||++|++||++|.|.++.+|..|+.+||.||..||
T Consensus         4 ~~~~~i~~~v~~~~d~~g~~l~~~F~~~p~~~~~pdYy~~I~~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn   83 (104)
T cd05522           4 ARIKNILKGLRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN   83 (104)
T ss_pred             HHHHHHHHHHHHHhCcCCCcccHHHhcCCCccccCcHHHHhCCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHC
Confidence            355566666654      35688999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHH
Q psy5115         140 PRESPFFKHAHQLEMFFVQK  159 (171)
Q Consensus       140 ~~~s~~~~~a~~l~~~f~~~  159 (171)
                      +++|.++.+|..|++.|+++
T Consensus        84 ~~~s~i~~~A~~l~~~f~~l  103 (104)
T cd05522          84 ENDSQEYKDAVLLEKEARLL  103 (104)
T ss_pred             CCCCHHHHHHHHHHHHHHHh
Confidence            99999999999999999874

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

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

Probab=99.93  E-value=9.5e-26  Score=144.75  Aligned_cols=84  Identities=43%  Similarity=0.861  Sum_probs=79.7

Q ss_pred             HHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHH
Q psy5115          68 LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFK  147 (171)
Q Consensus        68 ~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~  147 (171)
                      |..+++.|++++.+++|..||++..+|+|+.+|+.||||++|++||++|.|.++++|..||++||.||..||+++|.+++
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            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHH
Q psy5115         148 HAHQ  151 (171)
Q Consensus       148 ~a~~  151 (171)
                      +|.+
T Consensus        81 ~A~~   84 (84)
T PF00439_consen   81 AAEK   84 (84)
T ss_dssp             HHHH
T ss_pred             HhcC
Confidence            9974

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=99.93  E-value=2.5e-25  Score=147.91  Aligned_cols=95  Identities=29%  Similarity=0.467  Sum_probs=85.8

Q ss_pred             HHHHHHHHHHHHhCcC------CCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          65 FESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~~------~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      .+.|..+++.+...+.      +.+|..+|+...+|+||++|++||||++|++||++  |.|+++|.+|+.+||+||..|
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            4567777777776543      46899999888999999999999999999999998  999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESPFFKHAHQLEMFFVQKVK  161 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~~~  161 (171)
                      |+++|.++.+|..|++.|.+.+.
T Consensus        81 N~~~s~i~~~A~~le~~~~~~~~  103 (106)
T cd05521          81 NTKGSVIYKYALILEKYINDVII  103 (106)
T ss_pred             cCCCCHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999998763

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

>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family

Probab=99.93  E-value=4.2e-25  Score=146.83  Aligned_cols=96  Identities=17%  Similarity=0.257  Sum_probs=85.3

Q ss_pred             HHHHHHHHh-CcCCCCCccCCCCC-----CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          69 RKLMKQIQA-HKSAWPFMEPVDPH-----EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        69 ~~~l~~l~~-~~~~~~F~~pv~~~-----~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      .-++..+.. .+...+|..||.+.     .+|+|+.+|++||||+||++||++|.|+++++|.+||.+||+||.+|||++
T Consensus         6 ~f~~~~~k~~lp~~~~~~~~v~~~~~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~N~~~yNg~~   85 (109)
T cd05492           6 KFIVSRMKSWLPPDTTNRAIVLNKRGKATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGAD   85 (109)
T ss_pred             HHHHHHHHhcCcccccccccccccCchhccCCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            344555555 46678999999632     489999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      |.++.+|+.|.......+.+++
T Consensus        86 s~~~~~A~~l~~d~~~el~Ei~  107 (109)
T cd05492          86 SEQYDAARWLYRDTCHDLRELR  107 (109)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999888875

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.

>cd04369 Bromodomain Bromodomain

Probab=99.92  E-value=6.4e-25  Score=144.44  Aligned_cols=95  Identities=44%  Similarity=0.780  Sum_probs=90.7

Q ss_pred             HHHHHHHHHHHHhC--cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          65 FESLRKLMKQIQAH--KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        65 ~~~~~~~l~~l~~~--~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      ...|..+++.+...  +.+.+|..||++...|+|+.+|++||||++|++|+++|.|.++.+|..|+++||.||..||+++
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            35688899999998  9999999999998999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQK  159 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~  159 (171)
                      |.++.+|..|+..|++.
T Consensus        82 ~~~~~~a~~l~~~~~~~   98 (99)
T cd04369          82 SPIYKDAKKLEKLFEKL   98 (99)
T ss_pred             CHHHHHHHHHHHHHHHh
Confidence            99999999999999875

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

>KOG1245|consensus

Probab=99.91  E-value=9.4e-25  Score=194.95  Aligned_cols=95  Identities=38%  Similarity=0.779  Sum_probs=91.6

Q ss_pred             HHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHH
Q psy5115          68 LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFK  147 (171)
Q Consensus        68 ~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~  147 (171)
                      |..|+..|..++.+|||++||++..+|+|++||++||||+||+.|+..|.|.++++|..||+|||.||..||++ |.+++
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            78999999999999999999999999999999999999999999999999999999999999999999999998 99999


Q ss_pred             HHHHHHHHHHHHHHHH
Q psy5115         148 HAHQLEMFFVQKVKIL  163 (171)
Q Consensus       148 ~a~~l~~~f~~~~~~~  163 (171)
                      ++..|+.+|.+.|+..
T Consensus      1385 ag~~l~~ff~~~~~~~ 1400 (1404)
T KOG1245|consen 1385 AGTCLRRFFHKRWRKK 1400 (1404)
T ss_pred             hcchHHHHHHHHHHhh
Confidence            9999999999966543

>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI

Probab=99.88  E-value=5.1e-22  Score=131.69  Aligned_cols=100  Identities=24%  Similarity=0.350  Sum_probs=89.1

Q ss_pred             hHHHHHHHHHHHHHhCc------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHh
Q psy5115          63 RDFESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCR  136 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~  136 (171)
                      ..+..+..++..++++.      .+.+|.+.|+  ..++|+.+|+.||||+.|++|+++|.|+++++|..|+.+||.||.
T Consensus         3 ~vq~~l~~l~~~V~~~~D~~Gr~~s~~f~~LP~--~~~~~~~~ik~Pi~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NAr   80 (110)
T cd05526           3 LVQELLATLFVSVMNHQDEEGRCYSDSLAELPE--LAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR   80 (110)
T ss_pred             HHHHHHHHHHHHHHhccCCCCCCchHHHHHCCC--cccCchhhhcCCccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHHH
Confidence            34567888888888775      4678998887  346778999999999999999999999999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         137 YYNPRESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       137 ~yn~~~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      .||+++|.++++|..|++.|.+.-+++-
T Consensus        81 ~yN~~~S~iy~dA~eLq~~f~~~rd~~~  108 (110)
T cd05526          81 RLSRTDSEIYEDAVELQQFFIKIRDELC  108 (110)
T ss_pred             HhCcccCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999998877764

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=99.82  E-value=5.8e-20  Score=147.41  Aligned_cols=89  Identities=35%  Similarity=0.705  Sum_probs=84.5

Q ss_pred             cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q psy5115          79 KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQ  158 (171)
Q Consensus        79 ~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~~  158 (171)
                      ..+.+|..+|+...+|+||.+|+.||||.+|+++|+++.|.++++|..|+.|||.||.+||+++|.++.+|..|++.|.+
T Consensus       164 ~~s~~F~~~p~k~~~PdYy~iIk~Pm~L~~i~kkl~~~~Y~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~~~~  243 (371)
T COG5076         164 FLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLK  243 (371)
T ss_pred             ccccccccCCccccCCChheeecchhhHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHHHHHHH
Confidence            45788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHh
Q psy5115         159 KVKILREKL  167 (171)
Q Consensus       159 ~~~~~~~~~  167 (171)
                      .+..+....
T Consensus       244 ~i~~~~~~~  252 (371)
T COG5076         244 LIEEIPEEM  252 (371)
T ss_pred             HHHhccccc
Confidence            999776544

>KOG1472|consensus

Probab=99.66  E-value=1.2e-16  Score=134.17  Aligned_cols=104  Identities=38%  Similarity=0.869  Sum_probs=98.1

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      .....+..++..|..+..+|||.+||+..++|+||.+|++||||.||+.+|+++.|..+..|..|+.++|.||+.||+++
T Consensus       606 ~~~s~~~~il~~l~~h~~awPf~~Pv~~~e~pdyy~~I~~pmDl~tM~~~l~~~~y~~~~~f~ad~~~vf~ncr~yn~~~  685 (720)
T KOG1472|consen  606 KLFSAIQNILDQLQNHGDAWPFLKPVNKKEVPDYYDVIKHPMDLRTMQNRLKDNQYTEVELFMADVVRVFANCRMYNGSD  685 (720)
T ss_pred             hhhHHHHhHHhhhhcCCccCCccCccccccCCcHHHHhcccccHHHHhhhccccchhhHHHHHHHHHHHHhhhhccCCcc
Confidence            45567888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKILREK  166 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~~~~  166 (171)
                      +..++.|..|...|...+.+....
T Consensus       686 ~~y~k~~~~le~~~~~k~~~~i~~  709 (720)
T KOG1472|consen  686 TQYYKCAQALEKFFLFKLNELILR  709 (720)
T ss_pred             chheecccchhhhhcchhhhhhhh
Confidence            999999999999999988876443

>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily

Probab=99.45  E-value=9.1e-14  Score=93.59  Aligned_cols=76  Identities=28%  Similarity=0.462  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHHHhCcCCCCCccCCCC--CCCCccccccCCCCCHHHHHHHHhcCCCCC-------HHHHHHHHHHHHHH
Q psy5115          64 DFESLRKLMKQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKK-------LSEFIGDMTKIFDN  134 (171)
Q Consensus        64 ~~~~~~~~l~~l~~~~~~~~F~~pv~~--~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s-------~~~f~~Dv~li~~N  134 (171)
                      ....+...+..+.+++.+++|..||++  ..+|+|+++|++||||+||+++|.++.++.       -....+++..+..|
T Consensus         4 ~~~~~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (114)
T cd05494           4 ALERVLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDLQIVQEDPADKQIDDEGR   83 (114)
T ss_pred             HHHHHHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhhcCCCCChHHHHHHHHccccccccccccccccccccccccccc
Confidence            456777788888888899999999999  789999999999999999999999975533       33444445555555


Q ss_pred             HhhhC
Q psy5115         135 CRYYN  139 (171)
Q Consensus       135 a~~yn  139 (171)
                      +..++
T Consensus        84 ~~~~~   88 (114)
T cd05494          84 RSPSN   88 (114)
T ss_pred             cCccc
Confidence            44444

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

>KOG0955|consensus

Probab=99.44  E-value=1.9e-13  Score=119.45  Aligned_cols=104  Identities=30%  Similarity=0.560  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHH
Q psy5115          66 ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPF  145 (171)
Q Consensus        66 ~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~  145 (171)
                      ..++.+++.+...+....|..|+++.++|+|.++|++||||.+++.++++|.|.++++|..|+.+|..||+.||..+..+
T Consensus       568 kLl~~~l~~lq~kD~~gif~~pvd~~e~pdy~~iik~pmd~~t~~~kl~s~~y~tle~ieed~~l~~~nc~~yn~~dtv~  647 (1051)
T KOG0955|consen  568 KLLQKSLDKLQKKDSYGIFAEPVDPSELPDYIDIIKKPMDFFTMRLKLESGAYSTLEPIEEDVNLIVSNCMEYNAKDTVY  647 (1051)
T ss_pred             HHHHHHHHHhhcccccCceeeccChhhcccHHHHhcCccchhhhhhhccccchhhhhHHHHhHhHhHhHHHHhhccCeeh
Confidence            34557788888888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhh
Q psy5115         146 FKHAHQLEMFFVQKVKILREKLVE  169 (171)
Q Consensus       146 ~~~a~~l~~~f~~~~~~~~~~~~~  169 (171)
                      ++.|..+++.....+...+.+.++
T Consensus       648 ~r~av~~~e~~~~~~~~arke~e~  671 (1051)
T KOG0955|consen  648 YRAAVRLRELIKKDFRNARKEPES  671 (1051)
T ss_pred             HhhhHHHHhhhhhHHHhcccchhh
Confidence            999999999999999887766554

>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi

Probab=99.41  E-value=2.9e-13  Score=90.22  Aligned_cols=42  Identities=31%  Similarity=0.453  Sum_probs=39.4

Q ss_pred             CCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115         101 KEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus       101 ~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      -.||||+||++||.+|.|.++.+|++||++||.||..||+++
T Consensus        62 ~y~MDL~tIe~RL~ng~Y~tp~~F~~DiklI~~Nc~~ynd~d  103 (119)
T cd05491          62 FYNMDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKTIGDRE  103 (119)
T ss_pred             EeccCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCHH
Confidence            358999999999999999999999999999999999999753

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.

>KOG0008|consensus

Probab=99.33  E-value=1.4e-12  Score=114.52  Aligned_cols=99  Identities=34%  Similarity=0.605  Sum_probs=87.5

Q ss_pred             HHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHH
Q psy5115          68 LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFK  147 (171)
Q Consensus        68 ~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~  147 (171)
                      +-.++.++..-+.+|+|.+||++...|+||..|++||||++|.+++..+.|.+.++|..||++|..|+..|||.++....
T Consensus      1387 ~d~~vs~~~~ipes~~f~~~v~~k~~~~yy~kik~pmdl~~i~~n~~~~~y~s~~e~l~dv~~i~~n~~~~ng~e~~y~~ 1466 (1563)
T KOG0008|consen 1387 LDNIVSQMKEIPESWPFHEPVNKKRVPDYYKKIKNPMDLETILKNIPPHKYDSRSEFLDDVNLIYVNSVEYNGAESAYTK 1466 (1563)
T ss_pred             hhhHHHHHHhcchhcccccccchhhchHHHHHhcChhhHHHHhhcCCccccccHHHHhhhhHhhcccceeecCccccccH
Confidence            44566777777899999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q psy5115         148 HAHQLEMFFVQKVKILREK  166 (171)
Q Consensus       148 ~a~~l~~~f~~~~~~~~~~  166 (171)
                      .|+.+-......+.+.-..
T Consensus      1467 k~~k~~ev~~~~~~e~~~~ 1485 (1563)
T KOG0008|consen 1467 KARKIGEVGLANLLEYIEH 1485 (1563)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            8888777766665554433

>KOG1827|consensus

Probab=99.30  E-value=1.2e-11  Score=103.04  Aligned_cols=103  Identities=26%  Similarity=0.473  Sum_probs=92.8

Q ss_pred             CCChhHHHHHHHHHHHHHhCc------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q psy5115          59 NLTPRDFESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIF  132 (171)
Q Consensus        59 ~l~~~~~~~~~~~l~~l~~~~------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~  132 (171)
                      .+....+.++..++..+....      .+..|.+.++....|+||..|..||.|+.|++|++.+.|.+.+.|..|+.+|+
T Consensus        48 ~i~~~~~~~f~~il~~~~~~~d~~gk~~~d~feklp~~~~~p~yy~~i~~pisl~~ik~kv~k~~y~~~~~f~~D~~lm~  127 (629)
T KOG1827|consen   48 VIDPPLIPKFKTILASLLDLKDDEGKQLFDKFEKLPSRKEFPEYYYVIQQPISLDQIKRKVKKGRYKRLSFFQLDFLLMT  127 (629)
T ss_pred             ccChHHHHHHHHHHHHHHhhccccCcccchhHhhccccccCCCcceeecCcccHHHHHHHHHhcccccHHHHHHHHHHHH
Confidence            346677778888888887664      36679999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHHHHHHHHH
Q psy5115         133 DNCRYYNPRESPFFKHAHQLEMFFVQKVK  161 (171)
Q Consensus       133 ~Na~~yn~~~s~~~~~a~~l~~~f~~~~~  161 (171)
                      .||+.||.++|.++++|..|+..|.....
T Consensus       128 ena~~~n~~ds~~~~~s~~l~~~~~~~~~  156 (629)
T KOG1827|consen  128 ENARLYNRPDSLIYKDSGELEKYFISLED  156 (629)
T ss_pred             HHHHHhcCcchhhhhhhhhhhcchhhhhc
Confidence            99999999999999999999999988654

>KOG0008|consensus

Probab=99.17  E-value=5.9e-11  Score=104.62  Aligned_cols=108  Identities=24%  Similarity=0.438  Sum_probs=94.2

Q ss_pred             ChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCC
Q psy5115          61 TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP  140 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~  140 (171)
                      +......+..++.++...+.+.+|..||+..++++||.+|+.||||.++++.+....|.+-+.|+.|+.+|+.|..+||+
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            34445567788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy5115         141 RESPFFKHAHQLEMFFVQKVKILREKLV  168 (171)
Q Consensus       141 ~~s~~~~~a~~l~~~f~~~~~~~~~~~~  168 (171)
                      +.+.+...+..+....-..|.+-..++.
T Consensus      1339 ~~~~~t~~~q~mls~~~~~~~ekedk~~ 1366 (1563)
T KOG0008|consen 1339 PLASLTRQQQSMLSLCFEKLKEKEDKLW 1366 (1563)
T ss_pred             chHHHHHHHHHHHHHHHHhhchhHHHHH
Confidence            9999999988877666555554444433

>KOG0386|consensus

Probab=99.13  E-value=1.2e-10  Score=100.68  Aligned_cols=99  Identities=25%  Similarity=0.444  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHHhC------cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhC
Q psy5115          66 ESLRKLMKQIQAH------KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYN  139 (171)
Q Consensus        66 ~~~~~~l~~l~~~------~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn  139 (171)
                      +.+..|+....++      ..+..|...++...+|+||.+|+.|+++..|.+++.++.|.+..+...|+.+++.||++||
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            4466666666533      4577899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         140 PRESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       140 ~~~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      ..+|.++.+|..|.+++.....++.
T Consensus      1107 ~egs~~y~d~~~l~~~~~~~~~~~~ 1131 (1157)
T KOG0386|consen 1107 EEGSRVYEDAIVLQSVFKSARQEIS 1131 (1157)
T ss_pred             cCCceechhHHHHHHHHhhhHHHHh
Confidence            9999999999999999998887765

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.05  E-value=5.5e-11  Score=68.77  Aligned_cols=45  Identities=29%  Similarity=0.747  Sum_probs=35.1

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCC-CCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADN-IDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~-~~~~~Cp~C~   48 (171)
                      .|.+ .++++.||+|+.|.+|||..|+++....... .+.|+|+.|.
T Consensus         4 vC~~-~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    4 VCGQ-SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             TTTS-SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             CCCC-cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            4656 5566779999999999999999887653332 3489999995

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

>smart00249 PHD PHD zinc finger

Probab=98.98  E-value=3.8e-10  Score=63.67  Aligned_cols=44  Identities=25%  Similarity=0.681  Sum_probs=35.6

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCcc
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC   47 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C   47 (171)
                      +|.+.+ +++.||.|+.|.+|||..|+++..........|.|+.|
T Consensus         4 ~C~~~~-~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~~C~~C   47 (47)
T smart00249        4 VCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC   47 (47)
T ss_pred             cCCCcC-CCCCEEECCCCCchhhhhhCCCcccCCCCCCCEECcCC
Confidence            466666 56669999999999999999887664456778999987

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

>KOG1472|consensus

Probab=98.96  E-value=8.1e-10  Score=93.60  Aligned_cols=68  Identities=37%  Similarity=0.694  Sum_probs=63.9

Q ss_pred             hCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCH
Q psy5115          77 AHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESP  144 (171)
Q Consensus        77 ~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~  144 (171)
                      +...+++|..+|+...+|+||.+|+.||||.++.+|+..+.|.+.++|+.|+.+||.||..||...+.
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            46789999999999999999999999999999999999999999999999999999999999985543

>KOG1828|consensus

Probab=98.66  E-value=2.2e-08  Score=78.76  Aligned_cols=89  Identities=11%  Similarity=0.025  Sum_probs=79.2

Q ss_pred             HHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCH
Q psy5115          65 FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESP  144 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~  144 (171)
                      ...+.....++...+....|..++....+|.|..+|++|+++.|+.+|..++.|.| -+|..|..+|..||.+||.++..
T Consensus       210 ~~l~~~q~~kl~~~~p~~~lnyg~tas~aP~YSm~Ik~~~~~~Tygdk~~andy~S-~~f~~D~kl~~l~amT~gehsk~  288 (418)
T KOG1828|consen  210 QQLQTLQEDKLNRVDPVAYLNYGPTASFAPGYSMTITEVEPPGTYGDKSSANDYES-LSFTQDRKLIALKAVTNGEHSKS  288 (418)
T ss_pred             HHHHHHHHHHhcccCchhhhcccchhhhcccccccccccCCCcchhhhhhhhhhhh-hhhhcccchhhHHHHhcCCcchH
Confidence            33444456777777888899999988899999999999999999999999999999 89999999999999999999999


Q ss_pred             HHHHHHHHHH
Q psy5115         145 FFKHAHQLEM  154 (171)
Q Consensus       145 ~~~~a~~l~~  154 (171)
                      +++.|+.+..
T Consensus       289 yyelank~lh  298 (418)
T KOG1828|consen  289 YYELANKQLH  298 (418)
T ss_pred             HHHHHHhhhh
Confidence            9999988765

>KOG1828|consensus

Probab=98.65  E-value=3.7e-09  Score=83.04  Aligned_cols=96  Identities=22%  Similarity=0.272  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHH
Q psy5115          66 ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPF  145 (171)
Q Consensus        66 ~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~  145 (171)
                      .....++.++.+.+.-..|.-|+...-.|+|.++|+.|||+.+++.|++.++|.+..+|..|.+++..||..||..++.+
T Consensus        22 ~~~ehhlrkl~sKdp~q~fafplt~~map~y~~iis~Pmd~~t~r~kidd~~yl~L~~m~~d~kl~~~na~~yn~~~Tv~  101 (418)
T KOG1828|consen   22 GDAEHHLRKLPSKDPKQKFAFPLTDKMAPNYLEIISEPMDRITKRSKIDDTRYLVLSQMEFDRKLPDGNATLYNLHPTVP  101 (418)
T ss_pred             hhHHHHHHhccccChhhhhccccchhhccchHhhhhcccccccccccCCCccceechhhhhhhcccccchhhhhcCCccc
Confidence            34555667777777777888888888899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q psy5115         146 FKHAHQLEMFFVQKVK  161 (171)
Q Consensus       146 ~~~a~~l~~~f~~~~~  161 (171)
                      +..|+.|.-+......
T Consensus       102 ~~aaKrL~~v~~~~~q  117 (418)
T KOG1828|consen  102 IVAAKRLCPVRLGMTQ  117 (418)
T ss_pred             cccccccchhhcchhh
Confidence            9999998766544443

>KOG1474|consensus

Probab=98.52  E-value=1.6e-08  Score=86.42  Aligned_cols=90  Identities=38%  Similarity=0.728  Sum_probs=81.9

Q ss_pred             HHhCcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHH
Q psy5115          75 IQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQL  152 (171)
Q Consensus        75 l~~~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l  152 (171)
                      +..+..+|+|..||+..  ..|.|+..|.+|||+.+|..++++..|.+..+-.+|+..+|.||..||.++..+..++..+
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            45678899999999965  5899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy5115         153 EMFFVQKVKILR  164 (171)
Q Consensus       153 ~~~f~~~~~~~~  164 (171)
                      +..|.+....+.
T Consensus        84 ~~~~~~~~~~~~   95 (640)
T KOG1474|consen   84 EKLFPKKLRSMP   95 (640)
T ss_pred             hhhccccccccc
Confidence            999877665543

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

Probab=98.21  E-value=3.5e-06  Score=57.57  Aligned_cols=62  Identities=18%  Similarity=0.335  Sum_probs=55.1

Q ss_pred             CCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         103 PMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       103 Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      |.||..|++|++.|.|+|+.+|..||-.|+.-++.-.+...++-+....++.+|.+.|.++-
T Consensus        59 p~dL~~V~kkl~~G~Y~sv~~F~~DvvkIiqa~l~~e~~~pe~~ka~s~~Ksf~ik~me~vf  120 (131)
T cd05493          59 PLDLEAVGKKLEAGFYTSVLDFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVF  120 (131)
T ss_pred             cccHHHHHHHHhccceehHHHHHHHHHHHHHHHHhhccCCccccCcchHHHHHHHHHHHHhc
Confidence            88999999999999999999999999999999998777677777777788888888887654

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.

>KOG4299|consensus

Probab=97.94  E-value=3.3e-06  Score=70.45  Aligned_cols=47  Identities=30%  Similarity=0.685  Sum_probs=37.1

Q ss_pred             CccccccCCCce--eEecCCCCceecccccCcc-ccCcCCCCCCCCCccC
Q psy5115           2 KFHTLAVIEPKF--YICCDTCQDWFHGRCVGIL-QSEADNIDEYICPNCN   48 (171)
Q Consensus         2 ~~~~~~~~~~~~--~i~C~~C~r~~H~~C~~~~-~~~~~~~~~~~Cp~C~   48 (171)
                      .||..|...+.|  .|+||+|++.||..|+.+. ..+.-+++.|+|+.|.
T Consensus       254 ~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~  303 (613)
T KOG4299|consen  254 DFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECK  303 (613)
T ss_pred             HHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCe
Confidence            378888777775  5999999999999999442 2334467899999998

>KOG1632|consensus

Probab=97.82  E-value=1.4e-06  Score=69.31  Aligned_cols=46  Identities=33%  Similarity=0.747  Sum_probs=41.7

Q ss_pred             ccccccCCCceeEecCCCCceecccc--cCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRC--VGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C--~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|.++.+.+++|+.|+.|..|||+.|  +++........+.|.|..|.
T Consensus        64 ~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~  111 (345)
T KOG1632|consen   64 KCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECK  111 (345)
T ss_pred             hcccccCchhhhhccccccccccccccccCchhhcCCccccccccccc
Confidence            46778888889999999999999999  99998888888999999998

>KOG4323|consensus

Probab=97.70  E-value=7e-06  Score=66.90  Aligned_cols=38  Identities=34%  Similarity=0.849  Sum_probs=28.3

Q ss_pred             eeEecCCCCceecccccCcc--ccCc-CCCCCCCCCccCCC
Q psy5115          13 FYICCDTCQDWFHGRCVGIL--QSEA-DNIDEYICPNCNNS   50 (171)
Q Consensus        13 ~~i~C~~C~r~~H~~C~~~~--~~~~-~~~~~~~Cp~C~~~   50 (171)
                      .||+|++|.-|||..|+...  +... +..-+|+|..|...
T Consensus       184 rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~  224 (464)
T KOG4323|consen  184 RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG  224 (464)
T ss_pred             eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence            59999999999999998332  2222 23448999999953

>KOG3612|consensus

Probab=97.64  E-value=1e-05  Score=66.52  Aligned_cols=121  Identities=16%  Similarity=0.144  Sum_probs=89.9

Q ss_pred             CceeEecCCCCceecccccCccccCcCCCCCCCCCccCCCCcccccccCC-------ChhHHHHHHHHHHHHHhCcCCCC
Q psy5115          11 PKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNL-------TPRDFESLRKLMKQIQAHKSAWP   83 (171)
Q Consensus        11 ~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~~~~~~~~~~l-------~~~~~~~~~~~l~~l~~~~~~~~   83 (171)
                      +|.++.|+.|.|+||..|....+...+....|.||.|...........++       .+.+...   .++...+  ...+
T Consensus        69 pg~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~k~~~~~nqp~gn~~~~~~~sd~Er---~~d~nsk--~~~~  143 (588)
T KOG3612|consen   69 PGAVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPYSFKVNELDNQPLGNTQNLETPSDPER---LLDHNSK--INQT  143 (588)
T ss_pred             CcceeeeehhhccccccccCcchhhccccccccCCcccccCCCccccccccchhcccccCchhh---HHhhhcc--cccc
Confidence            45589999999999999998888888888999999999543332211111       1111111   2222211  1111


Q ss_pred             CccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCH
Q psy5115          84 FMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESP  144 (171)
Q Consensus        84 F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~  144 (171)
                              -.+.|..+...|+|..++....-++.|++...|-++-..+..|..++.+.+++
T Consensus       144 --------~~~~~~~lkhep~D~~d~e~~v~eqk~~~q~klp~~t~~lq~~~~~~~gsdae  196 (588)
T KOG3612|consen  144 --------LLATTDFLKHEPIDWDDDEFFVCEQKGARQRKLPRITDELQSSLDSDEGSDAE  196 (588)
T ss_pred             --------cchhHHHhhcCccccccchhccccCcccccccccccccccccccccccCCCcc
Confidence                    24678889999999999999999999999999999999999999999998877

>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A

Probab=97.46  E-value=2.4e-05  Score=41.55  Aligned_cols=35  Identities=26%  Similarity=0.762  Sum_probs=19.2

Q ss_pred             ceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115          12 KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus        12 ~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      ..||.|+.|.-.+|..|=|+....  ..+.|+|..|+
T Consensus         2 n~ll~C~~C~v~VH~~CYGv~~~~--~~~~W~C~~C~   36 (36)
T PF13831_consen    2 NPLLFCDNCNVAVHQSCYGVSEVP--DGDDWLCDRCE   36 (36)
T ss_dssp             CEEEE-SSS--EEEHHHHT-SS----SS-----HHH-
T ss_pred             CceEEeCCCCCcCChhhCCcccCC--CCCcEECCcCC
Confidence            469999999999999999986543  33359998884

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

Probab=97.44  E-value=3.6e-05  Score=62.18  Aligned_cols=93  Identities=40%  Similarity=0.827  Sum_probs=83.9

Q ss_pred             HHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHH
Q psy5115          72 MKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQ  151 (171)
Q Consensus        72 l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~  151 (171)
                      +.....+..+|+|..+++....|.|++.+..+|++++.+.++..+.|+...+|..|..++++|+..||+.....+..+..
T Consensus       272 i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  351 (371)
T COG5076         272 ITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANV  351 (371)
T ss_pred             ccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhccc
Confidence            34445667789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q psy5115         152 LEMFFVQKVKILR  164 (171)
Q Consensus       152 l~~~f~~~~~~~~  164 (171)
                      +...+...++..+
T Consensus       352 ~~~~~~~~~~~~~  364 (371)
T COG5076         352 LEDFVIKKTRLIR  364 (371)
T ss_pred             hhhhHhhhhhhhh
Confidence            9988887776543

>KOG0383|consensus

Probab=97.36  E-value=6.8e-05  Score=64.39  Aligned_cols=46  Identities=28%  Similarity=0.634  Sum_probs=37.1

Q ss_pred             CCccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           1 MKFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         1 ~~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      +++|+-|.+++. ++.|+.|+.|||..|.+...... +.++|.|+.|.
T Consensus        47 ~e~c~ic~~~g~-~l~c~tC~~s~h~~cl~~pl~~~-p~~~~~c~Rc~   92 (696)
T KOG0383|consen   47 QEACRICADGGE-LLWCDTCPASFHASCLGPPLTPQ-PNGEFICPRCF   92 (696)
T ss_pred             hhhhhhhcCCCc-EEEeccccHHHHHHccCCCCCcC-Cccceeeeeec
Confidence            467999999887 88999999999999997654433 33449999995

>KOG1512|consensus

Probab=97.19  E-value=0.00018  Score=55.06  Aligned_cols=42  Identities=33%  Similarity=0.642  Sum_probs=33.9

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCC-ccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICP-NCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp-~C~   48 (171)
                      +|-+|-.+++ ++.||.|+|-||..|+|+..   -+.+.|.|. .|.
T Consensus       319 IC~~P~~E~E-~~FCD~CDRG~HT~CVGL~~---lP~G~WICD~~C~  361 (381)
T KOG1512|consen  319 ICLGPVIESE-HLFCDVCDRGPHTLCVGLQD---LPRGEWICDMRCR  361 (381)
T ss_pred             ccCCcccchh-eeccccccCCCCcccccccc---ccCccchhhhHHH
Confidence            4667766666 99999999999999999853   356799998 465

>KOG0644|consensus

Probab=97.09  E-value=0.00036  Score=60.44  Aligned_cols=65  Identities=17%  Similarity=0.274  Sum_probs=56.7

Q ss_pred             cccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q psy5115          96 YYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV  160 (171)
Q Consensus        96 Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~~~~  160 (171)
                      |..-..-|..++.|+.+|++..|++.+.|..||..|..||.+|.+.+..+...+..|...|...+
T Consensus      1046 ~~~~fpvpls~evi~~rlEn~yYrs~e~~~hdvs~mlsnae~~fg~~~~~~~ki~~l~~~~~~Tl 1110 (1113)
T KOG0644|consen 1046 VDNRFPVPLSLEVIRSRLENNYYRSQEALRHDVSVMLSNAETFFGRNKNVAIKISFLSPWFDRTL 1110 (1113)
T ss_pred             cCCCCCCcccHHHHHHHHHhhhhhhhHhhhcchhhhhcccceeecccccHHHHhhhcchhhhhhc
Confidence            44556778999999999999999999999999999999999999988877777777877776654

>KOG0825|consensus

Probab=96.84  E-value=0.0012  Score=57.09  Aligned_cols=37  Identities=27%  Similarity=0.741  Sum_probs=29.4

Q ss_pred             CceeEecCCCCce-ecccccCccccCcCCCCCCCCCccC
Q psy5115          11 PKFYICCDTCQDW-FHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus        11 ~~~~i~C~~C~r~-~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      ++.||.||.|... ||..|+.+... +.+..+|+|+.|.
T Consensus       227 EdVLLLCDsCN~~~YH~YCLDPdl~-eiP~~eWYC~NC~  264 (1134)
T KOG0825|consen  227 EDVLLLCDSCNKVYYHVYCLDPDLS-ESPVNEWYCTNCS  264 (1134)
T ss_pred             HHhheeecccccceeeccccCcccc-cccccceecCcch
Confidence            4559999999988 99999966322 2356789999998

>KOG1844|consensus

Probab=96.53  E-value=0.0012  Score=55.41  Aligned_cols=44  Identities=32%  Similarity=0.666  Sum_probs=34.7

Q ss_pred             cccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      |..-.+.+|+|++|+.|++|.|..|.|.....  .++.|.|..|..
T Consensus        91 c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~--~p~~y~c~~c~~  134 (508)
T KOG1844|consen   91 CGLEDDMEGLMIQCDWCGRWQHKICCGSFKST--KPDKYVCEICTP  134 (508)
T ss_pred             cccccCCCceeeCCcccCcccCceeeeecCCC--Cchhceeeeecc
Confidence            33334438899999999999999999875442  378999999993

>KOG0954|consensus

Probab=96.37  E-value=0.0013  Score=56.43  Aligned_cols=43  Identities=23%  Similarity=0.590  Sum_probs=35.1

Q ss_pred             ccccccCC----CceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIE----PKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~----~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|++|..+    ..+||.||.|.-..|..|-|+..-   +.+.|+|..|.
T Consensus       273 iCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~---p~gpWlCr~Ca  319 (893)
T KOG0954|consen  273 ICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEV---PEGPWLCRTCA  319 (893)
T ss_pred             eeceecCCCccccceeEEeccchhHHHHhhhceeec---CCCCeeehhcc
Confidence            46666666    556999999999999999999743   44789999887

>KOG2752|consensus

Probab=96.24  E-value=0.0025  Score=49.45  Aligned_cols=27  Identities=26%  Similarity=0.677  Sum_probs=23.2

Q ss_pred             cccccCC-----CceeEecCCCCceec-ccccC
Q psy5115           4 HTLAVIE-----PKFYICCDTCQDWFH-GRCVG   30 (171)
Q Consensus         4 ~~~~~~~-----~~~~i~C~~C~r~~H-~~C~~   30 (171)
                      |+++|++     +|.|+||-.|..||| ..|+.
T Consensus       133 Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~  165 (345)
T KOG2752|consen  133 CDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQ  165 (345)
T ss_pred             ecCCCCCccccccceeeeEEeccchhcccccCc
Confidence            5888887     778999999999999 77763

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

Probab=95.84  E-value=0.0094  Score=41.72  Aligned_cols=25  Identities=28%  Similarity=0.573  Sum_probs=19.0

Q ss_pred             ecccccCccccCcCCCCCCCCCccCC
Q psy5115          24 FHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        24 ~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      ||..|+.+.-. ..+.+.|+||.|..
T Consensus         2 ~H~~CL~Ppl~-~~P~g~W~Cp~C~~   26 (148)
T cd04718           2 FHLCCLRPPLK-EVPEGDWICPFCEV   26 (148)
T ss_pred             cccccCCCCCC-CCCCCCcCCCCCcC
Confidence            89999965433 34567899999994

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

>KOG0955|consensus

Probab=95.69  E-value=0.0074  Score=54.38  Aligned_cols=46  Identities=22%  Similarity=0.437  Sum_probs=36.9

Q ss_pred             ccccccCCCce----eEecCCCCceecccccCccccCcCCCCCCCCCccCCCC
Q psy5115           3 FHTLAVIEPKF----YICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSS   51 (171)
Q Consensus         3 ~~~~~~~~~~~----~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~~   51 (171)
                      .|..|.+++.+    .|.||.|.-.+|..|.|+.   ..+.+.|+|..|-.+.
T Consensus       221 ~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~---~ipeg~WlCr~Cl~s~  270 (1051)
T KOG0955|consen  221 VCCICLDGECQNSNVIVFCDGCNLAVHQECYGIP---FIPEGQWLCRRCLQSP  270 (1051)
T ss_pred             cceeecccccCCCceEEEcCCCcchhhhhccCCC---CCCCCcEeehhhccCc
Confidence            57777777654    8999999999999999964   3456689999998544

>KOG0957|consensus

Probab=95.35  E-value=0.0083  Score=49.54  Aligned_cols=44  Identities=20%  Similarity=0.441  Sum_probs=29.0

Q ss_pred             cccccCCCceeEecCCCCceecccccCcc--ccCcCC-CCCCCCCccC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGIL--QSEADN-IDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~--~~~~~~-~~~~~Cp~C~   48 (171)
                      |.+..|.. .+++||.|..-||.-|+.+.  ....+. .--|.|..|.
T Consensus       550 Ckks~dQH-ll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd  596 (707)
T KOG0957|consen  550 CKKSTDQH-LLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD  596 (707)
T ss_pred             eccchhhH-HHhhcchhhceeeccccCCccccCcccccCcceeecccc
Confidence            44433333 38999999999999998442  111111 2359999995

>KOG1473|consensus

Probab=95.27  E-value=0.012  Score=52.87  Aligned_cols=43  Identities=26%  Similarity=0.404  Sum_probs=34.0

Q ss_pred             cccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      |+.+-|.+. ++||+.|+|+||.+|+... ......+.|-|-.|.
T Consensus       347 crf~~d~~~-~lc~Et~prvvhlEcv~hP-~~~~~s~~~e~evc~  389 (1414)
T KOG1473|consen  347 CRFCHDLGD-LLCCETCPRVVHLECVFHP-RFAVPSAFWECEVCN  389 (1414)
T ss_pred             ccccCcccc-eeecccCCceEEeeecCCc-cccCCCccchhhhhh
Confidence            666666666 9999999999999999653 334466789999998

>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=94.30  E-value=0.035  Score=31.56  Aligned_cols=35  Identities=17%  Similarity=0.485  Sum_probs=18.3

Q ss_pred             eeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115          13 FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus        13 ~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .+|||+.|.+|=... .+........++.|+|..-.
T Consensus         2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~d~W~C~~n~   36 (50)
T PF07496_consen    2 YWVQCDSCLKWRRLP-EEVDPIREELPDPWYCSMNP   36 (50)
T ss_dssp             EEEE-TTT--EEEE--CCHHCTSCCSSTT--GGGSS
T ss_pred             eEEECCCCCceeeCC-hhhCcccccCCCeEEcCCCC
Confidence            589999999998776 33332223345689998743

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.

>KOG1632|consensus

Probab=93.70  E-value=0.0041  Score=49.81  Aligned_cols=42  Identities=43%  Similarity=1.059  Sum_probs=33.4

Q ss_pred             ceeEecCCCCceecccccCccccCcCCCCC----CCCCccCCCCcc
Q psy5115          12 KFYICCDTCQDWFHGRCVGILQSEADNIDE----YICPNCNNSSSN   53 (171)
Q Consensus        12 ~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~----~~Cp~C~~~~~~   53 (171)
                      .++++|+.|..|||+.|+.+.+........    |.|+.|......
T Consensus       253 ~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~~~~  298 (345)
T KOG1632|consen  253 KFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVLKFE  298 (345)
T ss_pred             HHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeecccc
Confidence            668899999999999999887765555555    999999854433

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A

Probab=93.42  E-value=0.0088  Score=32.92  Aligned_cols=40  Identities=18%  Similarity=0.372  Sum_probs=26.6

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      +|...++++..++... |..+||..|+..--..     ...||.|+
T Consensus         5 IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~-----~~~CP~CR   44 (44)
T PF13639_consen    5 ICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKR-----NNSCPVCR   44 (44)
T ss_dssp             TTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHH-----SSB-TTTH
T ss_pred             CCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHh-----CCcCCccC
Confidence            4556666566677776 9999999998432211     24999984

...

>KOG0732|consensus

Probab=92.83  E-value=0.1  Score=47.31  Aligned_cols=62  Identities=15%  Similarity=0.110  Sum_probs=54.9

Q ss_pred             CCCCccCCCCCC-----CCccccccCCCCCHHHHHHHHhcCCCCCHHHHHH--HHHHHHHHHhhhCCCC
Q psy5115          81 AWPFMEPVDPHE-----APDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIG--DMTKIFDNCRYYNPRE  142 (171)
Q Consensus        81 ~~~F~~pv~~~~-----~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~--Dv~li~~Na~~yn~~~  142 (171)
                      ...|..|++...     .++|...|+++||+...-.++..+.|.++.+|..  ++.+|+.|++.||+..
T Consensus       533 ~~~~s~Pl~~~~~~ll~~~~~~~~iq~~~~va~~~~k~~e~~~~~v~~~e~~~~i~lic~~~lli~~~~  601 (1080)
T KOG0732|consen  533 SVIFSRPLSTYLKPLLPFQDALEDIQGLMDVASSMAKIEEHLKLLVRSFESNFAIRLICRPRLLINGGK  601 (1080)
T ss_pred             ccCCCCCCCcceecccchHHHHHHhhcchhHHhhhhhHHHHhHHHHHhhhcccchhhhcCcHHhcCCCc
Confidence            556777777552     4588999999999999999999999999999999  9999999999999865

>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain

Probab=92.75  E-value=0.054  Score=38.60  Aligned_cols=29  Identities=17%  Similarity=0.422  Sum_probs=23.0

Q ss_pred             cccccC-----CCceeEecCCCCceecccccCcc
Q psy5115           4 HTLAVI-----EPKFYICCDTCQDWFHGRCVGIL   32 (171)
Q Consensus         4 ~~~~~~-----~~~~~i~C~~C~r~~H~~C~~~~   32 (171)
                      |.+|+.     .-|.||.|.+|...||..|+|..
T Consensus         2 C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~R   35 (175)
T PF15446_consen    2 CDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPR   35 (175)
T ss_pred             cccccCCCCCccCCCeEEcCccChHHHhhhcCCc
Confidence            666653     25679999999999999997653

>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []

Probab=92.23  E-value=0.15  Score=28.64  Aligned_cols=35  Identities=26%  Similarity=0.553  Sum_probs=20.3

Q ss_pred             EecCCCCceeccccc----Ccc--ccCcCCCCCCCCCccCC
Q psy5115          15 ICCDTCQDWFHGRCV----GIL--QSEADNIDEYICPNCNN   49 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~~--~~~~~~~~~~~Cp~C~~   49 (171)
                      -+|..|.-+|...=-    ++.  .+..+.++.|.||.|..
T Consensus         2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a   42 (47)
T PF00301_consen    2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGA   42 (47)
T ss_dssp             EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSS
T ss_pred             cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCC
Confidence            468889888887652    111  12345688999999973

The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....

>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain

Probab=92.07  E-value=0.081  Score=35.10  Aligned_cols=27  Identities=22%  Similarity=0.412  Sum_probs=23.4

Q ss_pred             ccccccCCCceeEecCC--CCceeccccc
Q psy5115           3 FHTLAVIEPKFYICCDT--CQDWFHGRCV   29 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~--C~r~~H~~C~   29 (171)
                      -|..|....|..|+|..  |.++||..|.
T Consensus        57 ~C~iC~~~~G~~i~C~~~~C~~~fH~~CA   85 (110)
T PF13832_consen   57 KCSICGKSGGACIKCSHPGCSTAFHPTCA   85 (110)
T ss_pred             cCcCCCCCCceeEEcCCCCCCcCCCHHHH
Confidence            46667777888999998  9999999996

>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []

Probab=91.97  E-value=0.29  Score=40.29  Aligned_cols=49  Identities=10%  Similarity=0.148  Sum_probs=35.6

Q ss_pred             CHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy5115         120 KLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLV  168 (171)
Q Consensus       120 s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~~~  168 (171)
                      .+++..+=|++=-..|.+|.....+.-+-|..|+.+....-.++.+++.
T Consensus       351 ~~eeLESIVRiKqAEA~MFQ~kAdEARrEAE~LqrI~~aK~~k~EEEYa  399 (446)
T PF07227_consen  351 QIEELESIVRIKQAEAKMFQLKADEARREAEGLQRIALAKSEKIEEEYA  399 (446)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            4566666677777788888877777778888887777777666666554

Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.

>COG5141 PHD zinc finger-containing protein [General function prediction only]

Probab=91.72  E-value=0.087  Score=43.67  Aligned_cols=35  Identities=26%  Similarity=0.584  Sum_probs=29.1

Q ss_pred             CceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115          11 PKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus        11 ~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      ....|.||+|.-..|..|-|+..   -+.+.|+|..|.
T Consensus       207 ~naiVfCdgC~i~VHq~CYGI~f---~peG~WlCrkCi  241 (669)
T COG5141         207 SNAIVFCDGCEICVHQSCYGIQF---LPEGFWLCRKCI  241 (669)
T ss_pred             cceEEEecCcchhhhhhccccee---cCcchhhhhhhc
Confidence            34589999999999999999853   245689999998

>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center

Probab=91.20  E-value=0.2  Score=28.44  Aligned_cols=34  Identities=26%  Similarity=0.544  Sum_probs=22.4

Q ss_pred             ecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCC
Q psy5115          16 CCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNN   49 (171)
Q Consensus        16 ~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~   49 (171)
                      +|..|.-+|+..=-    ++  ..+..+.++.|.||.|..
T Consensus         3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a   42 (50)
T cd00730           3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA   42 (50)
T ss_pred             CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence            68899988886431    11  112334688999999973

Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.

>KOG0956|consensus

Probab=90.89  E-value=0.12  Score=44.51  Aligned_cols=42  Identities=26%  Similarity=0.588  Sum_probs=34.4

Q ss_pred             cccccCCCc----eeEecC--CCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           4 HTLAVIEPK----FYICCD--TCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~----~~i~C~--~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      |=+|-|+.|    .+|-||  .|...+|.-|-||-+-   +.+.|+|..|.
T Consensus         8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqV---PtGpWfCrKCe   55 (900)
T KOG0956|consen    8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQV---PTGPWFCRKCE   55 (900)
T ss_pred             eeeecCcCCCccCceeeecCCCceeeeehhcceeEec---CCCchhhhhhh
Confidence            557777755    489999  7999999999998643   56789999998

>COG1773 Rubredoxin [Energy production and conversion]

Probab=89.36  E-value=0.45  Score=27.54  Aligned_cols=35  Identities=26%  Similarity=0.547  Sum_probs=23.1

Q ss_pred             EecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCC
Q psy5115          15 ICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNN   49 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~   49 (171)
                      -+|..|.-+|...=-    ++  .....+-++.|.||.|..
T Consensus         4 ~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg~   44 (55)
T COG1773           4 WRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECGV   44 (55)
T ss_pred             eEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCCC
Confidence            578899888865431    11  112345688999999984

>KOG0957|consensus

Probab=89.34  E-value=0.27  Score=41.02  Aligned_cols=42  Identities=21%  Similarity=0.574  Sum_probs=31.2

Q ss_pred             ccCCCceeEecCCCCceecccccCcccc-------CcCCCCCCCCCccC
Q psy5115           7 AVIEPKFYICCDTCQDWFHGRCVGILQS-------EADNIDEYICPNCN   48 (171)
Q Consensus         7 ~~~~~~~~i~C~~C~r~~H~~C~~~~~~-------~~~~~~~~~Cp~C~   48 (171)
                      ..++-|..|+||.|+--.|.-|-|..+-       .......|+|..|.
T Consensus       129 rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~  177 (707)
T KOG0957|consen  129 RSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL  177 (707)
T ss_pred             ccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHh
Confidence            3556666999999999999999776521       11134689999888

>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines

Probab=89.20  E-value=0.13  Score=25.78  Aligned_cols=25  Identities=16%  Similarity=0.438  Sum_probs=10.1

Q ss_pred             cccccCCCceeEecCCCCceeccccc
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCV   29 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~   29 (171)
                      |..+.++ +.+-.|..|.-.+|..|+
T Consensus         6 C~~~~~~-~~~Y~C~~Cdf~lH~~Ca   30 (30)
T PF07649_consen    6 CGKPIDG-GWFYRCSECDFDLHEECA   30 (30)
T ss_dssp             TS----S---EEE-TTT-----HHHH
T ss_pred             CCCcCCC-CceEECccCCCccChhcC
Confidence            4444444 468899999999999884

The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.

>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family

Probab=88.74  E-value=1  Score=27.35  Aligned_cols=28  Identities=18%  Similarity=0.369  Sum_probs=24.3

Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHHH
Q psy5115         107 KTIELRIAQQRYKKLSEFIGDMTKIFDN  134 (171)
Q Consensus       107 ~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  134 (171)
                      ..|+.++++|.|.|..++++|..+++.-
T Consensus        12 ~~i~~~V~sG~Y~s~SEVir~aLR~le~   39 (69)
T TIGR02606        12 SFIRSQVQSGRYGSASEVVRAALRLLEE   39 (69)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHH
Confidence            4588999999999999999998887654

This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=88.10  E-value=0.63  Score=23.85  Aligned_cols=10  Identities=30%  Similarity=1.162  Sum_probs=8.3

Q ss_pred             CCCCCCccCC
Q psy5115          40 DEYICPNCNN   49 (171)
Q Consensus        40 ~~~~Cp~C~~   49 (171)
                      +.|.||.|..
T Consensus        16 ~~~~CP~Cg~   25 (33)
T cd00350          16 APWVCPVCGA   25 (33)
T ss_pred             CCCcCcCCCC
Confidence            4799999974

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=87.46  E-value=0.37  Score=27.77  Aligned_cols=26  Identities=15%  Similarity=0.350  Sum_probs=20.4

Q ss_pred             cccccCCCceeEecCCCCceeccccc
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCV   29 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~   29 (171)
                      |..+..+++-.|.|..|.-.||..|-
T Consensus        11 Cg~~~~~~dDiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen   11 CGKKFKDGDDIVVCPECGAPYHRDCW   36 (54)
T ss_pred             hCCcccCCCCEEECCCCCCcccHHHH
Confidence            55555445558999999999999996

>KOG0644|consensus

Probab=87.42  E-value=0.13  Score=45.28  Aligned_cols=72  Identities=11%  Similarity=0.119  Sum_probs=56.9

Q ss_pred             CccCCCCCCCCccccccCCCCCHHHHHHHHhcCCC--------------C----------CHHH------HHHHHHHHHH
Q psy5115          84 FMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRY--------------K----------KLSE------FIGDMTKIFD  133 (171)
Q Consensus        84 F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y--------------~----------s~~~------f~~Dv~li~~  133 (171)
                      |.-+++....|.|..++..|.+|++++.+|.+..|              .          ++.+      ...-+..|-+
T Consensus        86 lv~~~d~~~pp~~~~~a~vpTlLgtg~qsLl~r~k~~~~~~~~~s~~~~~h~~~~~~~~~sl~s~~~~~~~h~~a~~i~~  165 (1113)
T KOG0644|consen   86 LVPMLDKPIPPRYCTIARVPTLLGTGRQSLLRRAKDIRHTVWKGSAFRWPHMHADQVRGVSLRSIGGGFEIHHRAPSIGC  165 (1113)
T ss_pred             hccCcCCCCCcceeeeecccchhcchhHHHHhhhhhcccccccccccccccccCcccccceeccCCcchhhhhcCccccc
Confidence            34556666778888899999999999999998877              2          3333      6778889999


Q ss_pred             HHhhhCCCCCHHHHHHHHHHHHH
Q psy5115         134 NCRYYNPRESPFFKHAHQLEMFF  156 (171)
Q Consensus       134 Na~~yn~~~s~~~~~a~~l~~~f  156 (171)
                      |+..++.|++ +++.++.+.++.
T Consensus       166 at~~~akPgt-mvqkmk~ikrLl  187 (1113)
T KOG0644|consen  166 ATFSIAKPGT-MVQKMKNIKRLL  187 (1113)
T ss_pred             ceeeecCcHH-HHHHHHHHHHHH
Confidence            9999999999 777776665554

>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression

Probab=86.47  E-value=0.36  Score=31.95  Aligned_cols=32  Identities=28%  Similarity=0.697  Sum_probs=22.3

Q ss_pred             CCC---Cceeccccc----CccccCcCCCCCCCCCccCC
Q psy5115          18 DTC---QDWFHGRCV----GILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        18 ~~C---~r~~H~~C~----~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      ..|   ..-|...|+    +....+.....+|.||.|+.
T Consensus        31 ~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg   69 (105)
T PF10497_consen   31 SSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG   69 (105)
T ss_pred             CCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence            677   888999996    33322333456899999983

This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger

Probab=85.38  E-value=0.38  Score=30.49  Aligned_cols=33  Identities=24%  Similarity=0.515  Sum_probs=20.6

Q ss_pred             eEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115          14 YICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      ++-+ .|...||..|+-.=..  .....-.||.|+.
T Consensus        47 lv~g-~C~H~FH~hCI~kWl~--~~~~~~~CPmCR~   79 (85)
T PF12861_consen   47 LVWG-KCSHNFHMHCILKWLS--TQSSKGQCPMCRQ   79 (85)
T ss_pred             eeec-cCccHHHHHHHHHHHc--cccCCCCCCCcCC
Confidence            3444 5999999999722111  1122459999984

>KOG1512|consensus

Probab=85.01  E-value=0.26  Score=38.14  Aligned_cols=36  Identities=22%  Similarity=0.599  Sum_probs=27.7

Q ss_pred             eeEecCCCCceecccccCccccCcCC--CCCCCCCccC
Q psy5115          13 FYICCDTCQDWFHGRCVGILQSEADN--IDEYICPNCN   48 (171)
Q Consensus        13 ~~i~C~~C~r~~H~~C~~~~~~~~~~--~~~~~Cp~C~   48 (171)
                      -||+|..|.-.+|+.|+..++....-  .=.|.|..|+
T Consensus       278 S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~  315 (381)
T KOG1512|consen  278 SWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCE  315 (381)
T ss_pred             cceeecccccCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence            39999999999999999765544332  3368888886

>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain

Probab=85.00  E-value=0.74  Score=29.15  Aligned_cols=29  Identities=21%  Similarity=0.351  Sum_probs=23.0

Q ss_pred             ccccccCCCceeEecC--CCCceecccccCc
Q psy5115           3 FHTLAVIEPKFYICCD--TCQDWFHGRCVGI   31 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~--~C~r~~H~~C~~~   31 (171)
                      -|..|....|-.|.|.  +|.+.||..|...
T Consensus        38 ~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~   68 (90)
T PF13771_consen   38 KCSICKKKGGACIGCSHPGCSRSFHVPCARK   68 (90)
T ss_pred             CCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence            4666666667799998  5999999999743

>KOG1827|consensus

Probab=84.86  E-value=0.11  Score=44.45  Aligned_cols=74  Identities=11%  Similarity=0.007  Sum_probs=65.8

Q ss_pred             CCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHH
Q psy5115          82 WPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMF  155 (171)
Q Consensus        82 ~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~  155 (171)
                      ..|...++...+|.|+.+++-||.+....+++..++|.....|..|....+.|+..|+....-+...+..+.+.
T Consensus       214 er~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~q~l~g~c~v~~~~~yi~~~p~~ls~~  287 (629)
T KOG1827|consen  214 ERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLVQRLLGKCYVMKPTEYISGDPENLSEE  287 (629)
T ss_pred             cccccCcccccccceeEeeCCccCccccccchhcccceecccccccHHHHhhcceEEeehhHhhhcCccccccc
Confidence            35667777888999999999999999999999999999999999999999999999998888888877766543

>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown

Probab=84.13  E-value=1.9  Score=27.06  Aligned_cols=27  Identities=26%  Similarity=0.480  Sum_probs=22.3

Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHH
Q psy5115         107 KTIELRIAQQRYKKLSEFIGDMTKIFD  133 (171)
Q Consensus       107 ~~I~~kl~~~~Y~s~~~f~~Dv~li~~  133 (171)
                      .-|+.++.+|.|.|..++++|.-.++.
T Consensus        15 ~~i~~~V~sG~Y~s~SEvvR~aLRlle   41 (80)
T PF03693_consen   15 AFIEEQVASGRYSSASEVVREALRLLE   41 (80)
T ss_dssp             HHHHHHHCTTS-SSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence            458999999999999999999777664

The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins. ; PDB: 3KXE_C.

>PF14372 DUF4413: Domain of unknown function (DUF4413)

Probab=82.80  E-value=8.9  Score=24.95  Aligned_cols=50  Identities=18%  Similarity=0.164  Sum_probs=41.8

Q ss_pred             cCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         115 QQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       115 ~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      ...|.|...|...+..|-..-...+..+..+..+|..+.+.|.+-|++..
T Consensus         3 ~~~~pTsn~~f~~i~~i~~~l~~~~~~d~~l~~ma~~M~~KfdKYw~~~~   52 (101)
T PF14372_consen    3 GSSYPTSNLYFHEIWKIKDLLRDWNNDDPDLKNMAKKMKEKFDKYWKDCN   52 (101)
T ss_pred             CCCcCcHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHhH
Confidence            45788998898888888887777776778899999999999999998653

>KOG4443|consensus

Probab=82.22  E-value=0.37  Score=41.37  Aligned_cols=38  Identities=24%  Similarity=0.580  Sum_probs=28.4

Q ss_pred             CceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115          11 PKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus        11 ~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|-|+.|+.|+.-||..||.+--....-..-|.||.|+
T Consensus        32 ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~cr   69 (694)
T KOG4443|consen   32 AGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCR   69 (694)
T ss_pred             cCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCce
Confidence            34499999999999999997432323334459999888

>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type

Probab=81.40  E-value=0.63  Score=22.28  Aligned_cols=13  Identities=23%  Similarity=0.603  Sum_probs=10.1

Q ss_pred             eEecCCCCceecc
Q psy5115          14 YICCDTCQDWFHG   26 (171)
Q Consensus        14 ~i~C~~C~r~~H~   26 (171)
                      |+.|..|+|.|..
T Consensus         2 l~~C~~CgR~F~~   14 (25)
T PF13913_consen    2 LVPCPICGRKFNP   14 (25)
T ss_pred             CCcCCCCCCEECH
Confidence            6788888888854

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	171
3qzv_A	174	Crystal Structure Of Bptf Phd-Linker-Bromo In Compl		7e-58
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		7e-58
2f6j_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		7e-56
3uv2_A	126	Crystal Structure Of The Bromodomain Of Human Nucle		2e-38
3qzt_A	115	Crystal Structure Of Bptf Bromo In Complex With His		4e-37
3qzs_A	115	Crystal Structure Of Bptf Bromo In Complex With His		1e-36
1e6i_A	121	Bromodomain From Gcn5 Complexed With Acetylated H4		4e-24
3gg3_A	119	Crystal Structure Of The Bromodomain Of Human Pcaf		3e-23
1n72_A	118	Structure And Ligand Of A Histone Acetyltransferase		9e-23
1f68_A	103	Nmr Solution Structure Of The Bromodomain From Huma		9e-21
3d7c_A	112	Crystal Structure Of The Bromodomain Of Human Gcn5,		9e-21
3nxb_A	116	Crystal Structure Of The Bromodomain Of Human Cecr2		5e-18
2wp2_A	120	Structure Of Brdt Bromodomain Bd1 Bound To A Diacet		1e-14
2rfj_A	119	Crystal Structure Of The Bromo Domain 1 In Human Br		7e-14
4don_A	145	Brd4 Bromodomain 1 Complex With A Fragment 3,4-dihy		2e-13
3jvj_A	131	Crystal Structure Of The Bromodomain 1 In Mouse Brd		2e-13
4hbw_A	127	Crystal Structure Of The First Bromodomain Of Human		3e-13
3g0l_A	117	Crystal Structure Of Human Bromodomain Adjacent To		3e-13
2oss_A	127	Crystal Structure Of The Bromo Domain 1 In Human Br		3e-13
2e7o_A	112	Solution Structure Of The Bromodomain From Human Br		3e-13
2l5e_A	128	Complex Between Bd1 Of Brd3 And Gata-1 C-Tail Lengt		4e-13
2ydw_A	153	Crystal Structure Of The First Bromodomain Of Human		5e-13
4a9e_A	154	N-Terminal Bromodomain Of Human Brd2 With 3-Methyl-		5e-13
2fui_A	62	Nmr Solution Structure Of Phd Finger Fragment Of Hu		5e-13
2yw5_A	138	Solution Structure Of The Bromodomain From Human Br		6e-13
3o33_A	184	Crystal Structure Of Trim24 Phd-Bromo In The Free S		9e-13
3rcw_A	135	Crystal Structure Of The Bromodomain Of Human Brd1		1e-12
2nxb_A	123	Crystal Structure Of Human Bromodomain Containing P		5e-12
3uv4_A	158	Crystal Structure Of The Second Bromodomain Of Huma		5e-11
3u5m_A	207	Crystal Structure Of Trim33 Phd-Bromo In The Free S		9e-11
1eqf_A	280	Crystal Structure Of The Double Bromodomain Module		1e-10
3aqa_A	128	Crystal Structure Of The Human Brd2 Bd1 Bromodomain		1e-10
3uv5_A	265	Crystal Structure Of The Tandem Bromodomains Of Hum		1e-10
2yyn_A	135	Crystal Sturcture Of Human Bromodomain Protein Leng		1e-10
1x0j_A	122	Crystal Structure Analysis Of The N-Terminal Bromod		1e-10
3aad_A	292	Structure Of The Histone Chaperone Cia/asf1-double		1e-10
3hmh_A	155	Crystal Structure Of The Second Bromodomain Of Huma		2e-10
2wp1_A	126	Structure Of Brdt Bromodomain 2 Bound To An Acetyla		3e-10
3i3j_A	124	Crystal Structure Of The Bromodomain Of Human Ep300		5e-10
3oni_A	114	Crystal Structure Of The Second Bromodomain Of Huma		6e-10
2dvv_A	112	Crystal Structure Of The Second Bromodomain Of The		6e-10
2g4a_A	116	Solution Structure Of A Bromodomain From Ring3 Prot		7e-10
3kv5_D	488	Structure Of Kiaa1718, Human Jumonji Demethylase, I		7e-10
2d9e_A	121	Solution Structure Of The Bromodomain Of Peregrin L		9e-10
3dwy_A	119	Crystal Structure Of The Bromodomain Of Human Crebb		2e-09
2oo1_A	113	Crystal Structure Of The Bromo Domain 2 Of Human Br		2e-09
1jsp_B	121	Nmr Structure Of Cbp Bromodomain In Complex With P5		2e-09
2e7n_A	117	Solution Structure Of The Second Bromodomain From H		2e-09
3tlp_A	150	Crystal Structure Of The Fourth Bromodomain Of Huma		2e-09
3jvl_A	120	Crystal Structure Of Bromodomain 2 Of Mouse Brd4 Le		4e-09
2i8n_A	114	Solution Structure Of The Second Bromodomain Of Brd		4e-09
3kv4_A	447	Structure Of Phf8 In Complex With Histone H3 Length		4e-09
3dai_A	130	Crystal Structure Of The Bromodomain Of The Human A		4e-09
3lxj_A	136	Crystal Structure Of The Bromodomain Of Human Aaa D		5e-09
2ouo_A	130	Crystal Structure Of The Bromo Domain 2 In Human Br		5e-09
2lsp_B	128	Solution Structures Of Brd4 Second Bromodomain With		6e-09
3kqi_A	75	Crystal Structure Of Phf2 Phd Domain Complexed With		2e-08
2r0v_A	346	Structure Of The Rsc4 Tandem Bromodomain Acetylated		2e-08
2r10_A	361	Structure Of An Acetylated Rsc4 Tandem Bromodomain		2e-08
2ktb_B	121	Solution Structure Of The Second Bromodomain Of Hum		2e-08
3ljw_A	120	Crystal Structure Of The Second Bromodomain Of Huma		2e-08
3hmf_A	116	Crystal Structure Of The Second Bromodomain Of Huma		3e-08
1we9_A	64	Solution Structure Of Phd Domain In Nucleic Acid Bi		4e-08
2dww_A	114	Crystal Structure Of Bromodomain-Containing Protein		6e-08
3fkm_X	166	Plasmodium Falciparum Bromodomain-Containing Protei		9e-08
3q2e_A	123	Crystal Structure Of The Second Bromodomain Of Huma		2e-07
1wem_A	76	Solution Structure Of Phd Domain In Death Inducer-		4e-07
3mb3_A	135	Crystal Structure Of The Second Bromodomain Of Plec		1e-06
3hme_A	123	Crystal Structure Of Human Bromodomain Containing 9		2e-06
2i7k_A	117	Solution Structure Of The Bromodomain Of Human Brd7		2e-06
2dkw_A	131	Solution Structure Of The Bromodomain Of Human Prot		2e-06
2r0y_A	311	Structure Of The Rsc4 Tandem Bromodomain In Complex		2e-06
2r0s_A	285	Crystal Structure Of The Rsc4 Tandem Bromodomain Le		3e-06
1wep_A	79	Solution Structure Of Phd Domain In Phf8 Length = 7		3e-06
3mqm_A	126	Crystal Structure Of The Bromodomain Of Human Ash1l		6e-06
3k2j_A	130	Crystal Structure Of The 3rd Bromodomain Of Human P		2e-05
3g0j_A	124	Crystal Structure Of The Fifth Bromodomain Of Human		5e-05
2yqd_A	120	Solution Structure Of The Fifth Bromodomain From Mo		5e-05
3iu5_A	116	Crystal Structure Of The First Bromodomain Of Human		7e-05
3n9l_A	528	Cekdm7a From C.Elegans, Complex With H3k4me3 Peptid		6e-04

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

Iteration: 1
 Score =  219 bits (557), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 93/155 (60%), Positives = 125/155 (80%)
Query: 10  EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
           E KFYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct: 19  ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 78
Query: 70  KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
           ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+KL+EF+ DMT
Sbjct: 79  RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMT 138
Query: 130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR 164
           KIFDNCRYYNP +SPF++ A  LE FFVQK+K  +
Sbjct: 139 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 173

>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 =  219 bits (557), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 93/155 (60%), Positives = 125/155 (80%)
Query: 10  EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
           E KFYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct: 19  ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 78
Query: 70  KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
           ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+KL+EF+ DMT
Sbjct: 79  RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMT 138
Query: 130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR 164
           KIFDNCRYYNP +SPF++ A  LE FFVQK+K  +
Sbjct: 139 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 173

>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 =  212 bits (540), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 91/155 (58%), Positives = 121/155 (78%)
Query: 10  EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
           E KFYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++      +  LT +D+E L+
Sbjct: 19  ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAXTVLTPLTEKDYEGLK 78
Query: 70  KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
           ++++ +QAHK AWPF+EPVDP++APDYY V+KEP DL T E R+ ++ Y+KL+EF+ D T
Sbjct: 79  RVLRSLQAHKXAWPFLEPVDPNDAPDYYGVIKEPXDLATXEERVQRRYYEKLTEFVADXT 138
Query: 130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR 164
           KIFDNCRYYNP +SPF++ A  LE FFVQK+K  +
Sbjct: 139 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 173

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

Iteration: 1
 Score =  154 bits (390), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 65/119 (54%), Positives = 93/119 (78%)
Query: 46  NCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMD 105
            C ++   +  +  LT +D+E L+++++ +QAHK AWPF+EPVDP++APDYY V+KEPMD
Sbjct: 3   QCQSTEDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMD 62
Query: 106 LKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR 164
           L T+E R+ ++ Y+KL+EF+ DMTKIFDNCRYYNP +SPF++ A  LE FFVQK+K  +
Sbjct: 63  LATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 121

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

Iteration: 1
 Score =  150 bits (379), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 64/105 (60%), Positives = 88/105 (83%)
Query: 60  LTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
           LT +D+E L+++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+
Sbjct: 10  LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYE 69
Query: 120 KLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR 164
           KL+EF+ DMTKIFDNCRYYNP +SPF++ A  LE FFVQK+K  +
Sbjct: 70  KLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 114

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

Iteration: 1
 Score =  148 bits (374), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 63/108 (58%), Positives = 88/108 (81%)
Query: 57  MKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQ 116
           +  LT +D+E L+++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++
Sbjct: 7   LTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRR 66
Query: 117 RYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR 164
            Y+KL+EF+ DMT IFDNCRYYNP +SPF++ A  LE FFVQK+K  +
Sbjct: 67  YYEKLTEFVADMTAIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 114

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

Iteration: 1
 Score =  107 bits (266), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 46/114 (40%), Positives = 78/114 (68%), Gaps = 1/114 (0%)
Query: 52  SNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIEL 111
           +N+A      P D  +++ ++ ++Q H +AWPF++PV+  E PDYY+ +KEPMDL T+E+
Sbjct: 3   ANIAQRPKRGPHD-AAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEI 61
Query: 112 RIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
           ++   +Y+K+ +FI D   +F+NCR YN   + ++K+A++LE FF  KVK + E
Sbjct: 62  KLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPE 115

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

Iteration: 1
 Score =  104 bits (259), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 48/113 (42%), Positives = 75/113 (66%), Gaps = 4/113 (3%)
Query: 53  NLANMKNLTPRD----FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKT 108
           ++   K+  PRD    + +L+ +++Q+++H+SAWPFMEPV   EAP YY V++ PMDLKT
Sbjct: 1   SMGKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKT 60
Query: 109 IELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           +  R+  + Y     F+ D+ ++F NC+ YNP ES ++K A+ LE FF  K+K
Sbjct: 61  MSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIK 113

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

Iteration: 1
 Score =  102 bits (255), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 47/104 (45%), Positives = 71/104 (68%), Gaps = 4/104 (3%)
Query: 62  PRD----FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQR 117
           PRD    + +L+ +++Q+++H+SAWPFMEPV   EAP YY V++ PMDLKT+  R+  + 
Sbjct: 8   PRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRY 67
Query: 118 YKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           Y     F+ D+ ++F NC+ YNP ES ++K A+ LE FF  K+K
Sbjct: 68  YVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIK 111

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

Iteration: 1
 Score = 95.9 bits (237), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 44/97 (45%), Positives = 64/97 (65%)
Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           + +L+ L+ QI++H SAWPFMEPV   EAPDYY V++ P+DLKT+  R+  + Y     F
Sbjct: 5   YTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLF 64
Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           + D+ ++  NCR YNP +S + + A  LE FF  K+K
Sbjct: 65  VADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLK 101

>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 = 95.9 bits (237), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 44/97 (45%), Positives = 64/97 (65%)
Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           + +L+ L+ QI++H SAWPFMEPV   EAPDYY V++ P+DLKT+  R+  + Y     F
Sbjct: 9   YTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLF 68
Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           + D+ ++  NCR YNP +S + + A  LE FF  K+K
Sbjct: 69  VADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLK 105

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

Iteration: 1
 Score = 87.0 bits (214), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 38/93 (40%), Positives = 58/93 (62%)
Query: 64  DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
           DF ++ K++  ++AHK +WPF+EPVD   AP+YY ++K PMD+ ++E ++    Y    E
Sbjct: 17  DFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEE 76
Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
           F+ DM  +F NCR YN   S + K +  LE  F
Sbjct: 77  FVNDMKTMFRNCRKYNGESSEYTKMSDNLERCF 109

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 53/94 (56%), Gaps = 2/94 (2%)
Query: 69  RKLMKQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIG 126
           R ++K +  H  +WPF +PVD    + PDYY ++K PMDL TI+ R+  + Y+K SE I 
Sbjct: 20  RVVLKALWKHGFSWPFQQPVDAVKLKLPDYYTIIKTPMDLNTIKKRLENKYYEKASECIE 79
Query: 127 DMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
           D   +F NC  YN         A  LE  F+QK+
Sbjct: 80  DFNTMFSNCYLYNKTGDDIVVMAQALEKLFMQKL 113

>pdb|2RFJ|A Chain A, Crystal Structure Of The Bromo Domain 1 In Human Bromodomain Containing Protein, Testis Specific (Brdt) Length = 119

Iteration: 1
 Score = 73.2 bits (178), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 37/92 (40%), Positives = 50/92 (54%), Gaps = 2/92 (2%)
Query: 71  LMKQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           ++K +  H  +WPF  PVD    + PDYY ++K PMDL TI+ R+  + Y K SE I D 
Sbjct: 21  VLKDLWKHSFSWPFQRPVDAVKLQLPDYYTIIKNPMDLNTIKKRLENKYYAKASECIEDF 80
Query: 129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
             +F NC  YN         A  LE  F+QK+
Sbjct: 81  NTMFSNCYLYNKPGDDIVLMAQALEKLFMQKL 112

>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 = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 38/98 (38%), Positives = 52/98 (53%), Gaps = 2/98 (2%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           LR ++K +  H+ AWPF +PVD  +   PDYY ++K PMD+ TI+ R+    Y    E I
Sbjct: 46  LRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECI 105
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
            D   +F NC  YN         A  LE  F+QK+  L
Sbjct: 106 QDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINEL 143

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 38/98 (38%), Positives = 52/98 (53%), Gaps = 2/98 (2%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           LR ++K +  H+ AWPF +PVD  +   PDYY ++K PMD+ TI+ R+    Y    E I
Sbjct: 30  LRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECI 89
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
            D   +F NC  YN         A  LE  F+QK+  L
Sbjct: 90  QDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINEL 127

>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 = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 38/98 (38%), Positives = 52/98 (53%), Gaps = 2/98 (2%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           LR ++K +  H+ AWPF +PVD  +   PDYY ++K PMD+ TI+ R+    Y    E I
Sbjct: 26  LRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECI 85
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
            D   +F NC  YN         A  LE  F+QK+  L
Sbjct: 86  QDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINEL 123

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

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 51/89 (57%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
           ++ +++ H+ AWPF+ PV+    P Y  V+K+PMD  TI  +++  +Y  L  F  D+  
Sbjct: 21  ILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRL 80
Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFFVQK 159
           +FDNC  +N  +S   +  H +  +F +K
Sbjct: 81  VFDNCETFNEDDSDIGRAGHNMRKYFEKK 109

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

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 38/98 (38%), Positives = 52/98 (53%), Gaps = 2/98 (2%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           LR ++K +  H+ AWPF +PVD  +   PDYY ++K PMD+ TI+ R+    Y    E I
Sbjct: 26  LRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECI 85
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
            D   +F NC  YN         A  LE  F+QK+  L
Sbjct: 86  QDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINEL 123

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 53/97 (54%)
Query: 63  RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLS 122
           +D      ++ +++ H+ AWPF+ PV+    P Y  V+K+PMD  TI  +++  +Y  L 
Sbjct: 10  KDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLE 69
Query: 123 EFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQK 159
            F  D+  +FDNC  +N  +S   +  H +  +F +K
Sbjct: 70  TFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKK 106

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 38/102 (37%), Positives = 56/102 (54%), Gaps = 2/102 (1%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           ++K +  H+ AWPF +PVD  +   PDY+ ++K PMD+ TI+ R+    Y   SE + D 
Sbjct: 27  VVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDF 86
Query: 129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
             +F NC  YN         A  LE  F+QKV  + ++ VEL
Sbjct: 87  NTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEEVEL 128

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 38/102 (37%), Positives = 56/102 (54%), Gaps = 2/102 (1%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           +MK +  H+ AWPF +PVD  +   PDY+ ++K+PMD+ TI+ R+    Y   SE + D 
Sbjct: 40  VMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDF 99
Query: 129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
             +F NC  YN         A  LE  F+QKV  + ++  EL
Sbjct: 100 NTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQEL 141

>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 = 70.5 bits (171), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 38/102 (37%), Positives = 56/102 (54%), Gaps = 2/102 (1%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           +MK +  H+ AWPF +PVD  +   PDY+ ++K+PMD+ TI+ R+    Y   SE + D 
Sbjct: 40  VMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDF 99
Query: 129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
             +F NC  YN         A  LE  F+QKV  + ++  EL
Sbjct: 100 NTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQEL 141

>pdb|2FUI|A Chain A, Nmr Solution Structure Of Phd Finger Fragment Of Human Bptf In Free State Length = 62

Iteration: 1
 Score = 70.1 bits (170), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 29/41 (70%), Positives = 35/41 (85%)
Query: 10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS 50
          E KFYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++
Sbjct: 19 ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST 59

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 38/102 (37%), Positives = 56/102 (54%), Gaps = 2/102 (1%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           ++K +  H+ AWPF +PVD  +   PDY+ ++K PMD+ TI+ R+    Y   SE + D 
Sbjct: 29  VVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDF 88
Query: 129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
             +F NC  YN         A  LE  F+QKV  + ++ VEL
Sbjct: 89  NTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEEVEL 130

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 50/169 (29%), Positives = 75/169 (44%), Gaps = 23/169 (13%)
Query: 15  ICCDTCQDWFHGRC-VGILQSEADNIDEYICPNC-----------------NNSSSNLAN 56
           +CC+ C   FH  C V  L +      E+IC  C                 N+       
Sbjct: 17  LCCEKCPKVFHLSCHVPTLTNFPSG--EWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEG 74
Query: 57  MKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ- 115
           +  LTP D     +L+  +  H+ +  F +PV P   PDYY ++K PMDL TI+ R+ + 
Sbjct: 75  LVKLTPIDKRKCERLLLFLYCHEMSLAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLQED 133
Query: 116 -QRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
              Y K  +F+ D   IF NC  +N  +S       +LE +F + +K L
Sbjct: 134 YSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNL 182

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 48/85 (56%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           LR ++ Q+Q    A  F +PV   E PDY + +K PMD  T+  R+  Q YK L EF  D
Sbjct: 18  LRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEED 77
Query: 128 MTKIFDNCRYYNPRESPFFKHAHQL 152
              I DNC  YN R++ F++ A +L
Sbjct: 78  FDLIIDNCMKYNARDTVFYRAAVRL 102

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 50/92 (54%), Gaps = 2/92 (2%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           ++K +  H+ AWPF +PVD  +   PDY+ ++K PMD+ TI+ R+    Y   SE + D 
Sbjct: 25  VVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDF 84
Query: 129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
             +F NC  YN         A  LE  F+QKV
Sbjct: 85  NTMFTNCYIYNKPTDDIVLMAQALEKIFLQKV 116

>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 = 63.5 bits (153), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 53/101 (52%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
           + +++ A   +WPF  PV+    PDYY V+  PMDL+TI   I++ +Y+    F+ D+  
Sbjct: 38  VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 97
Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
           I  N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 98  ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 138

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 61/121 (50%), Gaps = 9/121 (7%)
Query: 22  DWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSA 81
           DW    C  I + E     EY C N  +S       + L+P D     +L+  +  H+ +
Sbjct: 45  DWICTFCRDIGKPEV----EYDCDNLQHSKKG-KTAQGLSPVDQRKCERLLLYLYCHELS 99
Query: 82  WPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ---QRYKKLSEFIGDMTKIFDNCRYY 138
             F EPV P   P+YY ++K+PMDL T++ ++ +   Q Y+   +F+ D+  IF NC  +
Sbjct: 100 IEFQEPV-PASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERF 158
Query: 139 N 139
           N
Sbjct: 159 N 159

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 53/101 (52%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
           + +++ A   +WPF  PV+    PDYY V+  PMDL+TI   I++ +Y+    F+ D+  
Sbjct: 157 VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 216
Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
           I  N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 217 ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 257

>pdb|3AQA|A Chain A, Crystal Structure Of The Human Brd2 Bd1 Bromodomain In Complex With A Brd2-Interactive Compound, Bic1 Length = 128

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           + K +  H+ AWPF +PVD  +   PDY+ ++K+P D  TI+ R+    Y   SE   D 
Sbjct: 20  VXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRLENNYYWAASECXQDF 79
Query: 129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
              F NC  YN         A  LE  F+QKV
Sbjct: 80  NTXFTNCYIYNKPTDDIVLXAQTLEKIFLQKV 111

>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 = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 53/101 (52%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
           + +++ A   +WPF  PV+    PDYY V+  PMDL+TI   I++ +Y+    F+ D+  
Sbjct: 145 VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 204
Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
           I  N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 205 ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 245

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 37/110 (33%), Positives = 57/110 (51%), Gaps = 3/110 (2%)
Query: 56  NMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ 115
            +  LTP D     +L+  +  H+ +  F +PV P   PDYY ++K PMDL TI+ R+ +
Sbjct: 13  GLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPV-PLTVPDYYKIIKNPMDLSTIKKRLQE 71
Query: 116 --QRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKIL 163
               Y K  +F+ D   IF NC  +N  +S       +LE +F + +K L
Sbjct: 72  DYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNL 121

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           + K +  H+ AWPF +PVD  +   PDY+ ++K+P D  TI+ R+    Y   SE   D 
Sbjct: 14  VXKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPXDXGTIKRRLENNYYWAASECXQDF 73
Query: 129 TKIFDNCRYYNPRESPFFKHAHQLEMFFVQKV 160
              F NC  YN         A  LE  F+QKV
Sbjct: 74  NTXFTNCYIYNKPTDDIVLXAQTLEKIFLQKV 105

>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 = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 53/101 (52%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
           + +++ A   +WPF  PV+    PDYY V+  PMDL+TI   I++ +Y+    F+ D+  
Sbjct: 178 VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 237
Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
           I  N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 238 ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 278

>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 = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/101 (30%), Positives = 53/101 (52%)
Query: 71  LMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
           + +++ A   +WPF  PV+    PDYY ++  P+DL+TI   I++ +Y+    F+ D+  
Sbjct: 35  VTQKMMAVPDSWPFHHPVNKKFVPDYYKMIVNPVDLETIRKNISKHKYQSRESFLDDVNL 94
Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
           I  N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 95  ILANSVKYNGPESQYTKTAQEIVNICYQTITEYDEHLTQLE 135

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 50/92 (54%), Gaps = 5/92 (5%)
Query: 70  KLMKQIQAHKS---AWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           +++K++ A K    AWPF  PVD       +YY+VVK PMDL TI+ ++  Q YK   EF
Sbjct: 21  EILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEF 80
Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
             D+  +F NC  YNP +      A  L+  F
Sbjct: 81  AADVRLMFMNCYKYNPPDHEVVAMARTLQDVF 112

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 35/109 (32%), Positives = 63/109 (57%), Gaps = 7/109 (6%)
Query: 66  ESLRK-LMKQIQA----HKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRY 118
           E LR+ LM  ++A       + PF +PVDP     PDY+++VK PMDL TI+ ++   +Y
Sbjct: 15  EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQY 74
Query: 119 KKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL 167
           ++  +++ D+  +F+N   YN + S  +K+  +L   F Q++  + + L
Sbjct: 75  QEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSL 123

>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 = 60.1 bits (144), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 3/91 (3%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           L++L+ +  A   AWPF +PVD       DY++++K PMDL T++ ++  + Y+   EF 
Sbjct: 16  LKELLSKKHA-AYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFA 74
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
            D+  +F NC  YNP +      A +L+  F
Sbjct: 75  ADVRLMFSNCYKYNPPDHDVVAMARKLQDVF 105

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 3/91 (3%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           L++L+ +  A   AWPF +PVD       DY++++K PMDL T++ ++  + Y+   EF 
Sbjct: 14  LKELLSKKHA-AYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFA 72
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
            D+  +F NC  YNP +      A +L+  F
Sbjct: 73  ADVRLMFSNCYKYNPPDHDVVAMARKLQDVF 103

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 3/91 (3%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           L++L+ +  A   AWPF +PVD       DY++++K PMDL T++ ++  + Y+   EF 
Sbjct: 10  LKELLSKKHA-AYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFA 68
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
            D+  +F NC  YNP +      A +L+  F
Sbjct: 69  ADVRLMFSNCYKYNPPDHDVVAMARKLQDVF 99

>pdb|3KV5|D Chain D, Structure Of Kiaa1718, Human Jumonji Demethylase, In Complex With N-Oxalylglycine Length = 488

Iteration: 1
 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 12  KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN--NSSSNLANMKNLTPRDFESLR 69
           +F I CD C+DWFHG CVG+ +  A +ID Y CPNC   + SS +   +N    D+  + 
Sbjct: 50  RFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCAVLHGSSLMKKRRNWHRHDYTEID 109
Query: 70  KLMKQIQA 77
              K +QA
Sbjct: 110 DGSKPVQA 117

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 33/98 (33%), Positives = 52/98 (53%), Gaps = 3/98 (3%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           LRK ++Q+Q   +   F EPV   E PDY + +K+PMD  T++  +   RY    +F  D
Sbjct: 12  LRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEED 71
Query: 128 MTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
              I  NC  YN +++ F++ A +L     Q   +LR+
Sbjct: 72  FNLIVSNCLKYNAKDTIFYRAAVRLRE---QGGAVLRQ 106

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/109 (32%), Positives = 62/109 (56%), Gaps = 7/109 (6%)
Query: 66  ESLRK-LMKQIQA----HKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRY 118
           E LR+ LM  ++A       + PF +PVDP     PDY+++VK PMDL TI+ ++   +Y
Sbjct: 10  EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQY 69
Query: 119 KKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL 167
           ++  +++ D+  +F+N   YN + S  +K   +L   F Q++  + + L
Sbjct: 70  QEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 118

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 50/91 (54%), Gaps = 3/91 (3%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           LR+++ +  A   AWPF +PVD    E  DY++++K PMDL T++ ++  + Y     F 
Sbjct: 16  LREMLSKKHA-AYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFA 74
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
            D+  +F NC  YNP +      A +L+  F
Sbjct: 75  ADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 105

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/109 (32%), Positives = 62/109 (56%), Gaps = 7/109 (6%)
Query: 66  ESLRK-LMKQIQA----HKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRY 118
           E LR+ LM  ++A       + PF +PVDP     PDY+++VK PMDL TI+ ++   +Y
Sbjct: 12  EELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQY 71
Query: 119 KKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL 167
           ++  +++ D+  +F+N   YN + S  +K   +L   F Q++  + + L
Sbjct: 72  QEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 120

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 50/91 (54%), Gaps = 3/91 (3%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           LR+++ +  A   AWPF +PVD    E  DY++++K PMDL T++ ++  + Y     F 
Sbjct: 21  LREMLSKKHA-AYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFA 79
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
            D+  +F NC  YNP +      A +L+  F
Sbjct: 80  ADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 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 = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 44/87 (50%), Gaps = 7/87 (8%)
Query: 84  FMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES 143
           FM      + PDYY ++ EPMDLK IE  I   +Y      I DM  +F N R+YN   S
Sbjct: 52  FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGS 111
Query: 144 PFFKHAHQLEMFFVQKVKILREKLVEL 170
             +  AH LE       K+L+EK  EL
Sbjct: 112 QVYNDAHILE-------KLLKEKRKEL 131

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 81  AWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           AWPF +PVD       DY +++K PMD+ TI+ ++  + Y+   EF  D+  +F NC  Y
Sbjct: 30  AWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKY 89
Query: 139 NPRESPFFKHAHQLEMFF 156
           NP +      A +L+  F
Sbjct: 90  NPPDHEVVAMARKLQDVF 107

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 81  AWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           AWPF +PVD       DY +++K PMD+ TI+ ++  + Y+   EF  D+  +F NC  Y
Sbjct: 22  AWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKY 81
Query: 139 NPRESPFFKHAHQLEMFF 156
           NP +      A +L+  F
Sbjct: 82  NPPDHEVVAMARKLQDVF 99

>pdb|3KV4|A Chain A, Structure Of Phf8 In Complex With Histone H3 Length = 447

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 22/36 (61%), Positives = 27/36 (75%)
Query: 12 KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
          +F I CD CQDWFHG CVG+ + +A +ID Y CPNC
Sbjct: 18 RFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 42/77 (54%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           LR +  ++   K    F +PVDP E PDY  V+K+PMDL ++  +I   +Y  + +++ D
Sbjct: 15  LRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRD 74
Query: 128 MTKIFDNCRYYNPRESP 144
           +  I  N   YNP   P
Sbjct: 75  IDLICSNALEYNPDRDP 91

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 41/77 (53%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           LR + K++   K    F +PVD  E  DY  V+KEPMDL T+  +I +  Y    +F+ D
Sbjct: 17  LRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKD 76
Query: 128 MTKIFDNCRYYNPRESP 144
           +  I  N   YNP + P
Sbjct: 77  IDLICSNALEYNPDKDP 93

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 81  AWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           AWPF +PVD       DY +++K PMD+ TI+ ++  + Y+   EF  D+  +F NC  Y
Sbjct: 43  AWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKY 102
Query: 139 NPRESPFFKHAHQLEMFF 156
           NP +      A +L+  F
Sbjct: 103 NPPDHEVVAMARKLQDVF 120

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 81  AWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           AWPF +PVD       DY +++K PMD+ TI+ ++  + Y+   EF  D+  +F NC  Y
Sbjct: 41  AWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKY 100
Query: 139 NPRESPFFKHAHQLEMFF 156
           NP +      A +L+  F
Sbjct: 101 NPPDHEVVAMARKLQDVF 118

>pdb|3KQI|A Chain A, Crystal Structure Of Phf2 Phd Domain Complexed With H3k4me3 Peptide Length = 75

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 30/50 (60%)
Query: 12 KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLT 61
          +F I CD C+DWFHG CVG+ + EA +ID Y CPNC  +       K  T
Sbjct: 23 RFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHGKSTLKKKRT 72

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 42/78 (53%)
Query: 79  KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           K + PFME VD  E P+YY +V  PM L  ++  +   +Y K+ +FI DM  +F N   +
Sbjct: 214 KLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIF 273
Query: 139 NPRESPFFKHAHQLEMFF 156
           N   +  +K A  L  +F
Sbjct: 274 NDPSALIYKDATTLTNYF 291

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 42/78 (53%)
Query: 79  KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           K + PFME VD  E P+YY +V  PM L  ++  +   +Y K+ +FI DM  +F N   +
Sbjct: 229 KLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIF 288
Query: 139 NPRESPFFKHAHQLEMFF 156
           N   +  +K A  L  +F
Sbjct: 289 NDPSALIYKDATTLTNYF 306

>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 = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 94  PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQL- 152
           PDYY ++KEP+DLKTI  RI    YK +     D+  +  N + YN   S  FK A+ + 
Sbjct: 46  PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIK 105
Query: 153 EMFFVQKVKI 162
           ++F+++K +I
Sbjct: 106 KIFYMKKAEI 115

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 94  PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQL- 152
           PDYY ++KEP+DLKTI  RI    YK +     D+  +  N + YN   S  FK A+ + 
Sbjct: 45  PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIK 104
Query: 153 EMFFVQKVKI 162
           ++F+++K +I
Sbjct: 105 KIFYMKKAEI 114

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 94  PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQL- 152
           PDYY ++KEP+DLKTI  RI    YK +     D+  +  N + YN   S  FK A+ + 
Sbjct: 43  PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIK 102
Query: 153 EMFFVQKVKI 162
           ++F+++K +I
Sbjct: 103 KIFYMKKAEI 112

>pdb|1WE9|A Chain A, Solution Structure Of Phd Domain In Nucleic Acid Binding Protein-like Np_197993 Length = 64

Iteration: 1
 Score = 53.9 bits (128), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 31/41 (75%)
Query: 12 KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSS 52
          +F+ICCD C+ WFHG+CV I  + A++I +Y CP+C+N S 
Sbjct: 20 EFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG 60

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 81  AWPFMEPVDPHEAP--DYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           AWPF +PVD       DY +++K P D  TI+ ++  + Y+   EF  D+   F NC  Y
Sbjct: 28  AWPFYKPVDVEALGLHDYCDIIKHPXDXSTIKSKLESREYRDAQEFGADVRLXFSNCYKY 87
Query: 139 NPRESPFFKHAHQLEMFF 156
           NP +      A +L+  F
Sbjct: 88  NPPDHEVVAXARKLQDVF 105

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 2/90 (2%)
Query: 69  RKLMKQIQAHKSAWPFMEPVDPHEA--PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIG 126
            +L+  +  ++    F + VD  +   PDYY+V+K P     I+ ++ + +Y   SEF+ 
Sbjct: 27  NQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPXSFSCIKTKLKKGQYAYPSEFVK 86
Query: 127 DMTKIFDNCRYYNPRESPFFKHAHQLEMFF 156
           D+  IFDNC  YN   S        +E +F
Sbjct: 87  DVQLIFDNCSLYNTSNSVVAITGKNIETYF 116

>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 = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 1/94 (1%)
Query: 69  RKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDM 128
           ++L+  I   + + PF +PVD  E PDY +++  PMD  T+   +    Y    EF  D+
Sbjct: 16  KELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDI 75
Query: 129 TKIFDNCRYYNP-RESPFFKHAHQLEMFFVQKVK 161
             IF N + Y P + S  +    +L   F +K+K
Sbjct: 76  RLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMK 109

>pdb|1WEM|A Chain A, Solution Structure Of Phd Domain In Death Inducer- Obliterator 1(Dio-1) Length = 76

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 28/40 (70%), Gaps = 4/40 (10%)
Query: 12 KFYICCDTCQDWFHGRCVGILQSEA----DNIDEYICPNC 47
          +F ICCD C++WFHG CVGI ++       N ++YICPNC
Sbjct: 28 RFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 67

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 83  PFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP-R 141
           PF +PVD  E PDY +++  PMD  T+   +    Y+   E   D+  IF N + Y P +
Sbjct: 41  PFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPSK 100
Query: 142 ESPFFKHAHQLEMFFVQKV 160
            S  +  + +L  FF + +
Sbjct: 101 RSRIYSMSLRLSAFFEEHI 119

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 43/85 (50%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           L   ++Q+Q       F  PV    AP Y  ++K PMD  T++ +I    YK ++EF  D
Sbjct: 18  LEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKAD 77
Query: 128 MTKIFDNCRYYNPRESPFFKHAHQL 152
              + DN   YN  ++ ++K A ++
Sbjct: 78  FKLMCDNAMTYNRPDTVYYKLAKKI 102

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 53/104 (50%), Gaps = 3/104 (2%)
Query: 66  ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           E+L +LM+Q+Q    +  F  PV    AP Y  ++K PMD  T++ +I    Y+ + E  
Sbjct: 11  EALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELK 70
Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVE 169
            +   +  N   YN  E+ ++K A +L       +KIL ++ +E
Sbjct: 71  DNFKLMCTNAMIYNKPETIYYKAAKKL---LHSGMKILSQERLE 111

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           LR + K++   K    F +PV      DY  V+KEPMDL T+  +I +  Y    +F+ D
Sbjct: 17  LRDVTKRLATDKRFNIFSKPV-----SDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKD 71
Query: 128 MTKIFDNCRYYNPRESP 144
           +  I  N   YNP + P
Sbjct: 72  IDLICSNALEYNPDKDP 88

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 39/78 (50%)
Query: 79  KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           K + PF E VD  E P+YY +V  P  L  ++  +   +Y K+ +FI D   +F N   +
Sbjct: 179 KLSEPFXELVDKDELPEYYEIVHSPXALSIVKQNLEIGQYSKIYDFIIDXLLVFQNAHIF 238
Query: 139 NPRESPFFKHAHQLEMFF 156
           N   +  +K A  L  +F
Sbjct: 239 NDPSALIYKDATTLTNYF 256

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 39/78 (50%)
Query: 79  KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY 138
           K + PF E VD  E P+YY +V  P  L  ++  +   +Y K+ +FI D   +F N   +
Sbjct: 173 KLSEPFXELVDKDELPEYYEIVHSPXALSIVKQNLEIGQYSKIYDFIIDXLLVFQNAHIF 232
Query: 139 NPRESPFFKHAHQLEMFF 156
           N   +  +K A  L  +F
Sbjct: 233 NDPSALIYKDATTLTNYF 250

>pdb|1WEP|A Chain A, Solution Structure Of Phd Domain In Phf8 Length = 79

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/35 (60%), Positives = 24/35 (68%)
Query: 13 FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
          F I C  CQDWFHG CVGI +  A +ID Y CP+C
Sbjct: 26 FMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDC 60

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 37/76 (48%)
Query: 81  AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP 140
           A P +      +  DYY  + +P+DL TIE +I    YK +  F  DM K+F N   Y  
Sbjct: 33  AAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYYG 92
Query: 141 RESPFFKHAHQLEMFF 156
           R+SP  +   +L   +
Sbjct: 93  RKSPVGRDVCRLRKAY 108

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 40/88 (45%)
Query: 76  QAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNC 135
           Q    A PF       + PDYY  +K P+ L+ I  ++  Q Y+ L     D+  +F+N 
Sbjct: 36  QGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENA 95
Query: 136 RYYNPRESPFFKHAHQLEMFFVQKVKIL 163
           + YN   S  +K   +L+     K K L
Sbjct: 96  KRYNVPNSAIYKRVLKLQQVMQAKKKEL 123

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 35/67 (52%)
Query: 92  EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQ 151
           E PDYY  +K+PMD++ I   +   +Y+ +   + D   +F+N   YN  ES  +K A  
Sbjct: 50  ELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALV 109
Query: 152 LEMFFVQ 158
           L    ++
Sbjct: 110 LHKVLLE 116

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 32/58 (55%)
Query: 92  EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHA 149
           E PDYY  +K+PMD++ I   +   +Y+ +   + D   +F+N   YN  ES  +K A
Sbjct: 50  ELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDA 107

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 34/59 (57%)
Query: 94  PDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQL 152
           PDYY VV +P+DL  I+ ++  + Y  ++    D   +F+N + Y   +SP +K A +L
Sbjct: 42  PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKL 100

>pdb|3N9L|A Chain A, Cekdm7a From C.Elegans, Complex With H3k4me3 Peptide And Nog Length = 528

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 14  YICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDF 65
           +I CD+CQ W+H  C G+ Q E    +++ CP C   + +    K + P  +
Sbjct: 58  WIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRY 109

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	171
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	1e-62
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	4e-46
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	1e-44
3d7c_A	112	General control of amino acid synthesis protein 5;	1e-44
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	4e-44
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	9e-44
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	2e-43
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	7e-43
3uv4_A	158	Second bromodomain of human transcription initiat	2e-42
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	5e-42
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	7e-41
4alg_A	154	Bromodomain-containing protein 2; signaling protei	1e-40
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	3e-40
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	5e-40
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	6e-40
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	2e-33
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	1e-39
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	1e-39
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	4e-32
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	4e-39
3p1f_A	119	CREB-binding protein; structural genomics consorti	3e-38
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	8e-38
3mb3_A	135	PH-interacting protein; PHIP, pleckstrin homology	9e-38
3jvl_A	120	Bromodomain-containing protein 4; alpha helical, N	2e-37
2grc_A	129	Probable global transcription activator SNF2L4; br	3e-37
2dat_A	123	Possible global transcription activator SNF2L2; br	3e-37
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-36
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	1e-36
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-36
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	3e-36
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	4e-36
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	5e-36
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	2e-35
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	1e-34
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	4e-26
2r10_A	361	Chromatin structure-remodeling complex protein RSC	1e-34
2r10_A	361	Chromatin structure-remodeling complex protein RSC	3e-25
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	1e-31
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	6e-29
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	2e-26
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	1e-25
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	2e-24
1we9_A	64	PHD finger family protein; structural genomics, PH	7e-18
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	6e-15
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	1e-14
1wem_A	76	Death associated transcription factor 1; structura	2e-14
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	3e-13
3kv5_D	488	JMJC domain-containing histone demethylation prote	5e-13
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	2e-12
1wee_A	72	PHD finger family protein; structural genomics, PH	4e-12
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	5e-12
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	1e-11
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	2e-11
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	4e-11
1wew_A	78	DNA-binding family protein; structural genomics, P	8e-08
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	9e-08
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	7e-07
1weu_A	91	Inhibitor of growth family, member 4; structural g	3e-06
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	3e-06
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	6e-05
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	6e-05
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	1e-04
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	3e-04

>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 =  190 bits (483), Expect = 1e-62
 Identities = 93/155 (60%), Positives = 125/155 (80%)

Query: 10  EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLR 69
           E KFYI CD CQ+W+HGRCVGILQSEA+ IDEY+CP C ++   +  +  LT +D+E L+
Sbjct: 19  ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLK 78

Query: 70  KLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT 129
           ++++ +QAHK AWPF+EPVDP++APDYY V+KEPMDL T+E R+ ++ Y+KL+EF+ DMT
Sbjct: 79  RVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMT 138

Query: 130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR 164
           KIFDNCRYYNP +SPF++ A  LE FFVQK+K  +
Sbjct: 139 KIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFK 173

>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 =  146 bits (370), Expect = 4e-46
 Identities = 45/113 (39%), Positives = 76/113 (67%), Gaps = 1/113 (0%)

Query: 53  NLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELR 112
           N+A      P    +++ ++ ++Q H +AWPF++PV+  E PDYY+ +KEPMDL T+E++
Sbjct: 4   NIAQRPKRGP-HDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIK 62

Query: 113 IAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
           +   +Y+K+ +FI D   +F+NCR YN   + ++K+A++LE FF  KVK + E
Sbjct: 63  LESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPE 115

>2d9e_A Peregrin; four-helix bundle, transcription activator, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 121

 Score =  142 bits (360), Expect = 1e-44
 Identities = 31/110 (28%), Positives = 54/110 (49%)

Query: 61  TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKK 120
           +      LRK ++Q+Q   +   F EPV   E PDY + +K+PMD  T++  +   RY  
Sbjct: 5   SSGFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLN 64

Query: 121 LSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
             +F  D   I  NC  YN +++ F++ A +L       ++  R +  ++
Sbjct: 65  FDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKM 114

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

 Score =  142 bits (359), Expect = 1e-44
 Identities = 44/98 (44%), Positives = 64/98 (65%)

Query: 64  DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
            + +L+ L+ QI++H SAWPFMEPV   EAPDYY V++ P+DLKT+  R+  + Y     
Sbjct: 8   LYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKL 67

Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           F+ D+ ++  NCR YNP +S + + A  LE FF  K+K
Sbjct: 68  FVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLK 105

>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 =  140 bits (356), Expect = 4e-44
 Identities = 32/115 (27%), Positives = 58/115 (50%)

Query: 51  SSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIE 110
           S ++   K    +D      ++ +++ H+ AWPF+ PV+    P Y  V+K+PMD  TI 
Sbjct: 1   SMSVKKPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIR 60

Query: 111 LRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
            +++  +Y  L  F  D+  +FDNC  +N  +S   +  H +  +F +K     +
Sbjct: 61  EKLSSGQYPNLETFALDVRLVFDNCETFNEDDSDIGRAGHNMRKYFEKKWTDTFK 115

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

 Score =  140 bits (354), Expect = 9e-44
 Identities = 38/99 (38%), Positives = 60/99 (60%)

Query: 63  RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLS 122
            DF ++ K++  ++AHK +WPF+EPVD   AP+YY ++K PMD+ ++E ++    Y    
Sbjct: 16  DDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKE 75

Query: 123 EFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           EF+ DM  +F NCR YN   S + K +  LE  F + + 
Sbjct: 76  EFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMM 114

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

 Score =  139 bits (353), Expect = 2e-43
 Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 1/114 (0%)

Query: 54  LANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRI 113
           +A    LTP     LR ++ Q+Q    A  F +PV   E PDY + +K PMD  T+  R+
Sbjct: 5   VAMELRLTP-LTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRL 63

Query: 114 AQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL 167
             Q YK L EF  D   I DNC  YN R++ F++ A +L       ++  R ++
Sbjct: 64  EAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREV 117

>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 =  137 bits (348), Expect = 7e-43
 Identities = 34/122 (27%), Positives = 58/122 (47%), Gaps = 3/122 (2%)

Query: 50  SSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTI 109
           S   L+     TP   + L   ++Q+Q       F  PV    AP Y  ++K PMD  T+
Sbjct: 1   SMLKLSAENESTP-IQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTM 59

Query: 110 ELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVE 169
           + +I    YK ++EF  D   + DN   YN  ++ ++K A ++     + +   +E+L+ 
Sbjct: 60  KDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMS--KERLLA 117

Query: 170 LK 171
           LK
Sbjct: 118 LK 119

>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 =  138 bits (348), Expect = 2e-42
 Identities = 33/101 (32%), Positives = 53/101 (52%)

Query: 71  LMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK 130
           + +++ A   +WPF  PV+    PDYY V+  PMDL+TI   I++ +Y+    F+ D+  
Sbjct: 38  VTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNL 97

Query: 131 IFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
           I  N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 98  ILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 138

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

 Score =  135 bits (342), Expect = 5e-42
 Identities = 29/114 (25%), Positives = 53/114 (46%), Gaps = 1/114 (0%)

Query: 57  MKNLTPRDF-ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ 115
           M+ +      E+L +LM+Q+Q    +  F  PV    AP Y  ++K PMD  T++ +I  
Sbjct: 1   MEEVEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKN 60

Query: 116 QRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVE 169
             Y+ + E   +   +  N   YN  E+ ++K A +L    ++ +   R +   
Sbjct: 61  NDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERLEHHH 114

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

 Score =  133 bits (336), Expect = 7e-41
 Identities = 35/119 (29%), Positives = 57/119 (47%), Gaps = 3/119 (2%)

Query: 45  PNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPM 104
            + ++       +  LTP D     +L+  +  H+ +  F +PV     PDYY ++K PM
Sbjct: 2   SSGSSGKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPM 60

Query: 105 DLKTIE--LRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           DL TI+  L+     Y K  +F+ D   IF NC  +N  +S       +LE +F + +K
Sbjct: 61  DLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLK 119

>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 =  133 bits (337), Expect = 1e-40
 Identities = 39/115 (33%), Positives = 59/115 (51%), Gaps = 2/115 (1%)

Query: 58  KNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQ 115
             +T +     + +MK +  H+ AWPF +PVD      PDY+ ++K+PMD+ TI+ R+  
Sbjct: 27  GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLEN 86

Query: 116 QRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
             Y   SE + D   +F NC  YN         A  LE  F+QKV  + ++  EL
Sbjct: 87  NYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQEL 141

>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 =  131 bits (332), Expect = 3e-40
 Identities = 41/114 (35%), Positives = 56/114 (49%), Gaps = 2/114 (1%)

Query: 50  SSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLK 107
            +SN    K  T +    LR ++K +  H+ AWPF +PVD      PDYY ++K PMD+ 
Sbjct: 8   ETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMG 67

Query: 108 TIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           TI+ R+    Y    E I D   +F NC  YN         A  LE  F+QK+ 
Sbjct: 68  TIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKIN 121

>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 =  132 bits (334), Expect = 5e-40
 Identities = 46/166 (27%), Positives = 70/166 (42%), Gaps = 21/166 (12%)

Query: 15  ICCDTCQDWFHGRCVGILQSEADNIDEYICPNC-----------------NNSSSNLANM 57
           +CC+ C   FH  C     +      E+IC  C                 N+       +
Sbjct: 17  LCCEKCPKVFHLSCHVPTLTNFP-SGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGL 75

Query: 58  KNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIE--LRIAQ 115
             LTP D     +L+  +  H+ +  F +PV     PDYY ++K PMDL TI+  L+   
Sbjct: 76  VKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDY 134

Query: 116 QRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             Y K  +F+ D   IF NC  +N  +S       +LE +F + +K
Sbjct: 135 SMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLK 180

>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 =  135 bits (340), Expect = 6e-40
 Identities = 36/159 (22%), Positives = 62/159 (38%), Gaps = 9/159 (5%)

Query: 13  FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLM 72
                 +  D    +                      + + L +  +     F     + 
Sbjct: 96  LTQISQSMLDLCDEKLKEKED---------KLARLEKAINPLLDDDDQVAFSFILDNIVT 146

Query: 73  KQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIF 132
           +++ A   +WPF  PV+    PDYY V+  PMDL+TI   I++ +Y+    F+ D+  I 
Sbjct: 147 QKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLIL 206

Query: 133 DNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 207 ANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 245

>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 =  118 bits (297), Expect = 2e-33
 Identities = 23/101 (22%), Positives = 45/101 (44%)

Query: 66  ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
             L  ++  ++   + +PF  PV+     DYY ++  PMDL+T+   + ++ Y    EF 
Sbjct: 17  SILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFR 76

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREK 166
             +  I  N   YN  +    + +  +     +K+K   +K
Sbjct: 77  EHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDK 117

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

 Score =  131 bits (331), Expect = 1e-39
 Identities = 32/125 (25%), Positives = 56/125 (44%), Gaps = 2/125 (1%)

Query: 49  NSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDL 106
           +SS           + +    +L+  +  ++    F + VD      PDYY+V+K PM  
Sbjct: 7   HSSGRENLYFQGNKQWYLLANQLILSLSKYEGGHIFEKLVDAKKQNCPDYYDVIKNPMSF 66

Query: 107 KTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREK 166
             I+ ++ + +Y   SEF+ D+  IFDNC  YN   S        +E +F  ++ ++   
Sbjct: 67  SCIKTKLKKGQYAYPSEFVKDVQLIFDNCSLYNTSNSVVAITGKNIETYFNNQLIVMGYN 126

Query: 167 LVELK 171
              LK
Sbjct: 127 NFILK 131

>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 =  134 bits (339), Expect = 1e-39
 Identities = 36/159 (22%), Positives = 59/159 (37%), Gaps = 9/159 (5%)

Query: 13  FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLM 72
                 +  D    +        A                      +     F     + 
Sbjct: 129 LTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLD---------DDDQVAFSFILDNIVT 179

Query: 73  KQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIF 132
           +++ A   +WPF  PV+    PDYY V+  PMDL+TI   I++ +Y+    F+ D+  I 
Sbjct: 180 QKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLIL 239

Query: 133 DNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
            N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 240 ANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 278

>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 =  115 bits (289), Expect = 4e-32
 Identities = 22/97 (22%), Positives = 43/97 (44%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
              L  ++  ++   + +PF  PV+     DYY ++  PMDL+T+   + ++ Y    EF
Sbjct: 49  SSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEF 108

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
              +  I  N   YN  +    + +  +     +K+K
Sbjct: 109 REHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLK 145

>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 =  128 bits (323), Expect = 4e-39
 Identities = 29/103 (28%), Positives = 49/103 (47%), Gaps = 1/103 (0%)

Query: 66  ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           +  ++L+  I   + + PF +PVD  E PDY +++  PMD  T+   +    Y    EF 
Sbjct: 13  KQCKELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFC 72

Query: 126 GDMTKIFDNCRYYNPRE-SPFFKHAHQLEMFFVQKVKILREKL 167
            D+  IF N + Y P + S  +    +L   F +K+K +    
Sbjct: 73  KDIRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKISSDF 115

>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 =  126 bits (318), Expect = 3e-38
 Identities = 32/102 (31%), Positives = 57/102 (55%), Gaps = 5/102 (4%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
           L  L +Q      + PF +PVDP     PDY+++VK PMDL TI+ ++   +Y++  +++
Sbjct: 20  LEALYRQ---DPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYV 76

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL 167
            D+  +F+N   YN + S  +K   +L   F Q++  + + L
Sbjct: 77  DDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 118

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

 Score =  125 bits (315), Expect = 8e-38
 Identities = 29/116 (25%), Positives = 50/116 (43%), Gaps = 6/116 (5%)

Query: 61  TPRDFESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIA 114
             R  +  +++   I ++K       A P +      +  DYY  + +P+DL TIE +I 
Sbjct: 7   AARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQIL 66

Query: 115 QQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
              YK +  F  DM K+F N   Y  R+SP  +   +L   +         ++ E+
Sbjct: 67  TGYYKTVEAFDADMLKVFRNAEKYYGRKSPVGRDVCRLRKAYYNARHEASAQIDEI 122

>3mb3_A PH-interacting protein; PHIP, pleckstrin homology domain interacting protein, DCAF14 DDB1 and CUL4 associated factor 14, SGC; 2.25A {Homo sapiens} Length = 135

 Score =  125 bits (315), Expect = 9e-38
 Identities = 27/103 (26%), Positives = 47/103 (45%), Gaps = 1/103 (0%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
             +L+  I   + + PF +PVD  E PDY +++  PMD  T+   +    Y+   E   D
Sbjct: 26  CEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKD 85

Query: 128 MTKIFDNCRYYNPRE-SPFFKHAHQLEMFFVQKVKILREKLVE 169
           +  IF N + Y P + S  +  + +L  FF + +  +      
Sbjct: 86  VRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSDYKS 128

>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 =  123 bits (312), Expect = 2e-37
 Identities = 33/120 (27%), Positives = 58/120 (48%), Gaps = 5/120 (4%)

Query: 55  ANMKNLTPRDFESLRKLMKQIQAHK---SAWPFMEPVDPHE--APDYYNVVKEPMDLKTI 109
             M +      +    ++K++ A K    AWPF +PVD       DY +++K PMD+ TI
Sbjct: 1   GAMGSKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTI 60

Query: 110 ELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVE 169
           + ++  + Y+   EF  D+  +F NC  YNP +      A +L+  F  +   + ++  E
Sbjct: 61  KSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEE 120

>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 =  124 bits (312), Expect = 3e-37
 Identities = 20/102 (19%), Positives = 50/102 (49%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
            +++ K        + +  F++     E P+YY ++++P+D K I+ RI   +Y+ L++ 
Sbjct: 20  VDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDL 79

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREK 166
             D+  +  N + +N   S  ++ +  L+  F    + + ++
Sbjct: 80  EKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKE 121

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

 Score =  123 bits (311), Expect = 3e-37
 Identities = 21/107 (19%), Positives = 50/107 (46%), Gaps = 6/107 (5%)

Query: 61  TPRDFESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIA 114
            P+  + +  ++  +  +K       +  F++     E P+YY ++++P+D K I+ RI 
Sbjct: 11  PPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIR 70

Query: 115 QQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
             +Y+ L +   D+  +  N + +N   S  ++ +  L+  F    +
Sbjct: 71  NHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQ 117

>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 =  122 bits (307), Expect = 1e-36
 Identities = 26/113 (23%), Positives = 49/113 (43%), Gaps = 6/113 (5%)

Query: 60  LTPRDFESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRI 113
           +T        +L   I+ +K          F+        PDYY VV +P+DL  I+ ++
Sbjct: 2   MTVDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKL 61

Query: 114 AQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREK 166
             + Y  ++    D   +F+N + Y   +SP +K A +L   +++      +K
Sbjct: 62  KMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQK 114

>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 =  122 bits (309), Expect = 1e-36
 Identities = 32/97 (32%), Positives = 44/97 (45%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           F  + +  +     +    FM      + PDYY ++ EPMDLK IE  I   +Y      
Sbjct: 33  FNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGM 92

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           I DM  +F N R+YN   S  +  AH LE    +K K
Sbjct: 93  IEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRK 129

>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 =  121 bits (305), Expect = 2e-36
 Identities = 23/115 (20%), Positives = 49/115 (42%), Gaps = 10/115 (8%)

Query: 61  TPRDFESLRKLMKQI----------QAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIE 110
             +    +++ + ++          +  + +  F+      E PDYY  +K+PMD++ I 
Sbjct: 9   KSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIR 68

Query: 111 LRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
             +   +Y+ +   + D   +F+N   YN  ES  +K A  L    ++  + L  
Sbjct: 69  SHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLEG 123

>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 =  121 bits (305), Expect = 3e-36
 Identities = 31/114 (27%), Positives = 56/114 (49%), Gaps = 5/114 (4%)

Query: 58  KNLTPRDFESLRKLMKQIQAHK---SAWPFMEPVDPHE--APDYYNVVKEPMDLKTIELR 112
            +      +    ++K++ A K    AWPF +PVD       DY +++K PMD+ TI+ +
Sbjct: 17  SSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSK 76

Query: 113 IAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREK 166
           +  + Y+   EF  D+  +F NC  YNP +      A +L+  F  +   + ++
Sbjct: 77  LEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE 130

>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 =  121 bits (305), Expect = 4e-36
 Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 1/102 (0%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           ++++R      Q    A PF       + PDYY  +K P+ L+ I  ++  Q Y+ L   
Sbjct: 26  YDTVRSCRNN-QGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHL 84

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREK 166
             D+  +F+N + YN   S  +K   +L+     K K L  +
Sbjct: 85  ECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARR 126

>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 =  120 bits (303), Expect = 5e-36
 Identities = 33/108 (30%), Positives = 50/108 (46%), Gaps = 5/108 (4%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           LR +  ++   K    F +PVDP E PDY  V+K+PMDL ++  +I   +Y  + +++ D
Sbjct: 15  LRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRD 74

Query: 128 MTKIFDNCRYYNPRESP----FFKHAHQLEMFFVQKVK-ILREKLVEL 170
           +  I  N   YNP   P        A  L       +K  L E   +L
Sbjct: 75  IDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQL 122

>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 =  118 bits (299), Expect = 2e-35
 Identities = 31/106 (29%), Positives = 49/106 (46%), Gaps = 6/106 (5%)

Query: 66  ESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
           E L +L++ I    +      +  F +     + PDYY ++KEP+DLKTI  RI    YK
Sbjct: 11  EILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYK 70

Query: 120 KLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
            +     D+  +  N + YN   S  FK A+ ++  F  K   +  
Sbjct: 71  SIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEH 116

>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 =  122 bits (307), Expect = 1e-34
 Identities = 34/156 (21%), Positives = 58/156 (37%), Gaps = 4/156 (2%)

Query: 10  EPKFYICCDTCQ----DWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDF 65
           E    I  ++ Q      F       L+       E      +  +  +   +    +  
Sbjct: 106 EYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQAL 165

Query: 66  ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
                        K + PFME VD  E P+YY +V  PM L  ++  +   +Y K+ +FI
Sbjct: 166 LGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFI 225

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
            DM  +F N   +N   +  +K A  L  +F   ++
Sbjct: 226 IDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQ 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 =  100 bits (249), Expect = 4e-26
 Identities = 21/107 (19%), Positives = 44/107 (41%), Gaps = 3/107 (2%)

Query: 61  TPRDFESLRKLMKQI--QAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRY 118
            P+    +   +  +  +       F++       P YY  +++PM +  I+ R  +   
Sbjct: 26  IPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEY-E 84

Query: 119 KKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
              S F+ D+  +  NC+ YN  +S   K++ Q+ M    +V   + 
Sbjct: 85  DGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKN 131

>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A* Length = 361

 Score =  123 bits (309), Expect = 1e-34
 Identities = 33/156 (21%), Positives = 55/156 (35%), Gaps = 4/156 (2%)

Query: 10  EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFES-- 67
           E    I  ++ Q         +                      L  + + T +      
Sbjct: 156 EYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQAL 215

Query: 68  --LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
                        K + PFME VD  E P+YY +V  PM L  ++  +   +Y K+ +FI
Sbjct: 216 LGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFI 275

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
            DM  +F N   +N   +  +K A  L  +F   ++
Sbjct: 276 IDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQ 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 = 98.3 bits (244), Expect = 3e-25
 Identities = 23/112 (20%), Positives = 43/112 (38%), Gaps = 3/112 (2%)

Query: 49  NSSSNLANMKNLTPRDFESLRKLMKQIQAHKS--AWPFMEPVDPHEAPDYYNVVKEPMDL 106
           N  S L       P+    +   +  +          F++       P YY  +++PM +
Sbjct: 64  NPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSI 123

Query: 107 KTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQ 158
             I+ R  +      S F+ D+  +  NC+ YN  +S   K++ Q+ M    
Sbjct: 124 NEIKSRDYEY-EDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEF 174

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

 Score =  109 bits (274), Expect = 1e-31
 Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 5/102 (4%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           LR + K++   K    F +PV      DY  V+KEPMDL T+  +I +  Y    +F+ D
Sbjct: 17  LRDVTKRLATDKRFNIFSKPVS-----DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKD 71

Query: 128 MTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVE 169
           +  I  N   YNP + P  K               +    ++
Sbjct: 72  IDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELD 113

>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 =  104 bits (261), Expect = 6e-29
 Identities = 37/167 (22%), Positives = 67/167 (40%), Gaps = 17/167 (10%)

Query: 14  YICCDTCQDWFHGRCVGILQSEADNID-------------EYICPNCNNSSSNLANMKNL 60
            +CC+ C   FH  C         + D                  +    S      + L
Sbjct: 19  LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGL 78

Query: 61  TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ---QR 117
           +P D     +L+  +  H+ +  F EPV     P+YY ++K+PMDL T++ ++ +   Q 
Sbjct: 79  SPVDQRKCERLLLYLYCHELSIEFQEPVPAS-IPNYYKIIKKPMDLSTVKKKLQKKHSQH 137

Query: 118 YKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR 164
           Y+   +F+ D+  IF NC  +N        +A   E+      ++ +
Sbjct: 138 YQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQ 184

>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 = 98.1 bits (243), Expect = 2e-26
 Identities = 25/156 (16%), Positives = 57/156 (36%), Gaps = 18/156 (11%)

Query: 12  KFYICCDTCQDWFHGRCVGILQSEADNI------DEYICPNCNNSSSNLANMKNLTPRDF 65
              + C  C  W H +C  +     + +        Y C NC            L     
Sbjct: 19  SKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPA-EWRLALEKELQ 77

Query: 66  ESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFI 125
            SL++++  +   ++    +               ++P+DL+ ++ ++ Q  Y  + EF 
Sbjct: 78  ISLKQVLTALLNSRTTSHLLRYRQ-----------QQPLDLEGVKRKMDQGNYTSVLEFS 126

Query: 126 GDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
            D+ KI       +  +    K    ++ FF+++++
Sbjct: 127 DDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQME 162

>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 = 95.7 bits (237), Expect = 1e-25
 Identities = 24/164 (14%), Positives = 56/164 (34%), Gaps = 21/164 (12%)

Query: 15  ICCDTCQDWFHGRCVGILQSEADNIDEYICPNC--------------NNSSSNLANMKNL 60
           + C+ C+  FH  C      +    +E+ C  C               + + +   +  L
Sbjct: 15  VMCNQCEFCFHLDCHLPALQDV-PGEEWSCSLCHVLPDLKEEDGSLSLDGADSTGVVAKL 73

Query: 61  TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQR--- 117
           +P +     +++  +  H+   P  +           +     +DL  I  R+ ++    
Sbjct: 74  SPANQRKCERVLLALFCHEPCRPLHQLATDS--TFSLDQPGGTLDLTLIRARLQEKLSPP 131

Query: 118 YKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           Y    EF  D+ ++F         ++   +    L+ FF  ++ 
Sbjct: 132 YSSPQEFAQDVGRMFKQFNKLTEDKA-DVQSIIGLQRFFETRMN 174

>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 = 91.9 bits (228), Expect = 2e-24
 Identities = 23/107 (21%), Positives = 44/107 (41%), Gaps = 10/107 (9%)

Query: 66  ESLRKLMKQIQAHKSAW------PFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK 119
           E +  L   + +H+            E   P   P++ N  K P+    I   +   RY+
Sbjct: 10  ELIHNLFVSVMSHQDDEGRCYSDSLAEI--PAVDPNFPN--KPPLTFDIIRKNVENNRYR 65

Query: 120 KLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREK 166
           +L  F   M ++ +  R  N  +S  ++ A +L+ FF++    L + 
Sbjct: 66  RLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCKN 112

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Length = 64

 Score = 72.2 bits (177), Expect = 7e-18
 Identities = 21/41 (51%), Positives = 31/41 (75%)

Query: 12 KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSS 52
          +F+ICCD C+ WFHG+CV I  + A++I +Y CP+C+N S 
Sbjct: 20 EFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG 60

>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger, histone-binding, NUC protein; HET: M3L; 1.78A {Homo sapiens} Length = 75

 Score = 65.3 bits (159), Expect = 6e-15
 Identities = 22/36 (61%), Positives = 27/36 (75%)

Query: 12 KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
          +F I CD C+DWFHG CVG+ + EA +ID Y CPNC
Sbjct: 23 RFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNC 58

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2 Length = 79

 Score = 64.6 bits (157), Expect = 1e-14
 Identities = 21/35 (60%), Positives = 24/35 (68%)

Query: 13 FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
          F I C  CQDWFHG CVGI +  A +ID Y CP+C
Sbjct: 26 FMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDC 60

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2 Length = 76

 Score = 63.8 bits (155), Expect = 2e-14
 Identities = 20/40 (50%), Positives = 28/40 (70%), Gaps = 4/40 (10%)

Query: 12 KFYICCDTCQDWFHGRCVGILQSEADNID----EYICPNC 47
          +F ICCD C++WFHG CVGI ++    ++    +YICPNC
Sbjct: 28 RFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 67

>3pur_A Lysine-specific demethylase 7 homolog; oxidoreductase-oxidoreductase inhibitor complex; HET: 2HG; 2.10A {Caenorhabditis elegans} PDB: 3n9l_A 3n9m_A* 3n9o_A* 3n9p_A* 3n9q_A* 3n9n_A* 3puq_A* Length = 528

 Score = 65.5 bits (158), Expect = 3e-13
 Identities = 18/79 (22%), Positives = 33/79 (41%)

Query: 13  FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLM 72
            +I CD+CQ W+H  C G+ Q E    +++ CP C   + +    K + P  +       
Sbjct: 57  QWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNE 116

Query: 73  KQIQAHKSAWPFMEPVDPH 91
           K +     +  ++E     
Sbjct: 117 KHLGIEVGSKTWIEDFITR 135

>3kv5_D JMJC domain-containing histone demethylation protein 1D; epigenetics, histone CODE, jumonji lysine demethylase, metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo sapiens} PDB: 3kv6_A* Length = 488

 Score = 65.1 bits (157), Expect = 5e-13
 Identities = 24/113 (21%), Positives = 42/113 (37%)

Query: 12  KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKL 71
           +F I CD C+DWFHG CVG+ +  A +ID Y CPNC     +    K       +     
Sbjct: 50  RFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCAVLHGSSLMKKRRNWHRHDYTEID 109

Query: 72  MKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
                       F++ +     P    ++ +    +  +  + +  +      
Sbjct: 110 DGSKPVQAGTRTFIKELRSRVFPSADEIIIKMHGSQLTQRYLEKHGFDVPIMV 162

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens} Length = 52

 Score = 57.8 bits (140), Expect = 2e-12
 Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 2/38 (5%)

Query: 13 FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS 50
            I C+ C  W H  C  I +S     + ++C  C +S
Sbjct: 17 PMIECNECHTWIHLSCAKIRKSNVP--EVFVCQKCRDS 52

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Length = 72

 Score = 57.6 bits (139), Expect = 4e-12
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 12 KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
          +  + CD C  W H RC+GI  ++A    +++C  C
Sbjct: 29 ERMLACDGCGVWHHTRCIGINNADAL-PSKFLCFRC 63

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens} Length = 68

 Score = 57.2 bits (138), Expect = 5e-12
 Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 2/38 (5%)

Query: 13 FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS 50
            I C+ C  W H  C  I +S     + ++C  C +S
Sbjct: 32 PMIECNECHTWIHLSCAKIRKSNVP--EVFVCQKCRDS 67

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A* Length = 75

 Score = 56.8 bits (137), Expect = 1e-11
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 13 FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS 50
            I CD C DW+H  CVGI+ +  + +  + CP C N 
Sbjct: 32 PMIGCDDCDDWYHWPCVGIMAAPPEEMQ-WFCPKCANK 68

>3kv4_A PHD finger protein 8; epigenetics, histone CODE, covalent histone modifications, jumonji demethylase, mental retardation, metal-binding, zinc; HET: M3L MLY OGA; 2.19A {Homo sapiens} Length = 447

 Score = 60.4 bits (145), Expect = 2e-11
 Identities = 27/99 (27%), Positives = 38/99 (38%), Gaps = 3/99 (3%)

Query: 12  KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKL 71
           +F I CD CQDWFHG CVG+ + +A +ID Y CPNC               R        
Sbjct: 18  RFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHG---PSIMKKRRGSSKGHDT 74

Query: 72  MKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIE 110
            K       +  F+  +          V+ +P   +   
Sbjct: 75  HKGKPVKTGSPTFVRELRSRTFDSSDEVILKPTGNQLTV 113

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A* Length = 52

 Score = 54.5 bits (131), Expect = 4e-11
 Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 13 FYICCD-TCQDWFHGRCVGILQSEADNIDEYICPNC 47
           ++ CD  C +WFH  CVG+    A+N D YIC NC
Sbjct: 17 DWVQCDGGCDEWFHQVCVGVSPEMAENED-YICINC 51

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Length = 78

 Score = 46.6 bits (110), Expect = 8e-08
 Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 6/48 (12%)

Query: 10 EPKFYICCD--TCQDWFHGRCVGILQSEADNI----DEYICPNCNNSS 51
          E    I C+   C  W H  CV +     D      + + C  C  +S
Sbjct: 26 ETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS 73

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens} Length = 105

 Score = 47.2 bits (111), Expect = 9e-08
 Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 5/49 (10%)

Query: 15 ICCDTCQDWFHGRCVGILQS-----EADNIDEYICPNCNNSSSNLANMK 58
          +C  +CQ WFH  C G+ +S       +    + C  C  +     +  
Sbjct: 21 LCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEGSGSGS 69

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group} Length = 68

 Score = 43.8 bits (103), Expect = 7e-07
 Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 5/41 (12%)

Query: 12 KFYICCDT--CQDWFHGRCVGILQSEADNI---DEYICPNC 47
             I C+   CQ W H  CV I     ++      + C  C
Sbjct: 22 DSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELC 62

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2 Length = 91

 Score = 42.8 bits (100), Expect = 3e-06
 Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 6/36 (16%)

Query: 15 ICCDT---CQDWFHGRCVGILQSEADNIDEYICPNC 47
          I CD      +WFH  CVG+         ++ CP C
Sbjct: 50 IGCDNPDCSIEWFHFACVGLTTKP---RGKWFCPRC 82

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A Length = 71

 Score = 41.9 bits (98), Expect = 3e-06
 Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 6/36 (16%)

Query: 15 ICCDT---CQDWFHGRCVGILQSEADNIDEYICPNC 47
          I CD      +WFH  CVG+         ++ CP C
Sbjct: 30 IGCDNPDCSIEWFHFACVGLTTKP---RGKWFCPRC 62

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A* Length = 60

 Score = 38.3 bits (89), Expect = 6e-05
 Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 6/36 (16%)

Query: 15 ICCDT---CQDWFHGRCVGILQSEADNIDEYICPNC 47
          I CD      +WFH  CVG+         ++ CP C
Sbjct: 24 IGCDNPDCSIEWFHFACVGLTTKP---RGKWFCPRC 56

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A* Length = 59

 Score = 38.3 bits (89), Expect = 6e-05
 Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 6/36 (16%)

Query: 15 ICCDT---CQDWFHGRCVGILQSEADNIDEYICPNC 47
          I CD      +WFH  CV +         ++ CP C
Sbjct: 23 IGCDNPDCPIEWFHFACVDL---TTKPKGKWFCPRC 55

>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score = 37.9 bits (88), Expect = 1e-04
 Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 6/36 (16%)

Query: 15 ICCDTCQ---DWFHGRCVGILQSEADNIDEYICPNC 47
          + CD      +WFH  CVG+         ++ CP C
Sbjct: 20 VGCDNQDCPIEWFHYGCVGL---TEAPKGKWYCPQC 52

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A* Length = 65

 Score = 36.6 bits (84), Expect = 3e-04
 Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 6/39 (15%)

Query: 15 ICCDT-CQDWFHGRCVGILQS-----EADNIDEYICPNC 47
          I C+  CQ WFH  C G+ ++      A+    + C  C
Sbjct: 25 ILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	171
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	100.0
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	100.0
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	100.0
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	100.0
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	100.0
3g0l_A	117	Hwalp4, bromodomain adjacent to zinc finger domain	100.0
2d9e_A	121	Peregrin; four-helix bundle, transcription activat	100.0
3d7c_A	112	General control of amino acid synthesis protein 5;	100.0
3q2e_A	123	Bromodomain and WD repeat-containing protein 1; st	99.98
2i7k_A	117	Bromodomain-containing protein 7; helix, LEFT-hand	99.97
1e6i_A	121	Transcriptional activator GCN5; gene regulation, b	99.97
4alg_A	154	Bromodomain-containing protein 2; signaling protei	99.97
2oss_A	127	HUNK1 protein, bromodomain-containing protein 4; B	99.97
3rcw_A	135	Bromodomain-containing protein 1; transcription, s	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
3nxb_A	116	CAT eye syndrome critical region protein 2; struct	99.97
3iu5_A	116	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.97
2grc_A	129	Probable global transcription activator SNF2L4; br	99.97
3mb4_A	124	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.97
3mqm_A	126	Probable histone-lysine N-methyltransferase ASH1L;	99.97
2dat_A	123	Possible global transcription activator SNF2L2; br	99.97
3p1f_A	119	CREB-binding protein; structural genomics consorti	99.97
2yyn_A	135	Transcription intermediary factor 1-alpha; bromo d	99.97
2ouo_A	130	HUNK1 protein, bromodomain-containing protein 4; B	99.97
3ljw_A	120	Protein polybromo-1; alpha helix, alternative spli	99.97
3hme_A	123	Bromodomain-containing protein 9; BRD9, bromodomai	99.97
3fkm_X	166	Signaling protein; bromodomain, malaria, structura	99.97
3k2j_A	130	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.97
3uv4_A	158	Second bromodomain of human transcription initiat	99.97
3dai_A	130	ATPase family AAA domain-containing protein 2; anc	99.96
3tlp_A	150	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.96
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.95
2dkw_A	131	Hypothetical protein KIAA1240; bromodomain-like, f	99.95
3uv5_A	265	Transcription initiation factor TFIID subunit 1; t	99.95
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.94
3aad_A	292	Transcription initiation factor TFIID subunit 1; p	99.93
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.92
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.92
3iu6_A	147	Protein polybromo-1; PB1, polybromo 1 isoform 1, B	99.88
2r0y_A	311	Chromatin structure-remodeling complex protein RSC	99.87
2r10_A	361	Chromatin structure-remodeling complex protein RSC	99.87
1we9_A	64	PHD finger family protein; structural genomics, PH	99.53
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	99.53
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	99.47
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	99.47
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	99.46
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	99.42
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	99.39
1wee_A	72	PHD finger family protein; structural genomics, PH	99.36
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	99.32
1wew_A	78	DNA-binding family protein; structural genomics, P	99.3
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	99.27
1wem_A	76	Death associated transcription factor 1; structura	99.25
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	99.23
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	99.22
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	99.22
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	99.21
1weu_A	91	Inhibitor of growth family, member 4; structural g	99.19
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	99.18
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	99.17
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	99.08
3kv5_D	488	JMJC domain-containing histone demethylation prote	99.07
2jmi_A	90	Protein YNG1, ING1 homolog 1; PHD, histone, recogn	99.06
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	99.05
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	99.04
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	99.04
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	99.04
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	99.03
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	99.02
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	98.99
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	98.99
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	98.97
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	98.92
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	98.92
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	98.92
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	98.9
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	98.87
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	98.82
2yt5_A	66	Metal-response element-binding transcription facto	98.81
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	98.8
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	98.8
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	98.77
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	98.7
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	98.69
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	98.6
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	98.53
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	98.36
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.3
4bbq_A	117	Lysine-specific demethylase 2A; oxidoreductase, ub	98.26
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.2
3rsn_A	177	SET1/ASH2 histone methyltransferase complex subun;	98.17
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	97.94
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	97.87
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	97.13
3a1b_A	159	DNA (cytosine-5)-methyltransferase 3A, histone H3;	96.11
2pv0_B	386	DNA (cytosine-5)-methyltransferase 3-like; DNMT3L,	95.24
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	93.87
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	93.05
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	93.01
2l7p_A	100	Histone-lysine N-methyltransferase ASHH2; CW-domai	92.29
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	92.02
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	92.02
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	91.95
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	91.23
2e61_A	69	Zinc finger CW-type PWWP domain protein 1; ZF-CW d	90.7
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	90.56
1yk4_A	52	Rubredoxin, RD; electron transport; 0.69A {Pyrococ	90.08
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	89.76
1s24_A	87	Rubredoxin 2; electron transport; NMR {Pseudomonas	89.36
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	88.03
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	87.78
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	87.03
2lq6_A	87	Bromodomain-containing protein 1; PHD finger, meta	86.73
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	86.52
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	84.59
3nw0_A	238	Non-structural maintenance of chromosomes element	84.33
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	83.87
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	80.5

>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=100.00  E-value=5.1e-50  Score=289.54  Aligned_cols=162  Identities=57%  Similarity=1.143  Sum_probs=148.3

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCCCcccccccCCChhHHHHHHHHHHHHHhCcCCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQAHKSAW   82 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~~~~~~~~~~l~~~~~~~~~~~l~~l~~~~~~~   82 (171)
                      .|.+++|++|+||+||.|++|||..|+|++....+..+.|.||.|...........++++.+++.|..+|+.|.+++.++
T Consensus        12 ~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~l~~~~~~~l~~il~~l~~~~~~~   91 (174)
T 2ri7_A           12 ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAW   91 (174)
T ss_dssp             TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHHHHHHTTTSBCCHHHHHHHHHHHHHHHTSGGGT
T ss_pred             eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcchhccccccccCCHHHHHHHHHHHHHHHhhhhhh
Confidence            47888888999999999999999999999876666678999999985433333446799999999999999999999999


Q ss_pred             CCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHH
Q psy5115          83 PFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKI  162 (171)
Q Consensus        83 ~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~~~~~~  162 (171)
                      +|..||++..+|+|+++|++||||++|++||++|.|.|+++|.+||+|||+||.+||+++|.++++|..|++.|++.+++
T Consensus        92 ~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~  171 (174)
T 2ri7_A           92 PFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKG  171 (174)
T ss_dssp             TTSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTT
T ss_pred             hhhcCCCcccCCchHHHhCCcCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             HH
Q psy5115         163 LR  164 (171)
Q Consensus       163 ~~  164 (171)
                      ++
T Consensus       172 ~~  173 (174)
T 2ri7_A          172 FK  173 (174)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>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=100.00  E-value=9.8e-43  Score=253.33  Aligned_cols=159  Identities=30%  Similarity=0.570  Sum_probs=139.3

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCCCcc-----------------cccccCCChhH
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSN-----------------LANMKNLTPRD   64 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~~~~-----------------~~~~~~l~~~~   64 (171)
                      .+|.+|.+++. +++||+|+++||..|+++... ..+.+.|+||.|+.....                 ......+++.+
T Consensus         5 ~~C~~C~~~g~-ll~Cd~C~~~~H~~C~~p~l~-~~p~~~W~C~~C~~~~~~~~e~dc~~~~~~s~~~~~~~~~~l~~~~   82 (184)
T 3o36_A            5 DWCAVCQNGGE-LLCCEKCPKVFHLSCHVPTLT-NFPSGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPID   82 (184)
T ss_dssp             SSCTTTCCCSS-CEECSSSSCEECTTTSSSCCS-SCCSSCCCCTTTSCSSSCSSCCGGGCCSSCTTTSCCTTCCCCCHHH
T ss_pred             CccccCCCCCe-eeecCCCCcccCccccCCCCC-CCCCCCEECccccCccccccccccccccccccccccccccccCHHH
Confidence            47999987765 999999999999999965433 234568999999943210                 01123588999


Q ss_pred             HHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          65 FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ--QRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~--~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      ++.|..+|..|..++.+++|..||+.. +|+|+++|++||||++|++||++  |.|.++++|.+||+|||+||.+||+++
T Consensus        83 ~~~c~~il~~l~~~~~s~~F~~Pv~~~-~pdY~~iIk~PmdL~tI~~kl~~~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~  161 (184)
T 3o36_A           83 KRKCERLLLFLYCHEMSLAFQDPVPLT-VPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPD  161 (184)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHSCCCTT-STTHHHHCSSCCCHHHHHHHHHSTTCSCCSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHhchhhhhhccccccC-CCchhhhcCCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            999999999999999999999999865 89999999999999999999998  799999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      |.++++|..|++.|++.++++
T Consensus       162 s~v~~~a~~L~~~f~~~~~~~  182 (184)
T 3o36_A          162 SEVANAGIKLENYFEELLKNL  182 (184)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999876

>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=100.00  E-value=1.4e-41  Score=251.29  Aligned_cols=161  Identities=24%  Similarity=0.545  Sum_probs=140.4

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCCCc--------------ccccccCCChhHHHH
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSS--------------NLANMKNLTPRDFES   67 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~~~--------------~~~~~~~l~~~~~~~   67 (171)
                      .+|..|.+++. ||+||+|++|||..|+++... ..+.+.|+||.|.....              .......|++.+++.
T Consensus         8 ~~C~~C~~~g~-ll~Cd~C~~~~H~~Cl~p~l~-~~p~~~W~C~~C~~~~~~~~~~~c~~~~~s~k~~~~~~ls~~~~~~   85 (207)
T 3u5n_A            8 DWCAVCQNGGD-LLCCEKCPKVFHLTCHVPTLL-SFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRK   85 (207)
T ss_dssp             SSBTTTCCCEE-EEECSSSSCEECTTTSSSCCS-SCCSSCCCCTTTSCSSSCSSCCSCC----------CCSSCHHHHHH
T ss_pred             CCCCCCCCCCc-eEEcCCCCCccCCccCCCCCC-CCCCCCEEeCceeCccccccccccccccchhhhhhhhcccHHHHHH
Confidence            46889987654 999999999999999965332 33567899999994321              112235789999999


Q ss_pred             HHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHhhhCC----
Q psy5115          68 LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ---QRYKKLSEFIGDMTKIFDNCRYYNP----  140 (171)
Q Consensus        68 ~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~---~~Y~s~~~f~~Dv~li~~Na~~yn~----  140 (171)
                      |..+|..|.+++.+++|..||+. .+|+|+++|++||||++|++||++   |.|.++++|.+||+|||+||++||+    
T Consensus        86 c~~il~~l~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmdL~tI~~kl~~~~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~  164 (207)
T 3u5n_A           86 CERLLLYLYCHELSIEFQEPVPA-SIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKV  164 (207)
T ss_dssp             HHHHHHHHHTSTTCGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHSTTSTTCCSSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccchhhhhccCCh-hhccHhHHhCCccCHHHHHHHHhcccCCCcCCHHHHHHHHHHHHHHHHHHCCCcch
Confidence            99999999999999999999987 699999999999999999999997   7999999999999999999999999    


Q ss_pred             -------------CCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         141 -------------RESPFFKHAHQLEMFFVQKVKILRE  165 (171)
Q Consensus       141 -------------~~s~~~~~a~~l~~~f~~~~~~~~~  165 (171)
                                   ++|.++++|..|+..|++.|+++..
T Consensus       165 v~~~A~~l~~~~~~~s~i~~~a~~L~~~fe~~~~~~~p  202 (207)
T 3u5n_A          165 VQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYS  202 (207)
T ss_dssp             HC----------CCCCHHHHHHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHhcccccCHHHHHHHHHHHHHHHHHHHhCC
Confidence                         9999999999999999999998754

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

Probab=100.00  E-value=4.4e-41  Score=244.87  Aligned_cols=158  Identities=15%  Similarity=0.310  Sum_probs=136.5

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCCCc--------------ccccccCCChhHHHH
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSS--------------NLANMKNLTPRDFES   67 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~~~--------------~~~~~~~l~~~~~~~   67 (171)
                      .+|.+|.+++. +++||+|+++||..|+.+... ..+.+.|.|+.|.....              ......+|++.+++.
T Consensus         3 ~~C~~C~~~g~-ll~Cd~C~~~~H~~Cl~p~l~-~~p~g~W~C~~C~~~~~~~~~~g~~s~~~~~~~~~~~~m~~~~~~~   80 (189)
T 2ro1_A            3 TICRVCQKPGD-LVMCNQCEFCFHLDCHLPALQ-DVPGEEWSCSLCHVLPDLKEEDGSLSLDGADSTGVVAKLSPANQRK   80 (189)
T ss_dssp             CCBTTTCCCSS-CCCCTTTCCBCCSTTSTTCCS-SCCCTTCCTTTTSCSCCTTCSCSSCCSSSSSSSCSSCSSCHHHHHH
T ss_pred             CcCccCCCCCc-eeECCCCCchhccccCCCCcc-cCCCCCCCCcCccCCCCCCccccccccccccccccccCCCHHHHHH
Confidence            47999998765 999999999999999954322 23467899999994321              011234689999999


Q ss_pred             HHHHHHHHHhCcCCCCCccCCCCCCCCccccccC--CCCCHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          68 LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVK--EPMDLKTIELRIAQQ---RYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        68 ~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~--~Pmdl~~I~~kl~~~---~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      |..+|..|..++.+++|.+||+    |+||.+|+  +||||+||++||++|   .|.++++|.+||+|||+||++|| ++
T Consensus        81 c~~iL~~l~~~~~s~pF~~pV~----~~Yy~iIk~~~PMDL~tIk~kL~~~~~~~Y~s~~eF~~Dv~Lif~N~~~yN-~~  155 (189)
T 2ro1_A           81 CERVLLALFCHEPCRPLHQLAT----DSTFSLDQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLT-ED  155 (189)
T ss_dssp             HHHHHHHHHHSTTHHHHHSCSC----CTTCSSSCSSCCCCHHHHHHHHHTSSSSCCSCHHHHHHHHHHHHHHHHHHC-CS
T ss_pred             HHHHHhhcccCccchhhcCCCC----hhhhccccCCCcccHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHC-CC
Confidence            9999999999999999999997    67999998  899999999999999   99999999999999999999999 58


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKILREK  166 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~~~~  166 (171)
                      +.++.+|..|++.|++.|+++...
T Consensus       156 s~~~~~a~~L~~~Fe~~~~~~~~~  179 (189)
T 2ro1_A          156 KADVQSIIGLQRFFETRMNEAFGD  179 (189)
T ss_dssp             SCSSHHHHHHHHHHHHHHHHHTTT
T ss_pred             CHHHHHHHHHHHHHHHHHHHhcCc
Confidence            888999999999999999988643

>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=100.00  E-value=2.6e-36  Score=217.21  Aligned_cols=150  Identities=17%  Similarity=0.376  Sum_probs=126.7

Q ss_pred             ccccccCCCce---eEecCCCCceecccccCccccCcC------CCCCCCCCccCCCCcccccccCCChhHHHHHHHHHH
Q psy5115           3 FHTLAVIEPKF---YICCDTCQDWFHGRCVGILQSEAD------NIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMK   73 (171)
Q Consensus         3 ~~~~~~~~~~~---~i~C~~C~r~~H~~C~~~~~~~~~------~~~~~~Cp~C~~~~~~~~~~~~l~~~~~~~~~~~l~   73 (171)
                      .|.++|+++.+   ||+||.|.+|||+.|+|++....+      +...|.||.|........+ ..++.++.+.+..||.
T Consensus         7 iC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~~~~~-~~~~~el~~~l~~vl~   85 (183)
T 3lqh_A            7 LCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPAEWR-LALEKELQISLKQVLT   85 (183)
T ss_dssp             TTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSSCHHH-HHHHHHHHHHHHHHHH
T ss_pred             CCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCCHHHH-HHHHHHHHHHHHHHHH
Confidence            48999998764   999999999999999999763211      1237999999865443322 2456677788999999


Q ss_pred             HHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHH
Q psy5115          74 QIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLE  153 (171)
Q Consensus        74 ~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~  153 (171)
                      .|..++.++||...           .++.||||++|++||++|.|.|+.+|+.||.+||+||..||++++++.+++..|+
T Consensus        86 ~L~~~~~s~~~~~y-----------~~k~PmDL~~i~kKl~~~~Y~s~~eF~~Dv~lIf~n~~~~~~~~~e~~~ag~~l~  154 (183)
T 3lqh_A           86 ALLNSRTTSHLLRY-----------RQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVK  154 (183)
T ss_dssp             HHHTCHHHHHHHTC-----------CC--CCSHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHH
T ss_pred             HHHhccccHhhhhh-----------hhcCCccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhccCCChhhhhhhhHHH
Confidence            99999999999873           2599999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q psy5115         154 MFFVQKVKILR  164 (171)
Q Consensus       154 ~~f~~~~~~~~  164 (171)
                      ..|++.++++-
T Consensus       155 ~~f~~~l~~vf  165 (183)
T 3lqh_A          155 SFFIRQMERVF  165 (183)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHHHC
Confidence            99999999864

>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=100.00  E-value=3.6e-33  Score=188.89  Aligned_cols=110  Identities=28%  Similarity=0.571  Sum_probs=105.1

Q ss_pred             cccCCChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Q psy5115          56 NMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNC  135 (171)
Q Consensus        56 ~~~~l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  135 (171)
                      +.++.++.+++.|..+++.|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.++++|.+||+|||+||
T Consensus         6 k~~~~~~~~~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na   85 (117)
T 3g0l_A            6 KPKRDDSKDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNC   85 (117)
T ss_dssp             CCCCCCTTHHHHHHHHHHHHHTSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHHHHHHhCCCchhhcCcCChhhcCChHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         136 RYYNPRESPFFKHAHQLEMFFVQKVKILRE  165 (171)
Q Consensus       136 ~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~  165 (171)
                      ..||+++|.++.+|..|++.|++.|+++-.
T Consensus        86 ~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~  115 (117)
T 3g0l_A           86 ETFNEDDSDIGRAGHNMRKYFEKKWTDTFK  115 (117)
T ss_dssp             HHHSCSSSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999998753

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

Probab=100.00  E-value=1.5e-32  Score=186.56  Aligned_cols=109  Identities=28%  Similarity=0.466  Sum_probs=104.2

Q ss_pred             hhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCC
Q psy5115          62 PRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPR  141 (171)
Q Consensus        62 ~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~  141 (171)
                      ......|..+|+.|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.++++|.+||+|||+||.+||++
T Consensus         6 ~pl~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~   85 (121)
T 2d9e_A            6 SGFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAK   85 (121)
T ss_dssp             CHHHHHHHHHHHHHHHHCSSCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCT
T ss_pred             cHHHHHHHHHHHHHHcCCccHhhCCcCCccccCCHHHHcCCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5115         142 ESPFFKHAHQLEMFFVQKVKILREKLVEL  170 (171)
Q Consensus       142 ~s~~~~~a~~l~~~f~~~~~~~~~~~~~~  170 (171)
                      +|.++++|..|++.|++.++++++.+++.
T Consensus        86 ~s~~~~~A~~L~~~~~~~l~~~~~~~~~~  114 (121)
T 2d9e_A           86 DTIFYRAAVRLREQGGAVLRQARRQAEKM  114 (121)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999999988764

>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=100.00  E-value=2.2e-32  Score=183.62  Aligned_cols=103  Identities=43%  Similarity=0.797  Sum_probs=99.1

Q ss_pred             ChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCC
Q psy5115          61 TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP  140 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~  140 (171)
                      +.+....|..+++.|.+++.+++|..||++..+|+|+++|++||||+||++||++|.|.++++|.+||+|||+||..||+
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            35667899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Q psy5115         141 RESPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       141 ~~s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      ++|.++.+|..|++.|++.++++
T Consensus        85 ~~s~~~~~A~~L~~~f~~~~~~~  107 (112)
T 3d7c_A           85 PDSEYCRCASALEKFFYFKLKEG  107 (112)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHC
Confidence            99999999999999999999875

>3q2e_A Bromodomain and WD repeat-containing protein 1; structural genomics consortium, SGC, cell cycle progression, signal transduction, apoptosis; 1.74A {Homo sapiens}

Probab=99.98  E-value=7.3e-32  Score=183.85  Aligned_cols=109  Identities=27%  Similarity=0.465  Sum_probs=103.0

Q ss_pred             ChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCC
Q psy5115          61 TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP  140 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~  140 (171)
                      ...+++.|..+|+.|..++.+++|..||++..+|+|+++|++||||++|++||++|.|.++++|..||+|||+||..||+
T Consensus         8 ~~~~~~~c~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   87 (123)
T 3q2e_A            8 ESNWKKQCKELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTP   87 (123)
T ss_dssp             --CHHHHHHHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHhCCCcHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C-CCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5115         141 R-ESPFFKHAHQLEMFFVQKVKILREKLVE  169 (171)
Q Consensus       141 ~-~s~~~~~a~~l~~~f~~~~~~~~~~~~~  169 (171)
                      + +|.++.+|..|++.|++.++++.+++.+
T Consensus        88 ~~~s~i~~~A~~L~~~f~~~~~~~~~~~~~  117 (123)
T 3q2e_A           88 NKRSKIYSMTLRLSALFEEKMKKISSDFKI  117 (123)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6 8999999999999999999999988765

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

Probab=99.97  E-value=1.3e-31  Score=180.65  Aligned_cols=101  Identities=27%  Similarity=0.398  Sum_probs=97.0

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      .....|..+++.|.+++.+++|..||++..+|+|+++|++||||+||++||++|.|.|+++|.+||+|||.||.+||+++
T Consensus         8 ~l~~~l~~il~~L~~~~~~~~F~~PVd~~~~pdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Li~~Na~~yN~~~   87 (117)
T 2i7k_A            8 PLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPE   87 (117)
T ss_dssp             HHHHHHHHHHHHHHTSSGGGTSSSCCCTTTSSSHHHHCSCCCCHHHHHHHHTTTSCCSHHHHHHHHHHHHHHHHHTSCSS
T ss_pred             HHHHHHHHHHHHHHhCcccHHhcCCCCccccCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      |.++++|..|++.|++.++..
T Consensus        88 s~i~~~A~~L~~~f~~~~~~~  108 (117)
T 2i7k_A           88 TIYYKAAKKLLHSGMKILSQE  108 (117)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999998864

>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=5.7e-32  Score=183.75  Aligned_cols=102  Identities=40%  Similarity=0.883  Sum_probs=98.4

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      .....|..+|+.|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|.+||+|||+||.+||+++
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            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      |.++++|..|++.|++.+++++
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

>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=3.7e-32  Score=191.72  Aligned_cols=114  Identities=34%  Similarity=0.549  Sum_probs=106.1

Q ss_pred             ccCCChhHHHHHHHHHHHHHhCcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Q psy5115          57 MKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDN  134 (171)
Q Consensus        57 ~~~l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  134 (171)
                      .+.++.+....+..+|+.|.+++.+++|..||++.  .+|+|+++|++||||+||++||++|.|.++++|..||+|||.|
T Consensus        26 ~~r~t~~l~~~~~~il~~l~~~~~a~~F~~PVd~~~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N  105 (154)
T 4alg_A           26 PGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTN  105 (154)
T ss_dssp             CCCCBHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             CCcchHHHHHHHHHHHHHHHhCcCchhhcCCCChhhccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            34677888888888999999999999999999988  6999999999999999999999999999999999999999999


Q ss_pred             HhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5115         135 CRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL  170 (171)
Q Consensus       135 a~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~~~~~  170 (171)
                      |.+||+++|.++.+|..|++.|++.+++++....++
T Consensus       106 a~~YN~~~s~i~~~A~~L~~~f~~~~~~l~~~~~e~  141 (154)
T 4alg_A          106 CYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQEL  141 (154)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHTTSCSSCCBC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHCCchhccc
Confidence            999999999999999999999999999887665543

>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=1.1e-31  Score=183.63  Aligned_cols=108  Identities=37%  Similarity=0.620  Sum_probs=101.6

Q ss_pred             ccCCChhHHHHHHHHHHHHHhCcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Q psy5115          57 MKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDN  134 (171)
Q Consensus        57 ~~~l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  134 (171)
                      .+.++.+....|..+|+.|.+++.+++|..||++.  .+|+|+++|++||||++|++||++|.|.++++|.+||+|||+|
T Consensus        15 ~~r~~~~l~~~~~~il~~L~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~N   94 (127)
T 2oss_A           15 PKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTN   94 (127)
T ss_dssp             CCCCCHHHHHHHHTHHHHHHTSTTCGGGSSCCCTTTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHHHhCccchhhcCCCChhhccCccHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence            34677788888888999999999999999999975  7999999999999999999999999999999999999999999


Q ss_pred             HhhhCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         135 CRYYNPRESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       135 a~~yn~~~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      |.+||+++|.++.+|..|++.|++.+++++
T Consensus        95 a~~yN~~~s~i~~~A~~L~~~f~~~~~~lp  124 (127)
T 2oss_A           95 CYIYNKPGDDIVLMAEALEKLFLQKINELP  124 (127)
T ss_dssp             HHHHSCTTCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence            999999999999999999999999998764

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

Probab=99.97  E-value=2.8e-31  Score=183.80  Aligned_cols=108  Identities=33%  Similarity=0.523  Sum_probs=103.8

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      .....|..+|+.|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.++++|.+||+|||+||..||+++
T Consensus        13 ~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~   92 (135)
T 3rcw_A           13 PLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD   92 (135)
T ss_dssp             HHHHHHHHHHHHHHHTCTTCSSSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHHHhCCcchhhcCCCChhhcCCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            47788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5115         143 SPFFKHAHQLEMFFVQKVKILREKLVEL  170 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~~~~~~~~  170 (171)
                      |.++++|..|++.|++.++++++.++++
T Consensus        93 s~~~~~A~~L~~~~~~~~~~~~~~~~~~  120 (135)
T 3rcw_A           93 TVFYRAAVRLRDQGGVVLRQARREVDSI  120 (135)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999998877653

>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=1.5e-32  Score=186.64  Aligned_cols=110  Identities=28%  Similarity=0.584  Sum_probs=102.3

Q ss_pred             cCCChhHHHHHHHHHHHHHhCcC---CCCCccCCCCCC--CCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q psy5115          58 KNLTPRDFESLRKLMKQIQAHKS---AWPFMEPVDPHE--APDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIF  132 (171)
Q Consensus        58 ~~l~~~~~~~~~~~l~~l~~~~~---~~~F~~pv~~~~--~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~  132 (171)
                      +...+++++.|..+|..|..++.   +++|..||++..  +|+|+++|++||||++|++||++|.|.++++|.+||+|||
T Consensus         4 ~~~~~~~l~~c~~il~~l~~~~~~~~a~~F~~pvd~~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~   83 (120)
T 3jvl_A            4 GSKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMF   83 (120)
T ss_dssp             SCSSCHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCHHHHTCTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHhCcCccccchhcCCCCchhcCCCCHHHHcCCCCCHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence            35677889999999999998887   899999999986  9999999999999999999999999999999999999999


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5115         133 DNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL  167 (171)
Q Consensus       133 ~Na~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~~  167 (171)
                      +||.+||+++|.++.+|..|++.|++.+++++...
T Consensus        84 ~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~p~~~  118 (120)
T 3jvl_A           84 SNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEP  118 (120)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHTTCCC--
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            99999999999999999999999999999876543

>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=2.4e-31  Score=184.15  Aligned_cols=109  Identities=25%  Similarity=0.440  Sum_probs=104.5

Q ss_pred             ChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCC
Q psy5115          61 TPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNP  140 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~  140 (171)
                      .+...+.|..+|+.|..++.+++|..||++..+|+|+++|++||||+||++||++|.|.++++|..||+|||+||..||+
T Consensus        19 ~~~l~~~~~~il~~l~~~~~s~~F~~pv~~~~~pdY~~iI~~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~   98 (135)
T 3mb3_A           19 IQAWKKQCEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTP   98 (135)
T ss_dssp             SSTHHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHhCCCChhhcCCCChhhCCCHHHHhCCCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence            35688899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C-CCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5115         141 R-ESPFFKHAHQLEMFFVQKVKILREKLVE  169 (171)
Q Consensus       141 ~-~s~~~~~a~~l~~~f~~~~~~~~~~~~~  169 (171)
                      + +|.++.+|..|++.|++.++++.+++..
T Consensus        99 ~~~s~i~~~A~~L~~~f~~~~~~~~~~~~~  128 (135)
T 3mb3_A           99 SKRSRIYSMSLRLSAFFEEHISSVLSDYKS  128 (135)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7 8999999999999999999999887764

>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=1.5e-31  Score=180.60  Aligned_cols=101  Identities=38%  Similarity=0.762  Sum_probs=97.4

Q ss_pred             hhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCC
Q psy5115          62 PRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPR  141 (171)
Q Consensus        62 ~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~  141 (171)
                      .+..+.|..+|+.|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.++++|..||+|||+||..||++
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            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q psy5115         142 ESPFFKHAHQLEMFFVQKVKI  162 (171)
Q Consensus       142 ~s~~~~~a~~l~~~f~~~~~~  162 (171)
                      +|.++.+|..|++.|++.|.+
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            999999999999999998864

>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=99.97  E-value=1.3e-31  Score=180.86  Aligned_cols=106  Identities=24%  Similarity=0.443  Sum_probs=101.0

Q ss_pred             CChhHHHHHHHHHHHHHhCc------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Q psy5115          60 LTPRDFESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFD  133 (171)
Q Consensus        60 l~~~~~~~~~~~l~~l~~~~------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~  133 (171)
                      |+.++++.|..+++.|.+++      .+++|..||+...+|+|+++|++||||++|++||++|.|.++++|.+||+|||+
T Consensus         2 m~~~~~~~c~~il~~l~~~~d~~g~~~s~~F~~p~~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~   81 (116)
T 3iu5_A            2 MTVDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFN   81 (116)
T ss_dssp             CSCCHHHHHHHHHHHHHHCBCTTCCBGGGGGSSCCCGGGCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHhhccCCCeeeHHhcCCCCcccCCCHHHHhCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence            67788999999999999884      489999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         134 NCRYYNPRESPFFKHAHQLEMFFVQKVKILRE  165 (171)
Q Consensus       134 Na~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~  165 (171)
                      ||..||+++|.++++|..|++.|++.++++.+
T Consensus        82 Na~~yN~~~s~~~~~A~~L~~~f~~~~~~l~~  113 (116)
T 3iu5_A           82 NAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQ  113 (116)
T ss_dssp             HHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHh
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=3.8e-31  Score=181.57  Aligned_cols=111  Identities=20%  Similarity=0.412  Sum_probs=103.7

Q ss_pred             ccCCChhHHHHHHHHHHHHHhCc-------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHH
Q psy5115          57 MKNLTPRDFESLRKLMKQIQAHK-------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMT  129 (171)
Q Consensus        57 ~~~l~~~~~~~~~~~l~~l~~~~-------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~  129 (171)
                      +.+-.+...+.|..+|+.|.+++       .+++|..||+...+|+|+++|++||||+||++||++|.|.|+++|.+||+
T Consensus         5 ~~~~~~~l~~~~~~il~~l~~~~d~~~~~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~   84 (129)
T 2grc_A            5 LSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVM   84 (129)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHH
T ss_pred             cCCCcHHHHHHHHHHHHHHHhcccccccCeeeHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            34567788999999999999875       58899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5115         130 KIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL  167 (171)
Q Consensus       130 li~~Na~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~~  167 (171)
                      |||+||.+||+++|.++.+|..|++.|++.++++...-
T Consensus        85 Li~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~~  122 (129)
T 2grc_A           85 LLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKED  122 (129)
T ss_dssp             HHHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHccCCC
Confidence            99999999999999999999999999999999987643

>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=1.2e-31  Score=182.95  Aligned_cols=108  Identities=22%  Similarity=0.427  Sum_probs=101.1

Q ss_pred             ccCCChhHHHHHHHHHHHHHh------CcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHH
Q psy5115          57 MKNLTPRDFESLRKLMKQIQA------HKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTK  130 (171)
Q Consensus        57 ~~~l~~~~~~~~~~~l~~l~~------~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~l  130 (171)
                      ...+.+...+.|..+++.|.+      ++.+++|..||+...+|+|+++|++||||++|++||++|.|.++++|..||+|
T Consensus         9 ~~k~~~~l~~~~~~il~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~l   88 (124)
T 3mb4_A            9 KSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVM   88 (124)
T ss_dssp             -CCCCCHHHHHHHHHHHHHHHCBCTTSCBGGGGGSCCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHH
T ss_pred             ccccChHHHHHHHHHHHHHHhHhcccCCcccHHhhcCCCccccCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            346677888999999999998      45579999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         131 IFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       131 i~~Na~~yn~~~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      ||+||..||+++|.++++|..|++.|++.++++.
T Consensus        89 i~~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~l~  122 (124)
T 3mb4_A           89 MFNNACTYNEPESLIYKDALVLHKVLLETRRDLE  122 (124)
T ss_dssp             HHHHHHHHSCTTSHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999998875

>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=99.97  E-value=2e-31  Score=182.46  Aligned_cols=109  Identities=27%  Similarity=0.421  Sum_probs=102.6

Q ss_pred             hhHHHHHHHHHHHHHhCcC------CCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Q psy5115          62 PRDFESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNC  135 (171)
Q Consensus        62 ~~~~~~~~~~l~~l~~~~~------~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  135 (171)
                      ....+.|..+++.|.++..      +++|..||++..+|+|+++|++||||++|++||++|.|.++++|.+||+|||+||
T Consensus         8 ~~l~~~~~~i~~~l~~~~d~~g~~~s~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na   87 (126)
T 3mqm_A            8 ARLAQIFKEICDGIISYKDSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNA   87 (126)
T ss_dssp             HHHHHHHHHHHHHHHHCBCTTCCBTTGGGSSCCCGGGCTTHHHHCSSCCCHHHHHHHHHHTCCCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCcCCCChhHHhcCCCCcccCCCHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            4567788899999988754      8999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5115         136 RYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL  170 (171)
Q Consensus       136 ~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~~~~~  170 (171)
                      ..||+++|.++++|..|++.|++.++++.+.+.++
T Consensus        88 ~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~~l~~i  122 (126)
T 3mqm_A           88 EKYYGRKSPVGRDVCRLRKAYYNARHEASAQIDEI  122 (126)
T ss_dssp             HHHHCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999998875

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

Probab=99.97  E-value=1.4e-31  Score=182.38  Aligned_cols=107  Identities=20%  Similarity=0.393  Sum_probs=100.7

Q ss_pred             CCChhHHHHHHHHHHHHHhCc------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q psy5115          59 NLTPRDFESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIF  132 (171)
Q Consensus        59 ~l~~~~~~~~~~~l~~l~~~~------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~  132 (171)
                      ...+...+.|..+++.|.+++      .+++|..||+...+|+|+++|++||||++|++||++|.|.++++|.+||+|||
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            356788899999999999886      58999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         133 DNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE  165 (171)
Q Consensus       133 ~Na~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~  165 (171)
                      +||.+||+++|.++.+|..|++.|++.++++++
T Consensus        89 ~Na~~yN~~~s~i~~~A~~L~~~f~~~~~~~ps  121 (123)
T 2dat_A           89 HNAQTFNLEGSQIYEDSIVLQSVFKSARQSGPS  121 (123)
T ss_dssp             HHHHHHSCTTSHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHcCC
Confidence            999999999999999999999999999987653

>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=99.97  E-value=3e-31  Score=179.92  Aligned_cols=106  Identities=28%  Similarity=0.569  Sum_probs=99.5

Q ss_pred             hhHHHHHHHHHHHHHh-CcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          62 PRDFESLRKLMKQIQA-HKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        62 ~~~~~~~~~~l~~l~~-~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      .+..+.|..++..|.+ ++.+++|..||++.  ++|+|+++|++||||++|++||++|.|.++++|.+||+|||+||..|
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            3556779999999988 56999999999987  79999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5115         139 NPRESPFFKHAHQLEMFFVQKVKILREKL  167 (171)
Q Consensus       139 n~~~s~~~~~a~~l~~~f~~~~~~~~~~~  167 (171)
                      |+++|.++++|..|++.|++.++++...+
T Consensus        90 N~~~s~i~~~A~~L~~~f~~~~~~~~~~l  118 (119)
T 3p1f_A           90 NRKTSRVYKFCSKLAEVFEQEIDPVMQSL  118 (119)
T ss_dssp             SCTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999987764

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

Probab=99.97  E-value=4.6e-31  Score=182.45  Aligned_cols=107  Identities=34%  Similarity=0.601  Sum_probs=101.8

Q ss_pred             cCCChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHH
Q psy5115          58 KNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQ--QRYKKLSEFIGDMTKIFDNC  135 (171)
Q Consensus        58 ~~l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~--~~Y~s~~~f~~Dv~li~~Na  135 (171)
                      ..|++.+++.|..+|..|++++.+++|..||+. .+|+|+++|++||||++|++||++  |.|.++++|.+||+|||+||
T Consensus        15 ~~m~p~~~~~c~~il~~L~~~~~s~~F~~Pv~~-~~pdY~~iIk~PmDL~tI~~kL~~~~~~Y~s~~ef~~Dv~Lif~Na   93 (135)
T 2yyn_A           15 VKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPL-TVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNC   93 (135)
T ss_dssp             -CCCHHHHHHHHHHHHHHHTSGGGGGGSSCCCT-TSTTHHHHCSSCCCHHHHHHHHHSSSCCCSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHhCccchhhcCCCcc-cCCCHHHHcCCCCCHHHHHHHHhccccCCCCHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999987 699999999999999999999998  59999999999999999999


Q ss_pred             hhhCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         136 RYYNPRESPFFKHAHQLEMFFVQKVKILRE  165 (171)
Q Consensus       136 ~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~  165 (171)
                      .+||+++|.++.+|..|++.|++.++++..
T Consensus        94 ~~yN~~~s~i~~~A~~L~~~f~~~~~~~~~  123 (135)
T 2yyn_A           94 AEFNEPDSEVANAGIKLENYFEELLKNLYP  123 (135)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence            999999999999999999999999998754

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

Probab=99.97  E-value=1.4e-31  Score=183.90  Aligned_cols=106  Identities=29%  Similarity=0.608  Sum_probs=98.4

Q ss_pred             CChhHHHHHHHHHHHHHhCcC---CCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Q psy5115          60 LTPRDFESLRKLMKQIQAHKS---AWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDN  134 (171)
Q Consensus        60 l~~~~~~~~~~~l~~l~~~~~---~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  134 (171)
                      ..+.+++.|..+|+.|..++.   +++|..||++.  .+|+|+++|++||||+||++||++|.|.++++|.+||+|||+|
T Consensus        19 ~~~~~l~~c~~il~~L~~~~~~~~a~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~N   98 (130)
T 2ouo_A           19 KVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSN   98 (130)
T ss_dssp             CHHHHHHHHHHHHHHHTSGGGHHHHGGGSSCCCTTSTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhCCcchhHHHhcCCCChhhccCCcHHHHcCCCCCHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence            345677899999999998764   89999999987  4999999999999999999999999999999999999999999


Q ss_pred             HhhhCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         135 CRYYNPRESPFFKHAHQLEMFFVQKVKILRE  165 (171)
Q Consensus       135 a~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~  165 (171)
                      |.+||+++|.++.+|..|++.|++.+++++.
T Consensus        99 a~~yN~~~s~i~~~A~~L~~~f~~~~~~lp~  129 (130)
T 2ouo_A           99 CYKYNPPDHEVVAMARKLQDVFEMRFAKMPD  129 (130)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHHHCCC
Confidence            9999999999999999999999999987653

>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=99.97  E-value=7.9e-31  Score=177.99  Aligned_cols=107  Identities=29%  Similarity=0.434  Sum_probs=100.9

Q ss_pred             ChhHHHHHHHHHHHHHhCcC------CCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Q psy5115          61 TPRDFESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDN  134 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~~------~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  134 (171)
                      ...+...|..+++.|.+.+.      +++|..||+...+|+|+++|++||||++|++||++|.|.++++|..||+|||+|
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            45667789999999998876      999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5115         135 CRYYNPRESPFFKHAHQLEMFFVQKVKILREKL  167 (171)
Q Consensus       135 a~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~~  167 (171)
                      |..||+++|.++++|..|++.|++.++++++..
T Consensus        86 a~~yN~~~s~~~~~A~~L~~~f~~~~~~i~~~~  118 (120)
T 3ljw_A           86 AKTYNEPGSQVFKDANSIKKIFYMKKAEIEHHE  118 (120)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            999999999999999999999999999998754

>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=8.8e-31  Score=178.37  Aligned_cols=103  Identities=26%  Similarity=0.394  Sum_probs=98.4

Q ss_pred             hhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCC
Q psy5115          62 PRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPR  141 (171)
Q Consensus        62 ~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~  141 (171)
                      ......|..+++.|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.++++|..||+|||+||..||++
T Consensus        12 ~p~~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~   91 (123)
T 3hme_A           12 TPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRP   91 (123)
T ss_dssp             CHHHHHHHHHHHHHHTTCTTCSSSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCT
T ss_pred             CHHHHHHHHHHHHHHhCCccHhhcCCCChhhccCHHHHCCCCCCHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            44577899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         142 ESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       142 ~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      +|.++++|..|++.|++.+.+.+
T Consensus        92 ~s~~~~~A~~L~~~~~~~~~~~~  114 (123)
T 3hme_A           92 DTVYYKLAKKILHAGFKMMSKER  114 (123)
T ss_dssp             TSHHHHHHHHHHHHHHHHTCHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999988654

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

Probab=99.97  E-value=1.2e-30  Score=186.17  Aligned_cols=107  Identities=26%  Similarity=0.496  Sum_probs=100.1

Q ss_pred             cCCChhHHHHHHHHHHHHHhCcCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Q psy5115          58 KNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNC  135 (171)
Q Consensus        58 ~~l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  135 (171)
                      .++..+++..|..+|..|++++.+++|..||++.  .+|+|+++|++||||+||++||++|.|.++++|..||+|||.||
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            4788899999999999999999999999999976  59999999999999999999999999999999999999999999


Q ss_pred             hhhCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy5115         136 RYYNPRESPFFKHAHQLEMFFVQKVKILR  164 (171)
Q Consensus       136 ~~yn~~~s~~~~~a~~l~~~f~~~~~~~~  164 (171)
                      .+||+++|.++.+|..|++.|++.|+++.
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            99999999999999999999999998753

>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=99.97  E-value=1.8e-30  Score=178.26  Aligned_cols=106  Identities=25%  Similarity=0.464  Sum_probs=98.7

Q ss_pred             ChhHHHHHHHHHHHHHhCcC------CCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Q psy5115          61 TPRDFESLRKLMKQIQAHKS------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDN  134 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~~------~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  134 (171)
                      .......+..+++.+.+...      +++|..||+...+|+|+++|++||||++|++||++|.|.|+++|..||+|||+|
T Consensus        15 ~~kl~~~~~~l~~~l~~~~d~~g~~~s~~F~~pv~~~~~PdY~~iIk~PMdL~tI~~kL~~~~Y~s~~ef~~Dv~Lif~N   94 (130)
T 3k2j_A           15 TENLYFQSMQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFEN   94 (130)
T ss_dssp             HHHHHHHHHHHHHHHHTCBCSSSCBTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhcccCCCccHhhcCCCChhhCccHHHHcCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            34567778888888887654      899999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         135 CRYYNPRESPFFKHAHQLEMFFVQKVKILREK  166 (171)
Q Consensus       135 a~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~  166 (171)
                      |..||+++|.++++|..|++.|++.++++.++
T Consensus        95 a~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~~  126 (130)
T 3k2j_A           95 AKRYNVPNSAIYKRVLKLQQVMQAKKKELARR  126 (130)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999998765

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

Probab=99.97  E-value=1.3e-30  Score=184.34  Aligned_cols=108  Identities=31%  Similarity=0.569  Sum_probs=98.0

Q ss_pred             hHHHHHHHHHHH-----HHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhh
Q psy5115          63 RDFESLRKLMKQ-----IQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRY  137 (171)
Q Consensus        63 ~~~~~~~~~l~~-----l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~  137 (171)
                      .....|..+|..     +..++.+++|..||++..+|+|+++|++||||+||++||++|.|.++++|..||+|||+||.+
T Consensus        25 d~~~~l~~iL~~i~~~kl~~~~~s~~F~~PVd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~Na~~  104 (158)
T 3uv4_A           25 DDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVK  104 (158)
T ss_dssp             HHHHHHHHHHHHHHHHTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHcCCCchhhcCcCChhhcccHHHHcCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence            344555555544     455788999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5115         138 YNPRESPFFKHAHQLEMFFVQKVKILREKLVEL  170 (171)
Q Consensus       138 yn~~~s~~~~~a~~l~~~f~~~~~~~~~~~~~~  170 (171)
                      ||+++|.++++|..|.+.|++.++++++.+.++
T Consensus       105 yN~~~s~i~~~A~~L~~~~~~~l~e~~~~l~~l  137 (158)
T 3uv4_A          105 YNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQL  137 (158)
T ss_dssp             HHCTTCHHHHHHHHHHHHHHHHHHHTHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999888765

>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=2.5e-29  Score=172.79  Aligned_cols=106  Identities=30%  Similarity=0.465  Sum_probs=95.9

Q ss_pred             hhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCC
Q psy5115          62 PRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPR  141 (171)
Q Consensus        62 ~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~  141 (171)
                      .+....|..+++.|..++.+++|..||++..+|+|+++|++||||+||++||++|.|.++++|.+||+|||+||..||++
T Consensus         9 ~~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~   88 (130)
T 3dai_A            9 RELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPD   88 (130)
T ss_dssp             HHHHHHHHHHHHHHHTSGGGGGGSSCCCTTTCTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHCCS
T ss_pred             HHHHHHHHHHHHHHHcCCccHhhcCCCChhhcCCHHHHcCCCCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence            34566788899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHH----HHHHHHHHHHHHHHHH-HHHHHh
Q psy5115         142 ESPF----FKHAHQLEMFFVQKVK-ILREKL  167 (171)
Q Consensus       142 ~s~~----~~~a~~l~~~f~~~~~-~~~~~~  167 (171)
                      +|++    +..|..|++.+...++ ++.+++
T Consensus        89 ~s~~~~~i~~~A~~L~~~~~~~i~~el~~~~  119 (130)
T 3dai_A           89 RDPGDRLIRHRACALRDTAYAIIKEELDEDF  119 (130)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHHHHHSCHHH
T ss_pred             CChhHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence            9876    6888889988888885 444444

>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=99.96  E-value=4.3e-29  Score=175.70  Aligned_cols=103  Identities=32%  Similarity=0.494  Sum_probs=94.7

Q ss_pred             hHHHHHHHHHHHHHhCcC-------CCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Q psy5115          63 RDFESLRKLMKQIQAHKS-------AWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNC  135 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~-------~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na  135 (171)
                      .....|..++..+.+...       +++|..||+...+|+|+++|++||||++|++||++|.|.++++|..||+|||+||
T Consensus        24 ~~~~~~k~ll~~l~~~~~~~~~~~~~~~F~~~~~~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na  103 (150)
T 3tlp_A           24 IRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNA  103 (150)
T ss_dssp             HHHHHHHHHHHHHHHCBCTTTCCBGGGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHhcccCCcccHHhcCCCchhhCcCHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence            345667777777776654       8999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         136 RYYNPRESPFFKHAHQLEMFFVQKVKILRE  165 (171)
Q Consensus       136 ~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~  165 (171)
                      ..||+++|.++++|..|++.|++.++++..
T Consensus       104 ~~yN~~~s~i~~~A~~L~~~f~~~~~~l~~  133 (150)
T 3tlp_A          104 RHYNEEGSQVYNDAHILEKLLKEKRKELGP  133 (150)
T ss_dssp             HHHSCTTSHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHccC
Confidence            999999999999999999999999998763

>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=99.95  E-value=7.4e-28  Score=183.86  Aligned_cols=107  Identities=22%  Similarity=0.419  Sum_probs=102.2

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      .....|..+|..|..++.+++|..||++..+|+|+.+|++||||+||++||++|.|.++++|..||+|||+||.+||+++
T Consensus        14 ~l~~~l~~il~~l~~~~~~~~F~~pv~~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~~~~~f~~D~~li~~Na~~yN~~~   93 (265)
T 3uv5_A           14 TLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPK   93 (265)
T ss_dssp             HHHHHHHHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHHcCCCchhhhCCCChhhcCCHHHHhCCCCcHHHHHHHHHcCCCCCHHHHHHHHHHHHhhhhhcCCCC
Confidence            66778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5115         143 SPFFKHAHQLEMFFVQKVKILREKLVE  169 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~~~~~~~  169 (171)
                      |.++.+|..|.+.|++.++++...+.+
T Consensus        94 s~i~~~A~~l~~~~~~~~~~~~~~~~~  120 (265)
T 3uv5_A           94 HSLTQISQSMLDLCDEKLKEKEDKLAR  120 (265)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            999999999999999999988766654

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

Probab=99.95  E-value=3.7e-27  Score=161.70  Aligned_cols=98  Identities=30%  Similarity=0.420  Sum_probs=89.8

Q ss_pred             CCChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhh
Q psy5115          59 NLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYY  138 (171)
Q Consensus        59 ~l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~y  138 (171)
                      ....+....|..+++.|.+++.+++|..|     +|+|+++|++||||+||++||++|.|.++++|..||+|||+||..|
T Consensus         8 ~~~~~L~~~~~~il~~l~~~~~~~~F~~P-----~pdY~~iIk~PmDL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~y   82 (131)
T 2dkw_A            8 NTLRELRLFLRDVTKRLATDKRFNIFSKP-----VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEY   82 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSGGGCTTSSC-----CSSCTTSCSSCCCHHHHHHHHHTTCCCSSHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHhCccchhhcCc-----CccHHhHcCCCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            34456777899999999999999999998     7999999999999999999999999999999999999999999999


Q ss_pred             CCCCCH----HHHHHHHHHHHHHHHHH
Q psy5115         139 NPRESP----FFKHAHQLEMFFVQKVK  161 (171)
Q Consensus       139 n~~~s~----~~~~a~~l~~~f~~~~~  161 (171)
                      |+++|+    ++.+|..|++.|...++
T Consensus        83 N~~~s~~~~~i~~~A~~L~~~~~~~l~  109 (131)
T 2dkw_A           83 NPDKDPGDKIIRHRACTLKDTAHAIIA  109 (131)
T ss_dssp             CCCSSTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCChhHHHHHHHHHHHHHHHHHHHH
Confidence            999985    57889999998888774

>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=99.95  E-value=3.3e-27  Score=180.31  Aligned_cols=96  Identities=34%  Similarity=0.618  Sum_probs=92.1

Q ss_pred             HHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHH
Q psy5115          75 IQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEM  154 (171)
Q Consensus        75 l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~  154 (171)
                      +..++.+++|..||++..+|+|+++|++||||+||++||++|.|.++++|..||+|||+||..||+++|.++.+|..|++
T Consensus       149 l~~~~~~~~F~~pv~~~~~pdY~~iIk~Pmdl~tI~~kl~~~~Y~~~~~f~~D~~lif~Na~~yN~~~s~~~~~A~~l~~  228 (265)
T 3uv5_A          149 MMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVN  228 (265)
T ss_dssp             TTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHH
T ss_pred             HHhhhhhHHHhCCCChhHhCcHHHHhCCcccHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            66778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhc
Q psy5115         155 FFVQKVKILREKLVEL  170 (171)
Q Consensus       155 ~f~~~~~~~~~~~~~~  170 (171)
                      .|++.++++.+.+.++
T Consensus       229 ~~~~~~~~~~~~~~~~  244 (265)
T 3uv5_A          229 VCYQTLTEYDEHLTQL  244 (265)
T ss_dssp             HHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999998887654

>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=99.94  E-value=1.9e-26  Score=178.07  Aligned_cols=97  Identities=34%  Similarity=0.617  Sum_probs=92.7

Q ss_pred             HHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHH
Q psy5115          74 QIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLE  153 (171)
Q Consensus        74 ~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~  153 (171)
                      .|..++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|..||+|||+||..||+++|.++.+|..|+
T Consensus       181 ~l~~~~~s~~F~~pvd~~~~pdY~~iIk~PmdL~tI~~kl~~~~Y~s~~~f~~D~~Li~~Na~~yN~~~s~i~~~A~~L~  260 (292)
T 3aad_A          181 KMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIV  260 (292)
T ss_dssp             TGGGSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHH
T ss_pred             hhhcCcchhHHHhcccccccccHHHHcCCcCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence            36778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhc
Q psy5115         154 MFFVQKVKILREKLVEL  170 (171)
Q Consensus       154 ~~f~~~~~~~~~~~~~~  170 (171)
                      +.|++.++++.+.+.++
T Consensus       261 ~~~~~~~~~~~~~l~~l  277 (292)
T 3aad_A          261 NVCYQTLTEYDEHLTQL  277 (292)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999998887765

>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=7e-27  Score=180.56  Aligned_cols=106  Identities=23%  Similarity=0.421  Sum_probs=99.5

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      .....|..+|+.|..++.+++|..||++..+|+|+++|++||||+||++||++|.|.++.+|..||+|||+||.+||+++
T Consensus        47 ~l~~~~~~il~~l~~~~~a~~F~~pV~~~~~pdY~~iIk~PmDL~tIk~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~  126 (292)
T 3aad_A           47 TLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPK  126 (292)
T ss_dssp             HHHHHHHHHHHHHSSSTTCGGGSSSCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCSS
T ss_pred             HHHHHHHHHHHHHHhCCcchhhcCCCCchhcccHHHHcCCcCCHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHHHcCCc
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy5115         143 SPFFKHAHQLEMFFVQKVKILREKLV  168 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~~~~~~~  168 (171)
                      |.++.+|..|.+.|++.++++.+.+.
T Consensus       127 s~i~~~A~~L~~~~~~~~~~~~~~~~  152 (292)
T 3aad_A          127 HSLTQISQSMLDLCDEKLKEKEDKLA  152 (292)
T ss_dssp             SHHHHHHTHHHHTTTTTGGGSHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhhhcchhhhh
Confidence            99999999999999998887666544

>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=99.92  E-value=2.2e-25  Score=173.22  Aligned_cols=85  Identities=33%  Similarity=0.590  Sum_probs=82.8

Q ss_pred             CcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHH
Q psy5115          78 HKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFV  157 (171)
Q Consensus        78 ~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~  157 (171)
                      ++.+++|..||++..+|+|+++|++||||+||++||++|.|.++++|.+||+|||+||++||+++|.++.+|..|++.|+
T Consensus       178 ~~~s~~F~~pvd~~~~PdY~~iIk~PMDL~tI~~kl~~~~Y~s~~ef~~Dv~Lif~N~~~yN~~~s~i~~~A~~L~~~f~  257 (311)
T 2r0y_A          178 VKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFN  257 (311)
T ss_dssp             SCTTGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHHHHHTCCCBHHHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHH
T ss_pred             CccHHHHhCCCChhhcccHHHHhCCccCHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHH
Q psy5115         158 QKVKI  162 (171)
Q Consensus       158 ~~~~~  162 (171)
                      +.+++
T Consensus       258 ~~~~~  262 (311)
T 2r0y_A          258 YLIQK  262 (311)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99987

>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=99.92  E-value=6.5e-25  Score=173.97  Aligned_cols=85  Identities=33%  Similarity=0.590  Sum_probs=82.7

Q ss_pred             CcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHH
Q psy5115          78 HKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFV  157 (171)
Q Consensus        78 ~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l~~~f~  157 (171)
                      ++.+++|..||++..+|+||++|++||||++|++||++|.|.++++|..||+|||+||++||+++|.++.+|..|++.|+
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            45799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHH
Q psy5115         158 QKVKI  162 (171)
Q Consensus       158 ~~~~~  162 (171)
                      +.+++
T Consensus       308 ~~~~~  312 (361)
T 2r10_A          308 YLIQK  312 (361)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99987

>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=99.88  E-value=6.9e-22  Score=136.17  Aligned_cols=102  Identities=23%  Similarity=0.392  Sum_probs=92.8

Q ss_pred             ChhHHHHHHHHHHHHHhCc------CCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Q psy5115          61 TPRDFESLRKLMKQIQAHK------SAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDN  134 (171)
Q Consensus        61 ~~~~~~~~~~~l~~l~~~~------~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~N  134 (171)
                      +...+..+..++..+.++.      .+.+|...|+..  |+||.  ++||+|.+|++|+++|.|+++++|..|+.+||+|
T Consensus         5 ~~~lq~~l~~l~~~v~~~~De~GR~lsd~F~~LPsk~--pdYY~--k~Pi~l~~Ikkri~~~~Y~sld~f~~D~~lmf~N   80 (147)
T 3iu6_A            5 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLER   80 (147)
T ss_dssp             CCHHHHHHHHHHHHHHTCBCTTSCBGGGGGTTCCSSC--TTSTT--SCCCCHHHHHHHHHTTCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhcCCCCCcchHHHhHCCCCC--ccccC--CCCcCHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence            4556778888999998875      367899998877  78998  9999999999999999999999999999999999


Q ss_pred             HhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy5115         135 CRYYNPRESPFFKHAHQLEMFFVQKVKILREK  166 (171)
Q Consensus       135 a~~yn~~~s~~~~~a~~l~~~f~~~~~~~~~~  166 (171)
                      |++||.+||+|+++|..|++.|.+..+++..+
T Consensus        81 Ar~yN~e~S~IyeDAv~Lq~~f~~~r~eL~~~  112 (147)
T 3iu6_A           81 ARRMNRTDSEIYEDAVELQQFFIKIRDELCKN  112 (147)
T ss_dssp             HHHHSCTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999999999999999998765

>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=2.1e-22  Score=156.44  Aligned_cols=98  Identities=21%  Similarity=0.297  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHHHHhC--cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCC-CHHHHHHHHHHHHHHHhhhCC
Q psy5115          64 DFESLRKLMKQIQAH--KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK-KLSEFIGDMTKIFDNCRYYNP  140 (171)
Q Consensus        64 ~~~~~~~~l~~l~~~--~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~-s~~~f~~Dv~li~~Na~~yn~  140 (171)
                      ....+..+|..+.+.  ..+++|..||+...+|+||++|++||||+||++|+  +.|. ++++|..||+|||+||.+||+
T Consensus        29 ~~~~~~~~L~~~~~~~r~~~~~F~~p~~~~~~PdY~~iIk~PmDL~tI~~kl--~~y~~s~~~f~~D~~li~~Na~~yN~  106 (311)
T 2r0y_A           29 FNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAYNE  106 (311)
T ss_dssp             HHHHHHHHHHHHHHHSHHHHGGGSSCCCTTTCHHHHHHCSSCCCHHHHHHSC--CCSTTHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHcCCchhHHhcCCCCcccCCChHHHcCCCCCHHHHHHHH--hcccCCHHHHHHHHHHHHHHHHHccC
Confidence            334444455555432  36889999999999999999999999999999998  5555 899999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Q psy5115         141 RESPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       141 ~~s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      ++|.++++|..|++.|++.|.+.
T Consensus       107 ~~s~i~~~A~~l~~~~~~~~~k~  129 (311)
T 2r0y_A          107 YDSLIVKNSMQVVMLIEFEVLKA  129 (311)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999988765

>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=99.87  E-value=2.2e-22  Score=159.46  Aligned_cols=97  Identities=22%  Similarity=0.316  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHHHhC--cCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCC-CHHHHHHHHHHHHHHHhhhCCC
Q psy5115          65 FESLRKLMKQIQAH--KSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYK-KLSEFIGDMTKIFDNCRYYNPR  141 (171)
Q Consensus        65 ~~~~~~~l~~l~~~--~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~-s~~~f~~Dv~li~~Na~~yn~~  141 (171)
                      ...|..+|+.+.+.  ..+++|..||+...+|+||++|++||||+||++||  +.|. ++++|..||+|||+||..||++
T Consensus        80 ~~~~~~~l~~l~~~~~~~~~~F~~p~~~~~~PdY~~iIk~Pmdl~tI~~kl--~~y~~~~~~f~~D~~li~~Na~~yN~~  157 (361)
T 2r10_A           80 NRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRD--YEYEDGPSNFLLDVELLTKNCQAYNEY  157 (361)
T ss_dssp             HHHHHHHHHHHHHHTHHHHGGGSSCCCTTTCTTHHHHCSSCCCHHHHHTSC--CCSTTHHHHHHHHHHHHHHHHHHHBCS
T ss_pred             HHHHHHHHHHHHHcCCcccHHhcCCCCcccCCChHhhcCCCcCHHHHHHHh--hccCCCHHHHHHHHHHHHHHHhhcCCC
Confidence            34566777777553  35799999999999999999999999999999998  4555 8999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q psy5115         142 ESPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       142 ~s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      +|.++.+|..|++.|++.|.+.
T Consensus       158 ~s~i~~~a~~l~~~~~~~~~k~  179 (361)
T 2r10_A          158 DSLIVKNSMQVVMLIEFEVLKA  179 (361)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999988765

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=99.53  E-value=2.8e-15  Score=90.20  Aligned_cols=47  Identities=43%  Similarity=1.081  Sum_probs=41.5

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      .|.++++++++||+||.|.+|||..|++++....+..+.|+|+.|..
T Consensus        11 ~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A           11 ACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            57999998899999999999999999999876655568999999973

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=99.53  E-value=2.6e-15  Score=86.45  Aligned_cols=45  Identities=33%  Similarity=0.819  Sum_probs=38.6

Q ss_pred             ccccccCCCceeEecC-CCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCD-TCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~-~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|++||+++++||+|| .|.+|||..|+|++..... .+.|+||.|.
T Consensus         7 ~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~-~~~~~C~~C~   52 (52)
T 2kgg_A            7 NCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAE-NEDYICINCA   52 (52)
T ss_dssp             TCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHH-HSCCCCSCC-
T ss_pred             CCcCccCCCCcEEEeCCCCCccCcccccCCCccccC-CCCEECCCCC
Confidence            5899999999999999 8999999999999865432 3789999994

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=99.47  E-value=2.1e-14  Score=89.82  Aligned_cols=48  Identities=44%  Similarity=0.936  Sum_probs=42.1

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS   50 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~   50 (171)
                      +|.+++|++++||+||.|..|||..|++++......++.|+|+.|...
T Consensus        16 ~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~   63 (79)
T 1wep_A           16 LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV   63 (79)
T ss_dssp             TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTT
T ss_pred             EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccc
Confidence            478999888999999999999999999998776655789999999853

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens}

Probab=99.47  E-value=2e-14  Score=82.78  Aligned_cols=44  Identities=25%  Similarity=0.688  Sum_probs=37.0

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +|+++++ +++||+||.|..|||..|+|++...  .++.|+||.|..
T Consensus         8 ~C~~~~~-~~~MI~Cd~C~~W~H~~Cvgi~~~~--~~~~~~C~~C~~   51 (52)
T 3o7a_A            8 FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSN--VPEVFVCQKCRD   51 (52)
T ss_dssp             TTCCBCT-TCCEEECTTTCCEEETTTTTCCGGG--CCSSCCCHHHHT
T ss_pred             EeCCcCC-CCCEEEcCCCCccccccccCCCccc--CCCcEECcCCCC
Confidence            4688877 6679999999999999999998653  357999999963

>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger, histone-binding, NUC protein; HET: M3L; 1.78A {Homo sapiens} SCOP: g.50.1.2

Probab=99.46  E-value=8.7e-15  Score=90.68  Aligned_cols=46  Identities=50%  Similarity=1.107  Sum_probs=41.2

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      +|.+++|++++||+||.|..|||..|++++.......+.|+|+.|.
T Consensus        14 iC~~~~~~~~~MI~Cd~C~~WfH~~Cvg~~~~~~~~~~~~~C~~C~   59 (75)
T 3kqi_A           14 VCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCE   59 (75)
T ss_dssp             TTTEECCTTSCEEECTTTCCEEEHHHHTCCTTTGGGBSSCCCHHHH
T ss_pred             ECCCcCCCCCCEEEcCCCCCCEecccccccccccCCCCEEECCCCc
Confidence            5799999899999999999999999999987765556789999998

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=99.42  E-value=7.2e-14  Score=84.64  Aligned_cols=44  Identities=25%  Similarity=0.698  Sum_probs=36.8

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +|+++++ +++||+||.|..|||..|+|++..  ..++.|+||.|..
T Consensus        23 iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~--~~~~~~~C~~C~~   66 (68)
T 3o70_A           23 FCMKPFA-GRPMIECNECHTWIHLSCAKIRKS--NVPEVFVCQKCRD   66 (68)
T ss_dssp             TTCCCCT-TCCEEECTTTCCEEETTTTTCCTT--SCCSSCCCHHHHT
T ss_pred             ECCCcCC-CCCEEECCCCCccccccccCcCcc--cCCCcEECCCCCC
Confidence            4677777 567999999999999999999865  3467999999963

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=99.39  E-value=9.3e-15  Score=87.70  Aligned_cols=46  Identities=28%  Similarity=0.668  Sum_probs=39.3

Q ss_pred             ccccccCCCceeEecC-CCCceecccccCccccCc-----CCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCD-TCQDWFHGRCVGILQSEA-----DNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~-~C~r~~H~~C~~~~~~~~-----~~~~~~~Cp~C~   48 (171)
                      .|.+|++++.+||+|| .|.+|||..|+|++....     ++...|+||.|.
T Consensus        13 ~C~~p~~~~~~mI~CD~~C~~WfH~~Cvglt~~~~~~l~~e~~~~w~C~~C~   64 (65)
T 2vpb_A           13 ICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCM   64 (65)
T ss_dssp             TTCSBCCTTSCEEEBTTTTCCEEEHHHHTCCHHHHHHHHHCTTEEECCHHHH
T ss_pred             cCCCccCCCCCeEecccCccccCchhccCCCHHHHHHhhccCCCcEECcCcc
Confidence            5899999999999999 999999999999987532     234589999994

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=99.36  E-value=2.9e-13  Score=83.16  Aligned_cols=45  Identities=24%  Similarity=0.605  Sum_probs=38.4

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|.++++++++||+||.|.+|||..|++++... ..++.|+||.|.
T Consensus        20 ~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~-~~~~~~~C~~C~   64 (72)
T 1wee_A           20 KCGTKDDDGERMLACDGCGVWHHTRCIGINNAD-ALPSKFLCFRCI   64 (72)
T ss_dssp             TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTS-CCCSCCCCHHHH
T ss_pred             eCCCccCCCCcEEECCCCCCccCCeeeccCccc-cCCCcEECCCcc
Confidence            367888777789999999999999999997643 356899999997

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=99.32  E-value=9.7e-14  Score=91.23  Aligned_cols=46  Identities=28%  Similarity=0.652  Sum_probs=39.3

Q ss_pred             ccccccCCCceeEecC-CCCceecccccCccccCc-----CCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCD-TCQDWFHGRCVGILQSEA-----DNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~-~C~r~~H~~C~~~~~~~~-----~~~~~~~Cp~C~   48 (171)
                      .|++||++++.||+|| .|.+|||..|+|++....     +..+.|+||.|.
T Consensus         8 iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~   59 (105)
T 2xb1_A            8 ACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCL   59 (105)
T ss_dssp             TTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHH
T ss_pred             CCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECcccc
Confidence            5899998888999998 999999999999986432     234789999998

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=99.30  E-value=6e-13  Score=82.93  Aligned_cols=45  Identities=22%  Similarity=0.521  Sum_probs=37.0

Q ss_pred             ccccccCCCceeEecC--CCCceecccccCccccCc----CCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCD--TCQDWFHGRCVGILQSEA----DNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~--~C~r~~H~~C~~~~~~~~----~~~~~~~Cp~C~   48 (171)
                      +|.++ +++|+||+||  .|..|||..|++++....    +.++.|+|+.|.
T Consensus        20 iC~~~-~~~g~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~   70 (78)
T 1wew_A           20 VCGNS-LETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICR   70 (78)
T ss_dssp             SSCCC-CCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHH
T ss_pred             ECCCc-CCCCCEEEECCccCCccccCEEEccccccccccccCCCCEECCCCC
Confidence            35666 4567899999  999999999999987643    457899999997

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=99.27  E-value=2e-12  Score=83.98  Aligned_cols=44  Identities=32%  Similarity=0.829  Sum_probs=35.4

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +|.++.++ |.||+||.|.+|||..|+++...  ..++.|+||.|+.
T Consensus        32 iC~~~~~~-~~mi~Cd~C~~w~H~~C~~~~~~--~~p~~w~C~~C~~   75 (98)
T 2lv9_A           32 ICGFTHDD-GYMICCDKCSVWQHIDCMGIDRQ--HIPDTYLCERCQP   75 (98)
T ss_dssp             TTSCCSCS-SCEEEBTTTCBEEETTTTTCCTT--SCCSSBCCTTTSS
T ss_pred             ECCCccCC-CcEEEcCCCCCcCcCcCCCCCcc--CCCCCEECCCCcC
Confidence            36777654 56999999999999999998643  3456899999973

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=99.25  E-value=4.2e-13  Score=83.30  Aligned_cols=45  Identities=47%  Similarity=1.192  Sum_probs=36.5

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcC----CCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEAD----NIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~----~~~~~~Cp~C~   48 (171)
                      +|.++++ +++||+||.|.+|||..|++++.....    .++.|+|+.|.
T Consensus        20 ~C~~~~~-~~~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~   68 (76)
T 1wem_A           20 ICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCT   68 (76)
T ss_dssp             TTCCCCC-SSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHH
T ss_pred             ECCCccC-CCCEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCc
Confidence            4688877 457999999999999999999765321    35689999997

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=99.23  E-value=9.6e-12  Score=75.83  Aligned_cols=41  Identities=32%  Similarity=0.839  Sum_probs=32.5

Q ss_pred             cccccCCCceeEecCC--CC-ceecccccCccccCcCCCCCCCCCccCC
Q psy5115           4 HTLAVIEPKFYICCDT--CQ-DWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~--C~-r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      |+++.+  |+||+||.  |+ .|||..|++++..   +.+.|+||.|..
T Consensus        21 C~~~~~--g~MI~CD~~~C~~~wfH~~Cvgl~~~---p~g~w~Cp~C~~   64 (71)
T 1wen_A           21 CHQVSY--GEMIGCDNPDCSIEWFHFACVGLTTK---PRGKWFCPRCSQ   64 (71)
T ss_dssp             TCCCSC--SSEECCSCSSCSCCCEETTTTTCSSC---CSSCCCCTTTSS
T ss_pred             CCCCCC--CCEeEeeCCCCCCccEecccCCcCcC---CCCCEECCCCCc
Confidence            455543  67999999  88 6999999998644   346899999974

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=99.22  E-value=4e-12  Score=75.46  Aligned_cols=40  Identities=30%  Similarity=0.782  Sum_probs=32.3

Q ss_pred             cccccCCCceeEecCC--CC-ceecccccCccccCcCCCCCCCCCccC
Q psy5115           4 HTLAVIEPKFYICCDT--CQ-DWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~--C~-r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      |+++.+  |+||+||.  |+ +|||..|++++..   +.+.|+||.|.
T Consensus        16 C~~~~~--g~MI~CD~c~C~~~WfH~~Cvgl~~~---p~~~w~Cp~C~   58 (62)
T 2g6q_A           16 CNQVSY--GEMIGCDNEQCPIEWFHFSCVSLTYK---PKGKWYCPKCR   58 (62)
T ss_dssp             TTEECC--SEEEECSCTTCSSCEEETGGGTCSSC---CSSCCCCHHHH
T ss_pred             CCCCCC--CCeeeeeCCCCCcccEecccCCcCcC---CCCCEECcCcc
Confidence            556543  57999999  66 9999999998754   35789999996

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=99.22  E-value=5.1e-12  Score=78.18  Aligned_cols=44  Identities=32%  Similarity=0.741  Sum_probs=35.1

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|.++++ +++||+||.|.+|||..|++++.... ..+.|+||.|.
T Consensus        23 ~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~-~~~~w~C~~C~   66 (75)
T 2k16_A           23 GCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPP-EEMQWFCPKCA   66 (75)
T ss_dssp             TTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCC-SSSCCCCTTTH
T ss_pred             CCCCCCC-CCCEEEcCCCCcccccccCCCCccCC-CCCCEEChhcc
Confidence            3566655 45699999999999999999876543 35789999996

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=99.21  E-value=4.7e-12  Score=74.46  Aligned_cols=40  Identities=30%  Similarity=0.753  Sum_probs=32.1

Q ss_pred             cccccCCCceeEecCC--CC-ceecccccCccccCcCCCCCCCCCccC
Q psy5115           4 HTLAVIEPKFYICCDT--CQ-DWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~--C~-r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      |++++  .|+||+||.  |+ .|||..|+|++..   +.++|+||.|.
T Consensus        14 C~~~~--~g~mi~CD~~~C~~~wfH~~Cvgl~~~---p~~~w~Cp~C~   56 (59)
T 3c6w_A           14 CHQVS--YGEMIGCDNPDCPIEWFHFACVDLTTK---PKGKWFCPRCV   56 (59)
T ss_dssp             TTEEC--CSEEEECSCTTCSSCEEETGGGTCSSC---CSSCCCCHHHH
T ss_pred             CCCCC--CCCeeEeeCCCCCCCCEecccCCcccC---CCCCEECcCcc
Confidence            56664  367999999  88 6999999998754   34689999996

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=99.19  E-value=1.4e-11  Score=78.42  Aligned_cols=41  Identities=32%  Similarity=0.839  Sum_probs=32.7

Q ss_pred             cccccCCCceeEecCC--CC-ceecccccCccccCcCCCCCCCCCccCC
Q psy5115           4 HTLAVIEPKFYICCDT--CQ-DWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~--C~-r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      |+++++  |+||+||.  |+ .|||..|++++..   +.++|+||.|..
T Consensus        41 C~~~~~--g~MI~CD~~dC~~~WfH~~CVgl~~~---p~g~W~Cp~C~~   84 (91)
T 1weu_A           41 CHQVSY--GEMIGCDNPDCSIEWFHFACVGLTTK---PRGKWFCPRCSQ   84 (91)
T ss_dssp             TCCBCC--SCCCCCSCSSCSCCCCCSTTTTCSSC---CCSSCCCTTTCC
T ss_pred             CCCCCC--CCEeEecCCCCCCCCEecccCCcCcC---CCCCEECcCccC
Confidence            455553  67999999  87 7999999998754   346899999974

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=99.18  E-value=9.1e-12  Score=75.50  Aligned_cols=44  Identities=25%  Similarity=0.554  Sum_probs=34.0

Q ss_pred             cccccCCCceeEecC--CCCceecccccCccccCcC---CCCCCCCCccC
Q psy5115           4 HTLAVIEPKFYICCD--TCQDWFHGRCVGILQSEAD---NIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~--~C~r~~H~~C~~~~~~~~~---~~~~~~Cp~C~   48 (171)
                      |..+.+ +|+||+||  .|..|||..|+|++.....   .++.|+||.|+
T Consensus        15 C~~~~~-~g~mI~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~~~~C~~Cr   63 (68)
T 2rsd_A           15 CSSTMV-NDSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCR   63 (68)
T ss_dssp             TCCCSC-CSCEEECSCTTTCEEEETTTSCCCSSTTSCCCCCSSCCCHHHH
T ss_pred             CCCCcC-CCCEEEECCCCCCCeEchhhCCCCcccccccCCCCcEECcCcc
Confidence            455444 56799999  5999999999999765433   35689999996

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=99.17  E-value=9.9e-12  Score=73.37  Aligned_cols=41  Identities=32%  Similarity=0.849  Sum_probs=32.4

Q ss_pred             ccccccCCCceeEecCC--CC-ceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDT--CQ-DWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~--C~-r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      +|+++.+  |+||+||+  |+ +|||..|++++..   +.+.|+||.|.
T Consensus        14 ~C~~~~~--g~mi~CD~cdC~~~wfH~~Cvgl~~~---p~g~w~C~~C~   57 (60)
T 2vnf_A           14 LCHQVSY--GEMIGCDNPDCSIEWFHFACVGLTTK---PRGKWFCPRCS   57 (60)
T ss_dssp             TTTEECC--SEEEECSCTTCSSCEEETGGGTCSSC---CSSCCCCHHHH
T ss_pred             ECCCcCC--CCEEEeCCCCCCCceEehhcCCCCcC---CCCCEECcCcc
Confidence            3566643  67999999  77 8999999998643   34789999995

>3kv4_A PHD finger protein 8; epigenetics, histone CODE, covalent histone modifications, jumonji demethylase, mental retardation, metal-binding, zinc; HET: M3L MLY OGA; 2.19A {Homo sapiens}

Probab=99.08  E-value=8.4e-12  Score=100.83  Aligned_cols=46  Identities=50%  Similarity=1.105  Sum_probs=41.5

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      +|++++|++++||+||.|..|||..|+|++.......+.|+||.|.
T Consensus         9 iC~~~~d~~~~MIqCD~C~~WfH~~CVgi~~~~~~~~~~y~C~~C~   54 (447)
T 3kv4_A            9 LCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCE   54 (447)
T ss_dssp             TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTEEECCCHHHH
T ss_pred             eCCCcCCCCCCeEEcCCCCcccccccCCcCcccccCCCEEECCCCc
Confidence            4799999899999999999999999999987765556889999998

>3kv5_D JMJC domain-containing histone demethylation protein 1D; epigenetics, histone CODE, jumonji lysine demethylase, metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo sapiens} PDB: 3kv6_A*

Probab=99.07  E-value=1.3e-11  Score=100.89  Aligned_cols=46  Identities=46%  Similarity=0.999  Sum_probs=41.4

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      +|.+++|++++||+||.|..|||..|+|++.......+.|+|+.|.
T Consensus        41 ~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~   86 (488)
T 3kv5_D           41 VCRQPYDVNRFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCA   86 (488)
T ss_dssp             TTTEECCTTSCEEEBTTTCCEEEHHHHTCCGGGGGGEEEBCCHHHH
T ss_pred             eCCCcCCCCCCeEEccCCCCceeeeecCcCcccccCCCEEECCCCc
Confidence            4799999899999999999999999999987765556789999998

>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A*

Probab=99.06  E-value=7.2e-11  Score=74.93  Aligned_cols=40  Identities=28%  Similarity=0.698  Sum_probs=31.6

Q ss_pred             cccccCCCceeEecCCCC---ceecccccCccccCcCCCCCCCCCc-cC
Q psy5115           4 HTLAVIEPKFYICCDTCQ---DWFHGRCVGILQSEADNIDEYICPN-CN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~---r~~H~~C~~~~~~~~~~~~~~~Cp~-C~   48 (171)
                      |+++.+  |+||+||.|.   .|||..|++++...   .+.|+||. |.
T Consensus        31 C~~~~~--g~MI~CD~c~C~~eWfH~~CVgl~~~p---~~~W~Cp~cC~   74 (90)
T 2jmi_A           31 CRNVSY--GPMVACDNPACPFEWFHYGCVGLKQAP---KGKWYCSKDCK   74 (90)
T ss_dssp             TTCCCS--SSEECCCSSSCSCSCEETTTSSCSSCT---TSCCCSSHHHH
T ss_pred             eCCCCC--CCEEEecCCCCccccCcCccCCCCcCC---CCCccCChhhc
Confidence            455544  4699999966   89999999987543   46899999 96

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=99.05  E-value=1.4e-10  Score=66.21  Aligned_cols=45  Identities=24%  Similarity=0.454  Sum_probs=32.8

Q ss_pred             cccccCC--CceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           4 HTLAVIE--PKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         4 ~~~~~~~--~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      |.++..+  ++.||.||+|++|||..|+++... ..+.+.|+|+.|..
T Consensus         3 C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~-~~P~g~W~C~~C~~   49 (51)
T 1f62_A            3 CKVCRKKGEDDKLILCDECNKAFHLFCLRPALY-EVPDGEWQCPACQP   49 (51)
T ss_dssp             CTTTCCSSCCSCCEECTTTCCEECHHHHCTTCC-SCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCEEECCCCChhhCcccCCCCcC-CCCCCcEECcCccc
Confidence            4444432  456999999999999999965322 23456899999973

>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.04  E-value=3.6e-11  Score=73.06  Aligned_cols=40  Identities=28%  Similarity=0.741  Sum_probs=32.2

Q ss_pred             cccccCCCceeEecCCCC---ceecccccCccccCcCCCCCCCCCccC
Q psy5115           4 HTLAVIEPKFYICCDTCQ---DWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~---r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      |+++.  .|+||+||.|.   .|||..|++++..   +.+.|+||.|.
T Consensus        11 C~~~~--~g~MI~CD~cdC~~~WfH~~Cvgl~~~---p~~~w~Cp~C~   53 (70)
T 1x4i_A           11 CNQVS--YGEMVGCDNQDCPIEWFHYGCVGLTEA---PKGKWYCPQCT   53 (70)
T ss_dssp             TSCCC--CSSEECCSCTTCSCCCEEHHHHTCSSC---CSSCCCCHHHH
T ss_pred             cCCCC--CCCEeEeCCCCCCccCCcccccccCcC---CCCCEECCCCC
Confidence            45553  44899999974   9999999998753   36789999996

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=99.04  E-value=2.3e-10  Score=67.73  Aligned_cols=46  Identities=26%  Similarity=0.625  Sum_probs=36.6

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      .+|.+|.+++ .||.||.|+++||..|+++... ..+.+.|+|+.|..
T Consensus        10 ~~C~vC~~~g-~ll~Cd~C~~~fH~~Cl~ppl~-~~p~g~W~C~~C~~   55 (61)
T 1mm2_A           10 EFCRVCKDGG-ELLCCDTCPSSYHIHCLNPPLP-EIPNGEWLCPRCTC   55 (61)
T ss_dssp             SSCTTTCCCS-SCBCCSSSCCCBCSSSSSSCCS-SCCSSCCCCTTTTT
T ss_pred             CcCCCCCCCC-CEEEcCCCCHHHcccccCCCcC-cCCCCccCChhhcC
Confidence            3688888765 5999999999999999985433 23457899999974

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=99.04  E-value=1.1e-10  Score=69.20  Aligned_cols=45  Identities=22%  Similarity=0.510  Sum_probs=36.2

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .+|..|.++ +.||.||.|++|||..|+++... ..+.+.|+|+.|.
T Consensus        12 ~~C~vC~~~-g~ll~CD~C~~~fH~~Cl~p~l~-~~p~g~W~C~~C~   56 (61)
T 2l5u_A           12 DYCEVCQQG-GEIILCDTCPRAYHMVCLDPDME-KAPEGKWSCPHCE   56 (61)
T ss_dssp             SSCTTTSCC-SSEEECSSSSCEEEHHHHCTTCC-SCCCSSCCCTTGG
T ss_pred             CCCccCCCC-CcEEECCCCChhhhhhccCCCCC-CCCCCceECcccc
Confidence            368888875 46999999999999999987433 2356789999996

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=99.03  E-value=1.4e-10  Score=69.75  Aligned_cols=45  Identities=22%  Similarity=0.413  Sum_probs=36.1

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .+|.+|.+++ .||.||.|++|||..|+++... ..+.+.|+|+.|.
T Consensus         9 ~~C~vC~~~g-~ll~CD~C~~~fH~~Cl~ppl~-~~P~g~W~C~~C~   53 (66)
T 1xwh_A            9 DECAVCRDGG-ELICCDGCPRAFHLACLSPPLR-EIPSGTWRCSSCL   53 (66)
T ss_dssp             CSBSSSSCCS-SCEECSSCCCEECTTTSSSCCS-SCCSSCCCCHHHH
T ss_pred             CCCccCCCCC-CEEEcCCCChhhcccccCCCcC-cCCCCCeECcccc
Confidence            3688888765 5999999999999999985333 2345789999997

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=99.02  E-value=5.7e-10  Score=70.33  Aligned_cols=47  Identities=17%  Similarity=0.326  Sum_probs=37.2

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS   50 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~   50 (171)
                      .+|.+|.+++. +|.||.|++.||..|+.+... ..+.+.|+|+.|...
T Consensus        26 ~~C~vC~~~g~-LL~CD~C~~~fH~~Cl~PpL~-~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           26 TICRVCQKPGD-LVMCNQCEFCFHLDCHLPALQ-DVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SCCSSSCSSSC-CEECTTSSCEECTTSSSTTCC-CCCSSSCCCCSCCCC
T ss_pred             CcCcCcCCCCC-EEECCCCCCceecccCCCCCC-CCcCCCcCCccccCC
Confidence            47889998764 999999999999999954322 235678999999843

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=98.99  E-value=2.3e-10  Score=67.57  Aligned_cols=45  Identities=24%  Similarity=0.566  Sum_probs=35.9

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .+|.+|.+++ .||.||.|++|||..|+++... ..+.+.|+||.|.
T Consensus         6 ~~C~vC~~~g-~ll~Cd~C~~~fH~~Cl~ppl~-~~p~g~W~C~~C~   50 (60)
T 2puy_A            6 DFCSVCRKSG-QLLMCDTCSRVYHLDCLDPPLK-TIPKGMWICPRCQ   50 (60)
T ss_dssp             SSCTTTCCCS-SCEECSSSSCEECGGGSSSCCS-SCCCSCCCCHHHH
T ss_pred             CCCcCCCCCC-cEEEcCCCCcCEECCcCCCCcC-CCCCCceEChhcc
Confidence            3688888764 6999999999999999985333 2345789999996

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.99  E-value=2.7e-10  Score=66.31  Aligned_cols=45  Identities=24%  Similarity=0.566  Sum_probs=35.7

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .+|.++.+++ .||.||.|++|||..|+++... ..+.+.|+||.|.
T Consensus        10 ~~C~vC~~~g-~ll~Cd~C~~~~H~~Cl~ppl~-~~p~g~W~C~~C~   54 (56)
T 2yql_A           10 DFCSVCRKSG-QLLMCDTCSRVYHLDCLDPPLK-TIPKGMWICPRCQ   54 (56)
T ss_dssp             CSCSSSCCSS-CCEECSSSSCEECSSSSSSCCC-SCCCSSCCCHHHH
T ss_pred             CCCccCCCCC-eEEEcCCCCcceECccCCCCcC-CCCCCceEChhhh
Confidence            3688888764 6999999999999999985333 2345789999995

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=98.97  E-value=3.3e-10  Score=67.95  Aligned_cols=45  Identities=18%  Similarity=0.288  Sum_probs=35.3

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      -|..|.+++. ||.||.|+++||..|+.+... ..+.+.|+|+.|..
T Consensus        14 ~C~vC~~~~~-ll~Cd~C~~~~H~~Cl~P~l~-~~P~g~W~C~~C~~   58 (66)
T 2lri_C           14 RCGVCGDGTD-VLRCTHCAAAFHWRCHFPAGT-SRPGTGLRCRSCSG   58 (66)
T ss_dssp             CCTTTSCCTT-CEECSSSCCEECHHHHCTTTC-CCCSSSCCCTTTTT
T ss_pred             CcCCCCCCCe-EEECCCCCCceecccCCCccC-cCCCCCEECccccC
Confidence            4788887655 999999999999999965322 23456899999973

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=98.92  E-value=6.4e-10  Score=76.29  Aligned_cols=66  Identities=15%  Similarity=0.367  Sum_probs=48.0

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccC----c--CCCCCCCCCccCCCCcccccccCCChhHHHHHHHHHHHH
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSE----A--DNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQI   75 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~----~--~~~~~~~Cp~C~~~~~~~~~~~~l~~~~~~~~~~~l~~l   75 (171)
                      .+|+.|.++++ +++||.|+|+||..|+.+....    .  .+.+.|.|+.|...         .....++.+..+++.+
T Consensus        64 d~C~vC~~GG~-LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~---------pl~~l~~~c~~~~~~~  133 (142)
T 2lbm_A           64 EQCRWCAEGGN-LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE---------PLLDLVTACNSVFENL  133 (142)
T ss_dssp             CSCSSSCCCSS-EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC---------TTHHHHHHHHHHHHHH
T ss_pred             CeecccCCCCc-EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc---------cHHHHHHHHHHHHHHH
Confidence            47999999887 9999999999999999643221    0  35678999999732         2244556677776666


Q ss_pred             Hh
Q psy5115          76 QA   77 (171)
Q Consensus        76 ~~   77 (171)
                      ..
T Consensus       134 ~~  135 (142)
T 2lbm_A          134 EQ  135 (142)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=98.92  E-value=3.1e-10  Score=69.07  Aligned_cols=43  Identities=19%  Similarity=0.510  Sum_probs=35.0

Q ss_pred             ccccccCCC----ceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEP----KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~----~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|..|.+++    +.||.||+|++|||..|+++..   .+.+.|+|+.|.
T Consensus        18 ~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~---vP~g~W~C~~C~   64 (71)
T 2ku3_A           18 VCSICMDGESQNSNVILFCDMCNLAVHQECYGVPY---IPEGQWLCRHCL   64 (71)
T ss_dssp             SCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSS---CCSSCCCCHHHH
T ss_pred             CCCCCCCCCCCCCCCEEECCCCCCccccccCCCCc---CCCCCcCCccCc
Confidence            577776553    6799999999999999998753   345789999996

>3pur_A Lysine-specific demethylase 7 homolog; oxidoreductase-oxidoreductase inhibitor complex; HET: 2HG; 2.10A {Caenorhabditis elegans} PDB: 3n9l_A 3n9m_A* 3n9o_A* 3n9p_A* 3n9q_A* 3n9n_A* 3puq_A*

Probab=98.92  E-value=3.9e-10  Score=91.95  Aligned_cols=41  Identities=34%  Similarity=0.792  Sum_probs=36.6

Q ss_pred             cCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           8 VIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         8 ~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .+.+.+||+||.|..|||..|+|++....+..+.|+||.|.
T Consensus        52 ~n~~~~mI~CD~C~~WfH~~CVgi~~~~a~~~~~y~Cp~C~   92 (528)
T 3pur_A           52 KKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCV   92 (528)
T ss_dssp             TTSTTSEEECTTTCCEEEGGGTTCCGGGTTTEEECCCTTTH
T ss_pred             CCcCCCEEECCCCCcCCCCcCCCCChhHhcCCCeEECcCCc
Confidence            45677899999999999999999998776667899999999

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=98.90  E-value=1.8e-09  Score=65.59  Aligned_cols=38  Identities=32%  Similarity=0.741  Sum_probs=30.3

Q ss_pred             CCceeEecCCCCceecccccCccccCcCCCC-CCCCCccC
Q psy5115          10 EPKFYICCDTCQDWFHGRCVGILQSEADNID-EYICPNCN   48 (171)
Q Consensus        10 ~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~-~~~Cp~C~   48 (171)
                      +++.||.||+|+++||..|+++..... +.+ .|+||.|.
T Consensus        29 ~~~~ll~CD~C~~~yH~~Cl~Ppl~~~-P~g~~W~C~~C~   67 (70)
T 3asl_A           29 DPDKQLMCDECDMAFHIYCLDPPLSSV-PSEDEWYCPECR   67 (70)
T ss_dssp             CGGGEEECTTTCCEEEGGGSSSCCSSC-CSSSCCCCTTTS
T ss_pred             CCCCEEEcCCCCCceecccCCCCcCCC-CCCCCcCCcCcc
Confidence            466799999999999999998543322 345 89999997

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.87  E-value=1e-09  Score=70.24  Aligned_cols=45  Identities=20%  Similarity=0.384  Sum_probs=35.0

Q ss_pred             ccccccCCC--ceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEP--KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~--~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|.+|..++  +.||.||.|++|||..|+++... ..+.+.|+||.|.
T Consensus        18 ~C~vC~~~~~~~~ll~CD~C~~~~H~~Cl~Ppl~-~~P~g~W~C~~C~   64 (92)
T 2e6r_A           18 ICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLP-EIPRGIWRCPKCI   64 (92)
T ss_dssp             CCSSSCCSGGGGGCEECTTTCCEECSSSSSSCCS-SCCSSCCCCHHHH
T ss_pred             CCccCCCcCCCCCEEEcCCCCchhccccCCCCcc-cCCCCCcCCccCc
Confidence            576776654  46999999999999999985333 2345789999996

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=4.5e-09  Score=64.90  Aligned_cols=44  Identities=23%  Similarity=0.538  Sum_probs=32.6

Q ss_pred             cccccC--CCceeEecCCCCceecccccCccccCcCCCC-CCCCCccC
Q psy5115           4 HTLAVI--EPKFYICCDTCQDWFHGRCVGILQSEADNID-EYICPNCN   48 (171)
Q Consensus         4 ~~~~~~--~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~-~~~Cp~C~   48 (171)
                      |.++..  +++.||.||.|+++||..|+++.... .+.+ .|+||.|.
T Consensus        29 C~vC~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~-~P~g~~W~C~~C~   75 (77)
T 2e6s_A           29 CRVCGGKHEPNMQLLCDECNVAYHIYCLNPPLDK-VPEEEYWYCPSCK   75 (77)
T ss_dssp             CSSSCCCCCSTTEEECSSSCCEEETTSSSSCCSS-CCCSSCCCCTTTC
T ss_pred             CcCcCCcCCCCCEEEcCCCCccccccccCCCccC-CCCCCCcCCcCcc
Confidence            445543  45669999999999999999853332 2345 89999996

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=98.81  E-value=1.4e-09  Score=65.35  Aligned_cols=46  Identities=24%  Similarity=0.572  Sum_probs=35.3

Q ss_pred             ccccccCC----CceeEecCCCCceecccccCccccCc--CCCCCCCCCccC
Q psy5115           3 FHTLAVIE----PKFYICCDTCQDWFHGRCVGILQSEA--DNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~----~~~~i~C~~C~r~~H~~C~~~~~~~~--~~~~~~~Cp~C~   48 (171)
                      .|.+|..+    ++.||.||+|+++||..|+++.....  .+.+.|+|+.|.
T Consensus         8 ~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~   59 (66)
T 2yt5_A            8 VCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCV   59 (66)
T ss_dssp             CBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHH
T ss_pred             CCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCc
Confidence            56667655    47799999999999999998743221  145689999997

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=98.80  E-value=4e-09  Score=69.09  Aligned_cols=44  Identities=18%  Similarity=0.385  Sum_probs=35.3

Q ss_pred             CccccccCCCceeEecC--CCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           2 KFHTLAVIEPKFYICCD--TCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~--~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      .+|..+.++ |.||.||  .|++|||..|+++..   .+.+.|+||.|..
T Consensus        16 ~~C~~C~~~-G~ll~CD~~~Cp~~fH~~Cl~L~~---~P~g~W~Cp~c~C   61 (107)
T 4gne_A           16 DYCFQCGDG-GELVMCDKKDCPKAYHLLCLNLTQ---PPYGKWECPWHQC   61 (107)
T ss_dssp             SSCTTTCCC-SEEEECCSTTCCCEECTGGGTCSS---CCSSCCCCGGGBC
T ss_pred             CCCCcCCCC-CcEeEECCCCCCcccccccCcCCc---CCCCCEECCCCCC
Confidence            468888855 5699999  899999999998653   2457899998873

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=98.80  E-value=1.2e-09  Score=69.33  Aligned_cols=43  Identities=19%  Similarity=0.510  Sum_probs=35.1

Q ss_pred             ccccccCCC----ceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEP----KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~----~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|.+|.+++    +.||.||+|++|||..|+++..   .+.+.|+|+.|.
T Consensus        27 ~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~---vP~g~W~C~~C~   73 (88)
T 2l43_A           27 VCSICMDGESQNSNVILFCDMCNLAVHQECYGVPY---IPEGQWLCRHCL   73 (88)
T ss_dssp             CCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSS---CCSSCCCCHHHH
T ss_pred             cCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCc---cCCCceECcccc
Confidence            577777654    5799999999999999998753   345789999997

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=98.77  E-value=2.8e-09  Score=67.62  Aligned_cols=47  Identities=15%  Similarity=0.379  Sum_probs=36.6

Q ss_pred             CccccccCC----CceeEecCCCCceecccccCccccC---cCCCCCCCCCccC
Q psy5115           2 KFHTLAVIE----PKFYICCDTCQDWFHGRCVGILQSE---ADNIDEYICPNCN   48 (171)
Q Consensus         2 ~~~~~~~~~----~~~~i~C~~C~r~~H~~C~~~~~~~---~~~~~~~~Cp~C~   48 (171)
                      .+|.+|..+    ++.||.||+|++.||..|+++....   ..+.+.|+|+.|.
T Consensus        17 ~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~   70 (88)
T 1wev_A           17 LACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCT   70 (88)
T ss_dssp             CSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHH
T ss_pred             CcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCcccc
Confidence            367778766    3679999999999999999764321   1356789999997

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=98.70  E-value=1.7e-08  Score=62.20  Aligned_cols=37  Identities=30%  Similarity=0.702  Sum_probs=28.9

Q ss_pred             CceeEecCCCCceecccccCccccCcCCCCC-CCCCccC
Q psy5115          11 PKFYICCDTCQDWFHGRCVGILQSEADNIDE-YICPNCN   48 (171)
Q Consensus        11 ~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~-~~Cp~C~   48 (171)
                      ++.||.||.|+++||..|+++.-.. .+.+. |+|+.|+
T Consensus        38 ~~~ll~CD~C~~~yH~~Cl~PpL~~-~P~g~~W~C~~C~   75 (77)
T 3shb_A           38 PDKQLMCDECDMAFHIYCLDPPLSS-VPSEDEWYCPECR   75 (77)
T ss_dssp             GGGEEECTTTCCEEETTTSSSCCSS-CCSSSCCCCTTTC
T ss_pred             CcceeEeCCCCCccCcccCCCcccC-CCCCCceECcCcc
Confidence            4569999999999999999754332 23445 9999996

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=98.69  E-value=3.4e-09  Score=71.46  Aligned_cols=64  Identities=16%  Similarity=0.352  Sum_probs=45.7

Q ss_pred             CccccccCCCceeEecCCCCceecccccCcccc-----C-cCCCCCCCCCccCCCCcccccccCCChhHHHHHHHHHHHH
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQS-----E-ADNIDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQI   75 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~-----~-~~~~~~~~Cp~C~~~~~~~~~~~~l~~~~~~~~~~~l~~l   75 (171)
                      .+|+.|.|+++ +++||.|+|+||..|+.+...     . ..+.+.|.|+.|...         -...++..|..+++.|
T Consensus        58 ~~C~vC~dGG~-LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~---------pl~~L~~~C~~v~~~~  127 (129)
T 3ql9_A           58 EQCRWCAEGGN-LICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPE---------PLLDLVTACNSVYENL  127 (129)
T ss_dssp             SSCTTTCCCSE-EEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCG---------GGHHHHHHHHHHHTTC
T ss_pred             CcCeecCCCCe-eEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCH---------HHHHHHHHHHHHHHHh
Confidence            47999998866 999999999999999864311     1 125678999999632         2245566677766543

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=98.60  E-value=5e-08  Score=64.66  Aligned_cols=45  Identities=20%  Similarity=0.395  Sum_probs=33.9

Q ss_pred             ccccccC---CCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVI---EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~---~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|..+.+   +++.||.||.|+++||..|+.+... ..+.+.|+|+.|+
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~-~~P~~~W~C~~C~  110 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLT-RMPKGMWICQICR  110 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCS-SCCSSCCCCTTTS
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCC-CCCCCCeECCCCC
Confidence            4555554   3467999999999999999965322 2355689999997

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=98.53  E-value=4.6e-08  Score=65.03  Aligned_cols=45  Identities=18%  Similarity=0.352  Sum_probs=33.9

Q ss_pred             ccccccCC--CceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIE--PKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~--~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|..+...  ++.||.||+|+++||..|+++... ..+.+.|+|+.|.
T Consensus        60 ~C~~C~~~~~~~~ll~Cd~C~~~yH~~Cl~ppl~-~~P~g~W~C~~C~  106 (114)
T 2kwj_A           60 SCILCGTSENDDQLLFCDDCDRGYHMYCLNPPVA-EPPEGSWSCHLCW  106 (114)
T ss_dssp             CCTTTTCCTTTTTEEECSSSCCEEETTTSSSCCS-SCCSSCCCCHHHH
T ss_pred             ccCcccccCCCCceEEcCCCCccccccccCCCcc-CCCCCCeECcccc
Confidence            35555543  566999999999999999985322 3355789999996

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=98.36  E-value=9.6e-08  Score=65.16  Aligned_cols=36  Identities=25%  Similarity=0.812  Sum_probs=28.9

Q ss_pred             eEecCCCCceecccccCcccc------CcCCCCCCCCCccCC
Q psy5115          14 YICCDTCQDWFHGRCVGILQS------EADNIDEYICPNCNN   49 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~~~~~~------~~~~~~~~~Cp~C~~   49 (171)
                      ||+||.|.+|||..|+++++.      .......|.||.|..
T Consensus         2 mi~c~~c~~w~H~~c~~~~~~~~~~l~~lp~~~~~~c~~C~~   43 (140)
T 2ku7_A            2 MMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTE   43 (140)
T ss_dssp             CCCCSCCSSCHHHHHCCCCHHHHHHHHSSCTTTTCCSSCCTT
T ss_pred             ccccccCCCccCCcccccCHHHHHHHhhccccceeeCccccc
Confidence            899999999999999998752      222344799999983

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=98.30  E-value=3.7e-07  Score=60.33  Aligned_cols=45  Identities=20%  Similarity=0.441  Sum_probs=32.9

Q ss_pred             cccccCCC--ceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           4 HTLAVIEP--KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         4 ~~~~~~~~--~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      |..+...+  ..|+.||.|+++||..|+.+... ..+.+.|+||.|..
T Consensus        57 C~~C~~~~~~~~ll~Cd~C~~~yH~~Cl~ppl~-~~P~g~W~C~~C~~  103 (111)
T 2ysm_A           57 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMK-SVPTNGWKCKNCRI  103 (111)
T ss_dssp             CTTTCCCSCCTTEEECSSSCCEEEGGGSSSCCS-SCCSSCCCCHHHHC
T ss_pred             ccccCccCCCCCeeECCCCCcHHhHHhcCCccc-cCCCCCcCCcCCcC
Confidence            44444433  35999999999999999975433 23457899999973

>4bbq_A Lysine-specific demethylase 2A; oxidoreductase, ubiquitin, ligase, ubiquitination, demethyla ZF-CXXC DNA binding domain, CPG island, chromatin; 2.24A {Homo sapiens}

Probab=98.26  E-value=2.5e-07  Score=61.71  Aligned_cols=44  Identities=18%  Similarity=0.375  Sum_probs=33.5

Q ss_pred             cccCCCceeEecCCCCceecccccCccccC---cCCCCCCCCCccCC
Q psy5115           6 LAVIEPKFYICCDTCQDWFHGRCVGILQSE---ADNIDEYICPNCNN   49 (171)
Q Consensus         6 ~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~---~~~~~~~~Cp~C~~   49 (171)
                      ..++.+..|++|+.|.+|||..|+++....   .+.++.|.||.|..
T Consensus        67 ~~~~~~~~m~~C~~C~~~~H~~C~~~~~~~~~~~~~~~~~~C~~C~~  113 (117)
T 4bbq_A           67 ETQDFEKKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQ  113 (117)
T ss_dssp             HHCCGGGSCEEETTTCCEECGGGCCSCCCCEECSSSSSEEECTTTC-
T ss_pred             cccccCcceEEeeecCCeEECCCCCCCccccccccCCCCeECCCCcC
Confidence            345667779999999999999999875432   23455699999974

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=98.20  E-value=1.5e-06  Score=57.34  Aligned_cols=45  Identities=22%  Similarity=0.521  Sum_probs=35.0

Q ss_pred             ccccccCCCc--eeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPK--FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~--~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|..+.++++  .||.|+.|++.||..|+++.... .....|.|+.|.
T Consensus         9 ~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~~-~~~~~W~C~~C~   55 (111)
T 2ysm_A            9 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTP-LKRAGWQCPECK   55 (111)
T ss_dssp             CBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCCT-TTSTTCCCTTTC
T ss_pred             CCcCCCCCCCCcCCeECCCCCCCcChHHhCCcccc-ccccCccCCcCC
Confidence            5777777654  36999999999999999876542 235689999986

>3rsn_A SET1/ASH2 histone methyltransferase complex subun; PHD domain, winged helix domain, binding, transcription; 2.10A {Homo sapiens} PDB: 3s32_A

Probab=98.17  E-value=3e-06  Score=59.92  Aligned_cols=72  Identities=15%  Similarity=0.213  Sum_probs=44.6

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCC---CCCCCCCccCCCCcccccccCCChhHHHHHHHHHHHHH
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADN---IDEYICPNCNNSSSNLANMKNLTPRDFESLRKLMKQIQ   76 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~---~~~~~Cp~C~~~~~~~~~~~~l~~~~~~~~~~~l~~l~   76 (171)
                      ||..+++-+..|++|+.|.+|||..|+........+   .=.+.|..|.........  ++.....+.+.-+|-.|.
T Consensus         9 YCG~~~~~~~~mLqC~~C~qWFH~~Cl~~~~~~~lp~~~fY~F~C~~C~~~g~E~f~--R~~~~w~~v~~laLyNL~   83 (177)
T 3rsn_A            9 DEENGRQLGEVELQCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSGNTYFL--RKQANLKEMCLSALANLT   83 (177)
T ss_dssp             --CTTCCTTSCEEECTTTCCEEEGGGGTCCCTTCCTTCCSEEEECTTTSTTSSCEEE--ECCCCHHHHHHHHHHHHH
T ss_pred             EcCCCCCCCceeEeeccccceecHHHhcccccCccccceeEEEEccccCCCCcceeE--eccCCHHHHHHHHHHhhh
Confidence            678888888889999999999999999643221111   115779999754433222  334445555554444443

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=97.94  E-value=2.1e-06  Score=56.89  Aligned_cols=38  Identities=21%  Similarity=0.500  Sum_probs=29.2

Q ss_pred             CceeEecCCCCceecccccCccccC--cCCCCCCCCCccC
Q psy5115          11 PKFYICCDTCQDWFHGRCVGILQSE--ADNIDEYICPNCN   48 (171)
Q Consensus        11 ~~~~i~C~~C~r~~H~~C~~~~~~~--~~~~~~~~Cp~C~   48 (171)
                      ++.||.|+.|++.||..|+++....  ......|.|+.|.
T Consensus        20 ~~~Li~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   59 (114)
T 2kwj_A           20 PEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECK   59 (114)
T ss_dssp             CCCCEECSSSCCEECTTTTTCCHHHHHHHHHTTCCCGGGC
T ss_pred             CCCCeEeCCCCCccchhhCCChhhhhhccCCCccCccccC
Confidence            4679999999999999999875321  1134579999885

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=97.87  E-value=3.1e-06  Score=55.95  Aligned_cols=39  Identities=21%  Similarity=0.484  Sum_probs=30.1

Q ss_pred             CCceeEecCCCCceecccccCccccCc--CCCCCCCCCccC
Q psy5115          10 EPKFYICCDTCQDWFHGRCVGILQSEA--DNIDEYICPNCN   48 (171)
Q Consensus        10 ~~~~~i~C~~C~r~~H~~C~~~~~~~~--~~~~~~~Cp~C~   48 (171)
                      .++.||.|+.|++.||..|+++.+...  .....|.|+.|+
T Consensus        22 ~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A           22 KPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             CchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            456799999999999999997643221  135689999996

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=97.13  E-value=0.00027  Score=43.40  Aligned_cols=46  Identities=22%  Similarity=0.512  Sum_probs=31.1

Q ss_pred             cccccc--CCCceeEecCCCCceecccccCc---cc--------cCcCCCCCCCCCccCC
Q psy5115           3 FHTLAV--IEPKFYICCDTCQDWFHGRCVGI---LQ--------SEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~--~~~~~~i~C~~C~r~~H~~C~~~---~~--------~~~~~~~~~~Cp~C~~   49 (171)
                      .|.+|.  +. +.++.|-.|.|+||..|...   ..        .......-|.|+.|.+
T Consensus        17 ~C~VC~~~t~-~~l~pCRvC~RvfH~~CL~r~gy~~~~~a~e~~l~A~T~~GWSC~~Cen   75 (89)
T 1wil_A           17 MCDVCEVWTA-ESLFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDN   75 (89)
T ss_dssp             CCTTTCCCCS-SCCSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCC
T ss_pred             ccCccccccc-cceeccccccccccHhhcccccccccHHHHHHHHccCCCCCccccccch
Confidence            466665  43 44999999999999999622   11        1112345799999973

>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger, histone binding, chromosomal protein, DNA damag repair, DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens} PDB: 3a1a_A*

Probab=96.11  E-value=0.0022  Score=44.42  Aligned_cols=49  Identities=22%  Similarity=0.449  Sum_probs=36.7

Q ss_pred             CccccccCCCceeEecC--CCCceecccccCcccc-----CcCCCCCCCCCccCCCC
Q psy5115           2 KFHTLAVIEPKFYICCD--TCQDWFHGRCVGILQS-----EADNIDEYICPNCNNSS   51 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~--~C~r~~H~~C~~~~~~-----~~~~~~~~~Cp~C~~~~   51 (171)
                      .||+-|-+++ .++.|+  .|.|.|...|+.....     .....+.|.|=.|...+
T Consensus        80 ~yC~wC~~Gg-~l~~Cdn~~C~r~FC~~CI~~nvG~~~~~~i~~~d~W~Cy~C~P~~  135 (159)
T 3a1b_A           80 SYCTICCGGR-EVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKG  135 (159)
T ss_dssp             SSCTTTSCCS-EEEECSSTTTCCEEEHHHHHHHTCTTHHHHHHTSSSCCCTTTCSSC
T ss_pred             ceeeEecCCC-eEEeeCCCCCCCchhHHHHHHhcCHhHHHHHhccCCCEEEecCCcc
Confidence            4788888876 499999  8999999999722211     12356799999998544

>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated H3K4, de novo DNA methylation, transferase regulator; HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*

Probab=95.24  E-value=0.0045  Score=48.92  Aligned_cols=49  Identities=18%  Similarity=0.494  Sum_probs=36.9

Q ss_pred             CccccccCCCceeEecC--CCCceecccccCccccC-----cCCCCCCCCCccCCCC
Q psy5115           2 KFHTLAVIEPKFYICCD--TCQDWFHGRCVGILQSE-----ADNIDEYICPNCNNSS   51 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~--~C~r~~H~~C~~~~~~~-----~~~~~~~~Cp~C~~~~   51 (171)
                      .||+-|-+++. ++.||  .|.|+|...|+......     ....+.|.|=.|...+
T Consensus        94 ~yCr~C~~Gg~-l~~Cdn~~C~r~FC~~Ci~~n~g~~~~~~i~~~d~W~Cf~C~p~p  149 (386)
T 2pv0_B           94 SYCSICCSGET-LLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSS  149 (386)
T ss_dssp             CSCTTTCCCSS-CEECCSTTCCCEECHHHHHHHTCTTHHHHHHHCSSCCCTTTSSCC
T ss_pred             ccceEcCCCCe-EEEeCCCCCCcchHHHHHHHhcChhHHHHhhccCCceEEEcCCcc
Confidence            47888988765 99999  99999999997332211     1245789999998544

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=93.87  E-value=0.053  Score=29.46  Aligned_cols=34  Identities=18%  Similarity=0.416  Sum_probs=23.2

Q ss_pred             EecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115          15 ICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        15 i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      -+|..|+-+|...=-..+ ...+.++.|.||.|..
T Consensus         5 y~C~vCGyvyd~~~Gd~t-~f~~lP~dw~CP~Cg~   38 (46)
T 6rxn_A            5 YVCNVCGYEYDPAEHDNV-PFDQLPDDWCCPVCGV   38 (46)
T ss_dssp             EEETTTCCEECGGGGTTC-CGGGSCTTCBCTTTCC
T ss_pred             EECCCCCeEEeCCcCCCc-chhhCCCCCcCcCCCC
Confidence            478899988875422222 2345688899999984

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=93.05  E-value=0.067  Score=29.60  Aligned_cols=40  Identities=20%  Similarity=0.406  Sum_probs=26.3

Q ss_pred             cccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      |...+.++...+.-..|...||..|+..-..     ....||.|+
T Consensus        11 C~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~-----~~~~CP~Cr   50 (55)
T 1iym_A           11 CLAELEDGEEARFLPRCGHGFHAECVDMWLG-----SHSTCPLCR   50 (55)
T ss_dssp             TCCCCCTTSCCEECSSSCCEECTTHHHHTTT-----TCCSCSSSC
T ss_pred             CCccccCCCceEECCCCCCcccHHHHHHHHH-----cCCcCcCCC
Confidence            4444444444666667999999999843211     135899997

>4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A 1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A 1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A 1smw_A 1be7_A 1t9o_A ...

Probab=93.01  E-value=0.12  Score=29.14  Aligned_cols=36  Identities=22%  Similarity=0.516  Sum_probs=24.1

Q ss_pred             EecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCC
Q psy5115          15 ICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNS   50 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~   50 (171)
                      -.|..|.-+|...=-    ++  .....+.++.|.||.|...
T Consensus         4 y~C~vCGyvYd~~~Gdp~~gi~pGt~fe~lP~dw~CP~Cg~~   45 (54)
T 4rxn_A            4 YTCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVG   45 (54)
T ss_dssp             EEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             eECCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCcCCCCc
Confidence            478899988876531    11  1123456889999999853

>2l7p_A Histone-lysine N-methyltransferase ASHH2; CW-domain; NMR {Arabidopsis thaliana}

Probab=92.29  E-value=0.076  Score=33.82  Aligned_cols=38  Identities=21%  Similarity=0.529  Sum_probs=25.0

Q ss_pred             cCCCceeEecCCCCceecccccCccccCcCCCCCCCCCcc
Q psy5115           8 VIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC   47 (171)
Q Consensus         8 ~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C   47 (171)
                      +.....+|||+.|.+|=-.. .+.. .....++.|+|..-
T Consensus        22 ~~~~~~WVQCD~C~KWRrLP-~~~~-~~~~~pd~W~C~mN   59 (100)
T 2l7p_A           22 YSTESAWVRCDDCFKWRRIP-ASVV-GSIDESSRWICMNN   59 (100)
T ss_dssp             CSSSSEEEECTTTCCEEEEC-HHHH-TTSTTSSCCCGGGS
T ss_pred             CCCCCeEEeeCCCCccccCC-hhHc-cccCCCCCceeCCC
Confidence            44467799999999996554 2221 11235689999764

>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa}

Probab=92.02  E-value=0.18  Score=28.39  Aligned_cols=38  Identities=21%  Similarity=0.424  Sum_probs=24.1

Q ss_pred             EecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCCCc
Q psy5115          15 ICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNSSS   52 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~~~   52 (171)
                      -.|..|.-+|...=-    ++  -....+.++.|.||.|.....
T Consensus         4 y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cga~K~   47 (55)
T 2v3b_B            4 WQCVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVGKI   47 (55)
T ss_dssp             EEETTTCCEEETTTCBTTTTBCTTCCGGGSCTTCCCTTTCCCGG
T ss_pred             EEeCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCCCCCCCHH
Confidence            468889888876431    11  112344688999999985433

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=92.02  E-value=0.19  Score=30.74  Aligned_cols=39  Identities=26%  Similarity=0.464  Sum_probs=25.7

Q ss_pred             eEecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCCCc
Q psy5115          14 YICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNSSS   52 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~~~   52 (171)
                      .-.|..|.-+|...=-    ++  -.+..+.++.|.||.|.....
T Consensus        27 ~y~C~vCGyvYD~~~Gdp~~gI~pGT~fedlPddW~CPvCga~K~   71 (81)
T 2kn9_A           27 LFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKS   71 (81)
T ss_dssp             EEEETTTCCEEETTTCBTTTTBCTTCCTTTSCTTCCCTTTCCCGG
T ss_pred             eEEeCCCCEEEcCCcCCcccCcCCCCChhHCCCCCcCCCCCCCHH
Confidence            5779999988876431    11  112345688999999985443

>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution, thermostability; NMR {Desulfovibrio gigas} SCOP: g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A

Probab=91.95  E-value=0.27  Score=27.35  Aligned_cols=36  Identities=28%  Similarity=0.504  Sum_probs=22.5

Q ss_pred             EecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCC
Q psy5115          15 ICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNS   50 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~   50 (171)
                      -.|..|.-+|...=-    ++  .....+.++.|.||.|...
T Consensus         4 y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cg~~   45 (52)
T 1e8j_A            4 YVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGAS   45 (52)
T ss_dssp             EECSSSCCCCCTTTCCTTTTCCSSCCTTSSCTTCCCSSSCCC
T ss_pred             EEeCCCCeEEcCCcCCcccCcCCCCchHHCCCCCcCCCCCCc
Confidence            468888877764321    11  1123446889999999853

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.23  E-value=0.069  Score=32.59  Aligned_cols=38  Identities=18%  Similarity=0.380  Sum_probs=22.5

Q ss_pred             CCCceeEe---cCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           9 IEPKFYIC---CDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         9 ~~~~~~i~---C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      ++++.++.   |.+...+||..|+..=..   ..+...||.|+.
T Consensus        26 ~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~---~~~~~~CplCr~   66 (80)
T 2d8s_A           26 DDESPLITPCHCTGSLHFVHQACLQQWIK---SSDTRCCELCKY   66 (80)
T ss_dssp             CSSSCEECSSSCCSSSCCEETTHHHHHHH---HHCCSBCSSSCC
T ss_pred             cCCCeeEeccccCCcCCeeCHHHHHHHHh---hCCCCCCCCCCC
Confidence            33444542   334469999999832111   122469999984

>2e61_A Zinc finger CW-type PWWP domain protein 1; ZF-CW domain, structural genomics, NPPSFA, national project protein structural and functional analyses; NMR {Homo sapiens} PDB: 2rr4_A*

Probab=90.70  E-value=0.28  Score=29.02  Aligned_cols=34  Identities=18%  Similarity=0.394  Sum_probs=22.0

Q ss_pred             CCceeEecC--CCCceecccccCccccCcCCCCCCCCCc
Q psy5115          10 EPKFYICCD--TCQDWFHGRCVGILQSEADNIDEYICPN   46 (171)
Q Consensus        10 ~~~~~i~C~--~C~r~~H~~C~~~~~~~~~~~~~~~Cp~   46 (171)
                      ....+||||  .|.+|=-..= ++..  ...++.|+|..
T Consensus        14 ~~~~WVQCd~p~C~KWR~LP~-~~~~--~~lpd~W~C~m   49 (69)
T 2e61_A           14 QCLVWVQCSFPNCGKWRRLCG-NIDP--SVLPDNWSCDQ   49 (69)
T ss_dssp             CCCCEEECSSTTTCCEEECCS-SCCT--TTSCTTCCGGG
T ss_pred             CCCeEEEeCccccCcccCCcc-cccc--ccCCCcCEeCC
Confidence            345699999  9999955422 1111  22567999975

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=90.56  E-value=0.29  Score=29.00  Aligned_cols=37  Identities=24%  Similarity=0.543  Sum_probs=24.1

Q ss_pred             eEecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCC
Q psy5115          14 YICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNS   50 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~   50 (171)
                      .-.|..|.-+|...=-    ++  -.+..+.++.|.||.|...
T Consensus         7 ~y~C~vCGyiYd~~~Gdp~~gi~pGT~f~~lPddw~CP~Cga~   49 (70)
T 1dx8_A            7 KYECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSP   49 (70)
T ss_dssp             CEEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCB
T ss_pred             eEEeCCCCEEEcCCCCCcccCcCCCCchhhCCCCCcCCCCCCC
Confidence            4678999988875431    11  1123446889999999853

>1yk4_A Rubredoxin, RD; electron transport; 0.69A {Pyrococcus abyssi} PDB: 2pya_A 1yk5_A 1bq8_A 1bq9_A* 3kyu_A 3kyv_A 3kyw_A 3kyx_A 3kyy_A 3ryg_A 3rz6_A 3rzt_A 3ss2_A 1brf_A 1caa_A 1cad_A 1vcx_A 1zrp_A 1iu5_A 1iu6_A ...

Probab=90.08  E-value=0.26  Score=27.40  Aligned_cols=36  Identities=25%  Similarity=0.579  Sum_probs=22.7

Q ss_pred             EecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCC
Q psy5115          15 ICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNS   50 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~   50 (171)
                      -.|..|.-+|...=-    ++  .....+.++.|.||.|...
T Consensus         3 ~~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cg~~   44 (52)
T 1yk4_A            3 LSCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAP   44 (52)
T ss_dssp             EEESSSSCEEETTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             EEeCCCCeEECCCcCCcccCcCCCCCHhHCCCCCcCCCCCCC
Confidence            468888888765421    11  1123456889999999843

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=89.76  E-value=0.097  Score=28.87  Aligned_cols=34  Identities=24%  Similarity=0.568  Sum_probs=23.2

Q ss_pred             CCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115          10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus        10 ~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      +++..+..-.|...||..|+..-...     ...||.|+
T Consensus        17 ~~~~~~~~~~CgH~fc~~Ci~~~~~~-----~~~CP~Cr   50 (55)
T 2ecm_A           17 TSRVVAHVLPCGHLLHRTCYEEMLKE-----GYRCPLCS   50 (55)
T ss_dssp             TTTSCEEECTTSCEEETTHHHHHHHH-----TCCCTTSC
T ss_pred             CCCcCeEecCCCCcccHHHHHHHHHc-----CCcCCCCC
Confidence            33345666779999999998432111     26899997

>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans} SCOP: g.41.5.1

Probab=89.36  E-value=0.39  Score=29.70  Aligned_cols=38  Identities=24%  Similarity=0.500  Sum_probs=24.8

Q ss_pred             eEecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCCC
Q psy5115          14 YICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNSS   51 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~~   51 (171)
                      .-.|..|.-+|...=-    ++  -....+.++.|.||.|....
T Consensus        35 ~y~C~vCGyvYD~~~Gdp~~gI~pGT~fedlPddW~CPvCga~K   78 (87)
T 1s24_A           35 KWICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGATK   78 (87)
T ss_dssp             EEEETTTTEEEETTSCCTTTTCCSCCCGGGCCTTCCCSSSCCCG
T ss_pred             eEECCCCCeEecCCcCCcccCcCCCCChhHCCCCCCCCCCCCCH
Confidence            5679999988876421    11  11234568899999998543

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=88.03  E-value=0.073  Score=32.36  Aligned_cols=35  Identities=20%  Similarity=0.606  Sum_probs=22.6

Q ss_pred             CCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115          10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        10 ~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +++..+.-..|...||..|+..=-.  .   .-.||.|+.
T Consensus        38 ~~~~~~~~~~C~H~FH~~Ci~~Wl~--~---~~~CP~CR~   72 (81)
T 2ecl_A           38 QEDCVVVWGECNHSFHNCCMSLWVK--Q---NNRCPLCQQ   72 (81)
T ss_dssp             TTTCCEEEETTSCEEEHHHHHHHTT--T---CCBCTTTCC
T ss_pred             CCceEEEeCCCCCccChHHHHHHHH--h---CCCCCCcCC
Confidence            3443444457999999999843211  1   238999983

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=87.78  E-value=1.1  Score=28.47  Aligned_cols=44  Identities=20%  Similarity=0.347  Sum_probs=25.7

Q ss_pred             cccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS   50 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~   50 (171)
                      |..|.+.-...+. -.|+..||..|+...-.  .......||.|+..
T Consensus        24 C~IC~~~~~~p~~-~~CgH~fC~~Ci~~~~~--~~~~~~~CP~Cr~~   67 (112)
T 1jm7_A           24 CPICLELIKEPVS-TKCDHIFCKFCMLKLLN--QKKGPSQCPLCKND   67 (112)
T ss_dssp             CSSSCCCCSSCCB-CTTSCCCCSHHHHHHHH--SSSSSCCCTTTSCC
T ss_pred             CcccChhhcCeEE-CCCCCHHHHHHHHHHHH--hCCCCCCCcCCCCc
Confidence            4444443322222 37999999999843211  12335789999953

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=87.03  E-value=0.16  Score=32.65  Aligned_cols=36  Identities=19%  Similarity=0.434  Sum_probs=22.7

Q ss_pred             eEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115          14 YICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      .+.--.|..+||..|+..-...........||.|+.
T Consensus        55 ~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~   90 (114)
T 1v87_A           55 VGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT   90 (114)
T ss_dssp             CEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCC
T ss_pred             ceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCC
Confidence            444567999999999843211111123569999984

>2lq6_A Bromodomain-containing protein 1; PHD finger, metal binding protein; NMR {Homo sapiens}

Probab=86.73  E-value=0.29  Score=30.33  Aligned_cols=26  Identities=27%  Similarity=0.420  Sum_probs=20.7

Q ss_pred             cccccCC-CceeEecCC--CCceeccccc
Q psy5115           4 HTLAVIE-PKFYICCDT--CQDWFHGRCV   29 (171)
Q Consensus         4 ~~~~~~~-~~~~i~C~~--C~r~~H~~C~   29 (171)
                      |..|... .|--|+|..  |.+.||..|.
T Consensus        20 C~iC~~~~~GAciqC~~~~C~~~fHv~CA   48 (87)
T 2lq6_A           20 CYLCKQKGVGASIQCHKANCYTAFHVTCA   48 (87)
T ss_dssp             BTTTTBCCSSCEEECSCTTTCCEEEHHHH
T ss_pred             CcCCCCCCCcEeEecCCCCCCCcCcHHHH
Confidence            5566554 477999985  9999999996

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=86.52  E-value=0.36  Score=30.38  Aligned_cols=44  Identities=16%  Similarity=0.329  Sum_probs=30.3

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS   50 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~   50 (171)
                      .|..|.+.-...+.|..|+..||..|+..--...    ...||.|+..
T Consensus        24 ~C~IC~~~~~~p~~~~~CgH~FC~~Ci~~~~~~~----~~~CP~Cr~~   67 (100)
T 3lrq_A           24 RCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQ----RAQCPHCRAP   67 (100)
T ss_dssp             BCTTTCSBCSSEEECTTTCCEEEHHHHHHHHHHT----CSBCTTTCCB
T ss_pred             CCccCCccccCccccCCCCChhhHHHHHHHHHHC----cCCCCCCCCc
Confidence            3556666655578889999999999984321111    2689999943

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=84.59  E-value=0.55  Score=27.31  Aligned_cols=43  Identities=14%  Similarity=0.346  Sum_probs=26.4

Q ss_pred             cccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      |..|.+.-...+.- .|...||..|+.....  .......||.|+.
T Consensus        23 C~IC~~~~~~~~~~-~CgH~fC~~Ci~~~~~--~~~~~~~CP~Cr~   65 (73)
T 2ysl_A           23 CPICLDILQKPVTI-DCGHNFCLKCITQIGE--TSCGFFKCPLCKT   65 (73)
T ss_dssp             CTTTCSBCSSEEEC-TTCCEEEHHHHHHHCS--SSCSCCCCSSSCC
T ss_pred             eccCCcccCCeEEc-CCCChhhHHHHHHHHH--cCCCCCCCCCCCC
Confidence            44455443333333 8999999999843211  1234679999984

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=84.33  E-value=0.43  Score=35.23  Aligned_cols=45  Identities=27%  Similarity=0.421  Sum_probs=32.0

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +.|..|++==..=+.|..|..-||..|+..--   .....-.||.|..
T Consensus       181 ~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~---~~~~~~~CP~C~~  225 (238)
T 3nw0_A          181 KICNICHSLLIQGQSCETCGIRMHLPCVAKYF---QSNAEPRCPHCND  225 (238)
T ss_dssp             CBCTTTCSBCSSCEECSSSCCEECHHHHHHHT---TTCSSCBCTTTCC
T ss_pred             CcCcchhhHHhCCcccCccChHHHHHHHHHHH---HhCCCCCCCCCCC
Confidence            45777777655558899999999999983311   1223468999984

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=83.87  E-value=0.54  Score=28.14  Aligned_cols=44  Identities=25%  Similarity=0.388  Sum_probs=27.4

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      .|..|++-=..=+.|..|..-||..|+.--  .. ....-.||.|+.
T Consensus        17 ~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kW--l~-~~~~~~CP~Cr~   60 (74)
T 2ct0_A           17 ICNICHSLLIQGQSCETCGIRMHLPCVAKY--FQ-SNAEPRCPHCND   60 (74)
T ss_dssp             BCSSSCCBCSSSEECSSSCCEECHHHHHHH--ST-TCSSCCCTTTCS
T ss_pred             cCcchhhHcccCCccCCCCchhhHHHHHHH--HH-hcCCCCCCCCcC
Confidence            344455443333678899999999998321  11 111258999984

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=80.50  E-value=0.45  Score=29.36  Aligned_cols=36  Identities=25%  Similarity=0.588  Sum_probs=22.1

Q ss_pred             cCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           8 VIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         8 ~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +..+...+.- .|...||..|+..--.     ....||.|+.
T Consensus        50 ~~~~~~~~~l-~C~H~Fh~~Ci~~wl~-----~~~~CP~Cr~   85 (91)
T 2l0b_A           50 YVKGDVATEL-PCHHYFHKPCVSIWLQ-----KSGTCPVCRC   85 (91)
T ss_dssp             CCTTCEEEEE-TTTEEEEHHHHHHHHT-----TTCBCTTTCC
T ss_pred             hcCCCcEEec-CCCChHHHHHHHHHHH-----cCCcCcCcCc
Confidence            3333334333 4999999999843211     1348999983

---

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	171
d1eqfa1	139	a.29.2.1 (A:1359-1497) TAFII250 double bromodomain	5e-32
d1eqfa2	128	a.29.2.1 (A:1498-1625) TAFII250 double bromodomain	3e-30
d1e6ia_	111	a.29.2.1 (A:) GCN5 {Baker's yeast (Saccharomyces c	7e-30
d3d7ca1	102	a.29.2.1 (A:731-832) GCN5 {Human (Homo sapiens) [T	8e-30
d1wuma1	118	a.29.2.1 (A:715-832) P300/CAF histone acetyltransf	6e-29
d3dwya1	114	a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {	3e-26
d1we9a_	64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	7e-13
d1wepa_	79	g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus mus	3e-12
d1wema_	76	g.50.1.2 (A:) Death associated transcription facto	3e-10
d1weea_	72	g.50.1.2 (A:) PHD finger protein At1g33420 {Thale	1e-08
d1wewa_	78	g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale c	2e-07
d1mm2a_	61	g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens	6e-06
d1f62a_	51	g.50.1.2 (A:) Williams-Beuren syndrome transcripti	4e-05
d1fp0a1	70	g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-	4e-04
d1weva_	88	g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus mu	6e-04
d2pnxa1	51	g.50.1.2 (A:195-245) Inhibitor of growth protein 4	0.001

>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 =  109 bits (274), Expect = 5e-32
 Identities = 25/103 (24%), Positives = 47/103 (45%)

Query: 68  LRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGD 127
           L  ++  ++   + +PF  PV+     DYY ++  PMDL+T+   + ++ Y    EF   
Sbjct: 31  LESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREH 90

Query: 128 MTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVEL 170
           +  I  N   YN  +    + +  +     +K+K   +KL  L
Sbjct: 91  LELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARL 133

>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 =  104 bits (261), Expect = 3e-30
 Identities = 35/105 (33%), Positives = 54/105 (51%), Gaps = 1/105 (0%)

Query: 68  LRKLMKQ-IQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIG 126
           L  ++ Q + A   +WPF  PV+    PDYY V+  PMDL+TI   I++ +Y+    F+ 
Sbjct: 14  LDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLD 73

Query: 127 DMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKLVELK 171
           D+  I  N   YN  ES + K A ++     Q +    E L +L+
Sbjct: 74  DVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLE 118

>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 =  103 bits (258), Expect = 7e-30
 Identities = 42/102 (41%), Positives = 72/102 (70%)

Query: 64  DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSE 123
              +++ ++ ++Q H +AWPF++PV+  E PDYY+ +KEPMDL T+E+++   +Y+K+ +
Sbjct: 4   HDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMED 63

Query: 124 FIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILRE 165
           FI D   +F+NCR YN   + ++K+A++LE FF  KVK + E
Sbjct: 64  FIYDARLVFNNCRMYNGENTSYYKYANRLEKFFNNKVKEIPE 105

>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 =  103 bits (257), Expect = 8e-30
 Identities = 44/97 (45%), Positives = 64/97 (65%)

Query: 65  FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEF 124
           + +L+ L+ QI++H SAWPFMEPV   EAPDYY V++ P+DLKT+  R+  + Y     F
Sbjct: 4   YTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLF 63

Query: 125 IGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           + D+ ++  NCR YNP +S + + A  LE FF  K+K
Sbjct: 64  VADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLK 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 =  101 bits (252), Expect = 6e-29
 Identities = 45/110 (40%), Positives = 73/110 (66%)

Query: 52  SNLANMKNLTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIEL 111
           S+++       + + +L+ +++Q+++H+SAWPFMEPV   EAP YY V++ PMDLKT+  
Sbjct: 2   SHMSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSE 61

Query: 112 RIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVK 161
           R+  + Y     F+ D+ ++F NC+ YNP ES ++K A+ LE FF  K+K
Sbjct: 62  RLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIK 111

>d3dwya1 a.29.2.1 (A:1084-1197) CREB-binding protein, CBP {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: All alpha proteins
fold: Bromodomain-like
superfamily: Bromodomain
family: Bromodomain
domain: CREB-binding protein, CBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 94.3 bits (234), Expect = 3e-26
 Identities = 30/105 (28%), Positives = 59/105 (56%), Gaps = 3/105 (2%)

Query: 66  ESLRKLMKQIQAH-KSAWPFMEPVDP--HEAPDYYNVVKEPMDLKTIELRIAQQRYKKLS 122
           ++L   ++ +      + PF +PVDP     PDY+++VK PMDL TI+ ++   +Y++  
Sbjct: 9   QALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPW 68

Query: 123 EFIGDMTKIFDNCRYYNPRESPFFKHAHQLEMFFVQKVKILREKL 167
           +++ D+  +F+N   YN + S  +K   +L   F Q++  + + L
Sbjct: 69  QYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 113

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 58.5 bits (141), Expect = 7e-13
 Identities = 21/43 (48%), Positives = 31/43 (72%)

Query: 10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSS 52
            +F+ICCD C+ WFHG+CV I  + A++I +Y CP+C+N S 
Sbjct: 18 ADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG 60

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.4 bits (138), Expect = 3e-12
 Identities = 24/52 (46%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 12 KFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSSNLANMKNLTPR 63
           F I C  CQDWFHG CVGI +  A +ID Y CP+C       + MKN    
Sbjct: 25 HFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGP-SIMKNWHSG 75

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 76

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.6 bits (123), Expect = 3e-10
 Identities = 20/42 (47%), Positives = 28/42 (66%), Gaps = 4/42 (9%)

Query: 10 EPKFYICCDTCQDWFHGRCVGILQSEADNI----DEYICPNC 47
            +F ICCD C++WFHG CVGI ++    +    ++YICPNC
Sbjct: 26 NNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 67

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 72

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 47.3 bits (112), Expect = 1e-08
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
          + +  + CD C  W H RC+GI  ++A    +++C  C
Sbjct: 27 DGERMLACDGCGVWHHTRCIGINNADALP-SKFLCFRC 63

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 44.4 bits (104), Expect = 2e-07
 Identities = 8/46 (17%), Positives = 14/46 (30%), Gaps = 4/46 (8%)

Query: 10 EPKFYICCDTCQDWFHGRCVGI----LQSEADNIDEYICPNCNNSS 51
          +         C  W H  CV +    +       + + C  C  +S
Sbjct: 28 DSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS 73

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (93), Expect = 6e-06
 Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 15 ICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSS 51
          +CCDTC   +H  C+     E  N  E++CP C   +
Sbjct: 22 LCCDTCPSSYHIHCLNPPLPEIPN-GEWLCPRCTCPA 57

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]} Length = 51

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 4e-05
 Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 10 EPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSS 51
          E    I CD C   FH  C+     E  +  E+ CP C  ++
Sbjct: 11 EDDKLILCDECNKAFHLFCLRPALYEVPD-GEWQCPACQPAT 51

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 4e-04
 Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 1/38 (2%)

Query: 15 ICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNSSS 52
          + C+ C+  FH  C      +    +E+ C  C+    
Sbjct: 20 VMCNQCEFCFHLDCHLPALQDVPG-EEWSCSLCHVLPD 56

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]} Length = 88

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.2 bits (80), Expect = 6e-04
 Identities = 7/42 (16%), Positives = 14/42 (33%), Gaps = 3/42 (7%)

Query: 15 ICCDTCQDWFHGRCVGILQSEADNID---EYICPNCNNSSSN 53
          + C  C + +H  C     ++ +  D    + C  C      
Sbjct: 34 VECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKR 75

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]} Length = 51

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

 Score = 33.4 bits (76), Expect = 0.001
 Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 3/35 (8%)

Query: 13 FYICCDTCQDWFHGRCVGILQSEADNIDEYICPNC 47
               D   +WFH  CVG+         ++ CP C
Sbjct: 17 GCDNPDCSIEWFHFACVGL---TTKPRGKWFCPRC 48

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	171
d3d7ca1	102	GCN5 {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1eqfa1	139	TAFII250 double bromodomain module {Human (Homo sa	99.98
d1e6ia_	111	GCN5 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.97
d1wuma1	118	P300/CAF histone acetyltransferase bromodomain {Hu	99.97
d3dwya1	114	CREB-binding protein, CBP {Human (Homo sapiens) [T	99.97
d1eqfa2	128	TAFII250 double bromodomain module {Human (Homo sa	99.97
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	99.46
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	99.36
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	99.22
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	99.22
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	99.13
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	99.09
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	99.05
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	99.05
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	99.03
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	98.94
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	98.76
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	96.01
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	95.27
d1iroa_	53	Rubredoxin {Clostridium pasteurianum [TaxId: 1501]	94.15
d1brfa_	53	Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2	93.66
d1dx8a_	70	Rubredoxin {Guillardia theta [TaxId: 55529]}	93.53
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	93.31
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	93.2
d1s24a_	56	Two-iron rubredoxin {Pseudomonas oleovorans [TaxId	92.36
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	91.17
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	90.43
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	87.99
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	86.62
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	86.26
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	83.81
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	83.64
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	82.27
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	81.64

>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=100.00  E-value=1e-32  Score=180.58  Aligned_cols=100  Identities=44%  Similarity=0.837  Sum_probs=96.7

Q ss_pred             hHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCC
Q psy5115          63 RDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRE  142 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~  142 (171)
                      +....|..+|..|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|.+||++||+||..||+++
T Consensus         2 ~L~~~l~~il~~l~~~~~s~~F~~pv~~~~~pdY~~~I~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~   81 (102)
T d3d7ca1           2 QLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPD   81 (102)
T ss_dssp             HHHHHHHHHHHHHHHSGGGGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCCSHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             hHHHHHHHHHHHHHhCCCCCccCCCCChhhCcCHHHHcCCccCHHHHHHHhccCccCCHHHHHHHHHHHHHHHHHHCCCC
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q psy5115         143 SPFFKHAHQLEMFFVQKVKI  162 (171)
Q Consensus       143 s~~~~~a~~l~~~f~~~~~~  162 (171)
                      |.++++|..|++.|++.+++
T Consensus        82 s~~~~~A~~l~~~f~~~~ke  101 (102)
T d3d7ca1          82 SEYCRCASALEKFFYFKLKE  101 (102)
T ss_dssp             SHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999998875

>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=99.98  E-value=4.4e-32  Score=186.77  Aligned_cols=107  Identities=23%  Similarity=0.432  Sum_probs=103.0

Q ss_pred             HHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCC
Q psy5115          64 DFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRES  143 (171)
Q Consensus        64 ~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s  143 (171)
                      ....|..+++.|..++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|..||++||+||..||+++|
T Consensus        27 l~~~l~~il~~l~~~~~s~pF~~Pvd~~~~pdY~~iI~~PmdL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~s  106 (139)
T d1eqfa1          27 LSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKH  106 (139)
T ss_dssp             HHHHHHHHHHHHHTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHTCTTS
T ss_pred             HHHHHHHHHHHHHcCCCchhhhCCCChhhccCHHHHcCChhhHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence            45678889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5115         144 PFFKHAHQLEMFFVQKVKILREKLVEL  170 (171)
Q Consensus       144 ~~~~~a~~l~~~f~~~~~~~~~~~~~~  170 (171)
                      .++++|..|+..|++.|+++...+.++
T Consensus       107 ~i~~~A~~L~~~~~~~~~~~~~~~~~~  133 (139)
T d1eqfa1         107 SLTQISQSMLDLCDEKLKEKEDKLARL  133 (139)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999988775

>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=3.5e-32  Score=180.62  Aligned_cols=101  Identities=42%  Similarity=0.905  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCH
Q psy5115          65 FESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESP  144 (171)
Q Consensus        65 ~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~  144 (171)
                      ...|..+|..|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|..||++||+||..||+++|.
T Consensus         5 ~~~l~~il~~l~~~~~a~pF~~pvd~~~~pdY~~vI~~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~   84 (111)
T d1e6ia_           5 DAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTS   84 (111)
T ss_dssp             HHHHHHHHHHHHHSTTCGGGSSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHSCTTSH
T ss_pred             HHHHHHHHHHHHhCCCChhhcCCCCchhCcCHHHHcCCchhHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHCCCCCH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q psy5115         145 FFKHAHQLEMFFVQKVKILRE  165 (171)
Q Consensus       145 ~~~~a~~l~~~f~~~~~~~~~  165 (171)
                      ++.+|..|++.|++.++++++
T Consensus        85 i~~~A~~l~~~f~~~~~~ipe  105 (111)
T d1e6ia_          85 YYKYANRLEKFFNNKVKEIPE  105 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHTSGG
T ss_pred             HHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999988754

>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=99.97  E-value=7.6e-32  Score=180.74  Aligned_cols=104  Identities=42%  Similarity=0.836  Sum_probs=99.3

Q ss_pred             CChhHHHHHHHHHHHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhC
Q psy5115          60 LTPRDFESLRKLMKQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYN  139 (171)
Q Consensus        60 l~~~~~~~~~~~l~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn  139 (171)
                      ...+....|..+++.|.+++.+++|..||++..+|+|+++|++||||++|++||++|.|.|+++|.+||++||+||..||
T Consensus        10 ~~~~l~~~l~~il~~l~~~~~a~~F~~pv~~~~~pdY~~iI~~PmdL~~I~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yn   89 (118)
T d1wuma1          10 DPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYN   89 (118)
T ss_dssp             SHHHHHHHHHHHHHHHHHSSSCHHHHSCCCSSSSSSCTTTCSSCCCHHHHHHHHTTTCCCSSHHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHHHHhCCCcCcccCCCChhhCcCHHHHcCChhhHHHHHHHhcccccCchHHHHHHHHHHHHHHHHHC
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q psy5115         140 PRESPFFKHAHQLEMFFVQKVKIL  163 (171)
Q Consensus       140 ~~~s~~~~~a~~l~~~f~~~~~~~  163 (171)
                      +++|.++.+|..|++.|.+.++++
T Consensus        90 ~~~s~~~~~A~~l~~~f~~~~~e~  113 (118)
T d1wuma1          90 PPESEYYKCANILEKFFFSKIKEA  113 (118)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999875

>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=99.97  E-value=2.9e-31  Score=176.95  Aligned_cols=105  Identities=29%  Similarity=0.578  Sum_probs=98.6

Q ss_pred             hHHHHHHHHHHHHHhC-cCCCCCccCCCCC--CCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhC
Q psy5115          63 RDFESLRKLMKQIQAH-KSAWPFMEPVDPH--EAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYN  139 (171)
Q Consensus        63 ~~~~~~~~~l~~l~~~-~~~~~F~~pv~~~--~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn  139 (171)
                      +..+.|..+++.|.++ +.+++|..||++.  ++|+|+++|++||||++|++||++|.|.|+++|.+||++||+||..||
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            4567788999999876 5899999999976  689999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5115         140 PRESPFFKHAHQLEMFFVQKVKILREKL  167 (171)
Q Consensus       140 ~~~s~~~~~a~~l~~~f~~~~~~~~~~~  167 (171)
                      +++|.++.+|..|+..|++.+.++.+++
T Consensus        86 ~~~s~~~~~A~~L~~~f~~~~~~i~~~~  113 (114)
T d3dwya1          86 RKTSRVYKFCSKLAEVFEQEIDPVMQSL  113 (114)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999988765

>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=99.97  E-value=1.9e-31  Score=181.11  Aligned_cols=98  Identities=34%  Similarity=0.616  Sum_probs=92.1

Q ss_pred             HHHHhCcCCCCCccCCCCCCCCccccccCCCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHH
Q psy5115          73 KQIQAHKSAWPFMEPVDPHEAPDYYNVVKEPMDLKTIELRIAQQRYKKLSEFIGDMTKIFDNCRYYNPRESPFFKHAHQL  152 (171)
Q Consensus        73 ~~l~~~~~~~~F~~pv~~~~~p~Y~~~i~~Pmdl~~I~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yn~~~s~~~~~a~~l  152 (171)
                      ..+.+++.|+||..||++..+|+|+++|++||||++|++||++|.|.|+.+|..||++||+||..||+++|.++++|..|
T Consensus        20 ~~~~~~p~a~pF~~pVd~~~~PdY~~vIk~PmDL~tI~~kl~~~~Y~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~L   99 (128)
T d1eqfa2          20 QKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEI   99 (128)
T ss_dssp             HTTTTSTTCGGGTSCCCTTTSTTHHHHCSSCCCHHHHHHHHHTTCCSSHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHcCCCCChhcCCCCcccCcCHHHHcCCcccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence            34456678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhc
Q psy5115         153 EMFFVQKVKILREKLVEL  170 (171)
Q Consensus       153 ~~~f~~~~~~~~~~~~~~  170 (171)
                      .+.|++.++++++.+.++
T Consensus       100 ~~~~~~~l~~~~~~~~~l  117 (128)
T d1eqfa2         100 VNVCYQTLTEYDEHLTQL  117 (128)
T ss_dssp             HHHHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHH
Confidence            999999999998887664

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=1.2e-14  Score=89.46  Aligned_cols=47  Identities=45%  Similarity=0.963  Sum_probs=41.5

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +|.++++++++||+||.|.+|||..|+++........+.|+||.|..
T Consensus        16 iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~   62 (79)
T d1wepa_          16 LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEA   62 (79)
T ss_dssp             TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTT
T ss_pred             ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcC
Confidence            47889998999999999999999999999877666667899999984

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.36  E-value=1.2e-13  Score=81.56  Aligned_cols=47  Identities=43%  Similarity=1.081  Sum_probs=40.6

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      .|.+++++++.||+|+.|.+|||..|+++........+.|+|+.|..
T Consensus        11 ~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~   57 (64)
T d1we9a_          11 ACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcC
Confidence            47888888888999999999999999998766655667899999984

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.22  E-value=2.1e-12  Score=77.78  Aligned_cols=45  Identities=24%  Similarity=0.605  Sum_probs=38.3

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|.++++++..||+|+.|.+|||..|+++.... ..++.|+|+.|.
T Consensus        20 ~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~-~~~~~~~C~~C~   64 (72)
T d1weea_          20 KCGTKDDDGERMLACDGCGVWHHTRCIGINNAD-ALPSKFLCFRCI   64 (72)
T ss_dssp             TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTS-CCCSCCCCHHHH
T ss_pred             eCCCCcCCCCeEEEeCCCCCcCchhhcCCcccc-CCCCcEECcCCc
Confidence            477788888889999999999999999986543 356789999997

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=5.7e-12  Score=73.35  Aligned_cols=47  Identities=28%  Similarity=0.640  Sum_probs=37.2

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS   50 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~   50 (171)
                      .+|..+.+++ .||.||.|.+|||..|+++.... .+.+.|+||.|...
T Consensus        10 ~~C~~C~~~g-~lv~Cd~C~~~~H~~C~~~~~~~-~~~~~W~C~~C~~~   56 (61)
T d1mm2a_          10 EFCRVCKDGG-ELLCCDTCPSSYHIHCLNPPLPE-IPNGEWLCPRCTCP   56 (61)
T ss_dssp             SSCTTTCCCS-SCBCCSSSCCCBCSSSSSSCCSS-CCSSCCCCTTTTTT
T ss_pred             CCCcCCCCCC-eEEEeCCCCccCchhhcCCCcCc-CCCCcEECCCCcCc
Confidence            3788888765 59999999999999999765433 34568999999743

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=5.8e-11  Score=70.85  Aligned_cols=47  Identities=17%  Similarity=0.326  Sum_probs=36.4

Q ss_pred             CccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCCC
Q psy5115           2 KFHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNNS   50 (171)
Q Consensus         2 ~~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~   50 (171)
                      ..|..+.+++. ||.||+|.+|||..|+++... ..+.+.|+|+.|...
T Consensus         8 ~~C~~C~~~~~-ll~Cd~C~~~~H~~C~~p~l~-~~p~~~W~C~~C~~~   54 (70)
T d1fp0a1           8 TICRVCQKPGD-LVMCNQCEFCFHLDCHLPALQ-DVPGEEWSCSLCHVL   54 (70)
T ss_dssp             SCCSSSCSSSC-CEECTTSSCEECTTSSSTTCC-CCCSSSCCCCSCCCC
T ss_pred             CCCCCCCCcCE-EEECCCCChhhccccCCCCcC-cCCCCCEECcCCcCc
Confidence            35777776654 999999999999999986433 334568999999843

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=3.7e-11  Score=67.26  Aligned_cols=45  Identities=24%  Similarity=0.420  Sum_probs=34.0

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      .|.++.++ +.||.||+|.+|||..|+++... ..+.+.|+|+.|+.
T Consensus         5 vC~~~~~~-~~~i~Cd~C~~~~H~~C~~p~~~-~~p~~~W~C~~C~~   49 (51)
T d1f62a_           5 VCRKKGED-DKLILCDECNKAFHLFCLRPALY-EVPDGEWQCPACQP   49 (51)
T ss_dssp             TTCCSSCC-SCCEECTTTCCEECHHHHCTTCC-SCCSSCCSCTTTSC
T ss_pred             CcCCCCCC-CCEEEcCCCCCCCCCCCCCCCCC-cCCCCCEECcCCcC
Confidence            36555544 45999999999999999976433 23456899999974

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

Probab=99.05  E-value=2.8e-11  Score=67.67  Aligned_cols=41  Identities=29%  Similarity=0.740  Sum_probs=31.3

Q ss_pred             ccccccCCCceeEecCC---CCceecccccCccccCcCCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDT---CQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~---C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      +|+++++  +.||.|+.   |..|||..|+|++..   +.+.|+||.|.
T Consensus         6 ~C~~~~~--~~mi~Cd~~~C~~~WfH~~Cvgl~~~---p~~~w~C~~C~   49 (51)
T d2pnxa1           6 LCHQVSY--GEMIGCDNPDCSIEWFHFACVGLTTK---PRGKWFCPRCS   49 (51)
T ss_dssp             TTTEECC--SEEEECSCTTCSSCEEEGGGGTCSSC---CSSCCCCHHHH
T ss_pred             EcCCCCC--CCEEEEecCCCCCCCEeCCccCCCcC---CCCcEECcCCC
Confidence            3566654  34999986   578999999998653   35689999996

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.05  E-value=7.9e-11  Score=70.24  Aligned_cols=44  Identities=20%  Similarity=0.559  Sum_probs=31.8

Q ss_pred             ccccccCCCceeEecCCCC-ceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQ-DWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~-r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +|+++++++-.|+.|+.|. .|||..|++++..   +.+.|+||.|+.
T Consensus        20 iC~~~~~~~~i~c~~~~C~~~wfH~~Cvgl~~~---p~~~w~C~~C~~   64 (71)
T d1wesa_          20 LCNQVSYGEMIGCDNEQCPIEWFHFSCVSLTYK---PKGKWYCPKCRG   64 (71)
T ss_dssp             TTCCCCCSSEECCSCTTCSCCCEETTTTTCSSC---CSSCCCCTTTSS
T ss_pred             EeCCCCCCCEEEEECCCCCCcCccCccCCCCcC---CCCcEECcCCcc
Confidence            4566655554455567885 7999999998643   456899999974

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.03  E-value=9.2e-12  Score=75.72  Aligned_cols=45  Identities=47%  Similarity=1.205  Sum_probs=34.4

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCc----CCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEA----DNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~----~~~~~~~Cp~C~   48 (171)
                      +|.+++++ +.||+|+.|.+|||..|+++.....    ...+.|+|+.|.
T Consensus        20 iC~~~~~~-~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~   68 (76)
T d1wema_          20 ICRQPHNN-RFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCT   68 (76)
T ss_dssp             TTCCCCCS-SCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHH
T ss_pred             ECCCccCC-CeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCc
Confidence            46777765 4599999999999999998754321    134579999996

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.94  E-value=1.2e-10  Score=70.90  Aligned_cols=45  Identities=20%  Similarity=0.465  Sum_probs=33.6

Q ss_pred             ccccccCCCceeEecC--CCCceecccccCccccCc----CCCCCCCCCccC
Q psy5115           3 FHTLAVIEPKFYICCD--TCQDWFHGRCVGILQSEA----DNIDEYICPNCN   48 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~--~C~r~~H~~C~~~~~~~~----~~~~~~~Cp~C~   48 (171)
                      +|..+.++ +.||+|+  .|.+|||..|+|++....    ..++.|+||.|.
T Consensus        20 ~C~~~~~~-~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~   70 (78)
T d1wewa_          20 VCGNSLET-DSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICR   70 (78)
T ss_dssp             SSCCCCCC-SCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHH
T ss_pred             ECCCccCC-CcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCc
Confidence            35666654 4588876  899999999999875432    235679999997

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.76  E-value=1e-09  Score=68.25  Aligned_cols=45  Identities=16%  Similarity=0.461  Sum_probs=32.1

Q ss_pred             cccccC-CCceeEecCCCCceecccccCccccC---cCCCCCCCCCccC
Q psy5115           4 HTLAVI-EPKFYICCDTCQDWFHGRCVGILQSE---ADNIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~-~~~~~i~C~~C~r~~H~~C~~~~~~~---~~~~~~~~Cp~C~   48 (171)
                      |.+..+ +.+.||.|+.|.+|||..|+++....   ..+...|+|+.|.
T Consensus        22 C~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~   70 (88)
T d1weva_          22 CRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCT   70 (88)
T ss_dssp             SCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHH
T ss_pred             CCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccC
Confidence            444333 34679999999999999999754221   2234479999997

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=96.01  E-value=0.002  Score=35.25  Aligned_cols=42  Identities=19%  Similarity=0.364  Sum_probs=30.7

Q ss_pred             ccccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           3 FHTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         3 ~~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +|-..+++++.++.+..|...||..|+..--.     ..-.||.|+.
T Consensus        10 ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~-----~~~~CP~CR~   51 (55)
T d1iyma_          10 VCLAELEDGEEARFLPRCGHGFHAECVDMWLG-----SHSTCPLCRL   51 (55)
T ss_dssp             TTCCCCCTTSCCEECSSSCCEECTTHHHHTTT-----TCCSCSSSCC
T ss_pred             EECccccCCCEEEEeCCCCCcccHHHHHHHHH-----hCCcCCCCCC
Confidence            45666777777888888999999999854311     1347999983

>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]

Probab=95.27  E-value=0.0069  Score=31.51  Aligned_cols=34  Identities=18%  Similarity=0.349  Sum_probs=23.5

Q ss_pred             EecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115          15 ICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        15 i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      -+|..|.-+|+..= |...+..+.++.|.||.|..
T Consensus         4 y~C~~CgyiYd~~~-Gdgt~Fe~LP~dw~CP~C~a   37 (45)
T d6rxna_           4 YVCNVCGYEYDPAE-HDNVPFDQLPDDWCCPVCGV   37 (45)
T ss_dssp             EEETTTCCEECGGG-GTTCCGGGSCTTCBCTTTCC
T ss_pred             eEeCCCCeEECccc-CCCCCHHHCCCCCCCcCCCC
Confidence            46889998887632 11223456788999999984

>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Clostridium pasteurianum [TaxId: 1501]

Probab=94.15  E-value=0.025  Score=30.37  Aligned_cols=36  Identities=22%  Similarity=0.536  Sum_probs=24.4

Q ss_pred             EecCCCCceeccccc----Ccc--ccCcCCCCCCCCCccCCC
Q psy5115          15 ICCDTCQDWFHGRCV----GIL--QSEADNIDEYICPNCNNS   50 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~~--~~~~~~~~~~~Cp~C~~~   50 (171)
                      -.|..|.-+|...=-    ++.  .+..+-++.|.||.|...
T Consensus         4 y~C~~CgyiYd~~~Gd~~~gi~pGT~F~~LP~dw~CP~C~a~   45 (53)
T d1iroa_           4 YTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVG   45 (53)
T ss_dssp             EEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             eEcCCCCcEECcccCCcccCCCCCCCHHHCCCCCCCcCCCCc
Confidence            468889888877652    221  134456889999999843

>d1brfa_ g.41.5.1 (A:) Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.66  E-value=0.034  Score=29.81  Aligned_cols=36  Identities=22%  Similarity=0.552  Sum_probs=23.5

Q ss_pred             EecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCC
Q psy5115          15 ICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNS   50 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~   50 (171)
                      -+|..|.-+|...=-    ++  .....+.++.|.||.|...
T Consensus         3 y~C~~CgyiYd~~~Gd~~~gi~pGT~f~dLP~dw~CP~C~a~   44 (53)
T d1brfa_           3 WVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAP   44 (53)
T ss_dssp             EEETTTCCEEETTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             eECCCCCcEECcccCCcccCCCCCCCHHHCCCCCCCcCCCCc
Confidence            368888888876531    11  1123456889999999843

>d1dx8a_ g.41.5.1 (A:) Rubredoxin {Guillardia theta [TaxId: 55529]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Guillardia theta [TaxId: 55529]

Probab=93.53  E-value=0.038  Score=31.40  Aligned_cols=37  Identities=24%  Similarity=0.543  Sum_probs=25.3

Q ss_pred             eEecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCCC
Q psy5115          14 YICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNNS   50 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~~   50 (171)
                      --.|..|.-.|+..=-    ++  ..+..+-++.|.||.|...
T Consensus         7 ky~C~~CgyiYDp~~GD~~~gI~pGT~F~dLP~dW~CP~Cga~   49 (70)
T d1dx8a_           7 KYECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSP   49 (70)
T ss_dssp             CEEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCB
T ss_pred             eEEcCCCCeEECcccCCcccCCCCCCChHHCCCCCCCcCCCCc
Confidence            3578899988877641    11  1134556889999999844

>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=93.31  E-value=0.039  Score=29.43  Aligned_cols=35  Identities=26%  Similarity=0.497  Sum_probs=23.8

Q ss_pred             EecCCCCceeccccc----Cc--cccCcCCCCCCCCCccCC
Q psy5115          15 ICCDTCQDWFHGRCV----GI--LQSEADNIDEYICPNCNN   49 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~--~~~~~~~~~~~~Cp~C~~   49 (171)
                      -.|..|.-+|...=-    ++  .....+-++.|.||.|..
T Consensus         4 y~C~~CgyiYdp~~Gd~~~gi~pGT~F~~LP~~w~CP~C~a   44 (52)
T d2dsxa1           4 YVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGA   44 (52)
T ss_dssp             EEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCC
T ss_pred             EEeCCCCeEECcccCCcccCCCCCCCHHHCCCCCCCcCCCC
Confidence            468889888876542    11  113345688999999984

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.20  E-value=0.029  Score=32.74  Aligned_cols=36  Identities=31%  Similarity=0.755  Sum_probs=24.9

Q ss_pred             eEecCCCCceeccccc---Ccccc--------CcCCCCCCCCCccCC
Q psy5115          14 YICCDTCQDWFHGRCV---GILQS--------EADNIDEYICPNCNN   49 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~---~~~~~--------~~~~~~~~~Cp~C~~   49 (171)
                      .+.|-.|.|+||..|.   |-...        ......-|.|..|.+
T Consensus        29 l~pCRvCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~n   75 (89)
T d1wila_          29 LFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDN   75 (89)
T ss_dssp             CSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCC
T ss_pred             eecceeecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcc
Confidence            6799999999999995   21111        111234699999984

>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Two-iron rubredoxin
species: Pseudomonas oleovorans [TaxId: 301]

Probab=92.36  E-value=0.075  Score=28.73  Aligned_cols=36  Identities=25%  Similarity=0.575  Sum_probs=23.2

Q ss_pred             EecCCCCceeccccc----Ccc--ccCcCCCCCCCCCccCCC
Q psy5115          15 ICCDTCQDWFHGRCV----GIL--QSEADNIDEYICPNCNNS   50 (171)
Q Consensus        15 i~C~~C~r~~H~~C~----~~~--~~~~~~~~~~~Cp~C~~~   50 (171)
                      -+|..|.-.|+..=-    ++.  ....+.++.|.||.|...
T Consensus         5 y~C~~CgyiYdp~~Gd~~~gi~pGT~F~~LP~dw~CP~C~a~   46 (56)
T d1s24a_           5 WICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGAT   46 (56)
T ss_dssp             EEETTTTEEEETTSCCTTTTCCSCCCGGGCCTTCCCSSSCCC
T ss_pred             EECCCCCcEECcccCCcccCcCCCCChhhCCCCCCCcCCCCc
Confidence            368888877765531    221  123456889999999844

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.17  E-value=0.024  Score=35.30  Aligned_cols=35  Identities=20%  Similarity=0.442  Sum_probs=22.3

Q ss_pred             eEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115          14 YICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .+.--.|..+||..|+..--..........||.|+
T Consensus        55 ~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR   89 (114)
T d1v87a_          55 VGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCK   89 (114)
T ss_dssp             CEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTC
T ss_pred             ceEECCCCChhhHHHHHHHHHhcCcCCCCcccccc
Confidence            45556899999999973211111112346899998

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=90.43  E-value=0.0071  Score=33.41  Aligned_cols=30  Identities=17%  Similarity=0.360  Sum_probs=21.4

Q ss_pred             ecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115          16 CCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus        16 ~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      .|.+|..+||..|+..=-   ...+...||.|+
T Consensus        25 ~c~~c~h~~H~~Cl~~W~---~~~~~~~CP~Cr   54 (60)
T d1vyxa_          25 GCTGELENVHRSCLSTWL---TISRNTACQICG   54 (60)
T ss_dssp             CCSSGGGSCCHHHHHHHH---HHHTCSBCTTTC
T ss_pred             ccCCCCCEEcHHHHHHHH---hhCCCCCCcccC
Confidence            577899999999984311   112356899998

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.99  E-value=0.44  Score=28.64  Aligned_cols=30  Identities=27%  Similarity=0.548  Sum_probs=20.0

Q ss_pred             CCCceecccccCccccCcCCCCCCCCCccCCC
Q psy5115          19 TCQDWFHGRCVGILQSEADNIDEYICPNCNNS   50 (171)
Q Consensus        19 ~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~~   50 (171)
                      .|+..||..|+...-  ........||.|+..
T Consensus        38 ~CgH~fC~~Ci~~~~--~~~~~~~~CP~Cr~~   67 (103)
T d1jm7a_          38 KCDHIFCKFCMLKLL--NQKKGPSQCPLCKND   67 (103)
T ss_dssp             TTSCCCCSHHHHHHH--HSSSSSCCCTTTSCC
T ss_pred             CCCCchhhHHHHHHH--HHCCCCCcCcCCCCc
Confidence            599999999973211  112335789999843

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.62  E-value=0.55  Score=24.99  Aligned_cols=37  Identities=19%  Similarity=0.343  Sum_probs=23.4

Q ss_pred             cccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      |..|.+.-..-+.. .|+..||..|+..        ....||.|+.
T Consensus         9 C~IC~~~~~~p~~l-pCgH~fC~~Ci~~--------~~~~CP~Cr~   45 (56)
T d1bora_           9 CQQCQAEAKCPKLL-PCLHTLCSGCLEA--------SGMQCPICQA   45 (56)
T ss_dssp             CSSSCSSCBCCSCS-TTSCCSBTTTCSS--------SSSSCSSCCS
T ss_pred             CcccCcccCCCEEe-cCCCHHhHHHHHc--------CCCcCcCCCC
Confidence            44444443333333 5899999999832        1457999984

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.26  E-value=0.057  Score=31.97  Aligned_cols=31  Identities=23%  Similarity=0.509  Sum_probs=21.7

Q ss_pred             eEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115          14 YICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        14 ~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      .+....|..+||..|+..=-..     .-.||.|+.
T Consensus        51 ~~~~~~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~   81 (88)
T d3dplr1          51 TVAWGVCNHAFHFHCISRWLKT-----RQVCPLDNR   81 (88)
T ss_dssp             CEEEETTSCEEEHHHHHHHHTT-----CSBCSSSCS
T ss_pred             CeEEccccCcccHHHHHHHHHH-----CCcCCCCCC
Confidence            4667789999999998432111     236999983

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=83.81  E-value=0.15  Score=28.40  Aligned_cols=41  Identities=20%  Similarity=0.392  Sum_probs=27.2

Q ss_pred             cccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      |.-|.+.-...+.+-.|...||..|+..--. .    .-.||.|+.
T Consensus         8 C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~-~----~~~CP~CR~   48 (68)
T d1chca_           8 CPICLEDPSNYSMALPCLHAFCYVCITRWIR-Q----NPTCPLCKV   48 (68)
T ss_dssp             CSSCCSCCCSCEEETTTTEEESTTHHHHHHH-H----SCSTTTTCC
T ss_pred             CccCCcCccCCcEEeCCCCcCcHHHHHHHHH-h----CCcCCCCCc
Confidence            5555555434566789999999999843211 1    247999983

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.64  E-value=0.22  Score=23.09  Aligned_cols=10  Identities=30%  Similarity=0.770  Sum_probs=7.5

Q ss_pred             ceeEecCCCC
Q psy5115          12 KFYICCDTCQ   21 (171)
Q Consensus        12 ~~~i~C~~C~   21 (171)
                      |.++.|.+|.
T Consensus         1 G~~~~CaGC~   10 (30)
T d1j2oa1           1 GSLLTCGGCQ   10 (30)
T ss_dssp             CCCBCBSSSC
T ss_pred             CCCcccCCCC
Confidence            3478899995

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.27  E-value=1.3  Score=26.04  Aligned_cols=28  Identities=29%  Similarity=0.699  Sum_probs=19.8

Q ss_pred             EecCCCCceecccccCccccCcCCCCCCCCCccCC
Q psy5115          15 ICCDTCQDWFHGRCVGILQSEADNIDEYICPNCNN   49 (171)
Q Consensus        15 i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~~   49 (171)
                      +.+..|+..||..|+..-.       ...||.|+.
T Consensus        36 v~~~~CgH~fC~~Ci~~~~-------~~~CP~Cr~   63 (97)
T d1jm7b_          36 VCLGGCEHIFCSNCVSDCI-------GTGCPVCYT   63 (97)
T ss_dssp             BCCCSSSCCBCTTTGGGGT-------TTBCSSSCC
T ss_pred             ceeCCCCCchhHHHHHHHH-------hccccccCC
Confidence            4556799999999974321       125999984

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.64  E-value=0.093  Score=27.74  Aligned_cols=41  Identities=15%  Similarity=0.233  Sum_probs=24.8

Q ss_pred             cccccCCCceeEecCCCCceecccccCccccCcCCCCCCCCCccC
Q psy5115           4 HTLAVIEPKFYICCDTCQDWFHGRCVGILQSEADNIDEYICPNCN   48 (171)
Q Consensus         4 ~~~~~~~~~~~i~C~~C~r~~H~~C~~~~~~~~~~~~~~~Cp~C~   48 (171)
                      |-..+++++..+.-..|+..||..|+..-..    .....||.|+
T Consensus         6 Cl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~----~~~~~CP~CR   46 (52)
T d1ur6b_           6 CMEPLEIDDINFFPCTCGYQICRFCWHRIRT----DENGLCPACR   46 (52)
T ss_dssp             TTEECCGGGTTCCSSSSSCCCCHHHHHHHTT----TSCCBCTTTC
T ss_pred             CChhhhCCCceEEecCCCCccchHHHHHHHh----hcCCCCCccC
Confidence            4344444443333337999999999743211    1235799998