Query psy7377
Match_columns 83
No_of_seqs 101 out of 201
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 16:41:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7377.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7377hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1122|consensus 99.7 3.1E-17 6.8E-22 131.1 2.4 79 5-83 72-153 (460)
2 PF09288 UBA_3: Fungal ubiquit 85.9 0.34 7.4E-06 29.3 0.7 17 62-78 3-19 (55)
3 PF02671 PAH: Paired amphipath 85.1 4.7 0.0001 22.3 5.4 43 31-80 5-47 (47)
4 PF14225 MOR2-PAG1_C: Cell mor 77.9 6.2 0.00013 29.8 5.1 47 30-78 148-196 (262)
5 cd05520 Bromo_polybromo_III Br 62.4 28 0.0006 22.5 5.0 29 19-47 45-85 (103)
6 PF09862 DUF2089: Protein of u 61.9 17 0.00036 24.7 4.0 40 20-59 60-100 (113)
7 PF01402 RHH_1: Ribbon-helix-h 60.6 23 0.00049 18.4 4.8 16 46-61 21-36 (39)
8 cd05519 Bromo_SNF2 Bromodomain 57.4 42 0.00091 21.4 5.1 31 18-48 44-86 (103)
9 TIGR03031 cas_csx12 CRISPR-ass 56.9 11 0.00023 32.9 2.8 29 35-63 195-224 (802)
10 cd05492 Bromo_ZMYND11 Bromodom 56.0 47 0.001 22.0 5.3 14 19-32 45-58 (109)
11 cd05526 Bromo_polybromo_VI Bro 55.9 42 0.0009 22.5 5.0 31 17-47 44-86 (110)
12 COG2739 Uncharacterized protei 54.5 27 0.00059 23.6 3.9 56 19-78 43-101 (105)
13 cd02642 R3H_encore_like R3H do 54.5 15 0.00032 21.8 2.4 21 48-68 27-47 (63)
14 PF07761 DUF1617: Protein of u 49.7 33 0.00071 24.3 3.9 51 27-77 7-58 (143)
15 cd05515 Bromo_polybromo_V Brom 49.6 30 0.00065 22.3 3.5 29 19-47 45-85 (105)
16 PF13907 DUF4208: Domain of un 48.5 71 0.0015 20.5 5.4 45 19-64 11-55 (100)
17 cd05503 Bromo_BAZ2A_B_like Bro 47.7 63 0.0014 20.4 4.8 29 19-47 39-79 (97)
18 smart00297 BROMO bromo domain. 46.7 68 0.0015 19.7 5.4 15 18-32 45-59 (107)
19 cd05507 Bromo_brd8_like Bromod 46.3 77 0.0017 20.3 5.4 13 19-31 42-54 (104)
20 COG2344 AT-rich DNA-binding pr 46.3 1.2E+02 0.0025 22.9 6.6 59 24-82 9-82 (211)
21 TIGR01795 CM_mono_cladeE monof 46.0 79 0.0017 20.3 6.3 54 24-78 21-77 (94)
22 cd05502 Bromo_tif1_like Bromod 45.9 55 0.0012 21.1 4.3 29 19-47 42-85 (109)
23 cd05521 Bromo_Rsc1_2_I Bromodo 45.8 37 0.00081 22.2 3.5 14 19-32 46-59 (106)
24 PF07568 HisKA_2: Histidine ki 45.2 69 0.0015 19.4 5.2 44 22-65 32-76 (76)
25 cd05513 Bromo_brd7_like Bromod 44.4 44 0.00096 21.5 3.7 29 19-47 40-80 (98)
26 PF11888 DUF3408: Protein of u 43.7 56 0.0012 22.1 4.3 31 24-60 87-117 (136)
27 KOG2183|consensus 43.6 30 0.00065 28.9 3.4 48 22-69 266-334 (492)
28 cd05524 Bromo_polybromo_I Brom 42.9 76 0.0017 20.8 4.7 30 19-48 47-88 (113)
29 PF12180 EABR: TSG101 and ALIX 42.2 47 0.001 18.4 3.0 32 27-61 1-32 (35)
30 cd05024 S-100A10 S-100A10: A s 41.4 98 0.0021 20.1 6.2 51 26-78 3-56 (91)
31 PF10607 CLTH: CTLH/CRA C-term 39.8 69 0.0015 20.8 4.2 43 25-68 73-125 (145)
32 cd05497 Bromo_Brdt_I_like Brom 38.6 1.1E+02 0.0023 19.9 4.9 29 19-47 46-86 (107)
33 cd05505 Bromo_WSTF_like Bromod 38.4 1.1E+02 0.0023 19.6 5.4 29 19-47 39-79 (97)
34 PF08951 EntA_Immun: Enterocin 37.7 80 0.0017 18.1 3.8 35 32-66 24-58 (75)
35 PF07159 DUF1394: Protein of u 37.6 73 0.0016 24.9 4.5 70 10-79 10-92 (303)
36 PHA00617 ribbon-helix-helix do 35.9 1.1E+02 0.0023 19.6 4.4 28 24-60 48-75 (80)
37 PF09312 SurA_N: SurA N-termin 35.1 91 0.002 20.2 4.1 42 21-62 67-113 (118)
38 cd05508 Bromo_RACK7 Bromodomai 34.2 39 0.00085 21.8 2.2 14 19-32 41-54 (99)
39 cd05516 Bromo_SNF2L2 Bromodoma 32.8 68 0.0015 20.7 3.2 13 19-31 46-58 (107)
40 PF14846 DUF4485: Domain of un 32.5 36 0.00077 21.5 1.8 37 26-62 25-61 (85)
41 cd05518 Bromo_polybromo_IV Bro 31.5 31 0.00067 22.3 1.4 13 19-31 45-57 (103)
42 cd05525 Bromo_ASH1 Bromodomain 31.0 31 0.00067 22.5 1.3 13 19-31 47-59 (106)
43 PF09958 DUF2192: Uncharacteri 31.0 97 0.0021 23.6 4.1 32 26-59 6-37 (231)
44 cd05517 Bromo_polybromo_II Bro 30.4 30 0.00064 22.4 1.2 13 19-31 45-57 (103)
45 cd05496 Bromo_WDR9_II Bromodom 30.2 49 0.0011 22.1 2.2 13 19-31 44-56 (119)
46 KOG3377|consensus 30.1 1.8E+02 0.0038 20.7 5.1 43 22-64 77-120 (143)
47 PLN02999 photosystem II oxygen 28.7 1.3E+02 0.0027 22.4 4.3 41 20-63 83-132 (190)
48 PF01506 HCV_NS5a: Hepatitis C 28.7 37 0.00081 17.0 1.1 13 30-42 8-20 (23)
49 cd05500 Bromo_BDF1_2_I Bromodo 28.6 1.6E+02 0.0034 18.6 5.8 13 19-31 45-57 (103)
50 COG3526 Uncharacterized protei 26.6 48 0.001 22.0 1.6 17 20-36 68-84 (99)
51 smart00741 SapB Saposin (B) Do 26.4 1.2E+02 0.0027 16.7 3.9 31 51-81 23-66 (76)
52 PF14401 RLAN: RimK-like ATPgr 26.0 1.3E+02 0.0028 21.0 3.9 19 63-81 90-113 (153)
53 PF10273 WGG: Pre-rRNA-process 25.9 1.7E+02 0.0038 18.2 4.7 37 32-68 5-47 (82)
54 cd05504 Bromo_Acf1_like Bromod 24.9 2.1E+02 0.0045 18.7 5.0 13 19-31 51-63 (115)
55 PF02172 KIX: KIX domain; Int 24.8 1.9E+02 0.0042 18.3 4.2 36 27-62 37-73 (81)
56 PF02845 CUE: CUE domain; Int 24.7 61 0.0013 17.4 1.6 12 69-80 2-13 (42)
57 PF12174 RST: RCD1-SRO-TAF4 (R 24.6 1.2E+02 0.0025 18.7 3.0 25 36-60 30-54 (70)
58 PRK10901 16S rRNA methyltransf 23.8 1.1E+02 0.0025 24.0 3.6 23 58-80 134-156 (427)
59 PF08006 DUF1700: Protein of u 23.5 77 0.0017 21.9 2.3 15 48-62 1-15 (181)
60 cd00213 S-100 S-100: S-100 dom 23.0 1.8E+02 0.0038 17.3 6.7 57 25-81 2-62 (88)
61 PRK14902 16S rRNA methyltransf 22.7 44 0.00096 26.4 1.1 24 58-81 140-163 (444)
62 cd05509 Bromo_gcn5_like Bromod 22.7 2E+02 0.0044 17.9 5.4 29 19-47 40-80 (101)
63 PF14823 Sirohm_synth_C: Siroh 22.6 1.8E+02 0.0039 17.8 3.6 16 52-67 29-44 (70)
64 cd05511 Bromo_TFIID Bromodomai 22.5 70 0.0015 20.9 1.9 14 19-32 39-52 (112)
65 PF00439 Bromodomain: Bromodom 22.1 69 0.0015 18.8 1.6 13 19-31 35-47 (84)
66 PF07553 Lipoprotein_Ltp: Host 21.9 1.7E+02 0.0037 16.8 3.4 26 47-76 18-45 (48)
67 PRK07075 isochorismate-pyruvat 21.9 2.3E+02 0.005 18.2 5.9 53 24-77 26-80 (101)
68 PF11616 EZH2_WD-Binding: WD r 21.6 1.1E+02 0.0024 16.4 2.1 19 27-45 8-27 (30)
69 smart00546 CUE Domain that may 21.5 70 0.0015 17.1 1.5 13 69-81 3-15 (43)
70 cd04369 Bromodomain Bromodomai 21.3 1.8E+02 0.004 16.8 5.0 15 18-32 40-54 (99)
71 PF09793 AD: Anticodon-binding 21.2 2.1E+02 0.0046 17.9 3.9 32 20-51 4-35 (91)
72 KOG4204|consensus 21.1 3.6E+02 0.0077 20.1 5.6 52 25-80 136-191 (231)
73 cd05512 Bromo_brd1_like Bromod 21.0 74 0.0016 20.3 1.7 14 19-32 40-53 (98)
74 COG4709 Predicted membrane pro 20.4 87 0.0019 23.3 2.2 15 48-62 1-15 (195)
75 PRK14903 16S rRNA methyltransf 20.3 75 0.0016 25.3 1.9 23 59-81 126-148 (431)
No 1
>KOG1122|consensus
Probab=99.65 E-value=3.1e-17 Score=131.10 Aligned_cols=79 Identities=38% Similarity=0.735 Sum_probs=73.9
Q ss_pred cccccCCCChHHhc---cCCChHHHHHHHHHHHHHhhchhhccCCCCCHHHHHHHHHHHHHHHhcccHHHHHHHHhcCCC
Q psy7377 5 DHEVFAFPSEEEAD---KVLSIPDVEQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLKDLCTYFSYNEFLMERIMQIFPL 81 (83)
Q Consensus 5 ~~e~f~lp~~ee~e---~~~dl~~v~~RIk~iv~vL~~fk~~r~~grSR~eY~~~L~~Di~~yYgYn~fL~ek~~~LF~~ 81 (83)
+.+.|.||+.++.+ .+|||+.|+.||.+++.+|++||+++++|++|++|+.+|++|+|.||+||.|||++++++||+
T Consensus 72 ~~~~l~lp~~~~~~~~~~~P~L~~v~~~~~~~~~~l~dfk~l~~~~~~~~~~~~~l~~~~~~~y~y~~~l~~~~~e~~~~ 151 (460)
T KOG1122|consen 72 EGDPLLLPTLEEEEEKDSVPDLQNVDLRIVELVPVLGDFKNLKEPGRLRSEYCGQLKKDGAHYYAYGVFLAEKLMELFPL 151 (460)
T ss_pred ccccccCcccccccccccCCccchhhHHhhhhhhhhcchhcccccccchhhHHHHHHhcccceechHHHHHHHhcccccH
Confidence 46889999988665 678999999999999999999999999999999999999999999999999999999999997
Q ss_pred CC
Q psy7377 82 DE 83 (83)
Q Consensus 82 ~E 83 (83)
.|
T Consensus 152 ~e 153 (460)
T KOG1122|consen 152 VE 153 (460)
T ss_pred HH
Confidence 54
No 2
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=85.94 E-value=0.34 Score=29.32 Aligned_cols=17 Identities=6% Similarity=0.331 Sum_probs=11.5
Q ss_pred HHHhcccHHHHHHHHhc
Q psy7377 62 CTYFSYNEFLMERIMQI 78 (83)
Q Consensus 62 ~~yYgYn~fL~ek~~~L 78 (83)
+.|||||..|++.|.+|
T Consensus 3 ~~~~Gi~~~lVd~F~~m 19 (55)
T PF09288_consen 3 AALYGIDKDLVDQFENM 19 (55)
T ss_dssp SS----SHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHc
Confidence 57899999999999876
No 3
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=85.09 E-value=4.7 Score=22.31 Aligned_cols=43 Identities=21% Similarity=0.448 Sum_probs=33.0
Q ss_pred HHHHHHhhchhhccCCCCCHHHHHHHHHHHHHHHhcccHHHHHHHHhcCC
Q psy7377 31 KDVLMVLGNFKQYRDPARSRCEYTSLLLKDLCTYFSYNEFLMERIMQIFP 80 (83)
Q Consensus 31 k~iv~vL~~fk~~r~~grSR~eY~~~L~~Di~~yYgYn~fL~ek~~~LF~ 80 (83)
++.+.+|.+|++ ...|+++ +.+-++...+-.+.|++-|-..+|
T Consensus 5 ~~FL~il~~y~~---~~~~~~~----v~~~v~~Ll~~hpdLl~~F~~FlP 47 (47)
T PF02671_consen 5 NEFLKILNDYKK---GRISRSE----VIEEVSELLRGHPDLLEEFNRFLP 47 (47)
T ss_dssp HHHHHHHHHHHC---TCSCHHH----HHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred HHHHHHHHHHHh---cCCCHHH----HHHHHHHHHccCHHHHHHHHhhCc
Confidence 567889999976 3457777 566678889999999999887766
No 4
>PF14225 MOR2-PAG1_C: Cell morphogenesis C-terminal
Probab=77.86 E-value=6.2 Score=29.83 Aligned_cols=47 Identities=13% Similarity=0.255 Sum_probs=35.8
Q ss_pred HHHHHHHhhchhhccCCCCCHHHHHHHHHHHHHHHh--cccHHHHHHHHhc
Q psy7377 30 IKDVLMVLGNFKQYRDPARSRCEYTSLLLKDLCTYF--SYNEFLMERIMQI 78 (83)
Q Consensus 30 Ik~iv~vL~~fk~~r~~grSR~eY~~~L~~Di~~yY--gYn~fL~ek~~~L 78 (83)
..++-+|+..|.+.+= |++.+++.+..+.||.+| .|.-.....++.|
T Consensus 148 ~~~La~il~~ya~~~f--r~~~dfl~~v~~~l~~~f~P~~~~~~l~~Ll~l 196 (262)
T PF14225_consen 148 LPNLARILSSYAKGRF--RDKDDFLSQVVSYLREAFFPDHEFQILTFLLGL 196 (262)
T ss_pred CccHHHHHHHHHhcCC--CCHHHHHHHHHHHHHHHhCchhHHHHHHHHHHH
Confidence 4556677888865554 899999999999999999 5666666555554
No 5
>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III. 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.
Probab=62.41 E-value=28 Score=22.52 Aligned_cols=29 Identities=21% Similarity=0.505 Sum_probs=20.5
Q ss_pred cCCChHHHHHHH------------HHHHHHhhchhhccCCC
Q psy7377 19 KVLSIPDVEQRI------------KDVLMVLGNFKQYRDPA 47 (83)
Q Consensus 19 ~~~dl~~v~~RI------------k~iv~vL~~fk~~r~~g 47 (83)
.|+||.+|+.|+ .|+-.+.+|-+..+.+|
T Consensus 45 ~PmdL~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~ 85 (103)
T cd05520 45 NPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPN 85 (103)
T ss_pred CCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 789999999996 45555555555555555
No 6
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=61.93 E-value=17 Score=24.70 Aligned_cols=40 Identities=25% Similarity=0.312 Sum_probs=30.6
Q ss_pred CCChHHHHHHHHHHHHHhhchhh-ccCCCCCHHHHHHHHHH
Q psy7377 20 VLSIPDVEQRIKDVLMVLGNFKQ-YRDPARSRCEYTSLLLK 59 (83)
Q Consensus 20 ~~dl~~v~~RIk~iv~vL~~fk~-~r~~grSR~eY~~~L~~ 59 (83)
+..-++|++|+.++++.|+--.. -.+...+|.+.++.|.+
T Consensus 60 giSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~ 100 (113)
T PF09862_consen 60 GISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEK 100 (113)
T ss_pred CCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHc
Confidence 57789999999999999977222 23445688898888874
No 7
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=60.64 E-value=23 Score=18.43 Aligned_cols=16 Identities=25% Similarity=0.353 Sum_probs=13.3
Q ss_pred CCCCHHHHHHHHHHHH
Q psy7377 46 PARSRCEYTSLLLKDL 61 (83)
Q Consensus 46 ~grSR~eY~~~L~~Di 61 (83)
.|+||++++..+..+.
T Consensus 21 ~g~s~s~~ir~ai~~~ 36 (39)
T PF01402_consen 21 LGRSRSELIREAIREY 36 (39)
T ss_dssp HTSSHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHHHHH
Confidence 3899999999987754
No 8
>cd05519 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi. 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.
Probab=57.41 E-value=42 Score=21.39 Aligned_cols=31 Identities=16% Similarity=0.504 Sum_probs=21.9
Q ss_pred ccCCChHHHHHHHH------------HHHHHhhchhhccCCCC
Q psy7377 18 DKVLSIPDVEQRIK------------DVLMVLGNFKQYRDPAR 48 (83)
Q Consensus 18 e~~~dl~~v~~RIk------------~iv~vL~~fk~~r~~gr 48 (83)
..|+||.+|++|++ |+-.+.+|-+..+.+|.
T Consensus 44 k~Pmdl~~I~~kl~~~~Y~s~~~f~~D~~li~~Na~~yn~~~s 86 (103)
T cd05519 44 KRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGS 86 (103)
T ss_pred CCCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence 37899999999986 45555566555566653
No 9
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to PFAM model pfam01844, HNH endonuclease.
Probab=56.86 E-value=11 Score=32.90 Aligned_cols=29 Identities=24% Similarity=0.362 Sum_probs=23.9
Q ss_pred HHhhchhhccCC-CCCHHHHHHHHHHHHHH
Q psy7377 35 MVLGNFKQYRDP-ARSRCEYTSLLLKDLCT 63 (83)
Q Consensus 35 ~vL~~fk~~r~~-grSR~eY~~~L~~Di~~ 63 (83)
.||++|-+.-.+ +|+|+.|.+.++.||.+
T Consensus 195 eil~~fdKne~~G~r~R~~Yfeei~~~i~~ 224 (802)
T TIGR03031 195 EILGTFDKNEVEGHRHRKVYFEEIKSDITK 224 (802)
T ss_pred HHhhhhhhcccccCchHHHHHHHHHHHhhh
Confidence 468889766554 69999999999999975
No 10
>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family. 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.
Probab=55.97 E-value=47 Score=22.04 Aligned_cols=14 Identities=21% Similarity=0.601 Sum_probs=12.6
Q ss_pred cCCChHHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIKD 32 (83)
Q Consensus 19 ~~~dl~~v~~RIk~ 32 (83)
.|+||.+|++||+.
T Consensus 45 ~PmDL~tI~~kl~~ 58 (109)
T cd05492 45 THLDVADIQEKINS 58 (109)
T ss_pred CCCcHHHHHHHHHc
Confidence 79999999999974
No 11
>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI. 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.
Probab=55.85 E-value=42 Score=22.49 Aligned_cols=31 Identities=13% Similarity=0.261 Sum_probs=24.3
Q ss_pred hccCCChHHHHHHHH------------HHHHHhhchhhccCCC
Q psy7377 17 ADKVLSIPDVEQRIK------------DVLMVLGNFKQYRDPA 47 (83)
Q Consensus 17 ~e~~~dl~~v~~RIk------------~iv~vL~~fk~~r~~g 47 (83)
+..|+|+..|+.||+ |+-.++.|=+..+.+|
T Consensus 44 ik~Pi~l~~Ik~ki~~~~Y~~ld~~~~D~~lmf~NAr~yN~~~ 86 (110)
T cd05526 44 KKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERARRLSRTD 86 (110)
T ss_pred hcCCccHHHHHHHHHcCCcCcHHHHHHHHHHHHHHHHHhCccc
Confidence 448899999999985 5667777777777776
No 12
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.51 E-value=27 Score=23.64 Aligned_cols=56 Identities=18% Similarity=0.127 Sum_probs=41.0
Q ss_pred cCCChHHHHHHHHHHHHHhhchhhcc---CCCCCHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Q psy7377 19 KVLSIPDVEQRIKDVLMVLGNFKQYR---DPARSRCEYTSLLLKDLCTYFSYNEFLMERIMQI 78 (83)
Q Consensus 19 ~~~dl~~v~~RIk~iv~vL~~fk~~r---~~grSR~eY~~~L~~Di~~yYgYn~fL~ek~~~L 78 (83)
-...-+.|+.-|+.++.+|.+|...- +...-|++..++|+..+..= +.+.+.+-+|
T Consensus 43 ~~VSRqAIyDnIKr~~~~L~~YE~KL~l~~k~~~R~el~d~lk~~~~~~----~~l~~~l~~l 101 (105)
T COG2739 43 FNVSRQAIYDNIKRTEKILEDYEEKLKLYEKYKIRKELYDKLKELITDP----EELREILEDL 101 (105)
T ss_pred hCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCH----HHHHHHHHHh
Confidence 35678999999999999999986532 23457999999888877654 5565555443
No 13
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=54.47 E-value=15 Score=21.82 Aligned_cols=21 Identities=19% Similarity=0.426 Sum_probs=17.8
Q ss_pred CCHHHHHHHHHHHHHHHhccc
Q psy7377 48 RSRCEYTSLLLKDLCTYFSYN 68 (83)
Q Consensus 48 rSR~eY~~~L~~Di~~yYgYn 68 (83)
..-..|-.+|..++|.|||-.
T Consensus 27 ~pm~sy~RllvH~la~~~gL~ 47 (63)
T cd02642 27 PPMNSYYRLLAHRVAQYYGLD 47 (63)
T ss_pred CCCCcHHHHHHHHHHHHhCCe
Confidence 356789999999999999964
No 14
>PF07761 DUF1617: Protein of unknown function (DUF1617); InterPro: IPR011675 This entry is represented by Bacteriophage phi3396 (Streptococcus phage phi3396), Orf51 (Orf: phi3396_51). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry is found in a family of hypothetical bacterial and bacteriophage proteins. The region represented by this entry is approximately 150 residues long and is highly conserved throughout the family.
Probab=49.71 E-value=33 Score=24.29 Aligned_cols=51 Identities=14% Similarity=0.201 Sum_probs=42.7
Q ss_pred HHHHHHHHHHhhchhhcc-CCCCCHHHHHHHHHHHHHHHhcccHHHHHHHHh
Q psy7377 27 EQRIKDVLMVLGNFKQYR-DPARSRCEYTSLLLKDLCTYFSYNEFLMERIMQ 77 (83)
Q Consensus 27 ~~RIk~iv~vL~~fk~~r-~~grSR~eY~~~L~~Di~~yYgYn~fL~ek~~~ 77 (83)
..-|..++.+|.+++-.+ .+.|.|+=.+.+++.=+..|..=...|+..++.
T Consensus 7 N~eL~~i~~~L~~iklk~~kaSraRtKLi~~v~~k~~ey~kDe~dLi~~ya~ 58 (143)
T PF07761_consen 7 NKELNPIYNFLEKIKLKNMKASRARTKLIKLVEEKIKEYAKDEYDLISQYAL 58 (143)
T ss_pred hHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHhhhHHHHHHHHHh
Confidence 346788999999997764 678999999999999999998888888877653
No 15
>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V. 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.
Probab=49.59 E-value=30 Score=22.30 Aligned_cols=29 Identities=21% Similarity=0.578 Sum_probs=21.1
Q ss_pred cCCChHHHHHHHH------------HHHHHhhchhhccCCC
Q psy7377 19 KVLSIPDVEQRIK------------DVLMVLGNFKQYRDPA 47 (83)
Q Consensus 19 ~~~dl~~v~~RIk------------~iv~vL~~fk~~r~~g 47 (83)
.|+||.+|++||+ |+-.+.+|-+..+.+|
T Consensus 45 ~PmdL~tI~~kl~~~~Y~s~~ef~~D~~l~~~Na~~yN~~~ 85 (105)
T cd05515 45 KPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPD 85 (105)
T ss_pred CCcCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 7899999999964 5556666666666555
No 16
>PF13907 DUF4208: Domain of unknown function (DUF4208)
Probab=48.50 E-value=71 Score=20.50 Aligned_cols=45 Identities=18% Similarity=0.217 Sum_probs=36.5
Q ss_pred cCCChHHHHHHHHHHHHHhhchhhccCCCCCHHHHHHHHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLKDLCTY 64 (83)
Q Consensus 19 ~~~dl~~v~~RIk~iv~vL~~fk~~r~~grSR~eY~~~L~~Di~~y 64 (83)
..++....+..++-|-..|...+.. .+|.++.+.+..|++.|..-
T Consensus 11 ds~~~~~ck~~m~Pvkk~LkkL~~~-~~~l~~~e~a~~lk~~L~~I 55 (100)
T PF13907_consen 11 DSMDEDECKELMRPVKKSLKKLKKP-KKGLPRKERAKILKKELLKI 55 (100)
T ss_pred CccHHHHHHHHhHHHHHHHHHhccC-CCCCCHHHHHHHHHHHHHHH
Confidence 4577788999999999888888766 45889999999998887653
No 17
>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily. 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.
Probab=47.65 E-value=63 Score=20.37 Aligned_cols=29 Identities=17% Similarity=0.501 Sum_probs=21.8
Q ss_pred cCCChHHHHHHHH------------HHHHHhhchhhccCCC
Q psy7377 19 KVLSIPDVEQRIK------------DVLMVLGNFKQYRDPA 47 (83)
Q Consensus 19 ~~~dl~~v~~RIk------------~iv~vL~~fk~~r~~g 47 (83)
.|+||.+|++|++ |+-.|..|-+..+.+|
T Consensus 39 ~PmdL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~ 79 (97)
T cd05503 39 KPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDD 79 (97)
T ss_pred CCCCHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 7899999999985 5666666666666654
No 18
>smart00297 BROMO bromo domain.
Probab=46.72 E-value=68 Score=19.74 Aligned_cols=15 Identities=7% Similarity=0.514 Sum_probs=12.8
Q ss_pred ccCCChHHHHHHHHH
Q psy7377 18 DKVLSIPDVEQRIKD 32 (83)
Q Consensus 18 e~~~dl~~v~~RIk~ 32 (83)
..|+||.+|++|++.
T Consensus 45 ~~P~dl~~I~~kl~~ 59 (107)
T smart00297 45 KKPMDLSTIKKKLEN 59 (107)
T ss_pred cCCCCHHHHHHHHhc
Confidence 378999999999863
No 19
>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup. 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.
Probab=46.35 E-value=77 Score=20.30 Aligned_cols=13 Identities=8% Similarity=0.480 Sum_probs=11.9
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|++||+
T Consensus 42 ~PmDL~tI~~kl~ 54 (104)
T cd05507 42 RPMDLSTIKKNIE 54 (104)
T ss_pred CCcCHHHHHHHHh
Confidence 7899999999985
No 20
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=46.29 E-value=1.2e+02 Score=22.91 Aligned_cols=59 Identities=17% Similarity=0.255 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHhhchhhccCCCCCHHHHHH-------HHHHHHHHH-------hcccH-HHHHHHHhcCCCC
Q psy7377 24 PDVEQRIKDVLMVLGNFKQYRDPARSRCEYTS-------LLLKDLCTY-------FSYNE-FLMERIMQIFPLD 82 (83)
Q Consensus 24 ~~v~~RIk~iv~vL~~fk~~r~~grSR~eY~~-------~L~~Di~~y-------YgYn~-fL~ek~~~LF~~~ 82 (83)
+..-.|..-.-++|+.+.+-..+-.|-++.-+ ++++|.+.+ ||||- .|..-|-++++.+
T Consensus 9 ~AT~kRL~~YyR~le~l~a~~v~rvsS~els~~~~vdsatIRrDfSYFG~lGkrG~GYnV~~L~~ff~~~Lg~~ 82 (211)
T COG2344 9 KATAKRLPLYYRVLERLHASGVERVSSKELSEALGVDSATIRRDFSYFGELGKRGYGYNVKYLRDFFDDLLGQD 82 (211)
T ss_pred HHHHHHhHHHHHHHHHHHHcCCceecHHHHHHHhCCCHHHHhhhhHHHHhcCCCCCCccHHHHHHHHHHHhCCC
Confidence 34566888888999888777766667666654 568888876 89994 5666666666543
No 21
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=45.98 E-value=79 Score=20.28 Aligned_cols=54 Identities=19% Similarity=0.228 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHhhchhhccC-C--CCCHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Q psy7377 24 PDVEQRIKDVLMVLGNFKQYRD-P--ARSRCEYTSLLLKDLCTYFSYNEFLMERIMQI 78 (83)
Q Consensus 24 ~~v~~RIk~iv~vL~~fk~~r~-~--grSR~eY~~~L~~Di~~yYgYn~fL~ek~~~L 78 (83)
..+.+|++-+-.| +.+|.... + ...|...+-.=....+.=+|..+++++.|+.+
T Consensus 21 ~LL~~R~~~~~~i-a~~K~~~~~~v~dp~Re~~vl~~~~~~a~~~gl~p~~~e~i~~~ 77 (94)
T TIGR01795 21 HMLAERFKCTSQV-GVLKANAGLAPADPAREDYQIARLRRLAIDAGLDPEFAEKFLNF 77 (94)
T ss_pred HHHHHHHHHHHHH-HHHHHhCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 4466677655555 66666543 1 45677777777789999999999999999875
No 22
>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily. 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.
Probab=45.86 E-value=55 Score=21.05 Aligned_cols=29 Identities=7% Similarity=0.327 Sum_probs=21.4
Q ss_pred cCCChHHHHHHHHH---------------HHHHhhchhhccCCC
Q psy7377 19 KVLSIPDVEQRIKD---------------VLMVLGNFKQYRDPA 47 (83)
Q Consensus 19 ~~~dl~~v~~RIk~---------------iv~vL~~fk~~r~~g 47 (83)
.|+||.+|++|++. +-.|..|-+..+.+|
T Consensus 42 ~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~~yN~~~ 85 (109)
T cd05502 42 TPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNEED 85 (109)
T ss_pred CCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 78999999999985 444556666666665
No 23
>cd05521 Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. 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.
Probab=45.83 E-value=37 Score=22.16 Aligned_cols=14 Identities=29% Similarity=0.489 Sum_probs=12.5
Q ss_pred cCCChHHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIKD 32 (83)
Q Consensus 19 ~~~dl~~v~~RIk~ 32 (83)
.|+||.+|++|++.
T Consensus 46 ~PmdL~tI~~kl~~ 59 (106)
T cd05521 46 NPLSLNTVKKRLPH 59 (106)
T ss_pred CCCCHHHHHHHHHc
Confidence 89999999999874
No 24
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=45.17 E-value=69 Score=19.40 Aligned_cols=44 Identities=25% Similarity=0.363 Sum_probs=33.4
Q ss_pred ChHHHHHHHHHHHHHhhchhhccC-CCCCHHHHHHHHHHHHHHHh
Q psy7377 22 SIPDVEQRIKDVLMVLGNFKQYRD-PARSRCEYTSLLLKDLCTYF 65 (83)
Q Consensus 22 dl~~v~~RIk~iv~vL~~fk~~r~-~grSR~eY~~~L~~Di~~yY 65 (83)
-|..+..||+-+-.|=...-.-.. ...+=++|+..|..+++.=|
T Consensus 32 ~L~~~~~RI~aia~vh~~L~~~~~~~~v~l~~yl~~L~~~l~~sy 76 (76)
T PF07568_consen 32 ALEDAQNRIQAIALVHEQLYQSEDLSEVDLREYLEELCEDLRQSY 76 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCeecHHHHHHHHHHHHHHhC
Confidence 477888999998888776544333 34677899999999998755
No 25
>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup. 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.
Probab=44.44 E-value=44 Score=21.50 Aligned_cols=29 Identities=21% Similarity=0.463 Sum_probs=20.0
Q ss_pred cCCChHHHHHHHH------------HHHHHhhchhhccCCC
Q psy7377 19 KVLSIPDVEQRIK------------DVLMVLGNFKQYRDPA 47 (83)
Q Consensus 19 ~~~dl~~v~~RIk------------~iv~vL~~fk~~r~~g 47 (83)
.|+||.+|++|++ |+-.|.+|=...+.+|
T Consensus 40 ~PmDL~tI~~kl~~~~Y~s~~~f~~D~~li~~Na~~yN~~~ 80 (98)
T cd05513 40 HPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPD 80 (98)
T ss_pred CccCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 7899999999984 4555555555555554
No 26
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=43.71 E-value=56 Score=22.07 Aligned_cols=31 Identities=19% Similarity=0.418 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHhhchhhccCCCCCHHHHHHHHHHH
Q psy7377 24 PDVEQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLKD 60 (83)
Q Consensus 24 ~~v~~RIk~iv~vL~~fk~~r~~grSR~eY~~~L~~D 60 (83)
..++.||..||+++++ .+.|=+-|++.+..+
T Consensus 87 ~e~h~~l~~Iv~~ig~------~~~si~~yidNIL~~ 117 (136)
T PF11888_consen 87 RETHERLSRIVRVIGE------RKMSISGYIDNILRH 117 (136)
T ss_pred HHHHHHHHHHHHHHCC------CCCcHHHHHHHHHHH
Confidence 5689999999999964 478889999877654
No 27
>KOG2183|consensus
Probab=43.60 E-value=30 Score=28.92 Aligned_cols=48 Identities=17% Similarity=0.395 Sum_probs=36.2
Q ss_pred ChHHHHHHHHHHHHHhhc--------h-------------hhccCCCCCHHHHHHHHHHHHHHHhcccH
Q psy7377 22 SIPDVEQRIKDVLMVLGN--------F-------------KQYRDPARSRCEYTSLLLKDLCTYFSYNE 69 (83)
Q Consensus 22 dl~~v~~RIk~iv~vL~~--------f-------------k~~r~~grSR~eY~~~L~~Di~~yYgYn~ 69 (83)
|+..+++=+++....|+= | +.+..+|.++++.++++.+=+..||.|+-
T Consensus 266 d~~~l~d~l~ea~~ylAMVdYPy~t~Fl~pLPa~PV~~~C~~i~~~~~~~~~ll~~i~a~~~~yyNytg 334 (492)
T KOG2183|consen 266 DIGDLKDYLREAYEYLAMVDYPYPTSFLAPLPAWPVKVVCKYINAPGPNDSDLLDRIFAAVNLYYNYTG 334 (492)
T ss_pred cHHHHHHHHHHHHHHHHHhcCCCCccccCcCCCCcHHHHHHHhccCCCChHHHHHHHHHHhhheeccCC
Confidence 677777777766555531 1 23456789999999999999999999984
No 28
>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I. 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.
Probab=42.93 E-value=76 Score=20.77 Aligned_cols=30 Identities=20% Similarity=0.488 Sum_probs=22.6
Q ss_pred cCCChHHHHHHH------------HHHHHHhhchhhccCCCC
Q psy7377 19 KVLSIPDVEQRI------------KDVLMVLGNFKQYRDPAR 48 (83)
Q Consensus 19 ~~~dl~~v~~RI------------k~iv~vL~~fk~~r~~gr 48 (83)
.|+||.+|++|| .|+-.+.+|-+..+.+|.
T Consensus 47 ~Pmdl~tI~~kl~~~~Y~s~~~f~~D~~lm~~Na~~yN~~~s 88 (113)
T cd05524 47 NPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDS 88 (113)
T ss_pred CccCHHHHHHHhCcCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence 799999999997 456666666666666663
No 29
>PF12180 EABR: TSG101 and ALIX binding domain of CEP55; InterPro: IPR022008 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR. ; PDB: 3E1R_A.
Probab=42.16 E-value=47 Score=18.36 Aligned_cols=32 Identities=31% Similarity=0.501 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhhchhhccCCCCCHHHHHHHHHHHH
Q psy7377 27 EQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLKDL 61 (83)
Q Consensus 27 ~~RIk~iv~vL~~fk~~r~~grSR~eY~~~L~~Di 61 (83)
+++++++...-+.|-..- .||.+||.-|..=|
T Consensus 1 ~~ql~~v~e~N~qWq~YD---~qRE~YV~~L~~rl 32 (35)
T PF12180_consen 1 KQQLRDVLEKNQQWQKYD---QQREAYVRGLLARL 32 (35)
T ss_dssp HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHH---HhHHHHHHHHHHHH
Confidence 356777777777775553 48999998876543
No 30
>cd05024 S-100A10 S-100A10: A subgroup of the S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A10 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions.
Probab=41.42 E-value=98 Score=20.07 Aligned_cols=51 Identities=14% Similarity=0.397 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHhhchhhccCC-CCCHHHHHHHHHHHHHHHhcc--cHHHHHHHHhc
Q psy7377 26 VEQRIKDVLMVLGNFKQYRDP-ARSRCEYTSLLLKDLCTYFSY--NEFLMERIMQI 78 (83)
Q Consensus 26 v~~RIk~iv~vL~~fk~~r~~-grSR~eY~~~L~~Di~~yYgY--n~fL~ek~~~L 78 (83)
+.+=|..+|.|...|. +++ -.||+|..++|.+.+..+-+= ++..++++|+-
T Consensus 3 LE~ai~~lI~~FhkYa--G~~~tLsk~Elk~Ll~~Elp~~l~~~~d~~~vd~im~~ 56 (91)
T cd05024 3 LEHSMEKMMLTFHKFA--GEKNYLNRDDLQKLMEKEFSEFLKNQNDPMAVDKIMKD 56 (91)
T ss_pred HHHHHHHHHHHHHHHc--CCCCcCCHHHHHHHHHHHhHHHHcCCCCHHHHHHHHHH
Confidence 4556777888777775 344 369999999999999987764 56667777643
No 31
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=39.78 E-value=69 Score=20.83 Aligned_cols=43 Identities=14% Similarity=0.308 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHhh----------chhhccCCCCCHHHHHHHHHHHHHHHhccc
Q psy7377 25 DVEQRIKDVLMVLG----------NFKQYRDPARSRCEYTSLLLKDLCTYFSYN 68 (83)
Q Consensus 25 ~v~~RIk~iv~vL~----------~fk~~r~~grSR~eY~~~L~~Di~~yYgYn 68 (83)
.....|++++..|. .++.+-++ ..|....+.+.+.+|.+||++
T Consensus 73 ~~~~~l~~~~~lL~~~~~~~~~~s~~~~l~~~-~~~~~la~~~~~~~l~~~~~~ 125 (145)
T PF10607_consen 73 EFLEELKKLMSLLAYPDPEEPLPSPYKELLSP-ERREELAEEFNSAILKSYGLP 125 (145)
T ss_pred HHHHHHHHHHHHHHcCCcccccchHHHHHhCh-HHHHHHHHHHHHHHHHHhCcC
Confidence 35567888888872 33333333 358999999999999999997
No 32
>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I. 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.
Probab=38.63 E-value=1.1e+02 Score=19.85 Aligned_cols=29 Identities=17% Similarity=0.423 Sum_probs=20.5
Q ss_pred cCCChHHHHHHHH------------HHHHHhhchhhccCCC
Q psy7377 19 KVLSIPDVEQRIK------------DVLMVLGNFKQYRDPA 47 (83)
Q Consensus 19 ~~~dl~~v~~RIk------------~iv~vL~~fk~~r~~g 47 (83)
.|+||.+|+.|++ |+-.|.+|=...+.+|
T Consensus 46 ~PmDL~tI~~kL~~~~Y~s~~ef~~D~~li~~Na~~yN~~~ 86 (107)
T cd05497 46 TPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPG 86 (107)
T ss_pred CcccHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 7899999999984 5555555555555554
No 33
>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). 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.
Probab=38.43 E-value=1.1e+02 Score=19.58 Aligned_cols=29 Identities=14% Similarity=0.406 Sum_probs=19.7
Q ss_pred cCCChHHHHHHHH------------HHHHHhhchhhccCCC
Q psy7377 19 KVLSIPDVEQRIK------------DVLMVLGNFKQYRDPA 47 (83)
Q Consensus 19 ~~~dl~~v~~RIk------------~iv~vL~~fk~~r~~g 47 (83)
.|+||.+|+.|++ |+-.|..|=+..+.+|
T Consensus 39 ~PmDL~tI~~kl~~~~Y~s~~ef~~D~~li~~Na~~yN~~~ 79 (97)
T cd05505 39 NPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENG 79 (97)
T ss_pred CcCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 7899999999984 4444555555555555
No 34
>PF08951 EntA_Immun: Enterocin A Immunity; InterPro: IPR015046 Gram-positive lactobacilli produce bacteriocins to kill closely-related competitor species []. To protect themselves from the bacteriocidal activity of this molecule they co-express an immunity protein (for discussion of this operon see Bacteriocin_IIc PF10439 from PFAM). The immunity protein structure is a soluble, cytoplasmic, antiparallel four alpha-helical globular bundle with a fifth, more flexible and more divergent C-terminal helical hair-pin []. The C-terminal hair-pin recognises the C terminus of the producer bacteriocin and this interaction is sufficient to dis-orient the bacteriocin within the membrane and close up the permeabilising pore that on its own the bacteriocin creates []. These immunity proteins interact in the same way with other bacteriocins, family Bacteriocin_II, PF01721 from PFAM. Since many enterococci can produce more than one bacteriocin it seems likely that the whole operon can be carried on transferable plasmids []. ; PDB: 2BL8_C 2BL7_A 2K19_A 2FU2_A 1TDP_A 2IP6_A.
Probab=37.67 E-value=80 Score=18.15 Aligned_cols=35 Identities=20% Similarity=0.104 Sum_probs=28.8
Q ss_pred HHHHHhhchhhccCCCCCHHHHHHHHHHHHHHHhc
Q psy7377 32 DVLMVLGNFKQYRDPARSRCEYTSLLLKDLCTYFS 66 (83)
Q Consensus 32 ~iv~vL~~fk~~r~~grSR~eY~~~L~~Di~~yYg 66 (83)
++..+|..+++.-+.|..=...+..|..+|+.|.-
T Consensus 24 ~lr~iL~~a~~~l~~~~~~~~v~~~L~~~l~~~~~ 58 (75)
T PF08951_consen 24 ELRKILLKAKNELEKGENVPLVASRLNNDLSPYAL 58 (75)
T ss_dssp HHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHH
Confidence 55678888888888888888899999999988753
No 35
>PF07159 DUF1394: Protein of unknown function (DUF1394); InterPro: IPR009828 This family consists of several hypothetical eukaryotic proteins of around 320 residues in length. The function of this family is unknown.
Probab=37.56 E-value=73 Score=24.94 Aligned_cols=70 Identities=20% Similarity=0.269 Sum_probs=48.7
Q ss_pred CCCChHHhccCCChHHHHHHHHHHHHHhhchhhccC------CCCCHH-------HHHHHHHHHHHHHhcccHHHHHHHH
Q psy7377 10 AFPSEEEADKVLSIPDVEQRIKDVLMVLGNFKQYRD------PARSRC-------EYTSLLLKDLCTYFSYNEFLMERIM 76 (83)
Q Consensus 10 ~lp~~ee~e~~~dl~~v~~RIk~iv~vL~~fk~~r~------~grSR~-------eY~~~L~~Di~~yYgYn~fL~ek~~ 76 (83)
.-||.+|.+--..+..|-.+-..++..|..|+.-.+ ..-|+. +-+.=+..=|..||.|+..+...|.
T Consensus 10 a~Pt~~E~ev~~~v~~VL~~~~~iL~~L~~Yrgas~~Ir~Ai~~Ps~ee~qe~aw~al~P~V~kLk~Fy~Fs~~le~~~~ 89 (303)
T PF07159_consen 10 AQPTEEEREVYNEVNEVLEEGEQILQDLYTYRGASREIRQAISNPSDEELQEKAWEALEPLVKKLKEFYEFSQELEKVFP 89 (303)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhccCchHHHHHHHcCCChHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 568888887555667777788888888888854321 123555 3334456778899999999988876
Q ss_pred hcC
Q psy7377 77 QIF 79 (83)
Q Consensus 77 ~LF 79 (83)
.+.
T Consensus 90 ~ll 92 (303)
T PF07159_consen 90 KLL 92 (303)
T ss_pred HHH
Confidence 654
No 36
>PHA00617 ribbon-helix-helix domain containing protein
Probab=35.89 E-value=1.1e+02 Score=19.60 Aligned_cols=28 Identities=18% Similarity=0.383 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHhhchhhccCCCCCHHHHHHHHHHH
Q psy7377 24 PDVEQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLKD 60 (83)
Q Consensus 24 ~~v~~RIk~iv~vL~~fk~~r~~grSR~eY~~~L~~D 60 (83)
+.+.+|+..+... .|+||++++.+..++
T Consensus 48 ~eL~erLD~LA~~---------~GrsRSelIreAI~~ 75 (80)
T PHA00617 48 PELNAKLEQVAIK---------MKKSKSEIIREALEK 75 (80)
T ss_pred HHHHHHHHHHHHH---------hCcCHHHHHHHHHHH
Confidence 3456676666553 489999999887664
No 37
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=35.14 E-value=91 Score=20.19 Aligned_cols=42 Identities=19% Similarity=0.249 Sum_probs=27.9
Q ss_pred CChHHHHHHHHHHHHHh----hchhh-ccCCCCCHHHHHHHHHHHHH
Q psy7377 21 LSIPDVEQRIKDVLMVL----GNFKQ-YRDPARSRCEYTSLLLKDLC 62 (83)
Q Consensus 21 ~dl~~v~~RIk~iv~vL----~~fk~-~r~~grSR~eY~~~L~~Di~ 62 (83)
.+=+.|.+.|.++..-. +.|++ +...|.|-.+|.++++++|.
T Consensus 67 vsd~evd~~i~~ia~~n~ls~~ql~~~L~~~G~s~~~~r~~ir~~i~ 113 (118)
T PF09312_consen 67 VSDEEVDEAIANIAKQNNLSVEQLRQQLEQQGISYEEYREQIRKQIL 113 (118)
T ss_dssp --HHHHHHHHHHHHHHTT--HHHHHHHCHHCT--HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 45566777777776543 45665 34579999999999999985
No 38
>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily. 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.
Probab=34.18 E-value=39 Score=21.79 Aligned_cols=14 Identities=14% Similarity=0.510 Sum_probs=12.3
Q ss_pred cCCChHHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIKD 32 (83)
Q Consensus 19 ~~~dl~~v~~RIk~ 32 (83)
.|+||.+|++||+.
T Consensus 41 ~PmDL~tI~~kl~~ 54 (99)
T cd05508 41 KPMDLSTLEKNVRK 54 (99)
T ss_pred CCCCHHHHHHHHhc
Confidence 78999999999853
No 39
>cd05516 Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, specific to animals. 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.
Probab=32.82 E-value=68 Score=20.71 Aligned_cols=13 Identities=23% Similarity=0.565 Sum_probs=11.9
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|++|++
T Consensus 46 ~Pmdl~tI~~kl~ 58 (107)
T cd05516 46 KPVDFKKIKERIR 58 (107)
T ss_pred CCCCHHHHHHHHc
Confidence 7899999999985
No 40
>PF14846 DUF4485: Domain of unknown function (DUF4485)
Probab=32.50 E-value=36 Score=21.51 Aligned_cols=37 Identities=32% Similarity=0.268 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhhchhhccCCCCCHHHHHHHHHHHHH
Q psy7377 26 VEQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLKDLC 62 (83)
Q Consensus 26 v~~RIk~iv~vL~~fk~~r~~grSR~eY~~~L~~Di~ 62 (83)
-++|...++.=|..-..-..+.+.|..|+..|..-+.
T Consensus 25 ~k~~a~~Wl~KL~~~~~~~~~~~~RN~Y~~~Ll~~l~ 61 (85)
T PF14846_consen 25 EKQRAALWLKKLCEPPHNVEEKKNRNEYASLLLHCLQ 61 (85)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 5678888888777654333446899999999987653
No 41
>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV. 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.
Probab=31.53 E-value=31 Score=22.34 Aligned_cols=13 Identities=15% Similarity=0.508 Sum_probs=11.7
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|+.+++
T Consensus 45 ~Pmdl~tI~~kl~ 57 (103)
T cd05518 45 EPIDLKTIEHNIR 57 (103)
T ss_pred CCcCHHHHHHHHC
Confidence 7999999999985
No 42
>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family. 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.
Probab=30.98 E-value=31 Score=22.49 Aligned_cols=13 Identities=15% Similarity=0.406 Sum_probs=11.8
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|+++++
T Consensus 47 ~P~dL~tI~~kl~ 59 (106)
T cd05525 47 DPVDLSTIEKQIL 59 (106)
T ss_pred CCcCHHHHHHHHc
Confidence 7899999999984
No 43
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=30.97 E-value=97 Score=23.58 Aligned_cols=32 Identities=22% Similarity=0.227 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhhchhhccCCCCCHHHHHHHHHH
Q psy7377 26 VEQRIKDVLMVLGNFKQYRDPARSRCEYTSLLLK 59 (83)
Q Consensus 26 v~~RIk~iv~vL~~fk~~r~~grSR~eY~~~L~~ 59 (83)
-+.||+-.+.+|+.- ++..+.||.+-++.|++
T Consensus 6 ~r~RI~va~~l~~~i--l~~~~~~R~~lv~~L~~ 37 (231)
T PF09958_consen 6 YRKRIEVATDLWSRI--LRGEVLDREELVELLRE 37 (231)
T ss_pred HHHHHHHHHHHHHHH--HHhccCCHHHHHHHHHH
Confidence 366999999999875 44478999999999985
No 44
>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II. 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.
Probab=30.35 E-value=30 Score=22.38 Aligned_cols=13 Identities=23% Similarity=0.537 Sum_probs=12.0
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|+.|++
T Consensus 45 ~PmdL~tI~~kl~ 57 (103)
T cd05517 45 EPIDLKTIAQRIQ 57 (103)
T ss_pred CCcCHHHHHHHHC
Confidence 7999999999986
No 45
>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily. 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.
Probab=30.20 E-value=49 Score=22.10 Aligned_cols=13 Identities=8% Similarity=0.217 Sum_probs=11.8
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|++|++
T Consensus 44 ~PmDL~tIk~kL~ 56 (119)
T cd05496 44 TPMDLGTVKETLF 56 (119)
T ss_pred CcccHHHHHHHHh
Confidence 7899999999985
No 46
>KOG3377|consensus
Probab=30.15 E-value=1.8e+02 Score=20.72 Aligned_cols=43 Identities=14% Similarity=0.210 Sum_probs=36.8
Q ss_pred ChHHHHHHHHHHHHHhhc-hhhccCCCCCHHHHHHHHHHHHHHH
Q psy7377 22 SIPDVEQRIKDVLMVLGN-FKQYRDPARSRCEYTSLLLKDLCTY 64 (83)
Q Consensus 22 dl~~v~~RIk~iv~vL~~-fk~~r~~grSR~eY~~~L~~Di~~y 64 (83)
.|...+.|+...+.+=.| |+.--.+|-+|.++..++-.+...+
T Consensus 77 El~~FQ~RL~Rc~m~C~Dk~~~~~~~~~~~~~~~~~~e~Cvn~c 120 (143)
T KOG3377|consen 77 ELGKFQDRLNRCLMVCNDKFEASKLQGSKRLKAVQQFESCVNKC 120 (143)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHhcccCCchHHHHHHHHHHHHHH
Confidence 678899999999999876 9888888988999999998776543
No 47
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=28.73 E-value=1.3e+02 Score=22.41 Aligned_cols=41 Identities=32% Similarity=0.369 Sum_probs=28.3
Q ss_pred CCChHHHHHHHHHHHHHhhchhhccCCC---------CCHHHHHHHHHHHHHH
Q psy7377 20 VLSIPDVEQRIKDVLMVLGNFKQYRDPA---------RSRCEYTSLLLKDLCT 63 (83)
Q Consensus 20 ~~dl~~v~~RIk~iv~vL~~fk~~r~~g---------rSR~eY~~~L~~Di~~ 63 (83)
+...+.--.|||+...=|-+-|.+-++. |.|+.| |+.|+-+
T Consensus 83 ~lspeeAaaRiK~sA~dLl~vK~LId~~aW~YVq~~LRlkasy---LryDL~t 132 (190)
T PLN02999 83 GLSPEDAAARIKQTAEGLRDMREMLDHMSWRYVIFYIRLKQAY---LSQDLTN 132 (190)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHH---HHHHHHH
Confidence 4556666778888888777777776654 678888 4555543
No 48
>PF01506 HCV_NS5a: Hepatitis C virus non-structural 5a protein membrane anchor; InterPro: IPR002868 The molecular function of the non-structural 5a viral protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the dsRNA-dependent (interferon inducible) kinase PKR, P19525 from SWISSPROT [, ].; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1R7F_A 1R7E_A 1R7C_A 1R7G_A 1R7D_A.
Probab=28.72 E-value=37 Score=16.99 Aligned_cols=13 Identities=38% Similarity=0.322 Sum_probs=10.3
Q ss_pred HHHHHHHhhchhh
Q psy7377 30 IKDVLMVLGNFKQ 42 (83)
Q Consensus 30 Ik~iv~vL~~fk~ 42 (83)
..-++++|++|++
T Consensus 8 WdWvc~~l~~~~~ 20 (23)
T PF01506_consen 8 WDWVCRVLRDFKT 20 (23)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4568999999976
No 49
>cd05500 Bromo_BDF1_2_I Bromodomain. 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.
Probab=28.60 E-value=1.6e+02 Score=18.65 Aligned_cols=13 Identities=23% Similarity=0.585 Sum_probs=11.8
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|+.|++
T Consensus 45 ~P~dL~tI~~kl~ 57 (103)
T cd05500 45 KPMDLGTIERKLK 57 (103)
T ss_pred CCCCHHHHHHHHh
Confidence 7899999999986
No 50
>COG3526 Uncharacterized protein conserved in bacteria [Posttranslational modification, protein turnover, chaperones]
Probab=26.57 E-value=48 Score=22.03 Aligned_cols=17 Identities=18% Similarity=0.284 Sum_probs=14.4
Q ss_pred CCChHHHHHHHHHHHHH
Q psy7377 20 VLSIPDVEQRIKDVLMV 36 (83)
Q Consensus 20 ~~dl~~v~~RIk~iv~v 36 (83)
-|+...++||++++|.-
T Consensus 68 FP~ak~LKQrvRD~idP 84 (99)
T COG3526 68 FPEAKVLKQRVRDLIDP 84 (99)
T ss_pred CCchHHHHHHHHhhcCc
Confidence 48899999999998853
No 51
>smart00741 SapB Saposin (B) Domains. Present in multiple copies in prosaposin and in pulmonary surfactant-associated protein B. In plant aspartic proteinases, a saposin domain is circularly permuted. This causes the prediction algorithm to predict two such domains, where only one is truly present.
Probab=26.41 E-value=1.2e+02 Score=16.70 Aligned_cols=31 Identities=16% Similarity=0.229 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHhc-------------ccHHHHHHHHhcCCC
Q psy7377 51 CEYTSLLLKDLCTYFS-------------YNEFLMERIMQIFPL 81 (83)
Q Consensus 51 ~eY~~~L~~Di~~yYg-------------Yn~fL~ek~~~LF~~ 81 (83)
.+.+......+|.+.+ |-+.++..+.+-.+|
T Consensus 23 ~~~i~~~~~~~C~~~~~~~~~~C~~~v~~~~~~ii~~i~~~~~p 66 (76)
T smart00741 23 EEEIKKALEKVCKKLPKSLSDQCKEFVDQYGPEIIDLLEQGLDP 66 (76)
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHHHhCCCH
Confidence 4556666666777666 445555555554443
No 52
>PF14401 RLAN: RimK-like ATPgrasp N-terminal domain
Probab=26.02 E-value=1.3e+02 Score=20.95 Aligned_cols=19 Identities=32% Similarity=0.628 Sum_probs=15.4
Q ss_pred HHhccc-----HHHHHHHHhcCCC
Q psy7377 63 TYFSYN-----EFLMERIMQIFPL 81 (83)
Q Consensus 63 ~yYgYn-----~fL~ek~~~LF~~ 81 (83)
.|||-+ +.|+.++|+.||.
T Consensus 90 iyFG~~~~~~~~~lAr~lFe~F~~ 113 (153)
T PF14401_consen 90 IYFGQTPDPRLERLARQLFERFPC 113 (153)
T ss_pred EEECCCCCHHHHHHHHHHHHhCCC
Confidence 588877 4699999999984
No 53
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=25.91 E-value=1.7e+02 Score=18.19 Aligned_cols=37 Identities=19% Similarity=0.266 Sum_probs=28.1
Q ss_pred HHHHHhhchhhcc-----CC-CCCHHHHHHHHHHHHHHHhccc
Q psy7377 32 DVLMVLGNFKQYR-----DP-ARSRCEYTSLLLKDLCTYFSYN 68 (83)
Q Consensus 32 ~iv~vL~~fk~~r-----~~-grSR~eY~~~L~~Di~~yYgYn 68 (83)
-|-.||++|..++ .+ |+.-++=.+.|..+|+.||..|
T Consensus 5 ~V~~vl~~WtaL~lAVen~wGG~~s~~K~~~l~~~i~~~f~~~ 47 (82)
T PF10273_consen 5 GVRLVLNRWTALQLAVENGWGGPDSQEKADWLAEVIVDWFTEN 47 (82)
T ss_pred HHHHHHhcCHHHHHHHHhccCCccHHHHHHHHHHHHHHHHhcC
Confidence 3567888888775 23 5666777788999999999887
No 54
>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily. 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.
Probab=24.87 E-value=2.1e+02 Score=18.73 Aligned_cols=13 Identities=8% Similarity=0.468 Sum_probs=11.7
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|++|++
T Consensus 51 ~PmDL~tI~~kL~ 63 (115)
T cd05504 51 KPMDLGTIKEKLN 63 (115)
T ss_pred CcccHHHHHHHHc
Confidence 7899999999975
No 55
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=24.81 E-value=1.9e+02 Score=18.35 Aligned_cols=36 Identities=25% Similarity=0.410 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhhchhhcc-CCCCCHHHHHHHHHHHHH
Q psy7377 27 EQRIKDVLMVLGNFKQYR-DPARSRCEYTSLLLKDLC 62 (83)
Q Consensus 27 ~~RIk~iv~vL~~fk~~r-~~grSR~eY~~~L~~Di~ 62 (83)
..||++++.-.......- +...||.+|-.+|..=|.
T Consensus 37 d~rm~~l~~yarkvE~~~fe~A~sreeYY~llA~kiy 73 (81)
T PF02172_consen 37 DPRMKNLIEYARKVEKDMFETAQSREEYYHLLAEKIY 73 (81)
T ss_dssp SHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 458898888876654422 445699999999987554
No 56
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=24.70 E-value=61 Score=17.38 Aligned_cols=12 Identities=25% Similarity=0.775 Sum_probs=9.8
Q ss_pred HHHHHHHHhcCC
Q psy7377 69 EFLMERIMQIFP 80 (83)
Q Consensus 69 ~fL~ek~~~LF~ 80 (83)
+..++.+.+|||
T Consensus 2 ~~~v~~L~~mFP 13 (42)
T PF02845_consen 2 EEMVQQLQEMFP 13 (42)
T ss_dssp HHHHHHHHHHSS
T ss_pred HHHHHHHHHHCC
Confidence 567788999998
No 57
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=24.57 E-value=1.2e+02 Score=18.71 Aligned_cols=25 Identities=16% Similarity=0.308 Sum_probs=18.7
Q ss_pred HhhchhhccCCCCCHHHHHHHHHHH
Q psy7377 36 VLGNFKQYRDPARSRCEYTSLLLKD 60 (83)
Q Consensus 36 vL~~fk~~r~~grSR~eY~~~L~~D 60 (83)
+...|.++++...||.+.+..++.=
T Consensus 30 l~~~Y~~~k~~kIsR~~fvr~lR~I 54 (70)
T PF12174_consen 30 LQKHYEEFKKKKISREEFVRKLRQI 54 (70)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHH
Confidence 3445666677788999999988753
No 58
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=23.76 E-value=1.1e+02 Score=24.02 Aligned_cols=23 Identities=17% Similarity=0.480 Sum_probs=20.5
Q ss_pred HHHHHHHhcccHHHHHHHHhcCC
Q psy7377 58 LKDLCTYFSYNEFLMERIMQIFP 80 (83)
Q Consensus 58 ~~Di~~yYgYn~fL~ek~~~LF~ 80 (83)
..|+|..|+|.+.|++++.+.|+
T Consensus 134 ~~~~~~~~s~P~wl~~~~~~~~~ 156 (427)
T PRK10901 134 QADPVARYNHPSWLIKRLKKAYP 156 (427)
T ss_pred hhchHhHhcCCHHHHHHHHHHhH
Confidence 56889999999999999998874
No 59
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=23.49 E-value=77 Score=21.91 Aligned_cols=15 Identities=27% Similarity=0.189 Sum_probs=12.6
Q ss_pred CCHHHHHHHHHHHHH
Q psy7377 48 RSRCEYTSLLLKDLC 62 (83)
Q Consensus 48 rSR~eY~~~L~~Di~ 62 (83)
.+|++|+++|++.+.
T Consensus 1 M~k~efL~~L~~~L~ 15 (181)
T PF08006_consen 1 MNKNEFLNELEKYLK 15 (181)
T ss_pred CCHHHHHHHHHHHHH
Confidence 379999999988776
No 60
>cd00213 S-100 S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents th
Probab=22.96 E-value=1.8e+02 Score=17.28 Aligned_cols=57 Identities=19% Similarity=0.310 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHhhchhhc-cCCC-CCHHHHHHHHHHHHHHH--hcccHHHHHHHHhcCCC
Q psy7377 25 DVEQRIKDVLMVLGNFKQY-RDPA-RSRCEYTSLLLKDLCTY--FSYNEFLMERIMQIFPL 81 (83)
Q Consensus 25 ~v~~RIk~iv~vL~~fk~~-r~~g-rSR~eY~~~L~~Di~~y--YgYn~fL~ek~~~LF~~ 81 (83)
.+.+.|+++..+...|-+. ...| .|..++...++.-+... +++++.-++.++.-|..
T Consensus 2 ~~~~~~~~l~~~F~~~D~~~~~~G~Is~~el~~~l~~~~g~~~~~~~~~~ei~~i~~~~d~ 62 (88)
T cd00213 2 ELEKAIETIIDVFHKYSGKEGDKDTLSKKELKELLETELPNFLKNQKDPEAVDKIMKDLDV 62 (88)
T ss_pred hHHHHHHHHHHHHHHHhhccCCCCcCcHHHHHHHHHHHhhhhccCCCCHHHHHHHHHHhcc
Confidence 3567888888888888552 3334 68888888776533222 44667778888877654
No 61
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=22.74 E-value=44 Score=26.38 Aligned_cols=24 Identities=21% Similarity=0.333 Sum_probs=21.1
Q ss_pred HHHHHHHhcccHHHHHHHHhcCCC
Q psy7377 58 LKDLCTYFSYNEFLMERIMQIFPL 81 (83)
Q Consensus 58 ~~Di~~yYgYn~fL~ek~~~LF~~ 81 (83)
..+++..|++.+.|++++.+.|+.
T Consensus 140 ~~~~~~~~~~P~w~~~~~~~~~g~ 163 (444)
T PRK14902 140 VKRLSIKYSHPVWLVKRWIDQYGE 163 (444)
T ss_pred HHHHHHHhCChHHHHHHHHHHhCH
Confidence 456899999999999999999874
No 62
>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily. 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.
Probab=22.67 E-value=2e+02 Score=17.87 Aligned_cols=29 Identities=21% Similarity=0.615 Sum_probs=19.7
Q ss_pred cCCChHHHHHHHH------------HHHHHhhchhhccCCC
Q psy7377 19 KVLSIPDVEQRIK------------DVLMVLGNFKQYRDPA 47 (83)
Q Consensus 19 ~~~dl~~v~~RIk------------~iv~vL~~fk~~r~~g 47 (83)
.|+||++|+.|++ |+-.|..|=+..+.+|
T Consensus 40 ~PmdL~tI~~kl~~~~Y~s~~~f~~Dv~li~~Na~~yN~~~ 80 (101)
T cd05509 40 KPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80 (101)
T ss_pred CCCCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHCCCC
Confidence 7899999999986 4444455544455544
No 63
>PF14823 Sirohm_synth_C: Sirohaem biosynthesis protein C-terminal; PDB: 1KYQ_B.
Probab=22.64 E-value=1.8e+02 Score=17.81 Aligned_cols=16 Identities=19% Similarity=0.534 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHhcc
Q psy7377 52 EYTSLLLKDLCTYFSY 67 (83)
Q Consensus 52 eY~~~L~~Di~~yYgY 67 (83)
.+.-.=.+-+|.|||-
T Consensus 29 ~~RM~Wm~~vcd~w~l 44 (70)
T PF14823_consen 29 KRRMRWMSQVCDYWSL 44 (70)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcccCH
Confidence 3334444556666664
No 64
>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily. 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.
Probab=22.51 E-value=70 Score=20.88 Aligned_cols=14 Identities=7% Similarity=0.456 Sum_probs=12.3
Q ss_pred cCCChHHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIKD 32 (83)
Q Consensus 19 ~~~dl~~v~~RIk~ 32 (83)
.|+||.+|++|++.
T Consensus 39 ~PmdL~tI~~kl~~ 52 (112)
T cd05511 39 RPMDLQTIRKKISK 52 (112)
T ss_pred CCCCHHHHHHHHhc
Confidence 78999999999874
No 65
>PF00439 Bromodomain: Bromodomain; InterPro: IPR001487 Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins []. 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 ....
Probab=22.05 E-value=69 Score=18.80 Aligned_cols=13 Identities=0% Similarity=0.442 Sum_probs=9.6
Q ss_pred cCCChHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIK 31 (83)
Q Consensus 19 ~~~dl~~v~~RIk 31 (83)
.|+||.+|++|++
T Consensus 35 ~P~dL~~I~~kl~ 47 (84)
T PF00439_consen 35 NPMDLSTIRKKLE 47 (84)
T ss_dssp SS--HHHHHHHHH
T ss_pred hccchhhhhHHhh
Confidence 7899999999984
No 66
>PF07553 Lipoprotein_Ltp: Host cell surface-exposed lipoprotein; InterPro: IPR011434 This domain is found as 1-3 copies in a small family of proteins of unknown function.
Probab=21.93 E-value=1.7e+02 Score=16.76 Aligned_cols=26 Identities=12% Similarity=0.126 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHHHHHHHHh--cccHHHHHHHH
Q psy7377 47 ARSRCEYTSLLLKDLCTYF--SYNEFLMERIM 76 (83)
Q Consensus 47 grSR~eY~~~L~~Di~~yY--gYn~fL~ek~~ 76 (83)
+.||+...++|..+ | ||+++=+++-+
T Consensus 18 ~~Sk~~l~~QL~se----~ge~Ft~e~A~YAv 45 (48)
T PF07553_consen 18 HMSKQGLYDQLTSE----YGEGFTEEEAQYAV 45 (48)
T ss_pred cCCHHHHHHHHHhh----cccCCCHHHHHHHH
Confidence 58999999999887 5 78887776654
No 67
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=21.86 E-value=2.3e+02 Score=18.22 Aligned_cols=53 Identities=13% Similarity=0.146 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhhchhhccCC--CCCHHHHHHHHHHHHHHHhcccHHHHHHHHh
Q psy7377 24 PDVEQRIKDVLMVLGNFKQYRDP--ARSRCEYTSLLLKDLCTYFSYNEFLMERIMQ 77 (83)
Q Consensus 24 ~~v~~RIk~iv~vL~~fk~~r~~--grSR~eY~~~L~~Di~~yYgYn~fL~ek~~~ 77 (83)
..+.+|++-+-.| +.+|+...| ...|.+-+=.=....+.=+|.++.+++.+|.
T Consensus 26 ~LL~eR~~~~~~i-a~~K~~~~~i~d~~Re~~vl~~~~~~a~~~gl~~~~i~~if~ 80 (101)
T PRK07075 26 AALGRRMQYVKAA-SRFKPSEASIPAPERVAAMLPERRRWAEQAGLDADFVEKLFA 80 (101)
T ss_pred HHHHHHHHHHHHH-HHhcCcCCCCCChHHHHHHHHHHHHHhhcCCCCHHHHHHHHH
Confidence 4456666644444 677764322 3456555544445555559999999998875
No 68
>PF11616 EZH2_WD-Binding: WD repeat binding protein EZH2; InterPro: IPR021654 This family of proteins represents Enhancer of zest homologue 2, (EZH2) a 30 residue peptide which binds to a WD-repeat domain of EED by residues 39-68. EED is a component of PRC2 complex which is involved in gene expression []. This interaction is required for the HMTase activity of PCR2 []. ; GO: 0018024 histone-lysine N-methyltransferase activity; PDB: 2QXV_B.
Probab=21.57 E-value=1.1e+02 Score=16.38 Aligned_cols=19 Identities=26% Similarity=0.424 Sum_probs=11.8
Q ss_pred HHHHHHHHHHh-hchhhccC
Q psy7377 27 EQRIKDVLMVL-GNFKQYRD 45 (83)
Q Consensus 27 ~~RIk~iv~vL-~~fk~~r~ 45 (83)
++.|++=..+| ++||++|-
T Consensus 8 r~Ki~e~t~iLN~eWk~lRi 27 (30)
T PF11616_consen 8 RQKIQERTDILNEEWKKLRI 27 (30)
T ss_dssp HHHHHHHHHHHHHHHHH---
T ss_pred HHHHHHHHHHHHHHHHHhcc
Confidence 45677777888 56988874
No 69
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=21.51 E-value=70 Score=17.12 Aligned_cols=13 Identities=15% Similarity=0.434 Sum_probs=10.0
Q ss_pred HHHHHHHHhcCCC
Q psy7377 69 EFLMERIMQIFPL 81 (83)
Q Consensus 69 ~fL~ek~~~LF~~ 81 (83)
...++.+.+|||-
T Consensus 3 ~~~v~~L~~mFP~ 15 (43)
T smart00546 3 DEALHDLKDMFPN 15 (43)
T ss_pred HHHHHHHHHHCCC
Confidence 4567888899983
No 70
>cd04369 Bromodomain Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Probab=21.29 E-value=1.8e+02 Score=16.79 Aligned_cols=15 Identities=7% Similarity=0.505 Sum_probs=13.1
Q ss_pred ccCCChHHHHHHHHH
Q psy7377 18 DKVLSIPDVEQRIKD 32 (83)
Q Consensus 18 e~~~dl~~v~~RIk~ 32 (83)
..|+|+.+|++|++.
T Consensus 40 ~~P~~l~~I~~kl~~ 54 (99)
T cd04369 40 KNPMDLSTIKKKLKN 54 (99)
T ss_pred hCcccHHHHHHHHhc
Confidence 378999999999876
No 71
>PF09793 AD: Anticodon-binding domain; InterPro: IPR019181 Sm and Sm-like proteins of the Lsm (like Sm) domain family are generally involved in essential RNA-processing tasks []. All the LSM proteins are evolutionarily conserved in eukaryotes with an N-terminal Lsm domain to bind nucleic acids, followed by an as yet uncharacterised C-terminal region, some of which have a C-terminal methyltransferase domain. This entry represents the central region of approximately 100 residues, which is conserved from plants to humans and is frequently found in association with Lsm domain-containing proteins.
Probab=21.22 E-value=2.1e+02 Score=17.91 Aligned_cols=32 Identities=16% Similarity=0.144 Sum_probs=24.2
Q ss_pred CCChHHHHHHHHHHHHHhhchhhccCCCCCHH
Q psy7377 20 VLSIPDVEQRIKDVLMVLGNFKQYRDPARSRC 51 (83)
Q Consensus 20 ~~dl~~v~~RIk~iv~vL~~fk~~r~~grSR~ 51 (83)
..|++.+++|++..+.-...-.....+|.|..
T Consensus 4 ~l~i~~l~~r~~~ai~~~~~~~~~~~~~vs~e 35 (91)
T PF09793_consen 4 PLDIERLQKRLRKAIEEAKRKLSSIGPGVSPE 35 (91)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHhcCCCcCHH
Confidence 46899999999998887765555556777753
No 72
>KOG4204|consensus
Probab=21.08 E-value=3.6e+02 Score=20.08 Aligned_cols=52 Identities=17% Similarity=0.319 Sum_probs=33.7
Q ss_pred HHHHHHHHHHH----HhhchhhccCCCCCHHHHHHHHHHHHHHHhcccHHHHHHHHhcCC
Q psy7377 25 DVEQRIKDVLM----VLGNFKQYRDPARSRCEYTSLLLKDLCTYFSYNEFLMERIMQIFP 80 (83)
Q Consensus 25 ~v~~RIk~iv~----vL~~fk~~r~~grSR~eY~~~L~~Di~~yYgYn~fL~ek~~~LF~ 80 (83)
.|++|.+..=. +|..+...++..+|.++ ....++..+++.+.|+..|...+|
T Consensus 136 klk~rf~~~~~v~~s~l~il~~y~~~~ks~~e----~~~eV~~L~~~~~DL~~ef~~~lp 191 (231)
T KOG4204|consen 136 KLKTRFQGDDHVYKSFLEILRMYQEGNKSVSE----VYQEVEALLQGHEDLLEEFSHFLP 191 (231)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHhhccchHHH----HHHHHHHHHccCHHHHHHHHhhcc
Confidence 45566553112 22333334455566665 788889999999999999986554
No 73
>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily. 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.
Probab=20.97 E-value=74 Score=20.32 Aligned_cols=14 Identities=0% Similarity=0.361 Sum_probs=12.3
Q ss_pred cCCChHHHHHHHHH
Q psy7377 19 KVLSIPDVEQRIKD 32 (83)
Q Consensus 19 ~~~dl~~v~~RIk~ 32 (83)
.|+||.+|+.|++.
T Consensus 40 ~PmDL~tI~~kl~~ 53 (98)
T cd05512 40 QPMDFSTMRKKLES 53 (98)
T ss_pred CCcCHHHHHHHHhC
Confidence 78999999999863
No 74
>COG4709 Predicted membrane protein [Function unknown]
Probab=20.40 E-value=87 Score=23.31 Aligned_cols=15 Identities=20% Similarity=0.189 Sum_probs=11.7
Q ss_pred CCHHHHHHHHHHHHH
Q psy7377 48 RSRCEYTSLLLKDLC 62 (83)
Q Consensus 48 rSR~eY~~~L~~Di~ 62 (83)
.||.||+++|.+.+.
T Consensus 1 Mtk~efL~eL~~yL~ 15 (195)
T COG4709 1 MTKTEFLNELEQYLE 15 (195)
T ss_pred CCHHHHHHHHHHHHH
Confidence 479999999976553
No 75
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=20.29 E-value=75 Score=25.32 Aligned_cols=23 Identities=22% Similarity=0.340 Sum_probs=20.4
Q ss_pred HHHHHHhcccHHHHHHHHhcCCC
Q psy7377 59 KDLCTYFSYNEFLMERIMQIFPL 81 (83)
Q Consensus 59 ~Di~~yYgYn~fL~ek~~~LF~~ 81 (83)
.+++..|++.+.|++.+.+.|+.
T Consensus 126 ~~l~~~~s~P~wl~~~~~~~~g~ 148 (431)
T PRK14903 126 KELHLKYSHPKWLVNYWRSFLPE 148 (431)
T ss_pred hhhhhhhcCcHHHHHHHHHHcCH
Confidence 56888999999999999999874
Done!