Query 035311
Match_columns 68
No_of_seqs 119 out of 503
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 10:52:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035311.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035311hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0928 Pattern-formation prot 99.8 2.4E-20 5.1E-25 152.5 5.3 67 1-68 662-728 (1386)
2 KOG0930 Guanine nucleotide exc 99.4 1.9E-13 4.2E-18 100.2 3.8 57 2-58 209-269 (395)
3 KOG0931 Predicted guanine nucl 99.4 5E-13 1.1E-17 102.5 3.7 43 1-43 350-392 (627)
4 PLN03076 ARF guanine nucleotid 99.3 1.5E-12 3.3E-17 109.8 4.9 43 1-43 763-805 (1780)
5 KOG0929 Guanine nucleotide exc 99.1 2.8E-11 6.1E-16 101.0 3.9 43 1-43 662-704 (1514)
6 cd00171 Sec7 Sec7 domain; Doma 99.1 1.1E-10 2.3E-15 78.9 4.4 36 1-36 150-185 (185)
7 smart00222 Sec7 Sec7 domain. D 99.1 1.2E-10 2.6E-15 78.7 4.5 36 1-36 152-187 (187)
8 COG5307 SEC7 domain proteins [ 99.1 9.5E-11 2.1E-15 95.4 4.7 60 1-61 417-476 (1024)
9 PF01369 Sec7: Sec7 domain; I 99.1 1.1E-10 2.4E-15 78.8 3.6 36 1-36 155-190 (190)
10 KOG0932 Guanine nucleotide exc 98.9 1.7E-09 3.7E-14 84.8 3.3 42 1-42 422-463 (774)
11 PHA02885 putative interleukin 77.5 1.8 4E-05 28.2 1.8 41 6-46 78-118 (135)
12 COG4844 Uncharacterized protei 66.3 6.4 0.00014 23.7 2.3 20 17-36 58-77 (78)
13 PRK13669 hypothetical protein; 58.5 8.2 0.00018 23.3 1.8 20 17-36 58-77 (78)
14 TIGR01797 CM_P_1 chorismate mu 54.5 13 0.00027 21.9 2.1 26 9-34 52-77 (83)
15 PF07293 DUF1450: Protein of u 54.3 10 0.00023 22.7 1.7 19 18-36 59-77 (78)
16 PF08671 SinI: Anti-repressor 54.1 15 0.00032 18.4 2.0 15 51-65 2-16 (30)
17 COG4088 Predicted nucleotide k 54.0 13 0.00028 27.1 2.4 20 13-32 120-139 (261)
18 smart00830 CM_2 Chorismate mut 52.9 22 0.00047 20.0 2.9 28 7-34 46-73 (79)
19 PF10364 NKWYS: Putative capsu 50.1 11 0.00023 25.1 1.4 14 18-31 119-132 (141)
20 PRK07075 isochorismate-pyruvat 48.8 18 0.0004 22.2 2.3 28 10-37 61-88 (101)
21 TIGR01799 CM_T chorismate muta 48.2 19 0.00041 21.1 2.2 24 13-36 56-79 (83)
22 TIGR01803 CM-like chorismate m 46.7 12 0.00025 21.9 1.1 26 11-36 54-79 (82)
23 PF06881 Elongin_A: RNA polyme 46.7 12 0.00027 22.9 1.3 47 14-60 2-48 (109)
24 PF03823 Neurokinin_B: Neuroki 46.4 23 0.0005 20.4 2.3 13 19-31 46-58 (59)
25 PRK00083 frr ribosome recyclin 44.4 82 0.0018 21.4 5.1 47 18-64 69-120 (185)
26 PF12745 HGTP_anticodon2: Anti 43.7 22 0.00047 25.6 2.3 32 3-36 220-251 (273)
27 TIGR01807 CM_P2 chorismate mut 38.1 39 0.00085 19.3 2.4 15 17-31 61-75 (76)
28 TIGR01795 CM_mono_cladeE monof 36.0 13 0.00028 22.7 0.1 31 8-38 55-85 (94)
29 TIGR01863 cas_Csd1 CRISPR-asso 34.5 29 0.00064 27.3 1.9 28 7-34 399-426 (580)
30 PF12937 F-box-like: F-box-lik 32.7 41 0.00089 17.0 1.8 14 17-30 2-15 (47)
31 TIGR01791 CM_archaeal chorisma 32.4 36 0.00077 19.7 1.6 17 17-33 60-76 (83)
32 PRK09239 chorismate mutase; Pr 31.8 18 0.00038 22.5 0.3 29 10-38 64-92 (104)
33 PF13013 F-box-like_2: F-box-l 30.3 35 0.00075 21.6 1.4 18 17-34 23-40 (109)
34 PRK06285 chorismate mutase; Pr 29.3 54 0.0012 19.7 2.1 18 16-33 67-84 (96)
35 PF12174 RST: RCD1-SRO-TAF4 (R 28.9 47 0.001 19.3 1.7 15 1-15 42-56 (70)
36 COG0233 Frr Ribosome recycling 28.9 2E+02 0.0043 20.0 5.0 49 17-65 70-123 (187)
37 TIGR00496 frr ribosome recycli 28.3 1.9E+02 0.0041 19.4 5.2 47 18-64 60-111 (176)
38 PRK10391 oriC-binding nucleoid 28.1 1.1E+02 0.0025 18.2 3.3 29 1-34 1-29 (71)
39 TIGR01806 CM_mono2 chorismate 27.1 71 0.0015 20.0 2.5 27 8-34 45-71 (114)
40 PRK09071 hypothetical protein; 27.0 1.7E+02 0.0036 21.5 4.7 36 1-36 2-38 (323)
41 PF13319 DUF4090: Protein of u 26.6 61 0.0013 19.9 2.0 24 11-35 11-35 (84)
42 PF04940 BLUF: Sensors of blue 26.1 55 0.0012 19.6 1.8 16 20-35 53-68 (93)
43 PF15332 LIME1: Lck-interactin 26.1 32 0.00069 24.6 0.7 17 16-32 211-227 (228)
44 COG3530 Uncharacterized protei 25.8 96 0.0021 18.4 2.6 28 1-28 1-36 (71)
45 cd00520 RRF Ribosome recycling 25.6 2.1E+02 0.0046 19.1 5.3 47 18-64 65-116 (179)
46 COG1605 PheA Chorismate mutase 25.4 58 0.0013 19.8 1.8 24 10-33 63-86 (101)
47 KOG2120 SCF ubiquitin ligase, 25.4 42 0.0009 25.9 1.3 29 8-36 87-118 (419)
48 PF02512 UK: Virulence determi 25.3 53 0.0011 20.4 1.6 20 1-20 46-66 (96)
49 PF01817 CM_2: Chorismate muta 25.1 64 0.0014 18.3 1.8 18 16-33 55-72 (81)
50 TIGR01801 CM_A chorismate muta 24.5 91 0.002 19.1 2.6 21 17-37 64-84 (102)
51 PF08982 DUF1857: Domain of un 23.3 83 0.0018 20.7 2.3 18 51-68 21-38 (149)
52 PRK07248 hypothetical protein; 22.7 1E+02 0.0022 17.9 2.4 16 18-33 62-77 (87)
53 PF09709 Cas_Csd1: CRISPR-asso 22.1 64 0.0014 25.3 1.8 29 5-33 394-422 (574)
54 PF06348 DUF1059: Protein of u 22.0 1.5E+02 0.0034 16.2 3.2 28 6-33 29-56 (57)
55 PF00646 F-box: F-box domain; 21.8 57 0.0012 16.3 1.1 18 18-35 5-22 (48)
56 PF12637 TSCPD: TSCPD domain; 21.7 89 0.0019 18.8 2.1 17 1-17 55-71 (95)
57 COG3972 Superfamily I DNA and 21.3 69 0.0015 26.1 1.9 17 13-29 301-317 (660)
58 PF08579 RPM2: Mitochondrial r 21.3 68 0.0015 20.9 1.5 19 24-42 44-62 (120)
59 PRK10945 gene expression modul 21.3 1.7E+02 0.0036 17.5 3.1 28 1-33 6-33 (72)
60 PF06411 HdeA: HdeA/HdeB famil 20.1 38 0.00083 20.2 0.2 10 1-10 34-43 (94)
61 PF08486 SpoIID: Stage II spor 20.1 1.1E+02 0.0024 18.2 2.2 33 1-33 14-54 (96)
No 1
>KOG0928 consensus Pattern-formation protein/guanine nucleotide exchange factor [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.81 E-value=2.4e-20 Score=152.46 Aligned_cols=67 Identities=42% Similarity=0.688 Sum_probs=63.9
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCcccCCCCcCCCCccchHHHHHHHHHHHhhccCC
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEIGTTPEQCAGFPEITQSCWIDLMRSLRKQLHLL 68 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~~~~~~~~~~~~~~~~W~~l~~~~~~~~~~~ 68 (68)
||++||+||+||+|+|+|||++||.+||++||.+||.||+++ +++.+++.++|..|+.|+++|.|++
T Consensus 662 MT~dDf~rNlrg~n~g~DFpreyLseiY~SIk~~EIvmPee~-hG~~~~~~~~W~~L~~~sktt~~~~ 728 (1386)
T KOG0928|consen 662 MTFDDFIRNLRGINGGKDFPREYLSEIYQSIKTNEIVMPEEH-HGTEEMFEYRWINLISRSKTTEPFI 728 (1386)
T ss_pred CCHHHHhhhcccccCCCCCCHHHHHHHHHHHhhcceeccccc-CCchhhhHHHHHHHHhcccccCcee
Confidence 999999999999999999999999999999999999998887 4889999999999999999998874
No 2
>KOG0930 consensus Guanine nucleotide exchange factor Cytohesin, contains PH and Sec7 domains [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.40 E-value=1.9e-13 Score=100.21 Aligned_cols=57 Identities=33% Similarity=0.496 Sum_probs=52.7
Q ss_pred ChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCcccCCCCc----CCCCccchHHHHHHH
Q 035311 2 TEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEIGTTPEQC----AGFPEITQSCWIDLM 58 (68)
Q Consensus 2 t~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~~~~~~----~~~~~~~~~~W~~l~ 58 (68)
++|.||.||||||+|+|+|.|+|.++|+||+++++++|++.+ +.|-++++.||+.-+
T Consensus 209 ~lErfi~MNrgineggdlpee~LrnlyeSi~~epFkIPeddgndlthtffnpdREGWLlKl 269 (395)
T KOG0930|consen 209 TLERFIAMNRGINEGGDLPEELLRNLYESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKL 269 (395)
T ss_pred cHHHHHHHhhccccCCCCcHHHHHHHHHHhcCCCCCCCcccCCcchhhccCccccceeeee
Confidence 689999999999999999999999999999999999999876 458899999998655
No 3
>KOG0931 consensus Predicted guanine nucleotide exchange factor, contains Sec7 domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.35 E-value=5e-13 Score=102.48 Aligned_cols=43 Identities=37% Similarity=0.675 Sum_probs=42.0
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCcccCCCCc
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEIGTTPEQC 43 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~~~~~~ 43 (68)
|+++|||+|+||+++|.|+|+++|.+||++|+++|++..+||.
T Consensus 350 M~leDFikNLRGvDnGeDIpRell~GIYeRIqk~ELktndDHV 392 (627)
T KOG0931|consen 350 MKLEDFIKNLRGVDNGEDIPRELLVGIYERIQKRELKTNDDHV 392 (627)
T ss_pred hhHHHHHHhccCCCCcccCcHHHHHHHHHHHHHhhcccCcchH
Confidence 8999999999999999999999999999999999999999985
No 4
>PLN03076 ARF guanine nucleotide exchange factor (ARF-GEF); Provisional
Probab=99.32 E-value=1.5e-12 Score=109.77 Aligned_cols=43 Identities=47% Similarity=0.818 Sum_probs=41.6
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCcccCCCCc
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEIGTTPEQC 43 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~~~~~~ 43 (68)
||+++|++||||||+|+|||++||++||++|+++||++++++.
T Consensus 763 Mt~~~Fi~n~rgin~g~dlp~e~L~~iY~~I~~~ei~~~~~~~ 805 (1780)
T PLN03076 763 MSADDFIRNNRGIDDGKDLPEEFMRSLYERISKNEIKMKEDDL 805 (1780)
T ss_pred CCHHHHHHHhhCCCCCCCCCHHHHHHHHHHHHhCcccCccccc
Confidence 9999999999999999999999999999999999999999864
No 5
>KOG0929 consensus Guanine nucleotide exchange factor [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.15 E-value=2.8e-11 Score=100.97 Aligned_cols=43 Identities=47% Similarity=0.737 Sum_probs=41.7
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCcccCCCCc
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEIGTTPEQC 43 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~~~~~~ 43 (68)
||+++||+||||||+|+|+|.+||+.+|+.|..+||+|.++..
T Consensus 662 MTK~dFI~nnrgind~~dlp~e~L~~lYd~I~~~Eikm~~~~~ 704 (1514)
T KOG0929|consen 662 MTKADFIRNNRGINDGKDLPEEYLEALYDEIEYKEIKMKSDSL 704 (1514)
T ss_pred ccHHHHHHhcccccCcccChHHHHHHHHHHhhhcccccccccc
Confidence 9999999999999999999999999999999999999998875
No 6
>cd00171 Sec7 Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Probab=99.10 E-value=1.1e-10 Score=78.94 Aligned_cols=36 Identities=61% Similarity=0.922 Sum_probs=35.3
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCc
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei 36 (68)
||+++|++|++|+++|.+||.++|++||++|+++||
T Consensus 150 mt~~~Fi~~~~~~~~~~~~~~~~L~~iY~~I~~~~~ 185 (185)
T cd00171 150 MTLEDFIKNLRGINDGEDFPREFLKELYDSIKNNEI 185 (185)
T ss_pred CCHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhCCC
Confidence 899999999999999999999999999999999987
No 7
>smart00222 Sec7 Sec7 domain. Domain named after the S. cerevisiae SEC7 gene product, which is required for proper protein transport through the Golgi. The domain facilitates guanine nucleotide exchange on the small GTPases, ARFs (ADP ribosylation factors).
Probab=99.09 E-value=1.2e-10 Score=78.65 Aligned_cols=36 Identities=61% Similarity=0.895 Sum_probs=35.2
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCc
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei 36 (68)
||+++|++|++|+++|.|+|.++|++||++|+.+||
T Consensus 152 mt~~~Fi~~~~~~~~~~~~~~~~L~~iY~~I~~~~i 187 (187)
T smart00222 152 MTLEDFIKNVRGSNDGEDLPREFLEELYDSIKNNEI 187 (187)
T ss_pred CCHHHHHHHHhccCCCCCCCHHHHHHHHHHHHhCCC
Confidence 899999999999999999999999999999999986
No 8
>COG5307 SEC7 domain proteins [General function prediction only]
Probab=99.09 E-value=9.5e-11 Score=95.44 Aligned_cols=60 Identities=35% Similarity=0.486 Sum_probs=51.9
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCcccCCCCcCCCCccchHHHHHHHHHH
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEIGTTPEQCAGFPEITQSCWIDLMRSL 61 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~~~~~~~~~~~~~~~~W~~l~~~~ 61 (68)
||+++|++|+||+|+|+|||++||+.+|++|+++||.++++++ ....+...-|..+....
T Consensus 417 MT~~df~~N~~g~n~g~~~~~~~L~~~Y~~I~~kei~~~e~~~-~~~~~~~~~~~~~~ss~ 476 (1024)
T COG5307 417 MTFEDFSKNLRGENTGRDFPEEFLEEFYDNIKKKEIVLPEEHH-SSETSPEDNWPSLDSSF 476 (1024)
T ss_pred ccHHHHHhhhcccCCccccCHHHHHHHHHHHhhccccchhhcc-cccccccccchhhhhhh
Confidence 9999999999999999999999999999999999999999986 44445567777766443
No 9
>PF01369 Sec7: Sec7 domain; InterPro: IPR000904 The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ]. The 3D structure of the domain displays several alpha-helices []. It was found to be associated with other domains involved in guanine nucleotide exchange (e.g., CDC25, Dbl) in mammalian factors [].; GO: 0005086 ARF guanyl-nucleotide exchange factor activity, 0032012 regulation of ARF protein signal transduction, 0005622 intracellular; PDB: 3SWV_A 3L8N_A 2R09_A 2R0D_B 1RE0_B 3LTL_A 1KU1_A 1XSZ_A 1XT0_B 1R8Q_E ....
Probab=99.07 E-value=1.1e-10 Score=78.78 Aligned_cols=36 Identities=47% Similarity=0.846 Sum_probs=29.8
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCc
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei 36 (68)
||+++|++|++|+++|+|+|.++|+.||++|+++||
T Consensus 155 mt~~~Fi~~~~~~~~~~~~~~~~L~~iY~~I~~~~~ 190 (190)
T PF01369_consen 155 MTKEDFIKNTRGIDDGKDIPEEFLESIYDSIKANPF 190 (190)
T ss_dssp --HHHHHHHTTTTBTTBS--HHHHHHHHHHHHHS--
T ss_pred CcHHHHHHHhhcccCCCCCCHHHHHHHHHHHHhCCC
Confidence 899999999999999999999999999999999986
No 10
>KOG0932 consensus Guanine nucleotide exchange factor EFA6 [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.86 E-value=1.7e-09 Score=84.83 Aligned_cols=42 Identities=36% Similarity=0.621 Sum_probs=39.0
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCcccCCCC
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKNEIGTTPEQ 42 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~~~~~ 42 (68)
||+++||.|+.|+|+|.|||+|+|..+|++||++.+.+.-+.
T Consensus 422 MtcqdFI~Nl~glndG~dF~kelLKaLy~SIKneklewAide 463 (774)
T KOG0932|consen 422 MTCQDFITNLAGLNDGGDFPKELLKALYNSIKNEKLEWAIDE 463 (774)
T ss_pred ccHHHHHHHHhcccccCccHHHHHHHHHHHHhhhhhhhccCh
Confidence 999999999999999999999999999999999988876543
No 11
>PHA02885 putative interleukin binding protein; Provisional
Probab=77.46 E-value=1.8 Score=28.16 Aligned_cols=41 Identities=20% Similarity=0.204 Sum_probs=33.5
Q ss_pred HHHHhcCCCCCCCCCHHHHHHHHHHHhcCCcccCCCCcCCC
Q 035311 6 FIRSNGHINGGNDLPREFLSKLYHSICKNEIGTTPEQCAGF 46 (68)
Q Consensus 6 FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~~~~~~~~~ 46 (68)
|+.|+.|.+.|+|-..++=.++|..-+.--|...+-.+..|
T Consensus 78 f~enl~g~~egqd~t~algdd~ykhtrelniss~dytgknf 118 (135)
T PHA02885 78 FIENLEGANEGQDNTFALGDDCYKHTRELNISSADYTGKNF 118 (135)
T ss_pred eeecccccccCccchhhhhHHHHhhhHhcccccccccCCce
Confidence 89999999999999999999999988776676665444333
No 12
>COG4844 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.29 E-value=6.4 Score=23.68 Aligned_cols=20 Identities=25% Similarity=0.562 Sum_probs=18.0
Q ss_pred CCCCHHHHHHHHHHHhcCCc
Q 035311 17 NDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 17 ~Dlp~e~L~~iY~sI~~~ei 36 (68)
++-|.++++.||.-|..+++
T Consensus 58 Get~eeLv~NIY~~i~Enp~ 77 (78)
T COG4844 58 GETPEELVENIYTFIEENPM 77 (78)
T ss_pred CCCHHHHHHHHHHHHhccCC
Confidence 57899999999999998875
No 13
>PRK13669 hypothetical protein; Provisional
Probab=58.52 E-value=8.2 Score=23.33 Aligned_cols=20 Identities=20% Similarity=0.577 Sum_probs=17.1
Q ss_pred CCCCHHHHHHHHHHHhcCCc
Q 035311 17 NDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 17 ~Dlp~e~L~~iY~sI~~~ei 36 (68)
.+=|.+++++||..|..+++
T Consensus 58 a~t~eeL~~kI~~~i~e~~~ 77 (78)
T PRK13669 58 GETPEELVENIYAHLEENPM 77 (78)
T ss_pred cCCHHHHHHHHHHHHhhcCC
Confidence 35689999999999999875
No 14
>TIGR01797 CM_P_1 chorismate mutase domain of proteobacterial P-protein, clade 1. This model represents the chorismate mutase domain of the gamma and beta proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain.
Probab=54.51 E-value=13 Score=21.88 Aligned_cols=26 Identities=12% Similarity=0.300 Sum_probs=18.2
Q ss_pred HhcCCCCCCCCCHHHHHHHHHHHhcC
Q 035311 9 SNGHINGGNDLPREFLSKLYHSICKN 34 (68)
Q Consensus 9 nnrGin~G~Dlp~e~L~~iY~sI~~~ 34 (68)
+.+..+...+||++++..||..|-..
T Consensus 52 ~~~~~~~~~~l~~~~i~~if~~ii~~ 77 (83)
T TIGR01797 52 RLITLGKAYHLDAHYITRLFQLIIED 77 (83)
T ss_pred HHHHHhhhCCCCHHHHHHHHHHHHHH
Confidence 33444444779999999999888654
No 15
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=54.31 E-value=10 Score=22.71 Aligned_cols=19 Identities=26% Similarity=0.427 Sum_probs=16.7
Q ss_pred CCCHHHHHHHHHHHhcCCc
Q 035311 18 DLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 18 Dlp~e~L~~iY~sI~~~ei 36 (68)
+=|.++++.||..|+.+++
T Consensus 59 ~t~eeL~~kI~~~i~e~~~ 77 (78)
T PF07293_consen 59 ETAEELLEKIKEKIEENPM 77 (78)
T ss_pred CCHHHHHHHHHHHHhcccC
Confidence 5588999999999999886
No 16
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=54.14 E-value=15 Score=18.39 Aligned_cols=15 Identities=13% Similarity=0.578 Sum_probs=12.2
Q ss_pred hHHHHHHHHHHHhhc
Q 035311 51 QSCWIDLMRSLRKQL 65 (68)
Q Consensus 51 ~~~W~~l~~~~~~~~ 65 (68)
+..|..||..++..|
T Consensus 2 D~EW~~Li~eA~~~G 16 (30)
T PF08671_consen 2 DEEWVELIKEAKESG 16 (30)
T ss_dssp -HHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHHcC
Confidence 467999999998776
No 17
>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=53.99 E-value=13 Score=27.07 Aligned_cols=20 Identities=30% Similarity=0.569 Sum_probs=18.4
Q ss_pred CCCCCCCCHHHHHHHHHHHh
Q 035311 13 INGGNDLPREFLSKLYHSIC 32 (68)
Q Consensus 13 in~G~Dlp~e~L~~iY~sI~ 32 (68)
.+.|+.+|.|.|.++|++--
T Consensus 120 ~ergepip~Evl~qly~RfE 139 (261)
T COG4088 120 RERGEPIPEEVLRQLYDRFE 139 (261)
T ss_pred ccCCCCCCHHHHHHHHHhhc
Confidence 78999999999999999864
No 18
>smart00830 CM_2 Chorismate mutase type II. Chorismate mutase, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine PUBMED:9642265, PUBMED:9497350.
Probab=52.91 E-value=22 Score=19.99 Aligned_cols=28 Identities=14% Similarity=0.369 Sum_probs=19.1
Q ss_pred HHHhcCCCCCCCCCHHHHHHHHHHHhcC
Q 035311 7 IRSNGHINGGNDLPREFLSKLYHSICKN 34 (68)
Q Consensus 7 irnnrGin~G~Dlp~e~L~~iY~sI~~~ 34 (68)
+.+.+.......+|+++++.||..|-+.
T Consensus 46 l~~~~~~a~~~~l~~~~~~~if~~ii~~ 73 (79)
T smart00830 46 LERLRALAEGPGLDPELVERIFREIIEA 73 (79)
T ss_pred HHHHHHHcccCCcCHHHHHHHHHHHHHH
Confidence 3444445556678889999998887543
No 19
>PF10364 NKWYS: Putative capsular polysaccharide synthesis protein; InterPro: IPR018831 This entry contains proteins of no known function. They are found predominantly in Vibrio and cyanobacterial species and are characterised by having a NKWYS sequence motif.
Probab=50.08 E-value=11 Score=25.14 Aligned_cols=14 Identities=50% Similarity=0.968 Sum_probs=12.4
Q ss_pred CCCHHHHHHHHHHH
Q 035311 18 DLPREFLSKLYHSI 31 (68)
Q Consensus 18 Dlp~e~L~~iY~sI 31 (68)
+||+++|++||++=
T Consensus 119 ~l~~~~leemY~s~ 132 (141)
T PF10364_consen 119 RLPREYLEEMYDSP 132 (141)
T ss_pred CCCHHHHHHHHccH
Confidence 59999999999873
No 20
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=48.78 E-value=18 Score=22.19 Aligned_cols=28 Identities=18% Similarity=0.268 Sum_probs=20.3
Q ss_pred hcCCCCCCCCCHHHHHHHHHHHhcCCcc
Q 035311 10 NGHINGGNDLPREFLSKLYHSICKNEIG 37 (68)
Q Consensus 10 nrGin~G~Dlp~e~L~~iY~sI~~~ei~ 37 (68)
.+.......+|+++++.||..|-+.-|.
T Consensus 61 ~~~~a~~~gl~~~~i~~if~~Ii~~~i~ 88 (101)
T PRK07075 61 RRRWAEQAGLDADFVEKLFAQLIHWYIA 88 (101)
T ss_pred HHHHhhcCCCCHHHHHHHHHHHHHHHHH
Confidence 4444555789999999999888765443
No 21
>TIGR01799 CM_T chorismate mutase domain of T-protein. This model represents the chorismate mutase domain of the gamma proteobacterial "T-protein" which consists of an N-terminal chorismate mutase domain and a C-terminal prephenate dehydrogenase domain.
Probab=48.15 E-value=19 Score=21.08 Aligned_cols=24 Identities=0% Similarity=0.151 Sum_probs=17.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCc
Q 035311 13 INGGNDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 13 in~G~Dlp~e~L~~iY~sI~~~ei 36 (68)
.....++|+++++.||..|-...|
T Consensus 56 ~a~~~gl~~~~i~~if~~i~~~s~ 79 (83)
T TIGR01799 56 EAEKAGIAPDLIEDVLRRFMRESY 79 (83)
T ss_pred HhhcCCCCHHHHHHHHHHHHHHHH
Confidence 334467999999999988876544
No 22
>TIGR01803 CM-like chorismate mutase related enzymes. This subfamily includes two enzymes which are variants on the mechanism of chorismate mutase and are likely to have evolved from an ancestral chorismate mutase enzyme. 4-amino-4-deoxy-chorismate mutase produces amino-deoxy-prephenate which is subsequently converted to para-dimethylamino-phenylalanine, a component of the natural product pristinamycin. Isochorismate-pyruvate lyase presumably catalyzes the same type of 2+2+2 cyclo-rearrangement as chorismate mutase, but acting on isochorismate, this results in two broken bonds instead of one broken and one made. The product of this reaction is salicylate (2-hydroxy-benzoate) which is also incorporated into various natural products.
Probab=46.68 E-value=12 Score=21.94 Aligned_cols=26 Identities=23% Similarity=0.268 Sum_probs=18.5
Q ss_pred cCCCCCCCCCHHHHHHHHHHHhcCCc
Q 035311 11 GHINGGNDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 11 rGin~G~Dlp~e~L~~iY~sI~~~ei 36 (68)
+.......+|+++++.||..|-...|
T Consensus 54 ~~~a~~~gl~~~~~~~if~~ii~~si 79 (82)
T TIGR01803 54 ARWAEENGLDPPFVEGLFAQIIHWYI 79 (82)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 33333367999999999998876543
No 23
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=46.68 E-value=12 Score=22.92 Aligned_cols=47 Identities=15% Similarity=0.315 Sum_probs=31.4
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCcccCCCCcCCCCccchHHHHHHHHH
Q 035311 14 NGGNDLPREFLSKLYHSICKNEIGTTPEQCAGFPEITQSCWIDLMRS 60 (68)
Q Consensus 14 n~G~Dlp~e~L~~iY~sI~~~ei~~~~~~~~~~~~~~~~~W~~l~~~ 60 (68)
.+=+++|-++|.-|-..+..+.+.--++....+...|+..|+.++.|
T Consensus 2 ~dvG~~py~ll~piL~~~~~~QL~~iE~~np~l~~~tdeLW~~~i~r 48 (109)
T PF06881_consen 2 EDVGDVPYHLLRPILEKCSPEQLRRIEDNNPHLIEDTDELWKKLIKR 48 (109)
T ss_pred CccCCCCHHHHHHHHccCCHHHHHHHHHhCCCcchhhHHHHHHHHHh
Confidence 34467888888888877765555544444334555678888888765
No 24
>PF03823 Neurokinin_B: Neurokinin B; InterPro: IPR003635 Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. This family includes neurokinins, as well as many other peptides. Like other tachykinins, neurokinins are synthesized as larger protein precursors that are enzymatically converted to their mature forms.; GO: 0007217 tachykinin receptor signaling pathway
Probab=46.36 E-value=23 Score=20.39 Aligned_cols=13 Identities=46% Similarity=0.805 Sum_probs=11.8
Q ss_pred CCHHHHHHHHHHH
Q 035311 19 LPREFLSKLYHSI 31 (68)
Q Consensus 19 lp~e~L~~iY~sI 31 (68)
+|+.+|..+||+-
T Consensus 46 LPpslLRRLydsr 58 (59)
T PF03823_consen 46 LPPSLLRRLYDSR 58 (59)
T ss_pred CCHHHHHHHHhcc
Confidence 8999999999973
No 25
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=44.40 E-value=82 Score=21.38 Aligned_cols=47 Identities=17% Similarity=0.384 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHhcCCcccCCCCc-----CCCCccchHHHHHHHHHHHhh
Q 035311 18 DLPREFLSKLYHSICKNEIGTTPEQC-----AGFPEITQSCWIDLMRSLRKQ 64 (68)
Q Consensus 18 Dlp~e~L~~iY~sI~~~ei~~~~~~~-----~~~~~~~~~~W~~l~~~~~~~ 64 (68)
.|++.++..|+.+|.+.-+-+....+ -.++.+|..+-.++++..+..
T Consensus 69 p~D~~~i~~I~kAI~~s~lgl~P~~dg~~Iri~iP~lT~E~R~elvK~~k~~ 120 (185)
T PRK00083 69 PWDKSMLKAIEKAIRASDLGLNPSNDGTVIRLPIPPLTEERRKELVKQVKKE 120 (185)
T ss_pred eCCHhHHHHHHHHHHHCCCCCCcccCCCEEEecCCCCCHHHHHHHHHHHHHH
Confidence 48899999999999998888776443 358899999999999887654
No 26
>PF12745 HGTP_anticodon2: Anticodon binding domain of tRNAs; InterPro: IPR024435 This is an anticodon binding domain, found largely on Gcn2 proteins which bind tRNA to down regulate translation in certain stress situations [].; GO: 0000049 tRNA binding
Probab=43.74 E-value=22 Score=25.59 Aligned_cols=32 Identities=16% Similarity=0.368 Sum_probs=23.6
Q ss_pred hHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcCCc
Q 035311 3 EEDFIRSNGHINGGNDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 3 ~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ei 36 (68)
.+.|+|-.-+. ..-+|+.||.+||+.|.+...
T Consensus 220 ~d~W~Rkv~~~--~~~~~k~Y~~~I~~~L~k~~~ 251 (273)
T PF12745_consen 220 PDEWNRKVIQS--VPSTPKSYLQNIYDELSKEAS 251 (273)
T ss_pred HHHHHHHHHhh--cCccHHHHHHHHHHHHHHHHh
Confidence 45666655554 567899999999999995443
No 27
>TIGR01807 CM_P2 chorismate mutase domain of proteobacterial P-protein, clade 2. This model represents one of two separate clades of the chorismate mutase domain of the gamma and beta and epsilon proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. It is also found in Aquifex aolicus.
Probab=38.14 E-value=39 Score=19.31 Aligned_cols=15 Identities=20% Similarity=0.558 Sum_probs=13.5
Q ss_pred CCCCHHHHHHHHHHH
Q 035311 17 NDLPREFLSKLYHSI 31 (68)
Q Consensus 17 ~Dlp~e~L~~iY~sI 31 (68)
+.+|+++++.||..|
T Consensus 61 ~~l~~~~i~~if~~I 75 (76)
T TIGR01807 61 GPLDQEAIARIFREI 75 (76)
T ss_pred CCCCHHHHHHHHHHH
Confidence 579999999999887
No 28
>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=35.97 E-value=13 Score=22.68 Aligned_cols=31 Identities=19% Similarity=0.163 Sum_probs=23.1
Q ss_pred HHhcCCCCCCCCCHHHHHHHHHHHhcCCccc
Q 035311 8 RSNGHINGGNDLPREFLSKLYHSICKNEIGT 38 (68)
Q Consensus 8 rnnrGin~G~Dlp~e~L~~iY~sI~~~ei~~ 38 (68)
.+.+.......+|++|.+.||..|-.+.+..
T Consensus 55 ~~~~~~a~~~gl~p~~~e~i~~~i~~esir~ 85 (94)
T TIGR01795 55 ARLRRLAIDAGLDPEFAEKFLNFIVTEVIKH 85 (94)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Confidence 3445556667899999999999988766554
No 29
>TIGR01863 cas_Csd1 CRISPR-associated protein, Csd1 family. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein that tends to be found near CRISPR repeats of the DVULG subtype of CRISPR/Cas locus. We designate this family Csd1 (CRISPR/Cas Subtype DVULG protein 1). The species range for this subtype, so far, is exclusively bacterial and mesophilic, although CRISPR loci in general are particularly common among archaea and thermophilic bacteria. In a few species (Xanthomonas axonopodis pv. citri str. 306 and Streptococcus mutans UA159), homology to this protein family is split across two tandem genes; the trusted cutoff to this family is set low enough to capture at least the longer of the two.
Probab=34.50 E-value=29 Score=27.28 Aligned_cols=28 Identities=29% Similarity=0.292 Sum_probs=24.4
Q ss_pred HHHhcCCCCCCCCCHHHHHHHHHHHhcC
Q 035311 7 IRSNGHINGGNDLPREFLSKLYHSICKN 34 (68)
Q Consensus 7 irnnrGin~G~Dlp~e~L~~iY~sI~~~ 34 (68)
-+..|.|-+|..+|.+++..+..+|++.
T Consensus 399 ~~ll~~Il~g~p~P~~L~~~~~~Rira~ 426 (580)
T TIGR01863 399 GRLLRSILDGGPYPRSLLSAALRRIRAD 426 (580)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHhcCc
Confidence 3566788999999999999999999975
No 30
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=32.70 E-value=41 Score=17.02 Aligned_cols=14 Identities=29% Similarity=0.624 Sum_probs=10.7
Q ss_pred CCCCHHHHHHHHHH
Q 035311 17 NDLPREFLSKLYHS 30 (68)
Q Consensus 17 ~Dlp~e~L~~iY~s 30 (68)
.+||.|.|..|+.-
T Consensus 2 ~~LP~Eil~~If~~ 15 (47)
T PF12937_consen 2 SSLPDEILLEIFSY 15 (47)
T ss_dssp CCS-HHHHHHHHTT
T ss_pred hHhHHHHHHHHHhc
Confidence 37999999999954
No 31
>TIGR01791 CM_archaeal chorismate mutase, archaeal type. This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase.
Probab=32.37 E-value=36 Score=19.68 Aligned_cols=17 Identities=12% Similarity=0.122 Sum_probs=12.5
Q ss_pred CCCCHHHHHHHHHHHhc
Q 035311 17 NDLPREFLSKLYHSICK 33 (68)
Q Consensus 17 ~Dlp~e~L~~iY~sI~~ 33 (68)
..+|++++..||..|-+
T Consensus 60 ~~l~~~~i~~if~~i~~ 76 (83)
T TIGR01791 60 LGLDVLKLKEIFEILMS 76 (83)
T ss_pred cCCCHHHHHHHHHHHHH
Confidence 45888888888877754
No 32
>PRK09239 chorismate mutase; Provisional
Probab=31.78 E-value=18 Score=22.49 Aligned_cols=29 Identities=21% Similarity=0.267 Sum_probs=20.7
Q ss_pred hcCCCCCCCCCHHHHHHHHHHHhcCCccc
Q 035311 10 NGHINGGNDLPREFLSKLYHSICKNEIGT 38 (68)
Q Consensus 10 nrGin~G~Dlp~e~L~~iY~sI~~~ei~~ 38 (68)
.+......++++++.+.||..|-.+.++-
T Consensus 64 ~~~~a~~~gl~p~~~~~i~~~ii~esir~ 92 (104)
T PRK09239 64 LRQLAKDANLDPDFAEKFLNFIIKEVIRH 92 (104)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Confidence 34445567888999999998887665543
No 33
>PF13013 F-box-like_2: F-box-like domain
Probab=30.33 E-value=35 Score=21.56 Aligned_cols=18 Identities=28% Similarity=0.418 Sum_probs=14.0
Q ss_pred CCCCHHHHHHHHHHHhcC
Q 035311 17 NDLPREFLSKLYHSICKN 34 (68)
Q Consensus 17 ~Dlp~e~L~~iY~sI~~~ 34 (68)
.|||.|+|+.|++.=...
T Consensus 23 ~DLP~ELl~~I~~~C~~~ 40 (109)
T PF13013_consen 23 LDLPWELLQLIFDYCNDP 40 (109)
T ss_pred hhChHHHHHHHHhhcCcH
Confidence 589999999998764433
No 34
>PRK06285 chorismate mutase; Provisional
Probab=29.28 E-value=54 Score=19.70 Aligned_cols=18 Identities=6% Similarity=0.154 Sum_probs=10.7
Q ss_pred CCCCCHHHHHHHHHHHhc
Q 035311 16 GNDLPREFLSKLYHSICK 33 (68)
Q Consensus 16 G~Dlp~e~L~~iY~sI~~ 33 (68)
...+|++++..||..|-.
T Consensus 67 ~~~l~~~~i~~if~~Ii~ 84 (96)
T PRK06285 67 EHNIDENIGLKIMKILME 84 (96)
T ss_pred hCCCCHHHHHHHHHHHHH
Confidence 355666666666665543
No 35
>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=28.92 E-value=47 Score=19.34 Aligned_cols=15 Identities=33% Similarity=0.693 Sum_probs=11.9
Q ss_pred CChHHHHHHhcCCCC
Q 035311 1 MTEEDFIRSNGHING 15 (68)
Q Consensus 1 Mt~e~FirnnrGin~ 15 (68)
+|.++|++..|+|-+
T Consensus 42 IsR~~fvr~lR~IVG 56 (70)
T PF12174_consen 42 ISREEFVRKLRQIVG 56 (70)
T ss_pred CCHHHHHHHHHHHHH
Confidence 467888888888766
No 36
>COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=28.90 E-value=2e+02 Score=20.05 Aligned_cols=49 Identities=14% Similarity=0.331 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHhcCCcccCCCCc-----CCCCccchHHHHHHHHHHHhhc
Q 035311 17 NDLPREFLSKLYHSICKNEIGTTPEQC-----AGFPEITQSCWIDLMRSLRKQL 65 (68)
Q Consensus 17 ~Dlp~e~L~~iY~sI~~~ei~~~~~~~-----~~~~~~~~~~W~~l~~~~~~~~ 65 (68)
+.|+...+..|+.+|...-+-+....+ -.++..|..+-++|++.++..+
T Consensus 70 ~p~Dks~~~~IekaI~~snLglnP~~dG~~IRv~~P~lTeErRkelvK~~k~~~ 123 (187)
T COG0233 70 KPFDKSMVKAIEKAILASNLGLNPNNDGNVIRVPLPPLTEERRKELVKVAKKYA 123 (187)
T ss_pred ecCccchHHHHHHHHHHcCCCCCcCcCCCeEEecCCCCCHHHHHHHHHHHHHHH
Confidence 357888899999999998888887654 3488999999999998876543
No 37
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=28.26 E-value=1.9e+02 Score=19.44 Aligned_cols=47 Identities=17% Similarity=0.409 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHhcCCcccCCCCc-----CCCCccchHHHHHHHHHHHhh
Q 035311 18 DLPREFLSKLYHSICKNEIGTTPEQC-----AGFPEITQSCWIDLMRSLRKQ 64 (68)
Q Consensus 18 Dlp~e~L~~iY~sI~~~ei~~~~~~~-----~~~~~~~~~~W~~l~~~~~~~ 64 (68)
.|++.++..|..+|.+.-+-+....+ -.++.+|.++-..+++..+..
T Consensus 60 p~D~~~~~~I~kAI~~s~lglnP~~dg~~Iri~iP~lT~E~RkelvK~~k~~ 111 (176)
T TIGR00496 60 PFDKSNINAIEKAIQRSDLGLNPNNDGSVIRVNFPPLTEERRKELVKHAKKI 111 (176)
T ss_pred cCChhhHHHHHHHHHHCCCCCCcccCCCEEEecCCCCCHHHHHHHHHHHHHH
Confidence 47899999999999988888776543 258889999999999887653
No 38
>PRK10391 oriC-binding nucleoid-associated protein; Provisional
Probab=28.10 E-value=1.1e+02 Score=18.18 Aligned_cols=29 Identities=28% Similarity=0.387 Sum_probs=23.0
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhcC
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICKN 34 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~~ 34 (68)
||+.+|+=..|-++. .|-|+.+|+..+..
T Consensus 1 mtk~eyLlkfRkcss-----~eTLEkv~e~~~y~ 29 (71)
T PRK10391 1 MTVQDYLLKFRKISS-----LESLEKLFDHLNYT 29 (71)
T ss_pred CcHHHHHHHHHhcCc-----HHHHHHHHHHhhcc
Confidence 788888888886664 68899999988743
No 39
>TIGR01806 CM_mono2 chorismate mutase, putative. This model represents a clade of probable chorismate mutases from alpha, beta and gamma proteobacteria as well as Mycobacterium tuberculosis and a clade of nematodes. Although the most likely function for the enzymes represented by this model is as a chorismate mutase, in no species are these enzymes the sole chorismate mutase in the genome. Also, in no case are these enzymes located in a region of the genome proximal to any other enzymes involved in chorismate pathways. Although the Pantoea enzyme has been shown to complement a CM-free mutant of E. coli, this was also shown to be the case with isochorismate-pyruvate lyase which only has a secondary (non-physiologically relevant) chorismate mutase activity. This enzyme is believed to be a homodimer and be localized to the periplasm.
Probab=27.12 E-value=71 Score=19.98 Aligned_cols=27 Identities=7% Similarity=0.214 Sum_probs=18.9
Q ss_pred HHhcCCCCCCCCCHHHHHHHHHHHhcC
Q 035311 8 RSNGHINGGNDLPREFLSKLYHSICKN 34 (68)
Q Consensus 8 rnnrGin~G~Dlp~e~L~~iY~sI~~~ 34 (68)
.+.+.......+++++++.||..|-+.
T Consensus 45 ~~~~~~a~~~gL~~~~i~~if~~Ii~~ 71 (114)
T TIGR01806 45 DSLRAQAQSAGLDPDYVTRFFQAQINA 71 (114)
T ss_pred HHHHHHhHcCCCCHHHHHHHHHHHHHH
Confidence 344444444679999999999988643
No 40
>PRK09071 hypothetical protein; Validated
Probab=27.04 E-value=1.7e+02 Score=21.51 Aligned_cols=36 Identities=22% Similarity=0.217 Sum_probs=31.0
Q ss_pred CChHHHHHHh-cCCCCCCCCCHHHHHHHHHHHhcCCc
Q 035311 1 MTEEDFIRSN-GHINGGNDLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 1 Mt~e~Firnn-rGin~G~Dlp~e~L~~iY~sI~~~ei 36 (68)
|++..||+-. ||-.+++||..+--.++++.|-+.++
T Consensus 2 ~~~~~~ik~vg~gk~~~~~Lt~eEa~~~~~~il~g~~ 38 (323)
T PRK09071 2 HPFAEYIRILGKGKRGRRSLTREEARQAMGMILDGEV 38 (323)
T ss_pred CcHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHcCCC
Confidence 5677888776 88899999999999999999987764
No 41
>PF13319 DUF4090: Protein of unknown function (DUF4090)
Probab=26.63 E-value=61 Score=19.85 Aligned_cols=24 Identities=29% Similarity=0.625 Sum_probs=18.0
Q ss_pred cCCC-CCCCCCHHHHHHHHHHHhcCC
Q 035311 11 GHIN-GGNDLPREFLSKLYHSICKNE 35 (68)
Q Consensus 11 rGin-~G~Dlp~e~L~~iY~sI~~~e 35 (68)
.||+ +|..+|.+.| ++|+.+-..|
T Consensus 11 ~GiDlDGspIP~~~L-~LY~~VM~lE 35 (84)
T PF13319_consen 11 AGIDLDGSPIPPAML-ELYNEVMDLE 35 (84)
T ss_pred hCcCCCCCcCCHHHH-HHHHHHHHHH
Confidence 4664 6889999998 4898876544
No 42
>PF04940 BLUF: Sensors of blue-light using FAD; InterPro: IPR007024 An FAD-binding domain, BLUF, exemplified by the N terminus of the AppA protein, (Q53119 from SWISSPROT), from Rhodobacter sphaeroides, is present in various proteins, primarily from Bacteria. The BLUF domain is involved in sensing blue-light (and possibly redox) using FAD and is similar to the flavin-binding PAS domains and cryptochromes. The predicted secondary structure reveals that the BLUF domain is a novel FAD-binding fold [].; PDB: 2IYG_A 2IYI_B 1X0P_A 2HFN_G 3MZI_A 2HFO_E 3GFZ_A 3GG1_B 2KB2_A 3GFY_A ....
Probab=26.10 E-value=55 Score=19.60 Aligned_cols=16 Identities=25% Similarity=0.519 Sum_probs=13.5
Q ss_pred CHHHHHHHHHHHhcCC
Q 035311 20 PREFLSKLYHSICKNE 35 (68)
Q Consensus 20 p~e~L~~iY~sI~~~e 35 (68)
|++-+..+|++|+.++
T Consensus 53 ~~~~v~~l~~rI~~D~ 68 (93)
T PF04940_consen 53 PEEAVDALFERIKQDP 68 (93)
T ss_dssp EHHHHHHHHHHHHT-T
T ss_pred CHHHHHHHHHHHhcCC
Confidence 7889999999999876
No 43
>PF15332 LIME1: Lck-interacting transmembrane adapter 1
Probab=26.08 E-value=32 Score=24.58 Aligned_cols=17 Identities=29% Similarity=0.399 Sum_probs=13.8
Q ss_pred CCCCCHHHHHHHHHHHh
Q 035311 16 GNDLPREFLSKLYHSIC 32 (68)
Q Consensus 16 G~Dlp~e~L~~iY~sI~ 32 (68)
|.+.....|+++|+||+
T Consensus 211 G~~~~~g~lENvYESI~ 227 (228)
T PF15332_consen 211 GLGMDNGPLENVYESIQ 227 (228)
T ss_pred cccCCCcchHhHHHhhc
Confidence 55666678999999996
No 44
>COG3530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.75 E-value=96 Score=18.37 Aligned_cols=28 Identities=32% Similarity=0.462 Sum_probs=17.9
Q ss_pred CChHHHHHHhc-----CCCCCC---CCCHHHHHHHH
Q 035311 1 MTEEDFIRSNG-----HINGGN---DLPREFLSKLY 28 (68)
Q Consensus 1 Mt~e~Firnnr-----Gin~G~---Dlp~e~L~~iY 28 (68)
|++++.++-.+ |=..|. |+|.+||-=.+
T Consensus 1 meke~L~~ia~t~MPFGKYqGR~liDLPe~YLlWFa 36 (71)
T COG3530 1 MEKEHLIEIANTPMPFGKYQGRVLIDLPEEYLLWFA 36 (71)
T ss_pred CCHHHHHHHHcCCCCcccccceeeecCCHHHHHHHH
Confidence 55666665443 445563 89999986554
No 45
>cd00520 RRF Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.
Probab=25.64 E-value=2.1e+02 Score=19.12 Aligned_cols=47 Identities=15% Similarity=0.374 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHhcCCcccCCCCcC-----CCCccchHHHHHHHHHHHhh
Q 035311 18 DLPREFLSKLYHSICKNEIGTTPEQCA-----GFPEITQSCWIDLMRSLRKQ 64 (68)
Q Consensus 18 Dlp~e~L~~iY~sI~~~ei~~~~~~~~-----~~~~~~~~~W~~l~~~~~~~ 64 (68)
.++..++..|+.+|.+..+-+....++ .++.+|..+-..+.+..+..
T Consensus 65 p~D~~~i~~I~kAI~~s~l~l~P~~dg~~iri~iP~lT~E~R~~lvK~~k~~ 116 (179)
T cd00520 65 PFDKSAIKAIEKAILNSDLGLNPNNDGAVIRVNLPPLTEERRKELVKDAKKI 116 (179)
T ss_pred ecchhhHHHHHHHHHHCCCCCCcCcCCCEEEecCCCCCHHHHHHHHHHHHHH
Confidence 477889999999999888888775442 58899999999999887654
No 46
>COG1605 PheA Chorismate mutase [Amino acid transport and metabolism]
Probab=25.45 E-value=58 Score=19.76 Aligned_cols=24 Identities=17% Similarity=0.261 Sum_probs=15.6
Q ss_pred hcCCCCCCCCCHHHHHHHHHHHhc
Q 035311 10 NGHINGGNDLPREFLSKLYHSICK 33 (68)
Q Consensus 10 nrGin~G~Dlp~e~L~~iY~sI~~ 33 (68)
.+.......+++++++.+|..|-.
T Consensus 63 ~~~~~~~~~l~~~~i~~~f~~i~~ 86 (101)
T COG1605 63 LRAEAEKGGLDPELIERLFREIME 86 (101)
T ss_pred HHHHHHhCCCCHHHHHHHHHHHHH
Confidence 333455667777777777777654
No 47
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]
Probab=25.41 E-value=42 Score=25.86 Aligned_cols=29 Identities=34% Similarity=0.659 Sum_probs=22.1
Q ss_pred HHhcCCCCCC---CCCHHHHHHHHHHHhcCCc
Q 035311 8 RSNGHINGGN---DLPREFLSKLYHSICKNEI 36 (68)
Q Consensus 8 rnnrGin~G~---Dlp~e~L~~iY~sI~~~ei 36 (68)
+++|-+|.|. .+|.|.|.+||...++.++
T Consensus 87 ~~~~~~npgv~~~slpDEill~IFs~L~kk~L 118 (419)
T KOG2120|consen 87 KLNRENNPGVSWDSLPDEILLGIFSCLCKKEL 118 (419)
T ss_pred chhcccCCCCCcccCCHHHHHHHHHhccHHHH
Confidence 3455566664 4999999999999887765
No 48
>PF02512 UK: Virulence determinant
Probab=25.29 E-value=53 Score=20.35 Aligned_cols=20 Identities=40% Similarity=0.655 Sum_probs=12.7
Q ss_pred CChHHHHHH-hcCCCCCCCCC
Q 035311 1 MTEEDFIRS-NGHINGGNDLP 20 (68)
Q Consensus 1 Mt~e~Firn-nrGin~G~Dlp 20 (68)
||-.++|.- -+||+-|.|+|
T Consensus 46 mtssewiaeywkgi~rgndvp 66 (96)
T PF02512_consen 46 MTSSEWIAEYWKGIKRGNDVP 66 (96)
T ss_pred hhhHHHHHHHHHhcccCCCCC
Confidence 444455543 36888888877
No 49
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=25.15 E-value=64 Score=18.26 Aligned_cols=18 Identities=22% Similarity=0.595 Sum_probs=15.4
Q ss_pred CCCCCHHHHHHHHHHHhc
Q 035311 16 GNDLPREFLSKLYHSICK 33 (68)
Q Consensus 16 G~Dlp~e~L~~iY~sI~~ 33 (68)
...+|+++++.||..|-+
T Consensus 55 ~~~l~~~~i~~if~~ii~ 72 (81)
T PF01817_consen 55 EGGLDPEFIERIFRAIIE 72 (81)
T ss_dssp HTTSEHHHHHHHHHHHHH
T ss_pred hCCCCHHHHHHHHHHHHH
Confidence 468999999999998864
No 50
>TIGR01801 CM_A chorismate mutase domain of gram positive AroA protein. This model represents a small clade of chorismate mutase domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some gram positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other trusted CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44% identity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the gram positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role.
Probab=24.51 E-value=91 Score=19.14 Aligned_cols=21 Identities=14% Similarity=0.430 Sum_probs=15.8
Q ss_pred CCCCHHHHHHHHHHHhcCCcc
Q 035311 17 NDLPREFLSKLYHSICKNEIG 37 (68)
Q Consensus 17 ~Dlp~e~L~~iY~sI~~~ei~ 37 (68)
+.+|.+++..||..|-+....
T Consensus 64 g~l~~~~i~~If~~I~~~Sr~ 84 (102)
T TIGR01801 64 GPFPTATIKGIFKEIFKASLA 84 (102)
T ss_pred CCCCHHHHHHHHHHHHHHHHH
Confidence 468999999999888754433
No 51
>PF08982 DUF1857: Domain of unknown function (DUF1857); InterPro: IPR015075 This protein has no known function. It is found in various hypothetical bacterial and fungal proteins. ; PDB: 2FFS_B.
Probab=23.30 E-value=83 Score=20.66 Aligned_cols=18 Identities=17% Similarity=0.375 Sum_probs=14.8
Q ss_pred hHHHHHHHHHHHhhccCC
Q 035311 51 QSCWIDLMRSLRKQLHLL 68 (68)
Q Consensus 51 ~~~W~~l~~~~~~~~~~~ 68 (68)
.+.|.-|++|++.+-+||
T Consensus 21 ~QlW~GL~~kar~p~~Fv 38 (149)
T PF08982_consen 21 EQLWRGLVLKARNPQLFV 38 (149)
T ss_dssp HHHHHHHHHHHH-GGGT-
T ss_pred HHHHHHHHHHHhChhhCc
Confidence 789999999999998886
No 52
>PRK07248 hypothetical protein; Provisional
Probab=22.66 E-value=1e+02 Score=17.94 Aligned_cols=16 Identities=19% Similarity=0.245 Sum_probs=8.9
Q ss_pred CCCHHHHHHHHHHHhc
Q 035311 18 DLPREFLSKLYHSICK 33 (68)
Q Consensus 18 Dlp~e~L~~iY~sI~~ 33 (68)
.++++++..||..|-+
T Consensus 62 ~~~~~~i~~if~~I~~ 77 (87)
T PRK07248 62 KAYQETIVATFKDIMK 77 (87)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 3444566666666543
No 53
>PF09709 Cas_Csd1: CRISPR-associated protein (Cas_Csd1); InterPro: IPR010144 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents the Csd1 (CRISPR/Cas Subtype DVULG protein 1) family of Cas proteins, which tend to be found near CRISPR repeats of the DVULG subtype of CRISPR/Cas locus. The species range for this subtype, so far, is exclusively bacterial and mesophilic, although CRISPR loci in general are particularly common among archaea and thermophilic bacteria.
Probab=22.08 E-value=64 Score=25.26 Aligned_cols=29 Identities=24% Similarity=0.164 Sum_probs=24.7
Q ss_pred HHHHHhcCCCCCCCCCHHHHHHHHHHHhc
Q 035311 5 DFIRSNGHINGGNDLPREFLSKLYHSICK 33 (68)
Q Consensus 5 ~FirnnrGin~G~Dlp~e~L~~iY~sI~~ 33 (68)
-.-+..|.|-.|..+|..++..+..+|++
T Consensus 394 l~~~Ll~~il~g~~~P~~l~~~~~~Rir~ 422 (574)
T PF09709_consen 394 LAGRLLRSILEGRPYPRSLLQAALRRIRN 422 (574)
T ss_pred HHHHHHHHHHcCCCChHHHHHHHHHHHHh
Confidence 34566788889999999999999999993
No 54
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=22.01 E-value=1.5e+02 Score=16.23 Aligned_cols=28 Identities=18% Similarity=0.409 Sum_probs=19.4
Q ss_pred HHHHhcCCCCCCCCCHHHHHHHHHHHhc
Q 035311 6 FIRSNGHINGGNDLPREFLSKLYHSICK 33 (68)
Q Consensus 6 FirnnrGin~G~Dlp~e~L~~iY~sI~~ 33 (68)
+....+-.-+=.++|++++..|=.+|+.
T Consensus 29 ~~~Ha~~~Hg~~~~~~el~~~ir~~I~~ 56 (57)
T PF06348_consen 29 VVEHAREVHGMTEIPEELREKIRSAIKD 56 (57)
T ss_pred HHHHHHHhcCCccCCHHHHHHHHHHhhc
Confidence 3444444445568899999999888864
No 55
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ]. This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme. The SCF complex (e.g., Skp1-Cullin-F-box) plays a similar role as an E3 ligase in the ubiquitin protein degradation pathway [, ]. Different F-box proteins as a part of SCF complex recruit particular substrates for ubiquitination through specific protein-protein interaction domains. Many mammalian F-box domains contain leucine-rich or WD-40 repeats (IPR001680 from INTERPRO). However, several F-box proteins either have other previously described domains such as Sec7 domain found in FBS protein or do not contain defined protein-protein interaction domains or motifs.; GO: 0005515 protein binding; PDB: 2E32_A 2E31_A 3V7D_B 1NEX_B 3MKS_D 3L2O_B.
Probab=21.85 E-value=57 Score=16.25 Aligned_cols=18 Identities=28% Similarity=0.541 Sum_probs=12.1
Q ss_pred CCCHHHHHHHHHHHhcCC
Q 035311 18 DLPREFLSKLYHSICKNE 35 (68)
Q Consensus 18 Dlp~e~L~~iY~sI~~~e 35 (68)
+||.+.+..|+....-.+
T Consensus 5 ~LP~~il~~Il~~l~~~~ 22 (48)
T PF00646_consen 5 DLPDEILQEILSYLDPKD 22 (48)
T ss_dssp HS-HHHHHHHHHTS-HHH
T ss_pred HCCHHHHHHHHHHCcHHH
Confidence 689999999987665444
No 56
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=21.75 E-value=89 Score=18.81 Aligned_cols=17 Identities=24% Similarity=0.296 Sum_probs=14.0
Q ss_pred CChHHHHHHhcCCCCCC
Q 035311 1 MTEEDFIRSNGHINGGN 17 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~ 17 (68)
|..+++++.++||..+.
T Consensus 55 ~~~~~ii~~L~gi~~~~ 71 (95)
T PF12637_consen 55 VPPEEIIDQLRGIRCGP 71 (95)
T ss_pred CCHHHHHHHhcCCCCCC
Confidence 57889999999987764
No 57
>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=21.34 E-value=69 Score=26.14 Aligned_cols=17 Identities=24% Similarity=0.647 Sum_probs=14.3
Q ss_pred CCCCCCCCHHHHHHHHH
Q 035311 13 INGGNDLPREFLSKLYH 29 (68)
Q Consensus 13 in~G~Dlp~e~L~~iY~ 29 (68)
|+.++|||.+|..=++-
T Consensus 301 IDE~QDFP~~F~~Lcf~ 317 (660)
T COG3972 301 IDESQDFPQSFIDLCFM 317 (660)
T ss_pred ecccccCCHHHHHHHHH
Confidence 78999999999876654
No 58
>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends. Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].
Probab=21.33 E-value=68 Score=20.90 Aligned_cols=19 Identities=26% Similarity=0.455 Sum_probs=15.2
Q ss_pred HHHHHHHHhcCCcccCCCC
Q 035311 24 LSKLYHSICKNEIGTTPEQ 42 (68)
Q Consensus 24 L~~iY~sI~~~ei~~~~~~ 42 (68)
.-.+|.+++.+.|.+|.-+
T Consensus 44 I~~lYqslkRN~i~lPsv~ 62 (120)
T PF08579_consen 44 INPLYQSLKRNGITLPSVE 62 (120)
T ss_pred HHHHHHHHHhcCCCCCcHH
Confidence 4579999999999887643
No 59
>PRK10945 gene expression modulator; Provisional
Probab=21.30 E-value=1.7e+02 Score=17.51 Aligned_cols=28 Identities=11% Similarity=0.148 Sum_probs=21.2
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHHHHHHHHhc
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLSKLYHSICK 33 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~~iY~sI~~ 33 (68)
||.++|+=..|-++ ..|-|+.+|+..+.
T Consensus 6 Mtk~dyL~~fRrcs-----s~eTLEkvie~~~~ 33 (72)
T PRK10945 6 LTKTDYLMRLRRCQ-----TIDTLERVIEKNKY 33 (72)
T ss_pred ccHHHHHHHHHhcC-----cHHHHHHHHHHhhc
Confidence 78888888887665 36788888887664
No 60
>PF06411 HdeA: HdeA/HdeB family; InterPro: IPR010486 HNS (histone-like nucleoid structuring)-dependent expression A (HdeA) protein is a stress response protein found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella []. HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria []. HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain. ; PDB: 1BG8_C 1DJ8_C 2XUV_C.
Probab=20.10 E-value=38 Score=20.20 Aligned_cols=10 Identities=30% Similarity=0.577 Sum_probs=6.2
Q ss_pred CChHHHHHHh
Q 035311 1 MTEEDFIRSN 10 (68)
Q Consensus 1 Mt~e~Firnn 10 (68)
||+++|+.++
T Consensus 34 mTC~eFl~ld 43 (94)
T PF06411_consen 34 MTCKEFLDLD 43 (94)
T ss_dssp -BHHHHHTS-
T ss_pred CcHHHHHcCC
Confidence 7888888644
No 61
>PF08486 SpoIID: Stage II sporulation protein; InterPro: IPR013693 This domain is found in the stage II sporulation protein SpoIID. SpoIID is necessary for membrane migration as well as for some of the earlier steps in engulfment during bacterial endospore formation []. The domain is also found in amidase enhancer proteins. Amidases, like SpoIID, are cell wall hydrolases [].
Probab=20.10 E-value=1.1e+02 Score=18.16 Aligned_cols=33 Identities=15% Similarity=0.183 Sum_probs=24.6
Q ss_pred CChHHHHHHhcCCCCCCCCCHHHHH--------HHHHHHhc
Q 035311 1 MTEEDFIRSNGHINGGNDLPREFLS--------KLYHSICK 33 (68)
Q Consensus 1 Mt~e~FirnnrGin~G~Dlp~e~L~--------~iY~sI~~ 33 (68)
|.+|+|+...=...=+.++|.|.|. -+|..+..
T Consensus 14 v~lEeYl~gVl~~E~~~~~~~EALKAQAV~aRTy~~~~~~~ 54 (96)
T PF08486_consen 14 VPLEEYLKGVLASEMPASWPEEALKAQAVAARTYAYYRMEH 54 (96)
T ss_pred ecHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 4678888877666667899999995 46666666
Done!