Query 046004
Match_columns 157
No_of_seqs 178 out of 435
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 07:44:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046004.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046004hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14009 DUF4228: Domain of un 100.0 4.1E-40 8.9E-45 253.0 12.8 153 1-155 1-181 (181)
2 PRK08053 sulfur carrier protei 73.6 10 0.00022 24.7 4.7 22 15-36 3-24 (66)
3 PRK06944 sulfur carrier protei 71.1 16 0.00035 23.2 5.3 54 15-68 3-60 (65)
4 PF02824 TGS: TGS domain; Int 70.5 7.6 0.00017 24.9 3.5 25 12-36 1-25 (60)
5 TIGR01683 thiS thiamine biosyn 59.6 24 0.00053 22.6 4.4 23 15-37 1-23 (64)
6 PRK06083 sulfur carrier protei 59.1 10 0.00022 26.4 2.6 23 15-37 21-43 (84)
7 PRK05659 sulfur carrier protei 54.0 15 0.00032 23.6 2.6 23 15-37 3-25 (66)
8 PRK07440 hypothetical protein; 50.4 19 0.0004 23.9 2.7 24 13-36 5-28 (70)
9 cd00565 ThiS ThiaminS ubiquiti 49.9 53 0.0012 21.0 4.8 23 15-37 2-24 (65)
10 PF13545 HTH_Crp_2: Crp-like h 43.0 45 0.00098 21.4 3.7 37 96-132 20-56 (76)
11 cd01668 TGS_RelA_SpoT TGS_RelA 40.4 40 0.00087 20.4 3.0 24 13-36 2-25 (60)
12 cd00178 STI Soybean trypsin in 39.8 23 0.00051 27.6 2.2 18 54-71 6-23 (172)
13 PRK05863 sulfur carrier protei 39.5 34 0.00075 22.1 2.6 23 15-37 3-25 (65)
14 PF00197 Kunitz_legume: Trypsi 38.8 25 0.00054 27.4 2.2 18 54-71 6-23 (176)
15 PF14237 DUF4339: Domain of un 35.0 15 0.00032 22.1 0.3 10 140-149 36-45 (45)
16 PRK07696 sulfur carrier protei 33.3 49 0.0011 21.6 2.6 22 15-36 3-25 (67)
17 PRK06437 hypothetical protein; 31.7 1.5E+02 0.0032 19.3 5.0 52 15-69 5-63 (67)
18 PF01402 RHH_1: Ribbon-helix-h 31.7 1E+02 0.0022 17.3 4.6 31 100-130 1-34 (39)
19 PF00325 Crp: Bacterial regula 31.5 53 0.0011 18.8 2.2 28 103-130 1-28 (32)
20 smart00452 STI Soybean trypsin 30.2 39 0.00084 26.4 2.0 18 54-71 5-22 (172)
21 PF10723 RepB-RCR_reg: Replica 28.9 1.6E+02 0.0035 20.3 4.8 36 96-131 39-77 (84)
22 PHA02843 hypothetical protein; 28.5 23 0.0005 23.4 0.4 14 1-14 1-14 (73)
23 PRK06488 sulfur carrier protei 24.6 83 0.0018 20.0 2.5 22 15-37 3-24 (65)
24 smart00419 HTH_CRP helix_turn_ 23.6 1E+02 0.0023 17.5 2.7 34 99-132 3-36 (48)
25 cd02980 TRX_Fd_family Thioredo 23.5 88 0.0019 20.1 2.5 33 1-36 44-76 (77)
26 COG2104 ThiS Sulfur transfer p 22.6 98 0.0021 20.6 2.6 23 15-37 5-27 (68)
27 PRK08364 sulfur carrier protei 21.9 2.4E+02 0.0051 18.3 5.0 52 15-69 7-66 (70)
28 cd03063 TRX_Fd_FDH_beta TRX-li 20.9 1.3E+02 0.0029 21.1 3.1 24 9-34 48-71 (92)
29 PF03990 DUF348: Domain of unk 20.4 1.6E+02 0.0036 17.3 3.1 23 15-37 4-27 (43)
No 1
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=100.00 E-value=4.1e-40 Score=253.05 Aligned_cols=153 Identities=37% Similarity=0.643 Sum_probs=115.3
Q ss_pred CCCcccc------CCceeEEEecCCcEEEEeCCCcHHHHHhhcCCcEEeCCC-----CCccCCCCCCccCCCCeEEEeeC
Q 046004 1 MGNCLVL------EEKVIKVMKTDGKILEYNQPIRVQDVLAEFSGHAISDSL-----PEIRHLRPDFKLVGGNLYFLVPV 69 (157)
Q Consensus 1 MGNC~~~------~~~~ikV~~~dG~v~e~~~pv~a~~vm~~~Pgh~v~~s~-----~~~~~L~~d~~L~~G~~YfLlP~ 69 (157)
||||++. ..++||||++||+|++|+.||+|+|||.+|||||||++. ..+++|+||++|++|++|||||.
T Consensus 1 MGn~~~~~~~~~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~h~v~~~~~~~~~~~~~~l~~d~~L~~G~~Y~llP~ 80 (181)
T PF14009_consen 1 MGNCVSCCLASSSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPGHFVCDSDSFRFGRRIKPLPPDEELQPGQIYFLLPM 80 (181)
T ss_pred CCCcccccccccCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCCCEEeccccccCCCcccCCCccCeecCCCEEEEEEc
Confidence 9999985 689999999999999999999999999999999998763 46799999999999999999999
Q ss_pred CCCCchhc---cccccccchhcc------------c--CCcCCCceEEEEEEeCHHHHHHHHHhccCCHHHHHHHHHhhc
Q 046004 70 PLPSQKVQ---KKKVRFSDEEAG------------A--GAKERGGVVRIKLVISKQELEELLQKQGVSVKDMVSRIQSKQ 132 (157)
Q Consensus 70 ~~~~~~~~---~~~vr~~~~~~~------------~--~~~~~~g~~rvkl~i~k~~L~~ll~~~~~s~e~~l~~l~~~~ 132 (157)
+....... .....+...... . ....++|++++|++++++||++++++. +.++++....+..
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~rvki~isk~el~~~l~~~--s~~~~~~~~~~~~ 158 (181)
T PF14009_consen 81 SRLQSVLSASDMASLASSASSASSSSSARKSSSRPFSRSRSSNGGVVRVKIVISKEELEELLSEG--SDEEMLSESCRRP 158 (181)
T ss_pred cccCcccccchhcccccchhhccccccccccccccccccccccCcccccccccCHHHHHHHHhcc--ccchhhhhhhccc
Confidence 98654211 111111111100 0 123467889999999999999999866 5666666555432
Q ss_pred cccccccCCCCCCccccCcCcCC
Q 046004 133 SADDFQSGDNTKAWKPELESIPE 155 (157)
Q Consensus 133 ~~~~~~~~~~~~~WrP~LeSIpE 155 (157)
.........+.++|||+||||||
T Consensus 159 ~~~~~~~~~~~~~WrP~LesI~E 181 (181)
T PF14009_consen 159 RRRSSRRGSRSRSWRPALESIPE 181 (181)
T ss_pred cccccccCCCCCCccCCCCCcCc
Confidence 21112233466999999999998
No 2
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=73.62 E-value=10 Score=24.68 Aligned_cols=22 Identities=9% Similarity=0.214 Sum_probs=20.0
Q ss_pred EecCCcEEEEeCCCcHHHHHhh
Q 046004 15 MKTDGKILEYNQPIRVQDVLAE 36 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~ 36 (157)
+..||+..++..++++.+++..
T Consensus 3 i~vNg~~~~~~~~~tl~~ll~~ 24 (66)
T PRK08053 3 ILFNDQPMQCAAGQTVHELLEQ 24 (66)
T ss_pred EEECCeEEEcCCCCCHHHHHHH
Confidence 5679999999999999999975
No 3
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=71.15 E-value=16 Score=23.21 Aligned_cols=54 Identities=20% Similarity=0.217 Sum_probs=32.3
Q ss_pred EecCCcEEEEeCCCcHHHHHhhc---CCcEE-eCCCCCccCCCCCCccCCCCeEEEee
Q 046004 15 MKTDGKILEYNQPIRVQDVLAEF---SGHAI-SDSLPEIRHLRPDFKLVGGNLYFLVP 68 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~~---Pgh~v-~~s~~~~~~L~~d~~L~~G~~YfLlP 68 (157)
|..||+..++....++++++... |+..+ .+..-..+.-..+..|+.|--.-++|
T Consensus 3 i~vNg~~~~~~~~~tl~~ll~~l~~~~~~~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 3 IQLNQQTLSLPDGATVADALAAYGARPPFAVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred EEECCEEEECCCCCcHHHHHHhhCCCCCeEEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 56799999999999999999864 33333 12211111233455666664444444
No 4
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=70.54 E-value=7.6 Score=24.93 Aligned_cols=25 Identities=36% Similarity=0.384 Sum_probs=22.5
Q ss_pred eEEEecCCcEEEEeCCCcHHHHHhh
Q 046004 12 IKVMKTDGKILEYNQPIRVQDVLAE 36 (157)
Q Consensus 12 ikV~~~dG~v~e~~~pv~a~~vm~~ 36 (157)
|+|..+||++.+|....|+.|+-..
T Consensus 1 I~v~lpdG~~~~~~~g~T~~d~A~~ 25 (60)
T PF02824_consen 1 IRVYLPDGSIKELPEGSTVLDVAYS 25 (60)
T ss_dssp EEEEETTSCEEEEETTBBHHHHHHH
T ss_pred CEEECCCCCeeeCCCCCCHHHHHHH
Confidence 5788899999999999999998766
No 5
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=59.65 E-value=24 Score=22.57 Aligned_cols=23 Identities=13% Similarity=0.384 Sum_probs=20.3
Q ss_pred EecCCcEEEEeCCCcHHHHHhhc
Q 046004 15 MKTDGKILEYNQPIRVQDVLAEF 37 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~~ 37 (157)
+..||+..++..+.++.+++...
T Consensus 1 i~iNg~~~~~~~~~tv~~ll~~l 23 (64)
T TIGR01683 1 ITVNGEPVEVEDGLTLAALLESL 23 (64)
T ss_pred CEECCeEEEcCCCCcHHHHHHHc
Confidence 35799999999999999999874
No 6
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=59.10 E-value=10 Score=26.36 Aligned_cols=23 Identities=4% Similarity=0.300 Sum_probs=20.7
Q ss_pred EecCCcEEEEeCCCcHHHHHhhc
Q 046004 15 MKTDGKILEYNQPIRVQDVLAEF 37 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~~ 37 (157)
+..||+..++..++++.+++..+
T Consensus 21 I~VNG~~~~~~~~~tl~~LL~~l 43 (84)
T PRK06083 21 ISINDQSIQVDISSSLAQIIAQL 43 (84)
T ss_pred EEECCeEEEcCCCCcHHHHHHHc
Confidence 67899999999999999999863
No 7
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=54.04 E-value=15 Score=23.56 Aligned_cols=23 Identities=22% Similarity=0.213 Sum_probs=20.5
Q ss_pred EecCCcEEEEeCCCcHHHHHhhc
Q 046004 15 MKTDGKILEYNQPIRVQDVLAEF 37 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~~ 37 (157)
+..||+..++..+.|+++++...
T Consensus 3 i~vNG~~~~~~~~~tl~~lL~~l 25 (66)
T PRK05659 3 IQLNGEPRELPDGESVAALLARE 25 (66)
T ss_pred EEECCeEEEcCCCCCHHHHHHhc
Confidence 67899999999999999999863
No 8
>PRK07440 hypothetical protein; Provisional
Probab=50.39 E-value=19 Score=23.93 Aligned_cols=24 Identities=13% Similarity=0.295 Sum_probs=21.0
Q ss_pred EEEecCCcEEEEeCCCcHHHHHhh
Q 046004 13 KVMKTDGKILEYNQPIRVQDVLAE 36 (157)
Q Consensus 13 kV~~~dG~v~e~~~pv~a~~vm~~ 36 (157)
.-+..||+..++..+.++.+++.+
T Consensus 5 m~i~vNG~~~~~~~~~tl~~lL~~ 28 (70)
T PRK07440 5 ITLQVNGETRTCSSGTSLPDLLQQ 28 (70)
T ss_pred eEEEECCEEEEcCCCCCHHHHHHH
Confidence 346679999999999999999986
No 9
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=49.92 E-value=53 Score=20.96 Aligned_cols=23 Identities=17% Similarity=0.378 Sum_probs=20.5
Q ss_pred EecCCcEEEEeCCCcHHHHHhhc
Q 046004 15 MKTDGKILEYNQPIRVQDVLAEF 37 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~~ 37 (157)
+..||+..++..+.++.+++...
T Consensus 2 i~iNg~~~~~~~~~tv~~ll~~l 24 (65)
T cd00565 2 ITVNGEPREVEEGATLAELLEEL 24 (65)
T ss_pred EEECCeEEEcCCCCCHHHHHHHc
Confidence 56799999999999999999774
No 10
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=42.97 E-value=45 Score=21.38 Aligned_cols=37 Identities=22% Similarity=0.484 Sum_probs=30.6
Q ss_pred CceEEEEEEeCHHHHHHHHHhccCCHHHHHHHHHhhc
Q 046004 96 GGVVRIKLVISKQELEELLQKQGVSVKDMVSRIQSKQ 132 (157)
Q Consensus 96 ~g~~rvkl~i~k~~L~~ll~~~~~s~e~~l~~l~~~~ 132 (157)
.+...+.+-+|.++|..++.-...++..+++.|....
T Consensus 20 ~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g 56 (76)
T PF13545_consen 20 GDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEG 56 (76)
T ss_dssp TTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTT
T ss_pred CCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4568899999999999999866567888888888764
No 11
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=40.39 E-value=40 Score=20.44 Aligned_cols=24 Identities=25% Similarity=0.297 Sum_probs=20.9
Q ss_pred EEEecCCcEEEEeCCCcHHHHHhh
Q 046004 13 KVMKTDGKILEYNQPIRVQDVLAE 36 (157)
Q Consensus 13 kV~~~dG~v~e~~~pv~a~~vm~~ 36 (157)
-|..+||...+|..+.++.+++..
T Consensus 2 ~~~~~~g~~~~~~~~~t~~~~~~~ 25 (60)
T cd01668 2 YVFTPKGEIIELPAGATVLDFAYA 25 (60)
T ss_pred EEECCCCCEEEcCCCCCHHHHHHH
Confidence 466789999999999999998865
No 12
>cd00178 STI Soybean trypsin inhibitor (Kunitz) family of protease inhibitors. Inhibit proteases by binding with high affinity to their active sites. Trefoil fold, common to interleukins and fibroblast growth factors.
Probab=39.80 E-value=23 Score=27.59 Aligned_cols=18 Identities=22% Similarity=0.433 Sum_probs=15.9
Q ss_pred CCCccCCCCeEEEeeCCC
Q 046004 54 PDFKLVGGNLYFLVPVPL 71 (157)
Q Consensus 54 ~d~~L~~G~~YfLlP~~~ 71 (157)
.+++|++|.-||++|+..
T Consensus 6 ~G~~l~~g~~YyI~p~~~ 23 (172)
T cd00178 6 DGNPLRNGGRYYILPAIR 23 (172)
T ss_pred CCCCCcCCCeEEEEEcee
Confidence 468999999999999975
No 13
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=39.46 E-value=34 Score=22.09 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=20.4
Q ss_pred EecCCcEEEEeCCCcHHHHHhhc
Q 046004 15 MKTDGKILEYNQPIRVQDVLAEF 37 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~~ 37 (157)
+..||+..++..+.++.+++...
T Consensus 3 i~vNG~~~~~~~~~tl~~ll~~l 25 (65)
T PRK05863 3 VVVNEEQVEVDEQTTVAALLDSL 25 (65)
T ss_pred EEECCEEEEcCCCCcHHHHHHHc
Confidence 56799999999999999999863
No 14
>PF00197 Kunitz_legume: Trypsin and protease inhibitor; InterPro: IPR002160 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The Kunitz-type soybean trypsin inhibitor (STI) family consists mainly of proteinase inhibitors from Leguminosae seeds []. They belong to MEROPS inhibitor family I3, clan IC. They exhibit proteinase inhibitory activity against serine proteinases; trypsin (MEROPS peptidase family S1, IPR001254 from INTERPRO) and subtilisin (MEROPS peptidase family S8, IPR000209 from INTERPRO), thiol proteinases (MEROPS peptidase family C1, IPR000668 from INTERPRO) and aspartic proteinases (MEROPS peptidase family A1, IPR001461 from INTERPRO) []. Inhibitors from cereals are active against subtilisin and endogenous alpha-amylases, while some also inhibit tissue plasminogen activator. The inhibitors are usually specific for either trypsin or chymotrypsin, and some are effective against both. They are thought to protect the seeds against consumption by animal predators, while at the same time existing as seed storage proteins themselves - all the actively inhibitory members contain 2 disulphide bridges. The existence of a member with no inhibitory activity, winged bean albumin 1, suggests that the inhibitors may have evolved from seed storage proteins. Proteins from the Kunitz family contain from 170 to 200 amino acid residues and one or two intra-chain disulphide bonds. The best conserved region is found in their N-terminal section. The crystal structures of soybean trypsin inhibitor (STI), trypsin inhibitor DE-3 from the Kaffir tree Erythrina caffra (ETI) [] and the bifunctional proteinase K/alpha-amylase inhibitor from wheat (PK13) have been solved, showing them to share the same 12-stranded beta-sheet structure as those of interleukin-1 and heparin-binding growth factors []. The beta-sheets are arranged in 3 similar lobes around a central axis, 6 strands forming an anti-parallel beta-barrel. Despite the structural similarity, STI shows no interleukin-1 bioactivity, presumably as a result of their primary sequence disparities. The active inhibitory site containing the scissile bond is located in the loop between beta-strands 4 and 5 in STI and ETI. The STIs belong to a superfamily that also contains the interleukin-1 proteins, heparin binding growth factors (HBGF) and histactophilin, all of which have very similar structures, but share no sequence similarity with the STI family.; GO: 0004866 endopeptidase inhibitor activity; PDB: 3TC2_B 3S8J_A 3S8K_A 1TIE_A 2GZB_A 3E8L_C 2IWT_B 3BX1_C 1AVA_D 3IIR_A ....
Probab=38.82 E-value=25 Score=27.45 Aligned_cols=18 Identities=22% Similarity=0.421 Sum_probs=14.7
Q ss_pred CCCccCCCCeEEEeeCCC
Q 046004 54 PDFKLVGGNLYFLVPVPL 71 (157)
Q Consensus 54 ~d~~L~~G~~YfLlP~~~ 71 (157)
.+++|++|.-||++|+..
T Consensus 6 ~G~~l~~g~~YyI~p~~~ 23 (176)
T PF00197_consen 6 DGNPLRNGGEYYILPAIR 23 (176)
T ss_dssp TSCB-BTTSEEEEEESST
T ss_pred CCCCCcCCCCEEEEeCcc
Confidence 368899999999999865
No 15
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=34.97 E-value=15 Score=22.11 Aligned_cols=10 Identities=30% Similarity=0.780 Sum_probs=6.1
Q ss_pred CCCCCCcccc
Q 046004 140 GDNTKAWKPE 149 (157)
Q Consensus 140 ~~~~~~WrP~ 149 (157)
+.+-..|+|+
T Consensus 36 ~~g~~~W~pl 45 (45)
T PF14237_consen 36 KEGMSDWKPL 45 (45)
T ss_pred CCChhhceEC
Confidence 3444678874
No 16
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=33.32 E-value=49 Score=21.61 Aligned_cols=22 Identities=23% Similarity=0.456 Sum_probs=19.1
Q ss_pred EecCCcEEEEeCC-CcHHHHHhh
Q 046004 15 MKTDGKILEYNQP-IRVQDVLAE 36 (157)
Q Consensus 15 ~~~dG~v~e~~~p-v~a~~vm~~ 36 (157)
+..||+..++..+ .++++++..
T Consensus 3 I~vNG~~~~~~~~~~tv~~lL~~ 25 (67)
T PRK07696 3 LKINGNQIEVPESVKTVAELLTH 25 (67)
T ss_pred EEECCEEEEcCCCcccHHHHHHH
Confidence 5679999999987 789999975
No 17
>PRK06437 hypothetical protein; Provisional
Probab=31.73 E-value=1.5e+02 Score=19.29 Aligned_cols=52 Identities=13% Similarity=0.268 Sum_probs=32.0
Q ss_pred EecCC---cEEEEeCCCcHHHHHhhc--C--CcEEeCCCCCccCCCCCCccCCCCeEEEeeC
Q 046004 15 MKTDG---KILEYNQPIRVQDVLAEF--S--GHAISDSLPEIRHLRPDFKLVGGNLYFLVPV 69 (157)
Q Consensus 15 ~~~dG---~v~e~~~pv~a~~vm~~~--P--gh~v~~s~~~~~~L~~d~~L~~G~~YfLlP~ 69 (157)
|..|| +..++..+.++++++.+. + +.++.- . -.+++++..|..|--.-++|.
T Consensus 5 ~~v~g~~~~~~~i~~~~tv~dLL~~Lgi~~~~vaV~v-N--g~iv~~~~~L~dgD~Veiv~~ 63 (67)
T PRK06437 5 IRVKGHINKTIEIDHELTVNDIIKDLGLDEEEYVVIV-N--GSPVLEDHNVKKEDDVLILEV 63 (67)
T ss_pred EEecCCcceEEEcCCCCcHHHHHHHcCCCCccEEEEE-C--CEECCCceEcCCCCEEEEEec
Confidence 55678 557788889999999863 2 122221 1 133457888887755555543
No 18
>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=31.66 E-value=1e+02 Score=17.34 Aligned_cols=31 Identities=19% Similarity=0.334 Sum_probs=22.2
Q ss_pred EEEEEeCHHHHHHH---HHhccCCHHHHHHHHHh
Q 046004 100 RIKLVISKQELEEL---LQKQGVSVKDMVSRIQS 130 (157)
Q Consensus 100 rvkl~i~k~~L~~l---l~~~~~s~e~~l~~l~~ 130 (157)
|+.|.|+++..++| -.+.|.|..+++..+..
T Consensus 1 Riti~l~~~~~~~l~~~a~~~g~s~s~~ir~ai~ 34 (39)
T PF01402_consen 1 RITIRLPDELYERLDELAKELGRSRSELIREAIR 34 (39)
T ss_dssp EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred CeEEEeCHHHHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 67788888766654 44668898888776654
No 19
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=31.53 E-value=53 Score=18.80 Aligned_cols=28 Identities=14% Similarity=0.405 Sum_probs=16.5
Q ss_pred EEeCHHHHHHHHHhccCCHHHHHHHHHh
Q 046004 103 LVISKQELEELLQKQGVSVKDMVSRIQS 130 (157)
Q Consensus 103 l~i~k~~L~~ll~~~~~s~e~~l~~l~~ 130 (157)
|.+|++|+..++.-.-.++-.+++.+.+
T Consensus 1 l~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 1 LPMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp EE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 5689999999987543345555555554
No 20
>smart00452 STI Soybean trypsin inhibitor (Kunitz) family of protease inhibitors.
Probab=30.23 E-value=39 Score=26.36 Aligned_cols=18 Identities=22% Similarity=0.449 Sum_probs=15.8
Q ss_pred CCCccCCCCeEEEeeCCC
Q 046004 54 PDFKLVGGNLYFLVPVPL 71 (157)
Q Consensus 54 ~d~~L~~G~~YfLlP~~~ 71 (157)
.+++|++|.-||++|+..
T Consensus 5 ~G~~l~~G~~YyI~p~~~ 22 (172)
T smart00452 5 DGNPLRNGGTYYILPAIR 22 (172)
T ss_pred CCCCCcCCCcEEEEEccc
Confidence 468999999999999964
No 21
>PF10723 RepB-RCR_reg: Replication regulatory protein RepB; InterPro: IPR019661 This family of proteins regulates the replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of the replication of the RCR plasmids occurs mainly at the initiation of leading strand synthesis at the dso, such that concentration of Rep protein controls plasmid replication []. ; PDB: 2KEL_B.
Probab=28.93 E-value=1.6e+02 Score=20.33 Aligned_cols=36 Identities=33% Similarity=0.544 Sum_probs=25.1
Q ss_pred CceEEEEEEeC---HHHHHHHHHhccCCHHHHHHHHHhh
Q 046004 96 GGVVRIKLVIS---KQELEELLQKQGVSVKDMVSRIQSK 131 (157)
Q Consensus 96 ~g~~rvkl~i~---k~~L~~ll~~~~~s~e~~l~~l~~~ 131 (157)
.+..++++.|+ |+.|.+|..+.|++.-+++..|+..
T Consensus 39 ~t~k~i~v~I~~~~K~~L~~lc~~~GlTQae~IE~LI~~ 77 (84)
T PF10723_consen 39 ETHKRINVFIPNELKERLEELCKEQGLTQAEMIERLIKS 77 (84)
T ss_dssp --EEEEEEEEEHHHHHHHHHHHHHS---HHHHHHHHHHH
T ss_pred hhcCeeEEEECHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence 34578999998 4577777788899999999888764
No 22
>PHA02843 hypothetical protein; Provisional
Probab=28.49 E-value=23 Score=23.41 Aligned_cols=14 Identities=50% Similarity=0.733 Sum_probs=9.8
Q ss_pred CCCccccCCceeEE
Q 046004 1 MGNCLVLEEKVIKV 14 (157)
Q Consensus 1 MGNC~~~~~~~ikV 14 (157)
||||.-.+.+.||-
T Consensus 1 mgncsrkqnknikt 14 (73)
T PHA02843 1 MGNCSRKQNKNIKT 14 (73)
T ss_pred CCccchhhccCccc
Confidence 89998766665553
No 23
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=24.56 E-value=83 Score=20.02 Aligned_cols=22 Identities=23% Similarity=0.385 Sum_probs=18.2
Q ss_pred EecCCcEEEEeCCCcHHHHHhhc
Q 046004 15 MKTDGKILEYNQPIRVQDVLAEF 37 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~~ 37 (157)
+..||+..++ .+.++.+++...
T Consensus 3 i~~Ng~~~~~-~~~tl~~Ll~~l 24 (65)
T PRK06488 3 LFVNGETLQT-EATTLALLLAEL 24 (65)
T ss_pred EEECCeEEEc-CcCcHHHHHHHc
Confidence 5679999999 568999999763
No 24
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=23.63 E-value=1e+02 Score=17.51 Aligned_cols=34 Identities=26% Similarity=0.520 Sum_probs=26.9
Q ss_pred EEEEEEeCHHHHHHHHHhccCCHHHHHHHHHhhc
Q 046004 99 VRIKLVISKQELEELLQKQGVSVKDMVSRIQSKQ 132 (157)
Q Consensus 99 ~rvkl~i~k~~L~~ll~~~~~s~e~~l~~l~~~~ 132 (157)
+++.+.+|..+|.+.+.-...++.+.+..|....
T Consensus 3 ~~~~~~~s~~~la~~l~~s~~tv~~~l~~L~~~g 36 (48)
T smart00419 3 IRVRLPLTRQEIAELLGLTRETVSRTLKRLEKEG 36 (48)
T ss_pred ceEEeccCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 5677889999999999865567788888887754
No 25
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=23.46 E-value=88 Score=20.07 Aligned_cols=33 Identities=24% Similarity=0.400 Sum_probs=15.6
Q ss_pred CCCccccCCceeEEEecCCcEEEEeCCCcHHHHHhh
Q 046004 1 MGNCLVLEEKVIKVMKTDGKILEYNQPIRVQDVLAE 36 (157)
Q Consensus 1 MGNC~~~~~~~ikV~~~dG~v~e~~~pv~a~~vm~~ 36 (157)
||+|- ...+-+|.++|.+...-.|-.+.+|+.+
T Consensus 44 lg~C~---~~P~v~i~~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 44 LGACG---LAPVVVVYPDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred cCccc---CCCEEEEeCCCeEEccCCHHHHHHHHHh
Confidence 45553 3444555566654433344444445543
No 26
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=22.64 E-value=98 Score=20.59 Aligned_cols=23 Identities=30% Similarity=0.515 Sum_probs=20.2
Q ss_pred EecCCcEEEEeCCCcHHHHHhhc
Q 046004 15 MKTDGKILEYNQPIRVQDVLAEF 37 (157)
Q Consensus 15 ~~~dG~v~e~~~pv~a~~vm~~~ 37 (157)
+..||+-.++..+.|++++|.+.
T Consensus 5 i~~ng~~~e~~~~~tv~dLL~~l 27 (68)
T COG2104 5 IQLNGKEVEIAEGTTVADLLAQL 27 (68)
T ss_pred EEECCEEEEcCCCCcHHHHHHHh
Confidence 45689999999999999999884
No 27
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=21.85 E-value=2.4e+02 Score=18.31 Aligned_cols=52 Identities=19% Similarity=0.299 Sum_probs=32.3
Q ss_pred EecCCc----EEEEeCCCcHHHHHhhcC----CcEEeCCCCCccCCCCCCccCCCCeEEEeeC
Q 046004 15 MKTDGK----ILEYNQPIRVQDVLAEFS----GHAISDSLPEIRHLRPDFKLVGGNLYFLVPV 69 (157)
Q Consensus 15 ~~~dG~----v~e~~~pv~a~~vm~~~P----gh~v~~s~~~~~~L~~d~~L~~G~~YfLlP~ 69 (157)
+..+|+ ..++....++++++.+.- +.+|.--. ..++++..|+.|--.-++|.
T Consensus 7 v~vng~~~~~~~~~~~~~tv~~ll~~l~~~~~~v~v~vNg---~iv~~~~~l~~gD~Veii~~ 66 (70)
T PRK08364 7 VKVIGRGIEKEIEWRKGMKVADILRAVGFNTESAIAKVNG---KVALEDDPVKDGDYVEVIPV 66 (70)
T ss_pred EEEeccccceEEEcCCCCcHHHHHHHcCCCCccEEEEECC---EECCCCcCcCCCCEEEEEcc
Confidence 344777 666778899999998642 11221111 23457788888876666664
No 28
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=20.86 E-value=1.3e+02 Score=21.13 Aligned_cols=24 Identities=25% Similarity=0.404 Sum_probs=17.0
Q ss_pred CceeEEEecCCcEEEEeCCCcHHHHH
Q 046004 9 EKVIKVMKTDGKILEYNQPIRVQDVL 34 (157)
Q Consensus 9 ~~~ikV~~~dG~v~e~~~pv~a~~vm 34 (157)
...+.|+.++|+ -||..|+..++=
T Consensus 48 ePlV~V~~p~g~--v~Y~~V~~edv~ 71 (92)
T cd03063 48 EPLVEVETPGGR--VAYGPVTPADVA 71 (92)
T ss_pred CCEEEEEeCCCc--EEEEeCCHHHHH
Confidence 455677779887 568888877743
No 29
>PF03990 DUF348: Domain of unknown function (DUF348) ; InterPro: IPR007137 This domain normally occurs as tandem repeats; however it is found as a single copy in the Saccharomyces cerevisiae (Baker's yeast) DNA-binding nuclear protein YCR593 (P25357 from SWISSPROT).
Probab=20.41 E-value=1.6e+02 Score=17.31 Aligned_cols=23 Identities=30% Similarity=0.342 Sum_probs=18.4
Q ss_pred EecCCcEEEEe-CCCcHHHHHhhc
Q 046004 15 MKTDGKILEYN-QPIRVQDVLAEF 37 (157)
Q Consensus 15 ~~~dG~v~e~~-~pv~a~~vm~~~ 37 (157)
+..||+...++ ..-+|+++|.+.
T Consensus 4 v~~dG~~~~v~T~a~tV~~~L~~~ 27 (43)
T PF03990_consen 4 VTVDGKEKTVYTTASTVGDALKEL 27 (43)
T ss_pred EEECCEEEEEEeCCCCHHHHHHhC
Confidence 34599888886 688999999875
Done!