Query T0638 3NXH, Bacillus subtilis, 269 residues
Match_columns 269
No_of_seqs 113 out of 1367
Neff 7.4
Searched_HMMs 11830
Date Thu Jul 22 15:08:52 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0638.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0638.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03816 LytR_cpsA_psr: Cell e 100.0 0 0 319.9 17.7 148 24-177 1-148 (148)
2 PF08597 eIF3_subunit: Transla 30.1 12 0.00099 14.3 4.0 51 165-215 144-194 (245)
3 PF01726 LexA_DNA_bind: LexA D 19.4 19 0.0016 13.1 3.3 47 161-212 5-51 (65)
4 PF03444 DUF293: Domain of unk 16.7 22 0.0019 12.7 5.6 48 161-214 3-50 (78)
5 PF04518 DUF582: Protein of un 14.2 26 0.0022 12.4 6.6 116 133-257 189-310 (379)
6 PF10869 DUF2666: Protein of u 12.9 28 0.0024 12.1 2.6 39 72-110 29-67 (131)
7 PF10758 DUF2586: Protein of u 12.4 24 0.0021 12.5 0.7 73 154-232 254-327 (363)
8 PF04363 DUF496: Protein of un 12.4 29 0.0024 12.0 6.5 36 183-218 33-68 (95)
9 PF08960 DUF1874: Domain of un 11.6 31 0.0026 11.9 1.7 18 72-89 44-61 (105)
10 PF02995 DUF229: Protein of un 11.1 32 0.0027 11.8 1.6 43 66-108 140-182 (498)
No 1
>PF03816 LytR_cpsA_psr: Cell envelope-related transcriptional attenuator domain; InterPro: IPR004474 This entry describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is protein psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. These proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor.
Probab=100.00 E-value=0 Score=319.94 Aligned_cols=148 Identities=51% Similarity=0.902 Sum_probs=140.6
Q ss_pred CCCEEEEEEEECCCCEEEEEEECCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHH
Q ss_conf 55189999980899879999971443356168898963015567643108999999998608984327998068999898
Q T0638 24 RSDSLIVVTLDPKNKTMKMLSIPRDTRVQLAGDTTGSKTKINAAYSKGGKDETVETVENFLQIPIDKYVTVDFDGFKDVI 103 (269)
Q Consensus 24 rsD~i~l~~i~~~~~~~~~isiPRDt~v~i~~~~~~~~~kln~ay~~gG~~~~~~~v~~l~gi~Id~yv~v~~~~f~~lv 103 (269)
|||+|||+++|+++++++++||||||+|++|+++..++.|||+||++||+++++++|++++|++|+||+.+||++|.++|
T Consensus 1 rtD~i~l~~i~~~~~~~~~~siPRDt~v~i~~~~~~~~~kin~ay~~GG~~~~~~~V~~l~gi~Id~yv~v~~~~f~~lv 80 (148)
T PF03816_consen 1 RTDTIMLVSINPKTKKVTLVSIPRDTYVDIPGGPETGYDKINAAYAYGGPEATVETVEDLLGIPIDYYVVVDFDGFVKLV 80 (148)
T ss_pred CCCEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCEEEEECHHHHHHHH
T ss_conf 98589999986999979999967874235789754205889998872483689999999879898779998288899999
Q ss_pred HHCCCEEEECCCCCCCCCCCCCCCCEEEECCCEEECHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 72098677348642226677776515870781485779999898621688986689999999999999999727
Q T0638 104 NEVGGIDVDVPFDFDEKSDVDESKRIYFKKGEMHLNGEEALAYARMRKQDKRGDFGRNDRQKQILNALIDRMSS 177 (269)
Q Consensus 104 D~lGGV~v~v~~~~~~~~~~~~~~~~~~~~G~q~LdG~qAl~y~R~R~~~~~gD~~R~~rQq~vl~al~~k~~~ 177 (269)
|++|||+||+|+++.+. ..+++|++|+|||||+||++|+|+|+.++ ||++|++|||+||+|+++|+++
T Consensus 81 D~lGGV~V~v~~~~~~~-----~~~~~~~~G~~~L~G~~Al~y~R~R~~~~-gD~~R~~RQq~~l~al~~k~~s 148 (148)
T PF03816_consen 81 DALGGVDVDVPQDMDYP-----DSGIDLPAGEQHLDGEQALAYVRYRHDDD-GDFGRMQRQQQVLKALLEKLKS 148 (148)
T ss_pred HHCCCEEEECCCCCCCC-----CCCEEECCCCEEECHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHC
T ss_conf 87189698368763136-----77666679759987789988898737998-6677999999999999999639
No 2
>PF08597 eIF3_subunit: Translation initiation factor eIF3 subunit; InterPro: IPR013906 This shows protein subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae (Baker's yeast) protein Q05775 from SWISSPROT has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p . ; PDB: 3bpj_B.
Probab=30.12 E-value=12 Score=14.34 Aligned_cols=51 Identities=6% Similarity=0.127 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHEEECCCHHHHHHHHHHHHCCC
Q ss_conf 999999999972765544699999987621063789899999999985368
Q T0638 165 KQILNALIDRMSSASNIAKIDKIAEKASENVETNIRITEGLALQQIYSGFT 215 (269)
Q Consensus 165 q~vl~al~~k~~~~~~~~~~~~l~~~~~~~i~Tnls~~~~~~l~~~~~~~~ 215 (269)
..|=.+|..++.+......+..++..+...+..+|+..++..+...+..+.
T Consensus 144 ~~l~~~l~~kl~~~~ks~~Y~~fl~~l~r~l~~~L~~~dikki~ssl~~l~ 194 (245)
T PF08597_consen 144 EELAKALAEKLTPFEKSPHYSSFLEDLIRDLCKPLSSEDIKKISSSLNVLS 194 (245)
T ss_dssp HH---HHHHHHGGGTTSTTHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf 999999999998404657799999999999983189999999999999999
No 3
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif . This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0008992 repressor LexA activity, 0006508 proteolysis; PDB: 1lea_A 1jhh_A 1jhf_A 1leb_A.
Probab=19.36 E-value=19 Score=13.11 Aligned_cols=47 Identities=15% Similarity=0.159 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHEEECCCHHHHHHHHHHHH
Q ss_conf 9999999999999972765544699999987621063789899999999985
Q T0638 161 NDRQKQILNALIDRMSSASNIAKIDKIAEKASENVETNIRITEGLALQQIYS 212 (269)
Q Consensus 161 ~~rQq~vl~al~~k~~~~~~~~~~~~l~~~~~~~i~Tnls~~~~~~l~~~~~ 212 (269)
..||++++..+.+-+....-+..+..|.+.++ .. |...+-.....+.
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~Pt~rEI~~~~g----l~-S~~tV~~~L~~Le 51 (65)
T PF01726_consen 5 TPRQQEVLDFIKDYIREHGYPPTVREIAEALG----LK-SPSTVHKHLKALE 51 (65)
T ss_dssp -HHHHHHHHHHHHHHHH------HHHHHHH---------SHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCC----CC-CCHHHHHHHHHHH
T ss_conf 99999999999999998388988999998819----99-8099999999999
No 4
>PF03444 DUF293: Domain of unknown function; InterPro: IPR005104 This domain is always found N-terminal to a pair of cystathionine-beta-synthase (CBS) domains IPR000644 from INTERPRO. This region may be distantly related to the HrcA proteins of prokaryotes.
Probab=16.69 E-value=22 Score=12.74 Aligned_cols=48 Identities=19% Similarity=0.163 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHEEECCCHHHHHHHHHHHHCC
Q ss_conf 999999999999997276554469999998762106378989999999998536
Q T0638 161 NDRQKQILNALIDRMSSASNIAKIDKIAEKASENVETNIRITEGLALQQIYSGF 214 (269)
Q Consensus 161 ~~rQq~vl~al~~k~~~~~~~~~~~~l~~~~~~~i~Tnls~~~~~~l~~~~~~~ 214 (269)
..||+++++++++.......+.+-..|++.+ +.|...+..-...+..+
T Consensus 3 t~rq~~IL~~lv~~Y~~~~~PVgSk~ia~~l------~~s~aTIRN~M~~Le~l 50 (78)
T PF03444_consen 3 TERQREILKALVELYIETGEPVGSKTIAEEL------DRSPATIRNEMADLEEL 50 (78)
T ss_pred CHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH------CCCCHHHHHHHHHHHHC
T ss_conf 8899999999999999739977669999986------88908899999999987
No 5
>PF04518 DUF582: Protein of unknown function, DUF582; InterPro: IPR007606 This family contains several uncharacterised chlamydial proteins.
Probab=14.18 E-value=26 Score=12.35 Aligned_cols=116 Identities=13% Similarity=0.217 Sum_probs=62.6
Q ss_pred CCCEEECHHHHHHHHH---HCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHH--HHHHHHHHHHHEE-ECCCHHHHHH
Q ss_conf 7814857799998986---21688986689999999999999999727655446--9999998762106-3789899999
Q T0638 133 KGEMHLNGEEALAYAR---MRKQDKRGDFGRNDRQKQILNALIDRMSSASNIAK--IDKIAEKASENVE-TNIRITEGLA 206 (269)
Q Consensus 133 ~G~q~LdG~qAl~y~R---~R~~~~~gD~~R~~rQq~vl~al~~k~~~~~~~~~--~~~l~~~~~~~i~-Tnls~~~~~~ 206 (269)
.|.+.+.|..-.+..| .|. ....|+.|++|-+.++.+++.++.....++. -.++.+.+..+.. -|.-...+..
T Consensus 189 ~g~~~F~g~~~~a~~~l~~Ek~-~~~~di~~~~~A~~~l~~~~~~V~~d~~lT~~Qk~~i~d~l~~Y~~~l~~i~~qL~~ 267 (379)
T PF04518_consen 189 MGTDNFPGSYFEALDKLEKEKE-QIRRDIKSCERAKAVLEQQLARVKADAKLTSEQKSEILDTLNNYASNLNIISNQLSN 267 (379)
T ss_pred CCHHHCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 5421056519999999999999-999999999999999999999987250048999999999999799999999989999
Q ss_pred HHHHHHCCCCCCEEEEEEECCCCEECCCCEEEEEECHHHHHHHHHHHHHHC
Q ss_conf 999985368675268996301210057864899968799999999999852
Q T0638 207 LQQIYSGFTSKKIDTLSITGSDLYLGPNNTYYFEPDATNLEKVRKTLQEHL 257 (269)
Q Consensus 207 l~~~~~~~~~~~i~~~~lp~~~~~~~~~g~~~~~~d~~~~~~~~~~l~~~~ 257 (269)
|-..+..+. ....|+.+ +..+.+-+...++.|..-.+.|...+
T Consensus 268 L~~~L~~L~-----~~~~~~~~---~~~~~f~i~gg~~~Wi~~L~~lE~~v 310 (379)
T PF04518_consen 268 LQSYLAPLS-----IQGVPDNN---EVDGAFKIMGGSDDWIRTLQSLESFV 310 (379)
T ss_pred HHHHHHCCE-----EECCCCCC---CCCCCEEEEECCCHHHHHHHHHHHHH
T ss_conf 998631357-----51468988---76774588606402899999999998
No 6
>PF10869 DUF2666: Protein of unknown function (DUF2666)
Probab=12.90 E-value=28 Score=12.13 Aligned_cols=39 Identities=13% Similarity=0.404 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHCCCCCCEEEEECHHHHHHHHHHCCCEE
Q ss_conf 089999999986089843279980689998987209867
Q T0638 72 GKDETVETVENFLQIPIDKYVTVDFDGFKDVINEVGGID 110 (269)
Q Consensus 72 G~~~~~~~v~~l~gi~Id~yv~v~~~~f~~lvD~lGGV~ 110 (269)
.++.....|++.....|..|+.+|.+++..+.+.+-.+-
T Consensus 29 ~IArlLAsI~eTv~~KIp~yl~iDv~~i~e~~~~~~~~K 67 (131)
T PF10869_consen 29 DIARLLASINETVNSKIPEYLGIDVKGIEEIAEEIKKVK 67 (131)
T ss_pred HHHHHHHHHHHHHHHHCHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 999999998888876042110416999999998887630
No 7
>PF10758 DUF2586: Protein of unknown function (DUF2586)
Probab=12.44 E-value=24 Score=12.46 Aligned_cols=73 Identities=15% Similarity=0.209 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHEEECCCHHHHHHHHHHHHCCCC-CCEEEEEEECCCCEEC
Q ss_conf 986689999999999999999727655446999999876210637898999999999853686-7526899630121005
Q T0638 154 KRGDFGRNDRQKQILNALIDRMSSASNIAKIDKIAEKASENVETNIRITEGLALQQIYSGFTS-KKIDTLSITGSDLYLG 232 (269)
Q Consensus 154 ~~gD~~R~~rQq~vl~al~~k~~~~~~~~~~~~l~~~~~~~i~Tnls~~~~~~l~~~~~~~~~-~~i~~~~lp~~~~~~~ 232 (269)
+.|||..+++-|-+-|+. ++++-. .+.++.+-..++--+++-.. -..|.+-++.+++ ..|.-.++||+-..-.
T Consensus 254 ~ggDYq~iE~lRVvdKaa-R~VRi~----AI~~I~dr~lNSTp~siaa~-~~~f~~pLr~Msks~~i~g~~FPGei~pP~ 327 (363)
T PF10758_consen 254 EGGDYQVIENLRVVDKAA-RRVRIL----AIKRIADRSLNSTPTSIAAH-KTYFARPLREMSKSTTINGITFPGEIKPPK 327 (363)
T ss_pred CCCCHHEEEHHHHHHHHH-HHHHHH----HHHHHHCCCCCCCHHHHHHH-HHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 898611122257799999-999999----99874213335880639999-999867999999752407803775565999
No 8
>PF04363 DUF496: Protein of unknown function (DUF496); InterPro: IPR007458 Members of this family are uncharacterised proteins.
Probab=12.36 E-value=29 Score=12.03 Aligned_cols=36 Identities=11% Similarity=0.102 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHEEECCCHHHHHHHHHHHHCCCCCC
Q ss_conf 699999987621063789899999999985368675
Q T0638 183 KIDKIAEKASENVETNIRITEGLALQQIYSGFTSKK 218 (269)
Q Consensus 183 ~~~~l~~~~~~~i~Tnls~~~~~~l~~~~~~~~~~~ 218 (269)
+=..|++-+.++++.+||..++..+..+|.+.-...
T Consensus 33 KRV~LL~NL~~YI~~~Ms~e~i~~II~nM~~DYEdR 68 (95)
T PF04363_consen 33 KRVLLLDNLNDYIKPDMSIEEIRAIIENMRSDYEDR 68 (95)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 899999879998679998999999999978668774
No 9
>PF08960 DUF1874: Domain of unknown function (DUF1874); InterPro: IPR015055 This protein is found in a set of hypothetical viral and bacterial proteins. ; PDB: 2j85_B.
Probab=11.63 E-value=31 Score=11.89 Aligned_cols=18 Identities=28% Similarity=0.508 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHCCCCCC
Q ss_conf 089999999986089843
Q T0638 72 GKDETVETVENFLQIPID 89 (269)
Q Consensus 72 G~~~~~~~v~~l~gi~Id 89 (269)
|.+.+++.+++++|+.|.
T Consensus 44 GH~aTAqlls~Llgv~i~ 61 (105)
T PF08960_consen 44 GHQATAQLLSNLLGVNIP 61 (105)
T ss_dssp --HHHHHHHHHH------
T ss_pred CCHHHHHHHHHHHCCCCC
T ss_conf 629899999998585114
No 10
>PF02995 DUF229: Protein of unknown function (DUF229); InterPro: IPR004245 Members of this family are uncharacterised with a long conserved region that may contain several domains.
Probab=11.11 E-value=32 Score=11.79 Aligned_cols=43 Identities=14% Similarity=0.170 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHHHHCCC
Q ss_conf 6764310899999999860898432799806899989872098
Q T0638 66 AAYSKGGKDETVETVENFLQIPIDKYVTVDFDGFKDVINEVGG 108 (269)
Q Consensus 66 ~ay~~gG~~~~~~~v~~l~gi~Id~yv~v~~~~f~~lvD~lGG 108 (269)
.+...--...+.+.++++=.+.-.+|=.|.-+.+.+++=.+-|
T Consensus 140 r~~f~R~mPkT~~fl~~~~~~ef~GynkVgdnT~pNl~alltG 182 (498)
T PF02995_consen 140 RMNFRRSMPKTAEFLRQLGWFEFQGYNKVGDNTFPNLMALLTG 182 (498)
T ss_pred HHHHHHHCHHHHHHHHHCCCEEECCCCCCCCCCHHHHHHHHHC
T ss_conf 7889762628999996389689668400243326789999717
Done!