Query T0517 YP_755085.1, Syntrophomonas wolfei str. Goettingen, 159 residues
Match_columns 159
No_of_seqs 106 out of 278
Neff 6.2
Searched_HMMs 11830
Date Fri May 21 18:06:24 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0517.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0517.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02635 DrsE: DsrE/DsrF-like 99.4 7.9E-13 6.7E-17 97.8 10.3 109 4-157 1-117 (119)
2 PF04077 DsrH: DsrH like prote 77.1 1.6 0.00013 21.1 4.6 44 112-156 44-87 (88)
3 PF03749 SfsA: Sugar fermentat 60.8 1.4 0.00012 21.3 1.5 31 100-130 180-210 (215)
4 PF11814 DUF3335: Domain of un 46.2 7 0.00059 17.0 3.1 39 7-47 64-102 (227)
5 PF04127 DFP: DNA / pantothena 38.3 5.7 0.00048 17.5 1.7 39 1-41 1-52 (199)
6 PF07498 Rho_N: Rho terminatio 29.8 7.9 0.00066 16.7 1.2 30 101-138 5-34 (43)
7 PF11663 Toxin_YhaV: Toxin wit 24.1 18 0.0015 14.4 2.7 27 86-112 113-140 (140)
8 PF10678 DUF2492: Protein of u 20.2 21 0.0018 13.9 4.5 45 90-138 9-56 (78)
9 PF07076 DUF1344: Protein of u 19.0 13 0.0011 15.3 0.6 37 2-40 33-69 (81)
10 PF07021 MetW: Methionine bios 16.6 26 0.0022 13.4 7.6 90 3-122 73-167 (193)
No 1
>PF02635 DrsE: DsrE/DsrF-like family; InterPro: IPR003787 Four small, soluble proteins (DsrE, DsrF, DsrH and DsrC) are encoded in the dsr gene region of the phototrophic sulphur bacterium Chromatium vinosum D. The dsrAB genes encoding dissimilatory sulphite reductase are part of the gene cluster, dsrABEFHCMK. The remaining proteins that are encoded are a transmembrane protein (DsrM) with similarity to haem-b-binding polypeptides and a soluble protein (DsrK) resembling [4Fe-4S]-cluster-containing heterodisulphide reductase from methanogenic archaea. DsrE is a small soluble protein involved in intracellular sulphur reduction .; PDB: 2pd2_A 1l1s_A 2qs7_B 2d1p_G 2hyb_P 2hy5_A 1jx7_C 2fb6_A.
Probab=99.41 E-value=7.9e-13 Score=97.85 Aligned_cols=109 Identities=31% Similarity=0.408 Sum_probs=95.4
Q ss_pred CCEEEEEEEC--CHHHHHHHHHHHHHHHHCC---CCEEEEEEHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHCCC
Q ss_conf 7357998609--8888889999999998618---9448987412366551221112233332100001246765002254
Q T0517 4 KKMNLLLFSG--DYDKALASLIIANAAREME---IEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPL 78 (159)
Q Consensus 4 kkl~II~~sG--~~dk~~~~~ilA~~Aaa~g---~eV~iFfTf~Gl~~l~K~~~~~~~~~~~~~~~~~~~~p~~~~~lp~ 78 (159)
||+.+|.+|+ +-++.+.++.+++++++.| .||.|||..+|+.++++...
T Consensus 1 k~v~~v~~~~p~~~~~~~~~~~l~~~~~~~~~~~~~v~v~~~g~gv~~~~~~~~-------------------------- 54 (119)
T PF02635_consen 1 KKVFIVVSSGPYDDERAYMALALANAAAALGMYGHEVAVFFYGDGVKALLKQEP-------------------------- 54 (119)
T ss_dssp EEEEEEE-S---SSHHHHHHHHHHHHHHHHHHTTSEEEEEE-GGGGGGGBTT-C--------------------------
T ss_pred CEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEECHHHHHHHHCCC--------------------------
T ss_conf 989999627999998899999999999975998640899998439999873476--------------------------
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEEEECCHHHHHCCC-HHHCCCCCE--EECHHHHHHHHHCCCC
Q ss_conf 4357013458999999985689978999999987698998822016552788-667367640--5128899998745882
Q T0517 79 SKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYACQLSVEIMGFK-KEELFPEVQ--IMDVKEYLKNALESDL 155 (159)
Q Consensus 79 s~~~~~g~~~~~~~~~m~~~~v~~~~eLl~~a~e~Gvk~~aC~msm~l~gi~-~edLidgVe--i~Ga~tFl~~A~~a~v 155 (159)
...+.+++.+++++.++.||++|+|+.+++.+|++ + ||+ +++ +.|...+.+...+++.
T Consensus 55 -----------------~~~~~~~~~~~l~~l~~~gv~~~~C~~s~~~~gi~~~-~l~-~v~~~~~g~~~l~~~~~~g~~ 115 (119)
T PF02635_consen 55 -----------------NPKGDPPLQELLKELKEYGVKIYACQNSLKARGIDEP-DLI-GVEVVPSGMAELAELQNEGDK 115 (119)
T ss_dssp -----------------GGTTTHTHHHHHHHHHHTTEEEEEEHHHHHHTT-CCG-GBH-TCEEEEE-HHHHHHHHHHSSE
T ss_pred -----------------CCCCCCCHHHHHHHHHHCCCEEEECHHHHHHCCCCCC-CCC-CCEEEECCHHHHHHHHHCCCE
T ss_conf -----------------6556657999999999869969970899988699732-347-865998489999999983998
Q ss_pred EE
Q ss_conf 43
Q T0517 156 QL 157 (159)
Q Consensus 156 ~L 157 (159)
++
T Consensus 116 vi 117 (119)
T PF02635_consen 116 VI 117 (119)
T ss_dssp EE
T ss_pred EE
T ss_conf 96
No 2
>PF04077 DsrH: DsrH like protein; InterPro: IPR007215 DsrH is involved in oxidation of intracellular sulphur in the phototrophic sulphur bacterium Chromatium vinosum D .; PDB: 2d1p_F 2hyb_I 2hy5_C 1x9a_A 1rhx_A.
Probab=77.08 E-value=1.6 Score=21.05 Aligned_cols=44 Identities=20% Similarity=0.416 Sum_probs=38.4
Q ss_pred HCCCEEEEECCHHHHHCCCHHHCCCCCEEECHHHHHHHHHCCCCE
Q ss_conf 769899882201655278866736764051288999987458824
Q T0517 112 KKEVKFYACQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQ 156 (159)
Q Consensus 112 e~Gvk~~aC~msm~l~gi~~edLidgVei~Ga~tFl~~A~~a~v~ 156 (159)
+.++++||++--++-.|+ .+...++|++++-..|.+.+.+-+-+
T Consensus 44 ~~~~~vyaL~~Dl~ARGl-~~~~~~~v~~idy~~fV~Lt~~h~k~ 87 (88)
T PF04077_consen 44 ESGIKVYALKEDLEARGL-TDRISPGVKLIDYDGFVELTEKHDKV 87 (88)
T ss_dssp CSSSEEEEEHHHHHH----GGCBCTTSEEE-HHHHHHHHHHSSCE
T ss_pred CCCCEEEEEHHHHHHCCC-CCCCCCCCEEECHHHHHHHHHHHCCC
T ss_conf 479739987688985698-52026895487799999999971675
No 3
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli strain MK2001 to use maltose.
Probab=60.84 E-value=1.4 Score=21.28 Aligned_cols=31 Identities=23% Similarity=0.359 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHCCCEEEEECCHHHHHCCC
Q ss_conf 9978999999987698998822016552788
Q T0517 100 APKLSDLLSGARKKEVKFYACQLSVEIMGFK 130 (159)
Q Consensus 100 v~~~~eLl~~a~e~Gvk~~aC~msm~l~gi~ 130 (159)
-|.+.+.+..|++.||++||+...++.-++.
T Consensus 180 Dp~fa~~l~~A~~~GVev~a~~~~~~~~~i~ 210 (215)
T PF03749_consen 180 DPEFAEALREAAEAGVEVLAYRCRVTPEGIR 210 (215)
T ss_pred CHHHHHHHHHHHHCCCEEEEEEEEECCCEEE
T ss_conf 9999999999998799999999998100179
No 4
>PF11814 DUF3335: Domain of unknown function (DUF3335)
Probab=46.19 E-value=7 Score=16.98 Aligned_cols=39 Identities=23% Similarity=0.291 Sum_probs=28.8
Q ss_pred EEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHHH
Q ss_conf 79986098888889999999998618944898741236655
Q T0517 7 NLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLL 47 (159)
Q Consensus 7 ~II~~sG~~dk~~~~~ilA~~Aaa~g~eV~iFfTf~Gl~~l 47 (159)
+|..+||- --+.|+=+|.+|+.-|.+|.++..-.+...+
T Consensus 64 TIfMtsGh--GGC~P~GLAlAA~~rG~~v~v~v~~~~plfl 102 (227)
T PF11814_consen 64 TIFMTSGH--GGCGPYGLALAAARRGFKVEVWVSTDGPLFL 102 (227)
T ss_pred CCCCCCCC--CCCCHHHHHHHHHHCCCCEEEEECCCCCCCC
T ss_conf 00333788--8847889999999869946999779997413
No 5
>PF04127 DFP: DNA / pantothenate metabolism flavoprotein; InterPro: IPR007085 This entry represents the C-terminal domain found in DNA/pantothenate metabolism flavoproteins, which affects synthesis of DNA and pantothenate metabolism. These proteins contain ATP, phosphopantothenate, and cysteine binding sites. The structure of this domain has been determined in human phosphopantothenoylcysteine (PPC) synthetase and as the PPC synthase domain (CoaB) from the Escherichia coli coenzyme A bifunctional protein CoaBC . This domain adopts a 3-layer alpha/beta/alpha fold with mixed beta-sheets, which topologically resembles a combination of Rossmann-like and ribokinase-like folds. The structure of these proteins predicts a ping pong mechanism with initial formation of an acyladenylate intermediate, followed by release of pyrophosphate and attack by cysteine to form the final products PPC and AMP. ; PDB: 2gk4_A 1p9o_A 1u7w_C 1u80_A 1u7u_A 1u7z_C.
Probab=38.30 E-value=5.7 Score=17.53 Aligned_cols=39 Identities=26% Similarity=0.305 Sum_probs=28.3
Q ss_pred CCCCCEEEEEEEC-CHHHH------------HHHHHHHHHHHHCCCCEEEEEEH
Q ss_conf 9877357998609-88888------------89999999998618944898741
Q T0517 1 MENKKMNLLLFSG-DYDKA------------LASLIIANAAREMEIEVTIFCAF 41 (159)
Q Consensus 1 m~~kkl~II~~sG-~~dk~------------~~~~ilA~~Aaa~g~eV~iFfTf 41 (159)
|.+|| |++++| |.+.+ -.++.+|..+...|.+|+++..-
T Consensus 1 ~~gkk--VLITaG~T~E~ID~VR~itN~SSGkmG~~iA~~~~~~Ga~V~li~g~ 52 (199)
T PF04127_consen 1 MKGKK--VLITAGPTREPIDPVRFITNRSSGKMGYAIAEEAYRRGADVTLIHGP 52 (199)
T ss_dssp --T-E--EEEEE---EEESSSSEEEEES-------HHHHHHHH---EEEEEEET
T ss_pred CCCCE--EEEECCCCCCCCCCCCEECCCCCHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf 97429--99954885204577215566895699999999998649989999768
No 6
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers . This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0003715 transcription termination factor activity, 0006353 transcription termination; PDB: 1pvo_F 1xpo_C 2a8v_B 1pv4_D 1a62_A 1a8v_A 1xpr_C 1xpu_D 1a63_A 2ht1_B ....
Probab=29.79 E-value=7.9 Score=16.65 Aligned_cols=30 Identities=20% Similarity=0.241 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHCCCEEEEECCHHHHHCCCHHHCCCCC
Q ss_conf 97899999998769899882201655278866736764
Q T0517 101 PKLSDLLSGARKKEVKFYACQLSVEIMGFKKEELFPEV 138 (159)
Q Consensus 101 ~~~~eLl~~a~e~Gvk~~aC~msm~l~gi~~edLidgV 138 (159)
.++.||.+.|++.|+.- .-+++++|||..+
T Consensus 5 ~t~~eL~~iA~elgI~~--------~s~mrK~eLI~~I 34 (43)
T PF07498_consen 5 MTLAELREIAKELGIEN--------YSKMRKQELIFAI 34 (43)
T ss_dssp S-HHHHHH--------S--------GTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHCCCCC--------CCCCCHHHHHHHH
T ss_conf 77999999999959988--------5647899999999
No 7
>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV
Probab=24.11 E-value=18 Score=14.43 Aligned_cols=27 Identities=22% Similarity=0.363 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHCCCC-CHHHHHHHHHH
Q ss_conf 4589999999856899-78999999987
Q T0517 86 IGKKMLLEMMKEEKAP-KLSDLLSGARK 112 (159)
Q Consensus 86 ~~~~~~~~~m~~~~v~-~~~eLl~~a~e 112 (159)
.+=...++|++..+.| +|.+|+.+|++
T Consensus 113 DaY~vF~kML~~G~pPddW~~Ll~~a~~ 140 (140)
T PF11663_consen 113 DAYAVFRKMLERGNPPDDWDALLKEARQ 140 (140)
T ss_pred CHHHHHHHHHHCCCCCCCHHHHHHHHCC
T ss_conf 7899999998489897459999998609
No 8
>PF10678 DUF2492: Protein of unknown function (DUF2492)
Probab=20.20 E-value=21 Score=13.94 Aligned_cols=45 Identities=16% Similarity=0.245 Sum_probs=28.7
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHH-CC--CEEEEECCHHHHHCCCHHHCCCCC
Q ss_conf 99999985689978999999987-69--899882201655278866736764
Q T0517 90 MLLEMMKEEKAPKLSDLLSGARK-KE--VKFYACQLSVEIMGFKKEELFPEV 138 (159)
Q Consensus 90 ~~~~~m~~~~v~~~~eLl~~a~e-~G--vk~~aC~msm~l~gi~~edLidgV 138 (159)
.|.-+++..+.-+-++|.+...+ .| ++||.|+.. +++.++|++..
T Consensus 9 VL~mml~~~~~~t~~~L~~~i~~~FG~~arFhTCsae----~m~~~~Li~FL 56 (78)
T PF10678_consen 9 VLNMMLASGEPYTRESLKQAIHQKFGEDARFHTCSAE----DMDADELIEFL 56 (78)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEECCCC----CCCHHHHHHHH
T ss_conf 9999997689738999999999985866437555746----79999999999
No 9
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=18.96 E-value=13 Score=15.32 Aligned_cols=37 Identities=8% Similarity=0.124 Sum_probs=21.9
Q ss_pred CCCCEEEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf 877357998609888888999999999861894489874
Q T0517 2 ENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCA 40 (159)
Q Consensus 2 ~~kkl~II~~sG~~dk~~~~~ilA~~Aaa~g~eV~iFfT 40 (159)
+.+..+|.+-+|.--++-+-|-+ .+..-|.+|.|||+
T Consensus 33 d~~~~tItLdDGkty~lp~e~~~--~~L~~G~kV~V~yd 69 (81)
T PF07076_consen 33 DKETLTITLDDGKTYQLPEEFDF--EGLKPGVKVVVTYD 69 (81)
T ss_pred CCCCCEEEECCCCEEECCCCCCH--HHCCCCCEEEEEEE
T ss_conf 47774799669976656876564--24268998999998
No 10
>PF07021 MetW: Methionine biosynthesis protein MetW; InterPro: IPR010743 This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells .
Probab=16.57 E-value=26 Score=13.42 Aligned_cols=90 Identities=12% Similarity=0.092 Sum_probs=55.7
Q ss_pred CCCEEEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEEEHHHH-----HHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHCC
Q ss_conf 773579986098888889999999998618944898741236-----655122111223333210000124676500225
Q T0517 3 NKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGL-----LLLRDPEKASQEDKSLYEQAFSSLTPREAEELP 77 (159)
Q Consensus 3 ~kkl~II~~sG~~dk~~~~~ilA~~Aaa~g~eV~iFfTf~Gl-----~~l~K~~~~~~~~~~~~~~~~~~~~p~~~~~lp 77 (159)
.+..-.|+.|.+++-+..|--+=.--+..|.++.|-|-.+|- .++.+++.+..+. +|-.|..-|
T Consensus 73 d~~FD~VIlsqtLqh~~~P~~vL~emLrvg~~~IVsfPNf~~w~~r~~l~~~GrmP~t~~-----------lp~~WydTp 141 (193)
T PF07021_consen 73 DQSFDYVILSQTLQHLRNPDKVLREMLRVGREAIVSFPNFGHWRVRLQLLFRGRMPVTEF-----------LPYEWYDTP 141 (193)
T ss_pred CCCCCEEEEHHHHHHHHHHHHHHHHHHHHCCEEEEECCCHHHHHHHHHHHHCCCCCCCCC-----------CCCCCCCCC
T ss_conf 888889973678883656899999998738979997477378999999996699997888-----------887434899
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEEEECC
Q ss_conf 443570134589999999856899789999999876989988220
Q T0517 78 LSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYACQL 122 (159)
Q Consensus 78 ~s~~~~~g~~~~~~~~~m~~~~v~~~~eLl~~a~e~Gvk~~aC~m 122 (159)
. -+.-++.||.+.|.+.|+++.-+..
T Consensus 142 -------n------------Ih~~T~~DF~~lc~~~~~~i~~~~~ 167 (193)
T PF07021_consen 142 -------N------------IHFCTIKDFEELCRELGIRILERVA 167 (193)
T ss_pred -------C------------CCCEEHHHHHHHHHHCCCEEEEEEE
T ss_conf -------8------------0302099999999987998999999
Done!