Query 537021.9.peg.1044_1
Match_columns 42
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Fri May 20 16:20:53 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_1044.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02124 hypE hydrogenase exp 20.3 28 0.00071 17.9 -0.1 28 7-34 87-114 (345)
2 PRK10523 lipoprotein involved 15.3 88 0.0022 15.6 1.5 32 1-32 98-138 (234)
3 cd05791 S1_CSL4 S1_CSL4: CSL4, 14.3 1.1E+02 0.0029 15.1 1.8 12 6-17 74-85 (92)
4 pfam02175 7TM_GPCR_Srb Serpent 13.9 61 0.0015 16.3 0.4 24 12-35 207-230 (236)
5 TIGR02080 O_succ_thio_ly O-suc 12.8 58 0.0015 16.4 -0.0 16 10-25 24-39 (383)
6 pfam09467 Yopt Hypothetical pr 8.6 1.1E+02 0.0028 15.1 0.2 17 20-36 29-45 (71)
7 TIGR02495 NrdG2 anaerobic ribo 7.5 1.9E+02 0.0049 14.0 1.1 13 2-14 96-108 (220)
8 COG4288 Uncharacterized protei 7.2 1.9E+02 0.0048 14.1 0.9 15 2-16 16-30 (124)
9 TIGR01748 rhaA L-rhamnose isom 7.2 1.8E+02 0.0045 14.2 0.7 20 20-39 210-229 (415)
10 COG5533 UBP5 Ubiquitin C-termi 6.5 1.7E+02 0.0042 14.3 0.3 32 4-35 180-211 (415)
No 1
>TIGR02124 hypE hydrogenase expression/formation protein HypE; InterPro: IPR011854 This family contains HypE (or HupE), a protein required for expression of catalytically active hydrogenase in many systems. It appears to be an accessory protein involved in maturation rather than a regulatory protein involved in expression. HypE shows considerable homology to the thiamine-monophosphate kinase ThiL (IPR006283 from INTERPRO) and other enzymes..
Probab=20.26 E-value=28 Score=17.86 Aligned_cols=28 Identities=39% Similarity=0.554 Sum_probs=19.5
Q ss_pred CCCCCEEEECCEEHHHHHCCCCHHHHHH
Q ss_conf 8987468650101213310211899999
Q 537021.9.peg.1 7 NGSKPYYLSTSYELEKISENYQLSKIVS 34 (42)
Q Consensus 7 ngskpyylstsyelekisenyqlskivs 34 (42)
-|.||-|||.+.=||.=-+--.|.+||.
T Consensus 87 ~GA~P~YLs~gfIlEEGfp~e~L~~iv~ 114 (345)
T TIGR02124 87 SGAKPLYLSCGFILEEGFPIEDLERIVK 114 (345)
T ss_pred CCCHHHHHCCCEEEEECCCHHHHHHHHH
T ss_conf 3844578507201340787678999999
No 2
>PRK10523 lipoprotein involved with copper homeostasis and adhesion; Provisional
Probab=15.32 E-value=88 Score=15.57 Aligned_cols=32 Identities=38% Similarity=0.649 Sum_probs=23.1
Q ss_pred CEEEECCCCCCEEEECCEEHHHH---------HCCCCHHHH
Q ss_conf 68870789874686501012133---------102118999
Q 537021.9.peg.1 1 LILLNSNGSKPYYLSTSYELEKI---------SENYQLSKI 32 (42)
Q Consensus 1 lillnsngskpyylstsyeleki---------senyqlski 32 (42)
|+|.+++|.|.||....-.|+-. .-||+|.+.
T Consensus 98 lvLt~s~gek~yfr~~g~~L~mLD~~G~pI~S~lNY~L~~v 138 (234)
T PRK10523 98 LVLTDSKGEKSYYRAKGDALEMLDREGNPIESQLNYTLEPV 138 (234)
T ss_pred EEEECCCCCEEEEEECCCEEEEECCCCCCCCCCCCCEEEEC
T ss_conf 89747998740135628804671568980214788622022
No 3
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=14.26 E-value=1.1e+02 Score=15.08 Aligned_cols=12 Identities=42% Similarity=0.706 Sum_probs=8.8
Q ss_pred CCCCCCEEEECC
Q ss_conf 789874686501
Q 537021.9.peg.1 6 SNGSKPYYLSTS 17 (42)
Q Consensus 6 sngskpyylsts 17 (42)
-..+++|||||.
T Consensus 74 lgd~~~y~LSTa 85 (92)
T cd05791 74 LGDASSYYLSTA 85 (92)
T ss_pred CCCCCEEEEEEC
T ss_conf 478724999853
No 4
>pfam02175 7TM_GPCR_Srb Serpentine type 7TM GPCR chemoreceptor Srb. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srb is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Probab=13.87 E-value=61 Score=16.32 Aligned_cols=24 Identities=42% Similarity=0.577 Sum_probs=17.1
Q ss_pred EEEECCEEHHHHHCCCCHHHHHHH
Q ss_conf 686501012133102118999998
Q 537021.9.peg.1 12 YYLSTSYELEKISENYQLSKIVSL 35 (42)
Q Consensus 12 yylstsyelekisenyqlskivsl 35 (42)
--||+.||+|.++..-..+-+|+.
T Consensus 207 ~sLS~rYqmEEi~~SskFt~~vsf 230 (236)
T pfam02175 207 SSLSTKYQLEEISQSSMFTLIVTF 230 (236)
T ss_pred CCEEHHHHHHHHHHHCCEEHHHHH
T ss_conf 750045568777631312021241
No 5
>TIGR02080 O_succ_thio_ly O-succinylhomoserine (thiol)-lyase; InterPro: IPR011821 Proteins in this entry are important in the interconversion of the sulphur-containing amino acids L-cysteine and L-methionine in bacteria. In bacteria, inorganic sulphur is reduced to sulphide, which is then used to displace the acetyl group of O-acetyl-L-serine to form the essential amino acid L-cysteine. Biosynthesis of L-methionine then occurs via the transsulphuration pathway which involves the sequential action of two pyridoxal 5'-phosphate (PLP) enzymes, cystathionine gamma-synthase (CGS) and cystathionine beta-lyase (CBL). Firstly CGS catalyses the formation of the intermediate cystathione from a homoserine ester and L-cysteine. This intermediate is then converted by CBL to L-homoserine, which is subsequently methylated by methionine synthase to form L-methionine. For more information see . The CGS enzyme (P00935 from SWISSPROT) from Escherichia coli is, like other CGS enzymes, a homotetramer composed of two catalytically active dimers . The active site of each dimer is found at the interface between the monomers and involves residues from each monomer. Catalysis occurs by alpha,gamma-elimination/replacement reactions..
Probab=12.79 E-value=58 Score=16.43 Aligned_cols=16 Identities=44% Similarity=0.820 Sum_probs=11.8
Q ss_pred CCEEEECCEEHHHHHC
Q ss_conf 7468650101213310
Q 537021.9.peg.1 10 KPYYLSTSYELEKISE 25 (42)
Q Consensus 10 kpyylstsyelekise 25 (42)
-|-||||.|+...-.+
T Consensus 24 PPIyLSttY~F~gF~~ 39 (383)
T TIGR02080 24 PPIYLSTTYNFAGFNE 39 (383)
T ss_pred CCCCCCCCCCCCCCCC
T ss_conf 8863566767556777
No 6
>pfam09467 Yopt Hypothetical protein Yopt. This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms homo-dimers, with each monomer consisting of one alpha helix and three beta strands.
Probab=8.59 E-value=1.1e+02 Score=15.14 Aligned_cols=17 Identities=53% Similarity=0.639 Sum_probs=14.1
Q ss_pred HHHHHCCCCHHHHHHHH
Q ss_conf 21331021189999988
Q 537021.9.peg.1 20 LEKISENYQLSKIVSLL 36 (42)
Q Consensus 20 lekisenyqlskivsll 36 (42)
...|.||.-|||-||.|
T Consensus 29 vtricenlllskevsfl 45 (71)
T pfam09467 29 VTRICENLLLSKEVSFL 45 (71)
T ss_pred HHHHHHHHHHHHHHHHE
T ss_conf 99999988766343201
No 7
>TIGR02495 NrdG2 anaerobic ribonucleoside-triphosphate reductase activating protein; InterPro: IPR012840 This enzyme is a member of the radical-SAM family. It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, IPR009161 from INTERPRO) and presumably fulfils the identical function as NrdG , , which utilises S-adenosyl methionine, an iron-sulphur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centred radical in NrdD..
Probab=7.47 E-value=1.9e+02 Score=14.01 Aligned_cols=13 Identities=46% Similarity=0.789 Sum_probs=7.6
Q ss_pred EEEECCCCCCEEE
Q ss_conf 8870789874686
Q 537021.9.peg.1 2 ILLNSNGSKPYYL 14 (42)
Q Consensus 2 illnsngskpyyl 14 (42)
|=|++||+.|--|
T Consensus 96 vkLdTNG~~P~~L 108 (220)
T TIGR02495 96 VKLDTNGSNPRVL 108 (220)
T ss_pred EEEECCCCCHHHH
T ss_conf 8560678867899
No 8
>COG4288 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=7.22 E-value=1.9e+02 Score=14.06 Aligned_cols=15 Identities=53% Similarity=0.886 Sum_probs=11.8
Q ss_pred EEEECCCCCCEEEEC
Q ss_conf 887078987468650
Q 537021.9.peg.1 2 ILLNSNGSKPYYLST 16 (42)
Q Consensus 2 illnsngskpyylst 16 (42)
|-+.|||..||..|.
T Consensus 16 IP~~sng~ep~~vSh 30 (124)
T COG4288 16 IPLESNGPEPYLVSH 30 (124)
T ss_pred CCCCCCCCCCCEEEC
T ss_conf 355458998623303
No 9
>TIGR01748 rhaA L-rhamnose isomerase; InterPro: IPR009308 This family consists of several bacterial L-rhamnose isomerase proteins (5.3.1.14 from EC). This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including Escherichia coli, this is the first step in rhamnose catabolism. Sequential steps are catalyzed by rhamnulose kinase (rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to yield glycerone phosphate and (S)-lactaldehyde. ; GO: 0008740 L-rhamnose isomerase activity, 0030145 manganese ion binding, 0019299 rhamnose metabolic process.
Probab=7.18 E-value=1.8e+02 Score=14.19 Aligned_cols=20 Identities=40% Similarity=0.424 Sum_probs=15.7
Q ss_pred HHHHHCCCCHHHHHHHHHHH
Q ss_conf 21331021189999988764
Q 537021.9.peg.1 20 LEKISENYQLSKIVSLLFFL 39 (42)
Q Consensus 20 lekisenyqlskivsllffl 39 (42)
-|||+|.|.+.-|-|-||=|
T Consensus 210 sEkl~e~h~~davESKLFGl 229 (415)
T TIGR01748 210 SEKLDEKHTLDAVESKLFGL 229 (415)
T ss_pred HHHCCCCCCHHHHHHHHHCC
T ss_conf 43057231400345534214
No 10
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=6.45 E-value=1.7e+02 Score=14.32 Aligned_cols=32 Identities=31% Similarity=0.365 Sum_probs=24.0
Q ss_pred EECCCCCCEEEECCEEHHHHHCCCCHHHHHHH
Q ss_conf 70789874686501012133102118999998
Q 537021.9.peg.1 4 LNSNGSKPYYLSTSYELEKISENYQLSKIVSL 35 (42)
Q Consensus 4 lnsngskpyylstsyelekisenyqlskivsl 35 (42)
||+|+|+.--+.-+-|.|...|...+|+.-.+
T Consensus 180 ln~N~Srs~i~~l~de~e~~Reel~l~~~S~~ 211 (415)
T COG5533 180 LNGNKSRSPILELKDEFEEVREELPLSHFSHH 211 (415)
T ss_pred HCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHH
T ss_conf 22775556532344379998763573101145
Done!