Query gi|254781015|ref|YP_003065428.1| hypothetical protein CLIBASIA_04585 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 78
No_of_seqs 10 out of 12
Neff 1.7
Searched_HMMs 39220
Date Mon May 30 03:00:39 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781015.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02535 hyp_Hser_kinase prop 53.8 6 0.00015 21.1 1.1 34 19-53 369-405 (431)
2 KOG4163 consensus 27.7 12 0.00029 19.6 -0.9 13 19-31 200-212 (551)
3 pfam00352 TBP Transcription fa 27.2 25 0.00065 17.7 0.8 34 10-44 29-62 (86)
4 pfam01376 Enterotoxin_b Heat-l 26.3 36 0.00091 16.9 1.4 26 37-62 32-59 (102)
5 TIGR00408 proS_fam_I prolyl-tR 23.0 26 0.00066 17.7 0.2 15 18-32 159-173 (533)
6 pfam03955 Adeno_PIX Adenovirus 15.2 94 0.0024 14.6 1.6 43 18-60 2-50 (109)
7 COG5362 Phage-related terminas 14.4 1.1E+02 0.0029 14.2 1.9 43 17-60 96-138 (202)
8 cd00652 TBP_TLF TATA box bindi 14.3 66 0.0017 15.5 0.6 30 11-41 28-57 (174)
9 pfam12147 Hydrolase_5 Putative 14.0 45 0.0012 16.4 -0.2 20 54-73 155-174 (311)
10 pfam11771 DUF3314 Protein of u 11.5 1.2E+02 0.003 14.1 1.2 37 1-52 1-37 (162)
No 1
>TIGR02535 hyp_Hser_kinase proposed homoserine kinase; InterPro: IPR013371 The genes encoding proteins in this entry are largely adjacent to genes involved in the biosynthesis of threonine (aspartate kinase, homoserine dehydrogenase and threonine synthase) in genomes which are lacking any other known homoserine kinase, and in which the presence of a homoserine kinase would indicate a complete pathway for the biosynthesis of threonine. These proteins are homologous to the archaeal form of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase and form part of a superfamily of metalloenzymes including phosphopentomutases, alkaline phosphatases and sulphatases. The proposal that these proteins encode a kinase is based on analogy to phosphomutases which are intramolecular phosphotransferases. A mutase active site could evolve to bring together homoserine and a phosphate donor such as phosphoenolpyruvate, resulting in kinase activity.; GO: 0004619 phosphoglycerate mutase activity.
Probab=53.82 E-value=6 Score=21.13 Aligned_cols=34 Identities=38% Similarity=0.781 Sum_probs=23.4
Q ss_pred CCCCCE-EEEC--CCCCHHHHHHCCCCCCCCCCEEEEE
Q ss_conf 887741-5630--8764022321787355357128999
Q gi|254781015|r 19 KHPSPI-FTTR--HPQSYRIFLGSGSEVSKDKGITFKV 53 (78)
Q Consensus 19 ~hpsp~-lrtr--~P~a~r~~lg~g~~ve~~~~TTF~I 53 (78)
-||+|+ +||- +|--+ ++.+.++..+.++|.+|-=
T Consensus 369 DHPTP~~~kTHt~~PVPf-~~~~~~~d~e~d~v~~fdE 405 (431)
T TIGR02535 369 DHPTPIELKTHTAEPVPF-LLYGSGKDVESDEVKTFDE 405 (431)
T ss_pred CCCCCCCCCCCCCCCCCE-EEECCCCCCCCCCCCCCCH
T ss_conf 788733210247788343-6456876423678741112
No 2
>KOG4163 consensus
Probab=27.71 E-value=12 Score=19.59 Aligned_cols=13 Identities=46% Similarity=0.759 Sum_probs=11.2
Q ss_pred CCCCCEEEECCCC
Q ss_conf 8877415630876
Q gi|254781015|r 19 KHPSPIFTTRHPQ 31 (78)
Q Consensus 19 ~hpsp~lrtr~P~ 31 (78)
.||.|+||||+=+
T Consensus 200 k~p~PFlRtrEFL 212 (551)
T KOG4163 200 KHPQPFLRTREFL 212 (551)
T ss_pred CCCCCCHHHHHHH
T ss_conf 4897512355777
No 3
>pfam00352 TBP Transcription factor TFIID (or TATA-binding protein, TBP).
Probab=27.25 E-value=25 Score=17.72 Aligned_cols=34 Identities=24% Similarity=0.424 Sum_probs=25.6
Q ss_pred CCHHHHCCCCCCCCEEEECCCCCHHHHHHCCCCCC
Q ss_conf 01022068988774156308764022321787355
Q gi|254781015|r 10 SNALWNQTGKHPSPIFTTRHPQSYRIFLGSGSEVS 44 (78)
Q Consensus 10 analwyq~g~hpsp~lrtr~P~a~r~~lg~g~~ve 44 (78)
.|+ -|.|..+|.-++|.++|.+.-+.+.+|.-+-
T Consensus 29 ~~~-~Y~Pe~fpgli~R~~~pk~t~liF~SGkivi 62 (86)
T pfam00352 29 ENA-EYEPEQFPGLVYRLREPKATALIFSSGKVVI 62 (86)
T ss_pred CCC-EECCCCCCCEEEECCCCCEEEEEECCCEEEE
T ss_conf 997-8995447756997478854999983885999
No 4
>pfam01376 Enterotoxin_b Heat-labile enterotoxin beta chain.
Probab=26.32 E-value=36 Score=16.92 Aligned_cols=26 Identities=35% Similarity=0.464 Sum_probs=19.7
Q ss_pred HHCCCCC--CCCCCEEEEEECCCCCCCE
Q ss_conf 2178735--5357128999416765430
Q gi|254781015|r 37 LGSGSEV--SKDKGITFKVEKVGDQHNK 62 (78)
Q Consensus 37 lg~g~~v--e~~~~TTF~IER~gd~~~~ 62 (78)
+|+++-| .-.+|.||.+|-||.||-+
T Consensus 32 agkremviisf~ngatfqvevpgsqh~~ 59 (102)
T pfam01376 32 AGKREMAIITFKNGATFQVEVPGSQHID 59 (102)
T ss_pred CCCEEEEEEEECCCCEEEEECCCCHHHH
T ss_conf 5760699999428967999668610134
No 5
>TIGR00408 proS_fam_I prolyl-tRNA synthetase; InterPro: IPR004499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by IPR002314 from INTERPRO, which recognises tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi (Lyme desease spirochete). The other family, IPR004500 from INTERPRO, includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis sp. (strain PCC6803), and one of the two prolyl-tRNA synthetases of Saccharomyces cerevisiae (Baker's yeast).; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=22.97 E-value=26 Score=17.69 Aligned_cols=15 Identities=33% Similarity=0.492 Sum_probs=11.9
Q ss_pred CCCCCCEEEECCCCC
Q ss_conf 988774156308764
Q gi|254781015|r 18 GKHPSPIFTTRHPQS 32 (78)
Q Consensus 18 g~hpsp~lrtr~P~a 32 (78)
-+|+-||||+|+=.+
T Consensus 159 ~kHTRPflR~rEf~t 173 (533)
T TIGR00408 159 KKHTRPFLRTREFLT 173 (533)
T ss_pred CCCCCCCHHHHHHHC
T ss_conf 178786102333210
No 6
>pfam03955 Adeno_PIX Adenovirus hexon-associated protein (IX). Hexon (PF01065) is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organized so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX.
Probab=15.24 E-value=94 Score=14.63 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=30.1
Q ss_pred CCCCCCEEEECCCC-C---HHH--HHHCCCCCCCCCCEEEEEECCCCCC
Q ss_conf 98877415630876-4---022--3217873553571289994167654
Q gi|254781015|r 18 GKHPSPIFTTRHPQ-S---YRI--FLGSGSEVSKDKGITFKVEKVGDQH 60 (78)
Q Consensus 18 g~hpsp~lrtr~P~-a---~r~--~lg~g~~ve~~~~TTF~IER~gd~~ 60 (78)
|.--+|+|.+|-|. + -++ ---.|+||.+-+..|.+-+..|...
T Consensus 2 G~V~t~fLT~RLP~WAGVRQNV~GS~vdGrPV~PanS~tl~yatv~~s~ 50 (109)
T pfam03955 2 GIVRTPFLTARLPSWAGVRQNVTGSNVDGRPVAPANSSTLTYATVGSST 50 (109)
T ss_pred CCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCC
T ss_conf 9630230112475422200134246778986578643101100025665
No 7
>COG5362 Phage-related terminase [General function prediction only]
Probab=14.43 E-value=1.1e+02 Score=14.17 Aligned_cols=43 Identities=26% Similarity=0.357 Sum_probs=24.5
Q ss_pred CCCCCCCEEEECCCCCHHHHHHCCCCCCCCCCEEEEEECCCCCC
Q ss_conf 89887741563087640223217873553571289994167654
Q gi|254781015|r 17 TGKHPSPIFTTRHPQSYRIFLGSGSEVSKDKGITFKVEKVGDQH 60 (78)
Q Consensus 17 ~g~hpsp~lrtr~P~a~r~~lg~g~~ve~~~~TTF~IER~gd~~ 60 (78)
.|+| .||+.--+|.+.-..+...----..+|-+|+||++||.-
T Consensus 96 dgk~-~~i~~~iEpkaaGk~~~q~Lk~~~~~g~~~r~epsgdKv 138 (202)
T COG5362 96 DGKY-QPIFVLIEPKAAGKQLIQDLKFLGGNGRVIRIEPSGDKV 138 (202)
T ss_pred CCCC-CCEEEECCCCCCCHHHHHHHHHCCEEEEEEEECCCCCCE
T ss_conf 0134-650456277644279999976332225898640378834
No 8
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=14.33 E-value=66 Score=15.48 Aligned_cols=30 Identities=27% Similarity=0.461 Sum_probs=21.1
Q ss_pred CHHHHCCCCCCCCEEEECCCCCHHHHHHCCC
Q ss_conf 1022068988774156308764022321787
Q gi|254781015|r 11 NALWNQTGKHPSPIFTTRHPQSYRIFLGSGS 41 (78)
Q Consensus 11 nalwyq~g~hpsp~lrtr~P~a~r~~lg~g~ 41 (78)
|+ -|.|..||.-++|.++|.+--+.+.+|.
T Consensus 28 n~-eY~P~~fp~~~~Rl~~Pk~t~lif~sGk 57 (174)
T cd00652 28 NA-EYNPKRFPGVIMRLREPKTTALIFSSGK 57 (174)
T ss_pred CC-EECCCCCCEEEEEECCCCEEEEEECCCC
T ss_conf 96-8883308679999479958999986883
No 9
>pfam12147 Hydrolase_5 Putative lysophospholipase. This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=14.04 E-value=45 Score=16.35 Aligned_cols=20 Identities=35% Similarity=0.513 Sum_probs=13.8
Q ss_pred ECCCCCCCEEEEEECCCCCC
Q ss_conf 41676543023221167886
Q gi|254781015|r 54 EKVGDQHNKILLKEYSSDNN 73 (78)
Q Consensus 54 ER~gd~~~~~~~~~~~~d~~ 73 (78)
+...+.+..|++||||+-|-
T Consensus 155 ~~~~~~~~~illRDys~~NV 174 (311)
T pfam12147 155 AKAPQRPDSILLRDYSPLNV 174 (311)
T ss_pred HHCCCCCCEEEECCCCHHHH
T ss_conf 85798874588514888779
No 10
>pfam11771 DUF3314 Protein of unknown function (DUF3314). This small family contains human, mouse and fish members but the function is not known.
Probab=11.46 E-value=1.2e+02 Score=14.12 Aligned_cols=37 Identities=19% Similarity=0.263 Sum_probs=0.0
Q ss_pred CEEEEEECCCCHHHHCCCCCCCCEEEECCCCCHHHHHHCCCCCCCCCCEEEE
Q ss_conf 9343141100102206898877415630876402232178735535712899
Q gi|254781015|r 1 MFLFFCWILSNALWNQTGKHPSPIFTTRHPQSYRIFLGSGSEVSKDKGITFK 52 (78)
Q Consensus 1 ~f~~F~fv~analwyq~g~hpsp~lrtr~P~a~r~~lg~g~~ve~~~~TTF~ 52 (78)
||+-|+||. |..-+|+|---++--.-...--+|++||
T Consensus 1 mfasfgfv~---------------lee~~plSvS~F~~Gq~~i~~~~vsiFr 37 (162)
T pfam11771 1 MFASFGFVD---------------LEEMNPLSVSHFAIGQFDIRGHEVSIFR 37 (162)
T ss_pred CCCCEEEEE---------------EECCCCCEEEEEEEEEEECCCCEEEEEE
T ss_conf 953031344---------------0016873477888852442675688999
Done!