Query gi|254780632|ref|YP_003065045.1| hypothetical protein CLIBASIA_02595 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 71
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Sun May 29 20:53:41 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780632.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03934 phosphatidylserine de 28.0 40 0.001 16.6 1.9 35 28-63 233-267 (267)
2 TIGR01049 rpsJ_bact ribosomal 19.2 74 0.0019 15.1 1.9 20 4-26 77-96 (99)
3 PRK06033 hypothetical protein; 16.4 69 0.0018 15.3 1.2 38 25-63 33-76 (87)
4 pfam06232 ATS3 Embryo-specific 16.1 86 0.0022 14.8 1.6 17 46-62 30-46 (126)
5 TIGR01088 aroQ 3-dehydroquinat 15.7 53 0.0014 15.9 0.5 12 41-52 115-126 (144)
6 cd07999 GH7_CBH_EG Glycosyl hy 15.1 84 0.0021 14.9 1.3 23 12-37 119-141 (386)
7 pfam00840 Glyco_hydro_7 Glycos 14.2 91 0.0023 14.6 1.4 22 12-36 125-146 (432)
8 COG3168 PilP Tfp pilus assembl 13.9 1.2E+02 0.0032 13.9 2.3 35 29-66 106-140 (170)
9 COG5522 Predicted integral mem 13.8 29 0.00073 17.4 -1.3 15 50-64 172-186 (236)
10 KOG2431 consensus 13.6 98 0.0025 14.5 1.4 38 4-41 445-497 (546)
No 1
>PRK03934 phosphatidylserine decarboxylase; Provisional
Probab=27.95 E-value=40 Score=16.62 Aligned_cols=35 Identities=26% Similarity=0.475 Sum_probs=21.3
Q ss_pred CCCCCEEEEECCHHHHHHCCCCEEEEEECCCCCEEE
Q ss_conf 377614664131133001025268889717622176
Q gi|254780632|r 28 GLGSSIVAVKPVVPYITDVARGQINVRLGDNYGVLH 63 (71)
Q Consensus 28 glgssivavkpvvpyitdvargqinvrlgdnygvlh 63 (71)
-+||++|-+-+---.--|+..|+. ||+|..-|-+|
T Consensus 233 ~~GSTVVllfe~~~~~~~l~~g~~-Vk~Gq~ig~~~ 267 (267)
T PRK03934 233 EMGSTIVLFSQKGSLEFNLKAGES-VKFGESIGKIH 267 (267)
T ss_pred CCCCEEEEEEECCCCCCCCCCCCE-EEEEHHHCCCC
T ss_conf 678849999518976326789999-88204320149
No 2
>TIGR01049 rpsJ_bact ribosomal protein S10; InterPro: IPR005731 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial transit peptide but contain additional sequence C-terminal to the ribosomal S10 protein region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=19.24 E-value=74 Score=15.13 Aligned_cols=20 Identities=30% Similarity=0.768 Sum_probs=14.8
Q ss_pred CHHHHHHHHEEEEECCCCEEEEE
Q ss_conf 46788753201374168326898
Q gi|254780632|r 4 GPETLESLMVSFRVDMSPAVQLQ 26 (71)
Q Consensus 4 gpetleslmvsfrvdmspavqlq 26 (71)
-|+|+++|| ++|+...|++.
T Consensus 77 ~~~t~daL~---~ldLPaGVDv~ 96 (99)
T TIGR01049 77 TPKTIDALM---KLDLPAGVDVE 96 (99)
T ss_pred CHHHHHHHH---CCCCCCCEEEE
T ss_conf 978989875---04788861688
No 3
>PRK06033 hypothetical protein; Validated
Probab=16.43 E-value=69 Score=15.31 Aligned_cols=38 Identities=21% Similarity=0.162 Sum_probs=22.2
Q ss_pred EEECCCCCEE----EEECCHHHHH--HCCCCEEEEEECCCCCEEE
Q ss_conf 9823776146----6413113300--1025268889717622176
Q gi|254780632|r 25 LQCGLGSSIV----AVKPVVPYIT--DVARGQINVRLGDNYGVLH 63 (71)
Q Consensus 25 lqcglgssiv----avkpvvpyit--dvargqinvrlgdnygvlh 63 (71)
|+-|-||-|- +-.|+--|+. -+|||.+-| .+|+|||--
T Consensus 33 L~L~~GsVIeLD~~~gepvdi~vN~~liArGEVvV-~~d~~gVri 76 (87)
T PRK06033 33 LRLSRGAIIELDATEADEVKILANNHPIASGVVLV-DRNRIAVEV 76 (87)
T ss_pred HCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEE-ECCEEEEEE
T ss_conf 35589868986567899489999999998885999-898889999
No 4
>pfam06232 ATS3 Embryo-specific protein 3, (ATS3). Family of plant seed-specific proteins.
Probab=16.12 E-value=86 Score=14.79 Aligned_cols=17 Identities=41% Similarity=0.745 Sum_probs=13.9
Q ss_pred CCCCEEEEEECCCCCEE
Q ss_conf 02526888971762217
Q gi|254780632|r 46 VARGQINVRLGDNYGVL 62 (71)
Q Consensus 46 vargqinvrlgdnygvl 62 (71)
-.|.||.++.||.||-.
T Consensus 30 ~T~D~ISi~FGDa~Gnq 46 (126)
T pfam06232 30 YTRDQISIAFGDAYGNQ 46 (126)
T ss_pred CCCCEEEEEEECCCCCE
T ss_conf 66643889984378899
No 5
>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales , and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=15.72 E-value=53 Score=15.94 Aligned_cols=12 Identities=50% Similarity=0.764 Sum_probs=9.7
Q ss_pred HHHHHCCCCEEE
Q ss_conf 330010252688
Q gi|254780632|r 41 PYITDVARGQIN 52 (71)
Q Consensus 41 pyitdvargqin 52 (71)
-|+.+||+|||-
T Consensus 115 S~~a~va~G~I~ 126 (144)
T TIGR01088 115 SYIAPVAKGVIV 126 (144)
T ss_pred CCCCCCCCCEEE
T ss_conf 542220353275
No 6
>cd07999 GH7_CBH_EG Glycosyl hydrolase family 7. Glycosyl hydrolase family 7 contains eukaryotic endoglucanases (EGs) and cellobiohydrolases (CBHs) that hydrolyze glycosidic bonds using a double-displacement mechanism. This leads to a net retention of the conformation at the anomeric carbon. Both enzymes work synergistically in the degradation of cellulose,which is the main component of plant cell wall, and is composed of beta-1,4 linked glycosyl units. EG cleaves the beta-1,4 linkages of cellulose and CBH cleaves off cellobiose disaccharide units from the reducing end of the chain. In general, the O-glycosyl hydrolases are a widespread group of enzymes that hydrolyze the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycoside hydrolase family 7.
Probab=15.08 E-value=84 Score=14.85 Aligned_cols=23 Identities=35% Similarity=0.709 Sum_probs=16.8
Q ss_pred HEEEEECCCCEEEEEECCCCCEEEEE
Q ss_conf 20137416832689823776146641
Q gi|254780632|r 12 MVSFRVDMSPAVQLQCGLGSSIVAVK 37 (71)
Q Consensus 12 mvsfrvdmspavqlqcglgssivavk 37 (71)
-.+|.|||| +|.||+-+.+--+.
T Consensus 119 EfTFDVD~S---~lpCG~NgALYfve 141 (386)
T cd07999 119 EFTFDVDMS---NLPCGMNGALYLSE 141 (386)
T ss_pred EEEEEEECC---CCCCCCCEEEEEEE
T ss_conf 688975335---78765300444663
No 7
>pfam00840 Glyco_hydro_7 Glycosyl hydrolase family 7.
Probab=14.25 E-value=91 Score=14.63 Aligned_cols=22 Identities=41% Similarity=0.762 Sum_probs=16.5
Q ss_pred HEEEEECCCCEEEEEECCCCCEEEE
Q ss_conf 2013741683268982377614664
Q gi|254780632|r 12 MVSFRVDMSPAVQLQCGLGSSIVAV 36 (71)
Q Consensus 12 mvsfrvdmspavqlqcglgssivav 36 (71)
-.+|.|||| +|.||+-..+--|
T Consensus 125 EftFdVD~S---~lpCGlNgALYfv 146 (432)
T pfam00840 125 EFTFDVDVS---KLPCGLNGALYFV 146 (432)
T ss_pred EEEEEECCC---CCCCCCCCEEEEE
T ss_conf 678874223---4885440034466
No 8
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=13.92 E-value=1.2e+02 Score=13.91 Aligned_cols=35 Identities=29% Similarity=0.403 Sum_probs=22.2
Q ss_pred CCCCEEEEECCHHHHHHCCCCEEEEEECCCCCEEEEEE
Q ss_conf 77614664131133001025268889717622176677
Q gi|254780632|r 29 LGSSIVAVKPVVPYITDVARGQINVRLGDNYGVLHSVD 66 (71)
Q Consensus 29 lgssivavkpvvpyitdvargqinvrlgdnygvlhsvd 66 (71)
-|.++.|+--.--+.-.|.+||. +|.|||-.-+++
T Consensus 106 ~g~~~~A~i~~~~~v~~V~vG~Y---lGqN~GrV~rI~ 140 (170)
T COG3168 106 SGQGVSALIEAPGGVYRVRVGQY---LGQNYGRVVRIT 140 (170)
T ss_pred CCCCEEEEEECCCCEEEEEECCE---EECCCCEEEEEC
T ss_conf 78836899973892699850107---502476688853
No 9
>COG5522 Predicted integral membrane protein [Function unknown]
Probab=13.76 E-value=29 Score=17.41 Aligned_cols=15 Identities=53% Similarity=0.634 Sum_probs=11.7
Q ss_pred EEEEEECCCCCEEEE
Q ss_conf 688897176221766
Q gi|254780632|r 50 QINVRLGDNYGVLHS 64 (71)
Q Consensus 50 qinvrlgdnygvlhs 64 (71)
-||-|||.||+-+..
T Consensus 172 finrrLGtNYlylsk 186 (236)
T COG5522 172 FINRRLGTNYLYLSK 186 (236)
T ss_pred HHHHHHCCCEEEEEC
T ss_conf 999874674357616
No 10
>KOG2431 consensus
Probab=13.64 E-value=98 Score=14.47 Aligned_cols=38 Identities=34% Similarity=0.418 Sum_probs=25.1
Q ss_pred CHHHHHHHHEEEEECCCCE---------------EEEEECCCCCEEEEECCHH
Q ss_conf 4678875320137416832---------------6898237761466413113
Q gi|254780632|r 4 GPETLESLMVSFRVDMSPA---------------VQLQCGLGSSIVAVKPVVP 41 (71)
Q Consensus 4 gpetleslmvsfrvdmspa---------------vqlqcglgssivavkpvvp 41 (71)
-|||.||++.-+|+.-.-. ..+.||-=+||-.|+...|
T Consensus 445 RPEtVESlfylYriT~D~kYqewGW~if~sfekytrv~~ggytSi~nV~~~~~ 497 (546)
T KOG2431 445 RPETVESLFYLYRITGDRKYQEWGWEIFQSFEKYTRVPSGGYTSIDNVKDQKP 497 (546)
T ss_pred CHHHHHHHHEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCC
T ss_conf 75777664304575387358887599999999855167888450454542588
Done!