Query 537021.9.peg.568_1 Match_columns 45 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Tue May 24 22:31:17 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_568.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR00213 GmhB_yaeD D,D-heptos 34.0 8.1 0.00021 20.5 -0.8 27 2-28 110-136 (178) 2 TIGR01021 rpsE_bact ribosomal 24.5 39 0.001 17.1 1.4 13 20-32 29-41 (157) 3 PRK12764 hypothetical protein; 15.6 1E+02 0.0026 15.1 1.9 13 20-32 430-442 (498) 4 TIGR01656 Histidinol-ppas hist 13.1 56 0.0014 16.4 -0.0 25 2-26 153-178 (208) 5 PRK06278 cobyrinic acid a,c-di 12.5 52 0.0013 16.5 -0.3 20 8-27 12-31 (482) 6 TIGR01649 hnRNP-L_PTB hnRNP-L/ 12.4 57 0.0015 16.3 -0.1 19 5-23 464-482 (557) 7 pfam08169 RBB1NT RBB1NT (NUC16 11.4 88 0.0022 15.4 0.6 23 2-31 24-46 (96) 8 TIGR02069 cyanophycinase cyano 10.9 88 0.0022 15.4 0.4 17 1-17 186-204 (297) 9 cd03075 GST_N_Mu GST_N family, 10.9 1E+02 0.0027 15.1 0.8 15 13-27 53-67 (82) 10 TIGR00459 aspS_bact aspartyl-t 10.0 1.9E+02 0.0048 13.8 2.1 17 17-33 36-53 (653) No 1 >TIGR00213 GmhB_yaeD D,D-heptose 1,7-bisphosphate phosphatase; InterPro: IPR004446 In a number of species, including Escherichia coli, the histidine biosynthetic enzymes imidazole glycerol phosphate dehydratase and histidinol phosphatase are found together in the bifunctional protein HisB. This family represents a protein closely related to the histidinol phosphatase domain of HisB. The protein is found both in Helicobacter pylori, for which the histidine biosynthetic pathway appears to be absent, and in species that also have a bifunctional HisB protein.. Probab=33.96 E-value=8.1 Score=20.52 Aligned_cols=27 Identities=33% Similarity=0.471 Sum_probs=23.5 Q ss_pred CCCEEECCHHEEEECCCCEEEEECCCC Q ss_conf 874683522106641686256707787 Q 537021.9.peg.5 2 SPGLILSPSCFIHFANLPSVIVGDKEG 28 (45) Q Consensus 2 spglilspscfihfanlpsvivgdkeg 28 (45) .||++|+..-..+..--.|..||||+. T Consensus 110 kp~~lL~A~~~~~I~~~~S~MvGDK~~ 136 (178) T TIGR00213 110 KPGLLLQAAKELKIDLEQSFMVGDKVE 136 (178) T ss_pred CHHHHHHHHHHHCCCHHHCEECCCCHH T ss_conf 613588777872135232222037778 No 2 >TIGR01021 rpsE_bact ribosomal protein S5; InterPro: IPR005712 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 , . This family includes chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=24.53 E-value=39 Score=17.14 Aligned_cols=13 Identities=54% Similarity=0.685 Sum_probs=10.1 Q ss_pred EEEEECCCCEEEE Q ss_conf 2567077874999 Q 537021.9.peg.5 20 SVIVGDKEGIVIV 32 (45) Q Consensus 20 svivgdkegiviv 32 (45) -|+|||++|-|=+ T Consensus 29 LvVVGd~~G~VG~ 41 (157) T TIGR01021 29 LVVVGDKKGRVGF 41 (157) T ss_pred EEEEECCCCEEEE T ss_conf 9997178743788 No 3 >PRK12764 hypothetical protein; Provisional Probab=15.60 E-value=1e+02 Score=15.14 Aligned_cols=13 Identities=46% Similarity=1.114 Sum_probs=10.2 Q ss_pred EEEEECCCCEEEE Q ss_conf 2567077874999 Q 537021.9.peg.5 20 SVIVGDKEGIVIV 32 (45) Q Consensus 20 svivgdkegiviv 32 (45) .+||||.+|.|.+ T Consensus 430 DiiVgD~DGvvVI 442 (498) T PRK12764 430 DVIVGDDDGVLVI 442 (498) T ss_pred CEEEECCCCEEEE T ss_conf 8899768845992 No 4 >TIGR01656 Histidinol-ppas histidinol-phosphate phosphatase family domain; InterPro: IPR006543 This is a group of authentic histidinol-phosphate phosphatases which are sometimes found as stand-alone entities and sometimes as fusions with imidazoleglycerol-phosphate dehydratase. Additionally, a family of proteins including YaeD from Escherichia coli and various other proteins are closely related but may not have the same substrate specificity. This protein is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing a conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the region modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a "capping" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3.; GO: 0004401 histidinol-phosphatase activity, 0000105 histidine biosynthetic process. Probab=13.14 E-value=56 Score=16.39 Aligned_cols=25 Identities=36% Similarity=0.513 Sum_probs=15.0 Q ss_pred CCCEEECCHHEEE-ECCCCEEEEECC Q ss_conf 8746835221066-416862567077 Q 537021.9.peg.5 2 SPGLILSPSCFIH-FANLPSVIVGDK 26 (45) Q Consensus 2 spglilspscfih-fanlpsvivgdk 26 (45) +||||+.----.. +--.-|.+|||+ T Consensus 153 ~Pgl~~~a~~~~~d~d~~~S~vVGD~ 178 (208) T TIGR01656 153 KPGLILEALKRLGDVDLSRSLVVGDR 178 (208) T ss_pred CCCHHHHHHHHCCCCCCCCEEEECCC T ss_conf 85268999964466552261576178 No 5 >PRK06278 cobyrinic acid a,c-diamide synthase; Validated Probab=12.49 E-value=52 Score=16.54 Aligned_cols=20 Identities=35% Similarity=0.828 Sum_probs=16.4 Q ss_pred CCHHEEEECCCCEEEEECCC Q ss_conf 52210664168625670778 Q 537021.9.peg.5 8 SPSCFIHFANLPSVIVGDKE 27 (45) Q Consensus 8 spscfihfanlpsvivgdke 27 (45) +-.||-+|.|||.-|+..+. T Consensus 12 slP~FE~FG~LPTkii~enn 31 (482) T PRK06278 12 TLPCFENFGNLPTKIIKENN 31 (482) T ss_pred CCCHHHHCCCCCHHHHCCCC T ss_conf 64113221678636644367 No 6 >TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family; InterPro: IPR006536 Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L . These proteins contain four RNA recognition motifs. ; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus. Probab=12.41 E-value=57 Score=16.34 Aligned_cols=19 Identities=32% Similarity=0.607 Sum_probs=15.6 Q ss_pred EEECCHHEEEECCCCEEEE Q ss_conf 6835221066416862567 Q 537021.9.peg.5 5 LILSPSCFIHFANLPSVIV 23 (45) Q Consensus 5 lilspscfihfanlpsviv 23 (45) -|.-|||-.||-|.|+-+- T Consensus 464 ~I~pPsatLHl~NiP~~v~ 482 (557) T TIGR01649 464 NIYPPSATLHLSNIPLSVS 482 (557) T ss_pred CCCCCCCHHHHHCCCCCCC T ss_conf 5788630223007889527 No 7 >pfam08169 RBB1NT RBB1NT (NUC162) domain. This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family. Probab=11.41 E-value=88 Score=15.42 Aligned_cols=23 Identities=39% Similarity=0.667 Sum_probs=14.1 Q ss_pred CCCEEECCHHEEEECCCCEEEEECCCCEEE Q ss_conf 874683522106641686256707787499 Q 537021.9.peg.5 2 SPGLILSPSCFIHFANLPSVIVGDKEGIVI 31 (45) Q Consensus 2 spglilspscfihfanlpsvivgdkegivi 31 (45) -|+|..+|||-- +|-++ |+-+.+ T Consensus 24 fPaLVVsPsc~d------~v~vk-KD~~lV 46 (96) T pfam08169 24 YPALVVSPSCND------DVTVK-KDQCLV 46 (96) T ss_pred EEEEEECCCCCC------CHHHC-CCEEEE T ss_conf 366887687664------01104-351898 No 8 >TIGR02069 cyanophycinase cyanophycinase; InterPro: IPR011811 This entry describes both cytosolic and extracellular cyanophycinases. The former are part of a system in many Cyanobacteria and a few other species of generating and later utilizing a storage polymer for nitrogen, carbon, and energy, called cyanophycin. The latter are found in species such as Pseudomonas anguilliseptica that can use external cyanophycin. The polymer has a backbone of L-aspartic acid, with most Asp side chain carboxyl groups attached to L-arginine.; GO: 0016787 hydrolase activity, 0044260 cellular macromolecule metabolic process. Probab=10.87 E-value=88 Score=15.43 Aligned_cols=17 Identities=53% Similarity=0.843 Sum_probs=9.4 Q ss_pred CCCCEEECCHHEE--EECC Q ss_conf 9874683522106--6416 Q 537021.9.peg.5 1 MSPGLILSPSCFI--HFAN 17 (45) Q Consensus 1 mspglilspscfi--hfan 17 (45) |+|||=|-|.-.| ||+| T Consensus 186 Ma~GLGl~~~v~iDQHF~~ 204 (297) T TIGR02069 186 MAPGLGLLKDVLIDQHFAQ 204 (297) T ss_pred HCCCCCCCCCCEEEECHHH T ss_conf 0467731687437306110 No 9 >cd03075 GST_N_Mu GST_N family, Class Mu subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The class Mu subfamily is composed of eukaryotic GSTs. In rats, at least six distinct class Mu subunits have been identified, with homologous genes in humans for five of these subunits. Class Mu GSTs can form homodimers and heterodimers, giving a large number of possible isoenzymes that can be formed, all with overlapping activities but different substrate specificities. They are the most abundant GSTs in human liver, skeletal muscle and brain, and are believed to provide protection against diseases inc Probab=10.85 E-value=1e+02 Score=15.06 Aligned_cols=15 Identities=47% Similarity=0.773 Sum_probs=12.0 Q ss_pred EEECCCCEEEEECCC Q ss_conf 664168625670778 Q 537021.9.peg.5 13 IHFANLPSVIVGDKE 27 (45) Q Consensus 13 ihfanlpsvivgdke 27 (45) .-|.|||-.+.||+. T Consensus 53 ~~f~nLP~l~dg~~~ 67 (82) T cd03075 53 LDFPNLPYYIDGDVK 67 (82) T ss_pred CCCCCCCEEEECCEE T ss_conf 957889989989999 No 10 >TIGR00459 aspS_bact aspartyl-tRNA synthetase; InterPro: IPR004524 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 . Aspartyl tRNA synthetase 184.108.40.206 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module . This family represents aspartyl-tRNA synthetases from the bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=10.05 E-value=1.9e+02 Score=13.78 Aligned_cols=17 Identities=41% Similarity=0.503 Sum_probs=0.0 Q ss_pred CCCEEEEECCCC-EEEEE Q ss_conf 686256707787-49998 Q 537021.9.peg.5 17 NLPSVIVGDKEG-IVIVC 33 (45) Q Consensus 17 nlpsvivgdkeg-ivivc 33 (45) ||-=++++||+| ||-|+ T Consensus 36 nliFidlRD~~GdivQv~ 53 (653) T TIGR00459 36 NLIFIDLRDRSGDIVQVV 53 (653) T ss_pred CEEEEEEECCCCCEEEEE T ss_conf 179998625888889998 Done!