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_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 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_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 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_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 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