Query         537021.9.peg.82_1
Match_columns 41
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 23 10:55:11 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_82.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01173 glmU UDP-N-acetylglu  25.3      23  0.0006   18.0   0.3   15   15-29    100-114 (461)
  2 PRK09729 hypothetical protein;  21.9      36 0.00091   17.2   0.7   34    2-35     32-65  (68)
  3 PRK09759 small toxic polypepti  10.9      97  0.0025   15.1   0.6   13    1-13      1-13  (50)
  4 TIGR00459 aspS_bact aspartyl-t  10.6      73  0.0019   15.7  -0.1   13   17-29    170-182 (653)
  5 PRK03853 DNA-directed RNA poly   8.6 1.6E+02  0.0041   14.0   1.1   26    3-28     19-45  (73)
  6 COG1207 GlmU N-acetylglucosami   7.4 1.4E+02  0.0037   14.2   0.4   16   15-30     99-114 (460)
  7 pfam04839 PSRP-3_Ycf65 Plastid   6.9 1.6E+02  0.0041   14.0   0.4   10   10-19     34-43  (49)
  8 COG4387 Mu-like prophage prote   6.1 2.3E+02  0.0059   13.2   0.9   21    2-24     87-107 (139)
  9 TIGR01801 CM_A chorismate muta   6.0 2.3E+02  0.0058   13.3   0.8   16   22-37     22-37  (104)
 10 TIGR00551 nadB L-aspartate oxi   5.7 1.5E+02  0.0038   14.2  -0.3   22    1-22     21-42  (546)

No 1  
>TIGR01173 glmU UDP-N-acetylglucosamine pyrophosphorylase; InterPro: IPR005882    N-Acetylglucosamine-1-PO(4) uridyltransferase (GlmU, 2.7.7.23 from EC) is a trimeric bifunctional enzyme that catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-GlcNAc.    The X-ray crystal structure of Escherichia coli GlmU in complex with UDP-GlcNAc and CoA has been determined to 2.1 A resolution and reveals a two-domain architecture that is responsible for these two reactions . The C-terminal domain is responsible for the CoA-dependent acetylation of Glc-1-PO(4) to GlcNAc-1-PO(4) and displays the longest left-handed parallel beta-helix observed to date. The acetyltransferase active site defined by the binding site for CoA makes use of residues from all three subunits and is positioned beneath an open cavity large enough to accommodate the Glc-1-PO(4) acetyl acceptor. The N-terminal domain catalyzes uridyl transfer from UTP to GlcNAc-1-PO(4) to form the final products UDP-GlcNAc and pyrophosphate. This domain is composed of a central seven-stranded beta-sheet surrounded by six alpha-helices in a Rossmann fold-like topology. ; GO: 0003977 UDP-N-acetylglucosamine diphosphorylase activity, 0009103 lipopolysaccharide biosynthetic process.
Probab=25.30  E-value=23  Score=18.04  Aligned_cols=15  Identities=40%  Similarity=0.676  Sum_probs=12.2

Q ss_pred             HHHHCCCCCCHHHHH
Q ss_conf             122148773022346
Q 537021.9.peg.8   15 TEVINGETPLLSKRT   29 (41)
Q Consensus        15 tevingetpllskrt   29 (41)
                      .=|+||.+||+++-|
T Consensus       100 vLvLyGDvPLi~~eT  114 (461)
T TIGR01173       100 VLVLYGDVPLISAET  114 (461)
T ss_pred             EEEEECCCCCCCHHH
T ss_conf             899958878775677


No 2  
>PRK09729 hypothetical protein; Provisional
Probab=21.87  E-value=36  Score=17.16  Aligned_cols=34  Identities=35%  Similarity=0.411  Sum_probs=24.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             6101002444321122148773022346788515
Q 537021.9.peg.8    2 PQRYRDTSLLSKKTEVINGETPLLSKRTEVITGI   35 (41)
Q Consensus         2 pqryrdtsllskktevingetpllskrtevitgi   35 (41)
                      |.-||..|||.|...|-...--||.+-.|..+..
T Consensus        32 ptfyrqisllake~pvegsplfllq~cme~l~~~   65 (68)
T PRK09729         32 PTFYRQISLLAKEKPVEGSPLFLLQMCMEQLVAI   65 (68)
T ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHC
T ss_conf             3799999998018998898289999999999870


No 3  
>PRK09759 small toxic polypeptide; Provisional
Probab=10.89  E-value=97  Score=15.07  Aligned_cols=13  Identities=54%  Similarity=0.779  Sum_probs=9.8

Q ss_pred             CCCCHHHHHHHHH
Q ss_conf             9610100244432
Q 537021.9.peg.8    1 MPQRYRDTSLLSK   13 (41)
Q Consensus         1 mpqryrdtsllsk   13 (41)
                      |||+|+--+|+--
T Consensus         1 MP~k~~l~~L~vi   13 (50)
T PRK09759          1 MPQKYRLLSLIVI   13 (50)
T ss_pred             CCCCHHHHHHHHH
T ss_conf             9820128989999


No 4  
>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 6.1.1.12 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=10.57  E-value=73  Score=15.65  Aligned_cols=13  Identities=46%  Similarity=0.687  Sum_probs=9.3

Q ss_pred             HHCCCCCCHHHHH
Q ss_conf             2148773022346
Q 537021.9.peg.8   17 VINGETPLLSKRT   29 (41)
Q Consensus        17 vingetpllskrt   29 (41)
                      -+.=|||.|+|-|
T Consensus       170 FleiETP~LtKsT  182 (653)
T TIGR00459       170 FLEIETPILTKST  182 (653)
T ss_pred             CCEEECCCCCCCC
T ss_conf             7065067777888


No 5  
>PRK03853 DNA-directed RNA polymerase subunit omega; Provisional
Probab=8.65  E-value=1.6e+02  Score=14.00  Aligned_cols=26  Identities=31%  Similarity=0.595  Sum_probs=18.3

Q ss_pred             CCHHHHHHHHHHH-HHHCCCCCCHHHH
Q ss_conf             1010024443211-2214877302234
Q 537021.9.peg.8    3 QRYRDTSLLSKKT-EVINGETPLLSKR   28 (41)
Q Consensus         3 qryrdtsllskkt-evingetpllskr   28 (41)
                      .||.-+.+.++.. +..||..||+...
T Consensus        19 DRY~Ls~~vakRa~qLanGA~PLv~~d   45 (73)
T PRK03853         19 DRYKLSLLVFKRAEQLANGAKPLVDMD   45 (73)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             089999999999999866886422468


No 6  
>COG1207 GlmU N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]
Probab=7.39  E-value=1.4e+02  Score=14.24  Aligned_cols=16  Identities=31%  Similarity=0.561  Sum_probs=12.7

Q ss_pred             HHHHCCCCCCHHHHHH
Q ss_conf             1221487730223467
Q 537021.9.peg.8   15 TEVINGETPLLSKRTE   30 (41)
Q Consensus        15 tevingetpllskrte   30 (41)
                      +-|++|.+||++..|-
T Consensus        99 vLVl~GD~PLit~~TL  114 (460)
T COG1207          99 VLVLYGDVPLITAETL  114 (460)
T ss_pred             EEEEECCCCCCCHHHH
T ss_conf             8999699666789999


No 7  
>pfam04839 PSRP-3_Ycf65 Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65). This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA.
Probab=6.88  E-value=1.6e+02  Score=14.01  Aligned_cols=10  Identities=60%  Similarity=0.899  Sum_probs=4.3

Q ss_pred             HHHHHHHHHC
Q ss_conf             4432112214
Q 537021.9.peg.8   10 LLSKKTEVIN   19 (41)
Q Consensus        10 llskktevin   19 (41)
                      ||.+-|||||
T Consensus        34 lLN~~TeiIn   43 (49)
T pfam04839        34 LLNQATEIIN   43 (49)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 8  
>COG4387 Mu-like prophage protein gp36 [Function unknown]
Probab=6.10  E-value=2.3e+02  Score=13.23  Aligned_cols=21  Identities=38%  Similarity=0.566  Sum_probs=13.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             61010024443211221487730
Q 537021.9.peg.8    2 PQRYRDTSLLSKKTEVINGETPL   24 (41)
Q Consensus         2 pqryrdtsllskktevingetpl   24 (41)
                      -|||+++-.+-++  |.+|+.+|
T Consensus        87 r~rYe~av~~L~~--va~G~V~l  107 (139)
T COG4387          87 RQRYEDAVRFLEK--VASGAVSL  107 (139)
T ss_pred             HHHHHHHHHHHHH--HHCCCCCC
T ss_conf             9999999999999--97688740


No 9  
>TIGR01801 CM_A chorismate mutase; InterPro: IPR010954   This entry represents chorismate mutase (CM) domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some Gram-positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44 0dentity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the Gram-positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role..
Probab=6.05  E-value=2.3e+02  Score=13.29  Aligned_cols=16  Identities=44%  Similarity=0.627  Sum_probs=11.9

Q ss_pred             CCCHHHHHHHHHHHHH
Q ss_conf             7302234678851575
Q 537021.9.peg.8   22 TPLLSKRTEVITGINR   37 (41)
Q Consensus        22 tpllskrtevitginr   37 (41)
                      -.|+|+|-||+.-|..
T Consensus        22 L~Lis~RGevv~~IG~   37 (104)
T TIGR01801        22 LKLISKRGEVVKKIGK   37 (104)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9998531189999757


No 10 
>TIGR00551 nadB L-aspartate oxidase; InterPro: IPR005288    L-aspartate oxidase is the B protein, NadB, of the quinolinate synthetase complex. Quinolinate synthetase makes a precursor of the pyridine nucleotide portion of NAD. This model identifies proteins that cluster as L-aspartate oxidase (a flavoprotein difficult to separate from the set of closely related flavoprotein subunits of succinate dehydrogenase and fumarate reductase) by both UPGMA and neighbour-joining trees.; GO: 0008734 L-aspartate oxidase activity, 0009435 NAD biosynthetic process, 0005737 cytoplasm.
Probab=5.75  E-value=1.5e+02  Score=14.19  Aligned_cols=22  Identities=32%  Similarity=0.631  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9610100244432112214877
Q 537021.9.peg.8    1 MPQRYRDTSLLSKKTEVINGET   22 (41)
Q Consensus         1 mpqryrdtsllskktevinget   22 (41)
                      +|..|+|-+++||+.++-++.|
T Consensus        21 l~~~~~~V~v~~K~a~~~~~~s   42 (546)
T TIGR00551        21 LAEKYRDVVVISKAAEVKESAS   42 (546)
T ss_pred             CCCCCCEEEEECCCCCCCCCCC
T ss_conf             3326863789758755556752


Done!