Query         537021.9.peg.36_1
Match_columns 29
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 22 15:15:45 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_36.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10397 hypothetical protein;  22.1      37 0.00095   17.1   0.9   24    6-29    106-129 (137)
  2 COG0608 RecJ Single-stranded D  16.9      78   0.002   15.5   1.6   26    1-26     38-63  (491)
  3 PRK01581 speE spermidine synth  14.0      52  0.0013   16.4   0.0   17    2-18    143-159 (363)
  4 PRK08605 D-lactate dehydrogena  14.0      38 0.00097   17.1  -0.6   24    3-26     41-64  (332)
  5 TIGR01083 nth endonuclease III  13.4   1E+02  0.0026   15.0   1.4   21    3-28     75-95  (192)
  6 KOG2193 consensus               12.2      58  0.0015   16.2  -0.1   14   13-26    249-262 (584)
  7 TIGR00088 trmD tRNA (guanine-N  10.5      64  0.0016   16.0  -0.4   20    2-21    109-129 (247)
  8 pfam07272 Orthoreo_P17 Orthore  10.0 1.6E+02   0.004   14.1   1.5   17    3-19    107-123 (146)
  9 KOG2152 consensus                9.1   1E+02  0.0026   15.0   0.2   26    3-28    551-578 (865)
 10 COG4689 Adc Acetoacetate decar   8.8 1.3E+02  0.0032   14.5   0.6   11    1-11    168-178 (247)

No 1  
>PRK10397 hypothetical protein; Provisional
Probab=22.06  E-value=37  Score=17.09  Aligned_cols=24  Identities=29%  Similarity=0.599  Sum_probs=19.2

Q ss_pred             EEECCEEEEHHHHHHHHHHHHHCC
Q ss_conf             510562320057898999997309
Q 537021.9.peg.3    6 GHYDGLAVRSTAKVTQSCCRMLKK   29 (29)
Q Consensus         6 ghydglavrstakvtqsccrmlkk   29 (29)
                      -||||+.....+.-|..|-.-|.|
T Consensus       106 L~YdgmtLqrv~rpT~ECa~~l~k  129 (137)
T PRK10397        106 LEYDGMTLQRVDRPTAECAAALDK  129 (137)
T ss_pred             EEECCEEEEECCCCCHHHHHHHHH
T ss_conf             876656888527885899999984


No 2  
>COG0608 RecJ Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]
Probab=16.92  E-value=78  Score=15.54  Aligned_cols=26  Identities=27%  Similarity=0.438  Sum_probs=20.1

Q ss_pred             CEEEEEEECCEEEEHHHHHHHHHHHH
Q ss_conf             90684510562320057898999997
Q 537021.9.peg.3    1 MVRIIGHYDGLAVRSTAKVTQSCCRM   26 (29)
Q Consensus         1 mvriighydglavrstakvtqsccrm   26 (29)
                      .++|+||||.=.+-|+|-....+.++
T Consensus        38 ~I~I~~d~DaDGitS~ail~~~L~~~   63 (491)
T COG0608          38 KILIYGDYDADGITSAAILAKALRRL   63 (491)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             69997878851778999999999976


No 3  
>PRK01581 speE spermidine synthase; Validated
Probab=14.01  E-value=52  Score=16.42  Aligned_cols=17  Identities=53%  Similarity=0.698  Sum_probs=13.7

Q ss_pred             EEEEEEECCEEEEHHHH
Q ss_conf             06845105623200578
Q 537021.9.peg.3    2 VRIIGHYDGLAVRSTAK   18 (29)
Q Consensus         2 vriighydglavrstak   18 (29)
                      |-|+|--||||+|.--|
T Consensus       143 VLILGGGDGLAlREVLK  159 (363)
T PRK01581        143 VLILGGGDGLALREVLK  159 (363)
T ss_pred             EEEEECCCHHHHHHHHC
T ss_conf             89980764399999871


No 4  
>PRK08605 D-lactate dehydrogenase; Validated
Probab=13.96  E-value=38  Score=17.05  Aligned_cols=24  Identities=13%  Similarity=0.425  Sum_probs=18.1

Q ss_pred             EEEEEECCEEEEHHHHHHHHHHHH
Q ss_conf             684510562320057898999997
Q 537021.9.peg.3    3 RIIGHYDGLAVRSTAKVTQSCCRM   26 (29)
Q Consensus         3 riighydglavrstakvtqsccrm   26 (29)
                      .+|.-|||+.+|++.+++..--.-
T Consensus        41 ~~~~~~D~i~v~~~~~i~~~vl~~   64 (332)
T PRK08605         41 EEVEGFDGLSLSQQIPLSEAIYKL   64 (332)
T ss_pred             HHHCCCCEEEEECCCCCCHHHHHH
T ss_conf             985799889997079779999996


No 5  
>TIGR01083 nth endonuclease III; InterPro: IPR005759    The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=13.37  E-value=1e+02  Score=14.97  Aligned_cols=21  Identities=43%  Similarity=0.646  Sum_probs=15.7

Q ss_pred             EEEEEECCEEEEHHHHHHHHHHHHHC
Q ss_conf             68451056232005789899999730
Q 537021.9.peg.3    3 RIIGHYDGLAVRSTAKVTQSCCRMLK   28 (29)
Q Consensus         3 riighydglavrstakvtqsccrmlk   28 (29)
                      +-||-|     |+-||--+++||+|-
T Consensus        75 k~iGlY-----r~KAk~I~~~~~~Lv   95 (192)
T TIGR01083        75 KSIGLY-----RNKAKNIIALCRKLV   95 (192)
T ss_pred             HCCCCC-----HHHHHHHHHHHHHHH
T ss_conf             225864-----568999999999999


No 6  
>KOG2193 consensus
Probab=12.21  E-value=58  Score=16.17  Aligned_cols=14  Identities=43%  Similarity=0.684  Sum_probs=5.3

Q ss_pred             EEHHHHHHHHHHHH
Q ss_conf             20057898999997
Q 537021.9.peg.3   13 VRSTAKVTQSCCRM   26 (29)
Q Consensus        13 vrstakvtqsccrm   26 (29)
                      |.||+.-+.+.|+|
T Consensus       249 vh~tpEg~s~Ac~~  262 (584)
T KOG2193         249 VHSTPEGTSKACKM  262 (584)
T ss_pred             EECCCHHHHHHHHH
T ss_conf             73373236799999


No 7  
>TIGR00088 trmD tRNA (guanine-N1)-methyltransferase; InterPro: IPR002649   In transfer RNA many different modified nucleosides are found, especially in the anticodon region. tRNA (guanine-N1-)-methyltransferase 2.1.1.31 from EC is one of several nucleases operating together with the tRNA-modifying enzymes before the formation of the mature tRNA. It catalyses the reaction:  S-adenosyl-L-methionine + tRNA -> S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine  methylating guanosine(G) to N1-methylguanine (1-methylguanosine (m1G)) at position 37 of tRNAs that read CUN (leucine), CCN(proline), and CGG (arginine) codons. The presence of m1G improves the cellular growth rate and the polypeptide steptime and also prevents the tRNA from shifting the reading frame .   The mechanism of the trmD3-induced frameshift involving mutant tRNA(Pro) and tRNA(Leu) species has been investigated . It has been suggested that the conformation of the anticodon loop may be a major determining element for the formation of m1G37 in vivo . ; GO: 0003723 RNA binding, 0008175 tRNA methyltransferase activity, 0008033 tRNA processing.
Probab=10.48  E-value=64  Score=15.98  Aligned_cols=20  Identities=35%  Similarity=0.559  Sum_probs=14.5

Q ss_pred             EEEEEEECCEEEEHHH-HHHH
Q ss_conf             0684510562320057-8989
Q 537021.9.peg.3    2 VRIIGHYDGLAVRSTA-KVTQ   21 (29)
Q Consensus         2 vriighydglavrsta-kvtq   21 (29)
                      |-|-|||.|.--|... .|++
T Consensus       109 vLiCGrYEG~DeR~~~~~vD~  129 (247)
T TIGR00088       109 VLICGRYEGFDERIIELLVDE  129 (247)
T ss_pred             EEEECCCCCCHHHHHHHHCCE
T ss_conf             899565036026645320786


No 8  
>pfam07272 Orthoreo_P17 Orthoreovirus P17 protein. This family consists of several Orthoreovirus P17 proteins. P17 is specified be ORF2 of the S1 gene and represents a nonstructural protein which associate with cell membranes.
Probab=10.05  E-value=1.6e+02  Score=14.09  Aligned_cols=17  Identities=35%  Similarity=0.587  Sum_probs=13.5

Q ss_pred             EEEEEECCEEEEHHHHH
Q ss_conf             68451056232005789
Q 537021.9.peg.3    3 RIIGHYDGLAVRSTAKV   19 (29)
Q Consensus         3 riighydglavrstakv   19 (29)
                      +++-||||-+---+||-
T Consensus       107 ~vVVH~d~~sQS~aAKR  123 (146)
T pfam07272       107 HVVVHYDGRTQSPAAKR  123 (146)
T ss_pred             EEEEEECCCCCCHHHHH
T ss_conf             69999689766866741


No 9  
>KOG2152 consensus
Probab=9.14  E-value=1e+02  Score=14.98  Aligned_cols=26  Identities=31%  Similarity=0.455  Sum_probs=20.5

Q ss_pred             EEEEEECCEEEEHH--HHHHHHHHHHHC
Q ss_conf             68451056232005--789899999730
Q 537021.9.peg.3    3 RIIGHYDGLAVRST--AKVTQSCCRMLK   28 (29)
Q Consensus         3 riighydglavrst--akvtqsccrmlk   28 (29)
                      +.|.+-+|.++-|.  +|.-|+||.|+.
T Consensus       551 yLis~gs~i~issl~~ak~lq~~~~~v~  578 (865)
T KOG2152         551 YLISLGSGILISSLRTAKALQSICKKVH  578 (865)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             8876178706575888887758999873


No 10 
>COG4689 Adc Acetoacetate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=8.80  E-value=1.3e+02  Score=14.54  Aligned_cols=11  Identities=45%  Similarity=0.866  Sum_probs=8.5

Q ss_pred             CEEEEEEECCE
Q ss_conf             90684510562
Q 537021.9.peg.3    1 MVRIIGHYDGL   11 (29)
Q Consensus         1 mvriighydgl   11 (29)
                      |..||-|+||-
T Consensus       168 llKIIPhvDGt  178 (247)
T COG4689         168 LLKIIPHVDGT  178 (247)
T ss_pred             EEEECCCCCCC
T ss_conf             57752467898


Done!