Query         537021.9.peg.993_1
Match_columns 52
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Wed May 25 04:47:54 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_993.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG2718 Uncharacterized conser  14.3 1.3E+02  0.0033   14.5   2.2   31    3-34    304-334 (423)
  2 pfam09054 consensus             13.6      41  0.0011   16.8  -0.5   27   21-47      2-28  (46)
  3 KOG4819 consensus               11.6      91  0.0023   15.2   0.7   19    8-26     83-101 (106)
  4 cd04877 ACT_TyrR N-terminal AC  10.3 1.8E+02  0.0047   13.8   2.2   25    8-32     35-65  (74)
  5 TIGR02062 RNase_B exoribonucle   8.7      42  0.0011   16.8  -1.9   37    4-40    624-662 (664)
  6 cd04896 ACT_ACR-like_3 ACT dom   7.6 1.8E+02  0.0046   13.9   1.0   19    2-20     44-62  (75)
  7 TIGR02863 spore_sspJ small, ac   6.6 1.7E+02  0.0042   14.0   0.4   17    1-17      1-17  (47)
  8 KOG1680 consensus                6.5 2.4E+02  0.0061   13.3   1.1   11   39-49     45-55  (290)
  9 pfam10805 DUF2730 Protein of u   6.1 2.3E+02  0.0058   13.4   0.8   14   14-27     91-104 (106)
 10 PHA00738 putative HTH transcri   5.7      84  0.0022   15.4  -1.6   25    2-26      3-27  (112)

No 1  
>COG2718 Uncharacterized conserved protein [Function unknown]
Probab=14.31  E-value=1.3e+02  Score=14.53  Aligned_cols=31  Identities=39%  Similarity=0.728  Sum_probs=24.3

Q ss_pred             EEEECCCCEEEECHHHHHHHHHHHHHEEEEHH
Q ss_conf             23312342389815799998612332231264
Q 537021.9.peg.9    3 YFFNQTKGKIIINDQLQLLMENIIKIRYVTQE   34 (52)
Q Consensus         3 yffnqtkgkiiindqlqllmeniikiryvtqe   34 (52)
                      +|..|..|--|+..-|. +|++||+-||-..|
T Consensus       304 FF~~~esGGTivSSAl~-~m~evi~ErYp~ae  334 (423)
T COG2718         304 FFYSQESGGTIVSSALK-LMLEVIKERYPPAE  334 (423)
T ss_pred             CEEECCCCCEEEHHHHH-HHHHHHHHHCCHHH
T ss_conf             02324789768688999-99999970388535


No 2  
>pfam09054 consensus
Probab=13.62  E-value=41  Score=16.81  Aligned_cols=27  Identities=26%  Similarity=0.469  Sum_probs=21.4

Q ss_pred             HHHHHHHHEEEEHHHHHHHCEEEEEEE
Q ss_conf             986123322312643411246557643
Q 537021.9.peg.9   21 LMENIIKIRYVTQEARSLLGITLIKIN   47 (52)
Q Consensus        21 lmeniikiryvtqearsllgitlikin   47 (52)
                      |++|+|-.||+-.+.+---+|..+|--
T Consensus         2 L~D~iilLr~~E~~g~l~R~i~VlK~R   28 (46)
T pfam09054         2 LADNVILLRYVELNGELRRALSVLKKR   28 (46)
T ss_pred             CEEEEEEEEEEEECCEEEEEEEEEEEC
T ss_conf             355799898752298999889999932


No 3  
>KOG4819 consensus
Probab=11.56  E-value=91  Score=15.24  Aligned_cols=19  Identities=47%  Similarity=0.707  Sum_probs=15.6

Q ss_pred             CCCEEEECHHHHHHHHHHH
Q ss_conf             3423898157999986123
Q 537021.9.peg.9    8 TKGKIIINDQLQLLMENII   26 (52)
Q Consensus         8 tkgkiiindqlqllmenii   26 (52)
                      -||.--.|||.++|.+-|-
T Consensus        83 kKGQPnln~qM~~LL~~Iq  101 (106)
T KOG4819          83 KKGQPNLNDQMQLLLKQIQ  101 (106)
T ss_pred             CCCCCCHHHHHHHHHHHHH
T ss_conf             2589867789999999999


No 4  
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence 
Probab=10.35  E-value=1.8e+02  Score=13.84  Aligned_cols=25  Identities=40%  Similarity=0.550  Sum_probs=18.2

Q ss_pred             CCCEEEE------CHHHHHHHHHHHHHEEEE
Q ss_conf             3423898------157999986123322312
Q 537021.9.peg.9    8 TKGKIII------NDQLQLLMENIIKIRYVT   32 (52)
Q Consensus         8 tkgkiii------ndqlqllmeniikiryvt   32 (52)
                      .+|+|-+      .+++|-||..|-+|.-|+
T Consensus        35 ~~g~IYl~~~~l~f~~~~~Lm~~ir~I~GV~   65 (74)
T cd04877          35 PKGRIYLNFPTIEFEKLQTLMPEIRRIDGVE   65 (74)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             6881899778789899999999984789831


No 5  
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804    This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=8.69  E-value=42  Score=16.78  Aligned_cols=37  Identities=24%  Similarity=0.487  Sum_probs=23.3

Q ss_pred             EEECCCCEEEECHHHHHHHHHHHH--HEEEEHHHHHHHC
Q ss_conf             331234238981579999861233--2231264341124
Q 537021.9.peg.9    4 FFNQTKGKIIINDQLQLLMENIIK--IRYVTQEARSLLG   40 (52)
Q Consensus         4 ffnqtkgkiiindqlqllmeniik--iryvtqearsllg   40 (52)
                      -|||-.|++.|...+-.-...+|+  +-=|-++.||+.|
T Consensus       624 ~~n~e~G~v~Ikge~~YKi~D~~~v~LtEv~~~tRSiva  662 (664)
T TIGR02062       624 VCNQEEGTVYIKGEVVYKIGDVIEVVLTEVREETRSIVA  662 (664)
T ss_pred             EEECCCCEEEEEEEEEEEEEEEEEEEEEEEECCCCCEEC
T ss_conf             650687638871078986610699998454013450112


No 6  
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=7.62  E-value=1.8e+02  Score=13.88  Aligned_cols=19  Identities=32%  Similarity=0.471  Sum_probs=15.1

Q ss_pred             CEEEECCCCEEEECHHHHH
Q ss_conf             4233123423898157999
Q 537021.9.peg.9    2 AYFFNQTKGKIIINDQLQL   20 (52)
Q Consensus         2 ayffnqtkgkiiindqlql   20 (52)
                      ..|+-|++||-|++.+-|-
T Consensus        44 dLFv~q~dGkKi~Dp~~q~   62 (75)
T cd04896          44 DLFIVQSDGKKIMDPKKQA   62 (75)
T ss_pred             EEEEECCCCCCCCCHHHHH
T ss_conf             8999727988636989999


No 7  
>TIGR02863 spore_sspJ small, acid-soluble spore protein, SspJ family; InterPro: IPR014220   This entry represents a group of small acid-soluble proteins (SASP) from Bacillus sp., which are present in spores but not in growing cells. The sspJ gene is transcribed in the forespore compartment by RNA polymerase with the forespore-specific sigmaG. Loss of SspJ causes a slight decrease in the rate of spore outgrowth in an otherwise wild-type background ..
Probab=6.56  E-value=1.7e+02  Score=14.04  Aligned_cols=17  Identities=41%  Similarity=0.682  Sum_probs=11.8

Q ss_pred             CCEEEECCCCEEEECHH
Q ss_conf             94233123423898157
Q 537021.9.peg.9    1 MAYFFNQTKGKIIINDQ   17 (52)
Q Consensus         1 mayffnqtkgkiiindq   17 (52)
                      |..|||..+|+---.++
T Consensus         1 mG~ffnkd~G~~~ek~~   17 (47)
T TIGR02863         1 MGIFFNKDKGKKSEKEK   17 (47)
T ss_pred             CCCCCCCCCCCCHHHHH
T ss_conf             97545544454002457


No 8  
>KOG1680 consensus
Probab=6.49  E-value=2.4e+02  Score=13.33  Aligned_cols=11  Identities=55%  Similarity=0.767  Sum_probs=7.7

Q ss_pred             HCEEEEEEEEE
Q ss_conf             24655764311
Q 537021.9.peg.9   39 LGITLIKINRL   49 (52)
Q Consensus        39 lgitlikinrl   49 (52)
                      -||++|.|||-
T Consensus        45 ~~I~lItlNRP   55 (290)
T KOG1680          45 NGIALITLNRP   55 (290)
T ss_pred             CCEEEEEECCH
T ss_conf             87689983786


No 9  
>pfam10805 DUF2730 Protein of unknown function (DUF2730). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=6.14  E-value=2.3e+02  Score=13.43  Aligned_cols=14  Identities=57%  Similarity=0.838  Sum_probs=8.5

Q ss_pred             ECHHHHHHHHHHHH
Q ss_conf             81579999861233
Q 537021.9.peg.9   14 INDQLQLLMENIIK   27 (52)
Q Consensus        14 indqlqllmeniik   27 (52)
                      ++.|.+||.||-+|
T Consensus        91 i~hq~~LLLE~~lk  104 (106)
T pfam10805        91 ISHQLELLLENELK  104 (106)
T ss_pred             HHHHHHHHHHHHHC
T ss_conf             88899999999864


No 10 
>PHA00738 putative HTH transcription regulator
Probab=5.65  E-value=84  Score=15.40  Aligned_cols=25  Identities=36%  Similarity=0.530  Sum_probs=20.1

Q ss_pred             CEEEECCCCEEEECHHHHHHHHHHH
Q ss_conf             4233123423898157999986123
Q 537021.9.peg.9    2 AYFFNQTKGKIIINDQLQLLMENII   26 (52)
Q Consensus         2 ayffnqtkgkiiindqlqllmenii   26 (52)
                      .|--|.-++||.-..-|||+.||-+
T Consensus         3 ~ynaN~iraki~RrKIl~LiaENY~   27 (112)
T PHA00738          3 DYNANEIRAKILRKKILELIAENYI   27 (112)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4118899999999999999999889


Done!