Query         537021.9.peg.1123_1
Match_columns 48
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Wed May 25 08:39:34 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_1123.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG0401 Uncharacterized homolo  30.9      16  0.0004   18.7   0.3   16   31-46     40-55  (56)
  2 TIGR01966 RNasePH ribonuclease  26.7      45  0.0012   16.6   2.0   41    4-47     68-121 (237)
  3 KOG1773 consensus               20.1      38 0.00096   17.0   0.6   17   31-47     42-58  (63)
  4 pfam09263 PEX-2N Peroxisome bi  16.7      78   0.002   15.5   1.5   23   21-43     58-80  (87)
  5 cd06811 PLPDE_III_yhfX_like Ty  14.6 1.2E+02   0.003   14.7   2.0   28   20-47      7-36  (382)
  6 pfam09173 eIF2_C Initiation fa  11.3      13 0.00032   19.2  -3.8   20   20-39     65-84  (88)
  7 COG0689 Rph RNase PH [Translat   8.3 2.2E+02  0.0057   13.3   3.6   16   32-47    111-126 (230)
  8 TIGR03001 Sig-70_gmx1 RNA poly   8.1 1.7E+02  0.0042   13.9   1.0   13   21-33    193-205 (249)
  9 pfam07347 CI-B14_5a NADH:ubiqu   7.6 2.1E+02  0.0055   13.4   1.3   28    8-35      3-30  (97)
 10 COG5257 GCD11 Translation init   7.5      33 0.00085   17.2  -2.8   19   20-38    388-406 (415)

No 1  
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=30.93  E-value=16  Score=18.73  Aligned_cols=16  Identities=50%  Similarity=0.696  Sum_probs=12.5

Q ss_pred             HHHHHCCEEEEEEEEE
Q ss_conf             5443062022478874
Q 537021.9.peg.1   31 IGQRTGIIHDCYVIEF   46 (48)
Q Consensus        31 igqrtgiihdcyvief   46 (48)
                      .|--.|+||.+|||--
T Consensus        40 Lg~~PGiiHA~yvi~~   55 (56)
T COG0401          40 LGYIPGIIHALYVILR   55 (56)
T ss_pred             HHHHHHHHHHEEEEEE
T ss_conf             9862455761377873


No 2  
>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381   Prokaryotic ribonuclease PH (2.7.7.56 from EC) (RNase PH) is a phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates . There is a similar protein in Caenorhabditis elegans that belongs to this group.   More information about these proteins can be found at Protein of the Month: RNA Exosomes .; GO: 0000049 tRNA binding, 0004549 tRNA-specific ribonuclease activity, 0008033 tRNA processing.
Probab=26.69  E-value=45  Score=16.58  Aligned_cols=41  Identities=39%  Similarity=0.605  Sum_probs=30.6

Q ss_pred             CHHHHHHHHHHHHHCHHHHHHHHHHHHHHH-------------HHCCEEEEEEEEEC
Q ss_conf             267888887676422012216899987544-------------30620224788740
Q 537021.9.peg.1    4 STNELTKNIRNSLLGREKRNRSAISRRIGQ-------------RTGIIHDCYVIEFD   47 (48)
Q Consensus         4 stneltknirnsllgrekrnrsaisrrigq-------------rtgiihdcyviefd   47 (48)
                      ||+  +.+.|.|..|+-.-----|+|-||-             || |.-||=||.=|
T Consensus        68 aT~--~R~~REa~~GK~~GRTqEIQRLIGRaLRavvDl~aLGErT-I~iDCDVlQAD  121 (237)
T TIGR01966        68 ATQ--TRNRREAAKGKQSGRTQEIQRLIGRALRAVVDLEALGERT-IWIDCDVLQAD  121 (237)
T ss_pred             HHC--CCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEE-EEEECCEEECC
T ss_conf             030--3124668617878750567778888988773462348502-79853343388


No 3  
>KOG1773 consensus
Probab=20.14  E-value=38  Score=16.96  Aligned_cols=17  Identities=47%  Similarity=0.811  Sum_probs=13.3

Q ss_pred             HHHHHCCEEEEEEEEEC
Q ss_conf             54430620224788740
Q 537021.9.peg.1   31 IGQRTGIIHDCYVIEFD   47 (48)
Q Consensus        31 igqrtgiihdcyviefd   47 (48)
                      .|--.|+||.||++-|.
T Consensus        42 L~~iPgiIhA~yii~~~   58 (63)
T KOG1773          42 LGFIPGIIHAIYIIFFR   58 (63)
T ss_pred             HHHHHHHHHHEEEEEEE
T ss_conf             99847878547789983


No 4  
>pfam09263 PEX-2N Peroxisome biogenesis factor 1, N-terminal. Members of this family adopt a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation.
Probab=16.68  E-value=78  Score=15.45  Aligned_cols=23  Identities=26%  Similarity=0.411  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHHHHCCEEEEEE
Q ss_conf             22168999875443062022478
Q 537021.9.peg.1   21 KRNRSAISRRIGQRTGIIHDCYV   43 (48)
Q Consensus        21 krnrsaisrrigqrtgiihdcyv   43 (48)
                      ..|.+.|+|.+||+-|+-|.--|
T Consensus        58 ~envaEinrq~gekLGl~dGeQv   80 (87)
T pfam09263        58 GENVAEINRQFAEKLGFSHGDQV   80 (87)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCEE
T ss_conf             62189999998887387756777


No 5  
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX. This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=14.64  E-value=1.2e+02  Score=14.65  Aligned_cols=28  Identities=39%  Similarity=0.521  Sum_probs=20.0

Q ss_pred             HHHHHHHHHH--HHHHHHCCEEEEEEEEEC
Q ss_conf             1221689998--754430620224788740
Q 537021.9.peg.1   20 EKRNRSAISR--RIGQRTGIIHDCYVIEFD   47 (48)
Q Consensus        20 ekrnrsaisr--rigqrtgiihdcyviefd   47 (48)
                      .|||..-|.-  ..-|.--|.-|+|||..|
T Consensus         7 ~krNp~LI~aA~~LhqqG~I~PdtYViDlD   36 (382)
T cd06811           7 LKRNPALIEAALTLHQSGAIPPDTYVIDLD   36 (382)
T ss_pred             HHHCHHHHHHHHHHHHCCCCCCCCEEEEHH
T ss_conf             566989999999999769979886897589


No 6  
>pfam09173 eIF2_C Initiation factor eIF2 gamma, C terminal. Members of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA.
Probab=11.31  E-value=13  Score=19.19  Aligned_cols=20  Identities=40%  Similarity=0.524  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHCCEE
Q ss_conf             12216899987544306202
Q 537021.9.peg.1   20 EKRNRSAISRRIGQRTGIIH   39 (48)
Q Consensus        20 ekrnrsaisrrigqrtgiih   39 (48)
                      ++-.|-||||||+.|--+|-
T Consensus        65 ~~g~rVaiSRrI~~rWRLIG   84 (88)
T pfam09173        65 EIGEKVAISRRVDKRWRLIG   84 (88)
T ss_pred             CCCCEEEEEEEECCEEEEEE
T ss_conf             89999999988688699998


No 7  
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=8.28  E-value=2.2e+02  Score=13.33  Aligned_cols=16  Identities=31%  Similarity=0.374  Sum_probs=13.5

Q ss_pred             HHHHCCEEEEEEEEEC
Q ss_conf             4430620224788740
Q 537021.9.peg.1   32 GQRTGIIHDCYVIEFD   47 (48)
Q Consensus        32 gqrtgiihdcyviefd   47 (48)
                      =-++.|--||+|++.|
T Consensus       111 ~p~~~I~i~~dVlqaD  126 (230)
T COG0689         111 LPESTIDIDCDVLQAD  126 (230)
T ss_pred             CCCCEEEEEEEEEECC
T ss_conf             4763899999999878


No 8  
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=8.09  E-value=1.7e+02  Score=13.91  Aligned_cols=13  Identities=38%  Similarity=0.588  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             2216899987544
Q 537021.9.peg.1   21 KRNRSAISRRIGQ   33 (48)
Q Consensus        21 krnrsaisrrigq   33 (48)
                      .-|||.+||+|-|
T Consensus       193 ~~~~STvsR~~~~  205 (249)
T TIGR03001       193 QVHRSTVSRWVAQ  205 (249)
T ss_pred             CCCCHHHHHHHHH
T ss_conf             5775078999999


No 9  
>pfam07347 CI-B14_5a NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a). This family contains the eukaryotic NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) (EC:1.6.5.3). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane. The main function of the complex is the transport of electrons from NADH to ubiquinone, accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space.
Probab=7.62  E-value=2.1e+02  Score=13.39  Aligned_cols=28  Identities=36%  Similarity=0.515  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHCHHHHHHHHHHHHHHHHH
Q ss_conf             8888767642201221689998754430
Q 537021.9.peg.1    8 LTKNIRNSLLGREKRNRSAISRRIGQRT   35 (48)
Q Consensus         8 ltknirnsllgrekrnrsaisrrigqrt   35 (48)
                      +-.-+||-|+||+..+---...-|..||
T Consensus         3 ~iq~lRnfl~Gr~~k~~lRy~d~is~RT   30 (97)
T pfam07347         3 LLQRLRNFLLGRQHKLALRYADGISKRT   30 (97)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHCCCCC
T ss_conf             8999999971210210000233133356


No 10 
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=7.54  E-value=33  Score=17.21  Aligned_cols=19  Identities=58%  Similarity=0.727  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHCCE
Q ss_conf             1221689998754430620
Q 537021.9.peg.1   20 EKRNRSAISRRIGQRTGII   38 (48)
Q Consensus        20 ekrnrsaisrrigqrtgii   38 (48)
                      |.-.|-||||||+.|--.|
T Consensus       388 e~g~rvaisRri~~rWRLI  406 (415)
T COG5257         388 EIGERVAISRRIGNRWRLI  406 (415)
T ss_pred             CCCCEEEEEEEECCEEEEE
T ss_conf             7787798775101537997


Done!