Query         537021.9.peg.232_1
Match_columns 46
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Wed May 25 16:22:16 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_232.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam06015 Chordopox_A30L Chord  32.0      25 0.00064   18.0   1.5   14    1-14     25-38  (71)
  2 TIGR01258 pgm_1 phosphoglycera  20.8      41   0.001   17.0   0.9   21    9-29    200-220 (248)
  3 TIGR02850 spore_sigG RNA polym  19.5      26 0.00066   17.9  -0.4   25   18-42     71-95  (254)
  4 PRK05087 D-alanine--poly(phosp  17.6 1.1E+02  0.0028   15.0   2.6   37    3-39     38-75  (78)
  5 TIGR02885 spore_sigF RNA polym  13.5      37 0.00095   17.2  -0.8   21   22-42     52-72  (231)
  6 pfam09010 AsiA Anti-Sigma Fact  12.9 1.4E+02  0.0035   14.6   1.9   32    1-32      1-32  (91)
  7 TIGR03215 ac_ald_DH_ac acetald  12.8      38 0.00097   17.2  -0.9   24   21-45     87-110 (285)
  8 PRK08300 acetaldehyde dehydrog  12.6      35  0.0009   17.3  -1.1   23   22-45     94-116 (298)
  9 COG4569 MhpF Acetaldehyde dehy  11.3      63  0.0016   16.2  -0.2   26   19-45     92-117 (310)
 10 pfam06972 DUF1296 Protein of u  10.6 1.8E+02  0.0047   14.0   2.8   36    3-38      7-43  (60)

No 1  
>pfam06015 Chordopox_A30L Chordopoxvirus A30L protein. This family consists of several short Chordopoxvirus proteins which are homologous to the A30L protein of Vaccinia virus. The vaccinia virus A30L protein is required for the association of electron-dense, granular, proteinaceous material with the concave surfaces of crescent membranes, an early step in viral morphogenesis. A30L is known to interact with the G7L protein and it has been shown that the stability of each is dependent on its association with the other.
Probab=32.05  E-value=25  Score=18.00  Aligned_cols=14  Identities=57%  Similarity=0.672  Sum_probs=12.0

Q ss_pred             CCHHHHHHHHHHHC
Q ss_conf             91399999999714
Q 537021.9.peg.2    1 MAATIQLVKEIISL   14 (46)
Q Consensus         1 maatiqlvkeiisl   14 (46)
                      .+||+-+|+|+||.
T Consensus        25 fsaTls~vkElIs~   38 (71)
T pfam06015        25 FAATLSTVKELISQ   38 (71)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             89999999999999


No 2  
>TIGR01258 pgm_1 phosphoglycerate mutase 1 family; InterPro: IPR005952    Most members of this family are phosphoglycerate mutase (5.4.2.1 from EC). This enzyme interconverts 2-phosphoglycerate and 3-phosphoglycerate.  2-phospho-D-glycerate + 2,3-diphosphoglycerate = 3-phospho-D-glycerate + 2,3-diphosphoglycerate. The enzyme is transiently phosphorylated on an active site histidine by 2,3-diphosphoglyerate, which is both substrate and product. Some members of this family have are phosphoglycerate mutase as a minor activity and act primarily as a bisphoglycerate mutase, interconverting 2,3-diphosphoglycerate and 1,3-diphosphoglycerate (5.4.2.4 from EC). ; GO: 0016868 intramolecular transferase activity phosphotransferases, 0006096 glycolysis.
Probab=20.82  E-value=41  Score=17.02  Aligned_cols=21  Identities=43%  Similarity=0.684  Sum_probs=17.8

Q ss_pred             HHHHHCCCCHHHCCHHHHCCC
Q ss_conf             999714561544063440577
Q 537021.9.peg.2    9 KEIISLNIPRAIANIDEIDMN   29 (46)
Q Consensus         9 keiislnipraianideidmn   29 (46)
                      ++|..||||.+|-=+=|.|-+
T Consensus       200 ~~Il~LNIPTGiPLvyeLd~~  220 (248)
T TIGR01258       200 EEILELNIPTGIPLVYELDEE  220 (248)
T ss_pred             HHHHHCCCCCCCCHHHHCCCC
T ss_conf             688504598755334100013


No 3  
>TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212   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 , .    Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=19.54  E-value=26  Score=17.94  Aligned_cols=25  Identities=36%  Similarity=0.705  Sum_probs=20.9

Q ss_pred             HHHCCHHHHCCCHHHHHHHHHHEEE
Q ss_conf             5440634405777786665420102
Q 537021.9.peg.2   18 RAIANIDEIDMNPKQKISKYVIPMV   42 (46)
Q Consensus        18 raianideidmnpkqkiskyvipmv   42 (46)
                      .-+..||..|+...-|.|.|.+||+
T Consensus        71 Gl~k~idnfdl~~nv~fstyavPmi   95 (254)
T TIGR02850        71 GLIKSIDNFDLSQNVKFSTYAVPMI   95 (254)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             7777655310111320011346678


No 4  
>PRK05087 D-alanine--poly(phosphoribitol) ligase subunit 2; Validated
Probab=17.62  E-value=1.1e+02  Score=15.00  Aligned_cols=37  Identities=32%  Similarity=0.399  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHH-CCCCHHHCCHHHHCCCHHHHHHHHHH
Q ss_conf             39999999971-45615440634405777786665420
Q 537021.9.peg.2    3 ATIQLVKEIIS-LNIPRAIANIDEIDMNPKQKISKYVI   39 (46)
Q Consensus         3 atiqlvkeiis-lnipraianideidmnpkqkiskyvi   39 (46)
                      +|+||.-++-+ ++|.-.+...+.-++|.-.||-.+|-
T Consensus        38 ~tVeLLveie~~fgI~vpvsEf~R~~w~TpnkIi~~v~   75 (78)
T PRK05087         38 GTVELLVELESRFDIEVPISEFDRDDWNTPNKIVAKVE   75 (78)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999999809856813633986148999999998


No 5  
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   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 , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=13.52  E-value=37  Score=17.21  Aligned_cols=21  Identities=38%  Similarity=0.752  Sum_probs=17.5

Q ss_pred             CHHHHCCCHHHHHHHHHHEEE
Q ss_conf             634405777786665420102
Q 537021.9.peg.2   22 NIDEIDMNPKQKISKYVIPMV   42 (46)
Q Consensus        22 nideidmnpkqkiskyvipmv   42 (46)
                      -||..|.+-.-|.|.|-.||.
T Consensus        52 AidkFD~~y~VKFSTYAVPmI   72 (231)
T TIGR02885        52 AIDKFDLSYDVKFSTYAVPMI   72 (231)
T ss_pred             HHHHCCCCCCEEEEECCCCHH
T ss_conf             554217677701552122202


No 6  
>pfam09010 AsiA Anti-Sigma Factor A. Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements.
Probab=12.92  E-value=1.4e+02  Score=14.60  Aligned_cols=32  Identities=25%  Similarity=0.264  Sum_probs=16.8

Q ss_pred             CCHHHHHHHHHHHCCCCHHHCCHHHHCCCHHH
Q ss_conf             91399999999714561544063440577778
Q 537021.9.peg.2    1 MAATIQLVKEIISLNIPRAIANIDEIDMNPKQ   32 (46)
Q Consensus         1 maatiqlvkeiislnipraianideidmnpkq   32 (46)
                      |.+++.+|+||++.-------..|+|-+|.+-
T Consensus         1 Mn~~~E~i~eIia~aSlLIK~~~edI~~~q~~   32 (91)
T pfam09010         1 MNKNIELIKDIIATASLLIKFGREDIVENQAN   32 (91)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf             97329999999999999998269999871999


No 7  
>TIGR03215 ac_ald_DH_ac acetaldehyde dehydrogenase (acetylating). Members of this protein family are acetaldehyde dehydrogenase (acetylating), EC 1.2.1.10. This enzyme oxidizes acetaldehyde, using NAD(+), and attaches coenzyme A (CoA), yielding acetyl-CoA. It occurs as a late step in the meta-cleavage pathways of a variety of compounds, including catechol, biphenyl, toluene, salicylate, etc.
Probab=12.83  E-value=38  Score=17.17  Aligned_cols=24  Identities=42%  Similarity=0.675  Sum_probs=16.3

Q ss_pred             CCHHHHCCCHHHHHHHHHHEEEECC
Q ss_conf             0634405777786665420102117
Q 537021.9.peg.2   21 ANIDEIDMNPKQKISKYVIPMVNLN   45 (46)
Q Consensus        21 anideidmnpkqkiskyvipmvnln   45 (46)
                      +.+--||+.|- ++..|++|-|||.
T Consensus        87 ~g~~~IDLTPA-aiGp~~VP~VNl~  110 (285)
T TIGR03215        87 LGKIVIDLTPA-AIGPYVVPAVNLD  110 (285)
T ss_pred             CCCEEEECCCC-CCCCEEECCCCHH
T ss_conf             59979978810-1597545553878


No 8  
>PRK08300 acetaldehyde dehydrogenase; Validated
Probab=12.58  E-value=35  Score=17.30  Aligned_cols=23  Identities=39%  Similarity=0.798  Sum_probs=15.4

Q ss_pred             CHHHHCCCHHHHHHHHHHEEEECC
Q ss_conf             634405777786665420102117
Q 537021.9.peg.2   22 NIDEIDMNPKQKISKYVIPMVNLN   45 (46)
Q Consensus        22 nideidmnpkqkiskyvipmvnln   45 (46)
                      .+--||+.|- +|..|++|-|||.
T Consensus        94 g~~~IDLTPA-aiGp~~VP~VNl~  116 (298)
T PRK08300         94 GVRVIDLTPA-AIGPYCVPAVNLD  116 (298)
T ss_pred             CCEEEECCCC-CCCCEEECCCCHH
T ss_conf             9879967700-2698787637789


No 9  
>COG4569 MhpF Acetaldehyde dehydrogenase (acetylating) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=11.31  E-value=63  Score=16.15  Aligned_cols=26  Identities=50%  Similarity=0.790  Sum_probs=18.7

Q ss_pred             HHCCHHHHCCCHHHHHHHHHHEEEECC
Q ss_conf             440634405777786665420102117
Q 537021.9.peg.2   19 AIANIDEIDMNPKQKISKYVIPMVNLN   45 (46)
Q Consensus        19 aianideidmnpkqkiskyvipmvnln   45 (46)
                      |-+.|.-||..|. .|..||+|.+|+.
T Consensus        92 ae~gi~~idltpa-aigp~vvp~~n~~  117 (310)
T COG4569          92 AEAGIRLIDLTPA-AIGPYVVPVVNLE  117 (310)
T ss_pred             HHCCCCEEECCHH-CCCCEECCCCCHH
T ss_conf             8649842305600-0487212654657


No 10 
>pfam06972 DUF1296 Protein of unknown function (DUF1296). This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=10.58  E-value=1.8e+02  Score=13.98  Aligned_cols=36  Identities=28%  Similarity=0.484  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHCCC-CHHHCCHHHHCCCHHHHHHHHH
Q ss_conf             39999999971456-1544063440577778666542
Q 537021.9.peg.2    3 ATIQLVKEIISLNI-PRAIANIDEIDMNPKQKISKYV   38 (46)
Q Consensus         3 atiqlvkeiislni-praianideidmnpkqkiskyv   38 (46)
                      .+||-.|||..-+- ..-.|-.-|-.|+|.....+..
T Consensus         7 k~iQ~iKEiv~~hSd~eIYa~L~ecnMDPnEtvqkLL   43 (60)
T pfam06972         7 KTIQSIKEVVGKHSDADIYAMLKECNMDPNETVQKLL   43 (60)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999998489789999999996798679999988


Done!