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!