Query 537021.9.peg.363_1 Match_columns 79 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Tue May 24 19:57:47 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_363.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01258 pgm_1 phosphoglycera 66.8 0.75 1.9E-05 24.8 -1.6 39 2-40 185-223 (248) 2 TIGR00845 caca sodium/calcium 30.7 25 0.00064 17.4 1.3 43 37-79 534-580 (1067) 3 TIGR02885 spore_sigF RNA polym 26.0 19 0.00049 17.9 0.0 26 54-79 47-72 (231) 4 cd04182 GT_2_like_f GT_2_like_ 20.0 15 0.00039 18.4 -1.4 35 33-67 152-186 (186) 5 COG2088 SpoVG Uncharacterized 18.3 33 0.00085 16.7 -0.0 35 38-76 42-76 (95) 6 TIGR01348 PDHac_trf_long pyruv 14.1 56 0.0014 15.7 0.2 12 25-36 440-451 (655) 7 TIGR02980 SigBFG RNA polymeras 13.3 61 0.0015 15.5 0.2 28 52-79 38-65 (229) 8 COG1274 PckA Phosphoenolpyruva 13.3 78 0.002 14.9 0.8 29 22-50 421-453 (608) 9 TIGR01661 ELAV_HUD_SF ELAV/HuD 12.5 96 0.0025 14.5 1.0 22 2-27 76-97 (436) 10 KOG2965 consensus 9.0 1.2E+02 0.003 14.1 0.5 14 58-71 138-151 (318) No 1 >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=66.81 E-value=0.75 Score=24.77 Aligned_cols=39 Identities=26% Similarity=0.291 Sum_probs=25.2 Q ss_pred CCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEECCCEEE Q ss_conf 742364735568663025861587312102330341333 Q 537021.9.peg.3 2 NSLRGIRPSNLSPTSTTTVSFSRPTTIPLVTQFSARSFL 40 (79) Q Consensus 2 nslrgirpsnlsptstttvsfsrpttiplvtqfsarsfl 40 (79) ||||++---=-.--...-+.+.-||-||||-.|...--. T Consensus 185 NSLRALvKhL~~~Sd~~Il~LNIPTGiPLvyeLd~~l~p 223 (248) T TIGR01258 185 NSLRALVKHLEGISDEEILELNIPTGIPLVYELDEELKP 223 (248) T ss_pred HHHHHHHHHHHCCCHHHHHHCCCCCCCCHHHHCCCCCCE T ss_conf 048999998612794688504598755334100013772 No 2 >TIGR00845 caca sodium/calcium exchanger 1; InterPro: IPR004836 Na^+/Ca^2+ exchange proteins are involved in maintaining Ca^2+ homeostasis in a wide variety of cell types. They are found in both the plasma membrane and intracellular organellar membranes, where they exchange Na^+ for Ca^2+ in an electrogenic manner. When located in the plasma membrane, they generally utilise the transmembrane (TM) Na^+ concentration gradient in order to extrude Ca^2+ from cells. Three mammalian isoforms have been cloned to date (NCX1-3), which consist of 920-970 amino acid residues that are predicted to possess 11 or 12 TM domains. Interestingly, they possess a short motif (~30 residues) that is similar to the Na^+/K^+-ATPase, although its function is unknown , . NCX1 has been found to be predominantly expressed in the heart, where it plays an important role in excitation-contraction coupling, but it is also abundant in a variety of other tissues . NCX2 and NCX3 transcripts have been detected in the brain and skeletal muscle , . Homologous Na^+/Ca^2+ exchange proteins have also been found in Caenorhabditis elegans, Drosophila melanogaster and Loligo opalescens (California market squid). ; GO: 0005432 calcium:sodium antiporter activity, 0006816 calcium ion transport, 0016020 membrane. Probab=30.68 E-value=25 Score=17.36 Aligned_cols=43 Identities=28% Similarity=0.495 Sum_probs=36.9 Q ss_pred CEEEEEECCCHHH-HHHCCCCHHHCCCCC---HHHHCCCCCCCCCCC Q ss_conf 1333432010221-110024001057862---232018620046459 Q 537021.9.peg.3 37 RSFLVKLSSRRVA-KSSRDGLVKDINTPD---KQQTKNPITSSVPII 79 (79) Q Consensus 37 rsflvklssrrva-kssrdglvkdintpd---kqqtknpitssvpii 79 (79) -.|+|+|+.-||. ..+.||+..+...-. +.|-.+|.+..|-|+ T Consensus 534 EhFy~RL~N~rv~~e~~~~G~~~~~~~~~~LP~a~L~~P~~ATv~IL 580 (1067) T TIGR00845 534 EHFYVRLSNLRVGSEQDEDGILEANTASAGLPVAQLASPLLATVMIL 580 (1067) T ss_pred CCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCEEEEEEE T ss_conf 33035552453256643367525665555788677479854688887 No 3 >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=25.96 E-value=19 Score=17.90 Aligned_cols=26 Identities=38% Similarity=0.378 Sum_probs=19.4 Q ss_pred CCCHHHCCCCCHHHHCCCCCCCCCCC Q ss_conf 24001057862232018620046459 Q 537021.9.peg.3 54 DGLVKDINTPDKQQTKNPITSSVPII 79 (79) Q Consensus 54 dglvkdintpdkqqtknpitssvpii 79 (79) =||||-||-=|..+.-.==|-.||+| T Consensus 47 iGLvKAidkFD~~y~VKFSTYAVPmI 72 (231) T TIGR02885 47 IGLVKAIDKFDLSYDVKFSTYAVPMI 72 (231) T ss_pred HHHHHHHHHCCCCCCEEEEECCCCHH T ss_conf 55666554217677701552122202 No 4 >cd04182 GT_2_like_f GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. Probab=20.00 E-value=15 Score=18.38 Aligned_cols=35 Identities=31% Similarity=0.458 Sum_probs=19.8 Q ss_pred EECCCEEEEEECCCHHHHHHCCCCHHHCCCCCHHH Q ss_conf 30341333432010221110024001057862232 Q 537021.9.peg.3 33 QFSARSFLVKLSSRRVAKSSRDGLVKDINTPDKQQ 67 (79) Q Consensus 33 qfsarsflvklssrrvakssrdglvkdintpdkqq 67 (79) ...+|+++-+.....+-.....+...|||||+.-| T Consensus 152 d~G~r~~l~~~~~~~~~~~~~~~~~~didTpeDl~ 186 (186) T cd04182 152 DKGARSLLRAHPDRVVVEVDDPGVLIDIDTPEDLR 186 (186) T ss_pred CCCHHHHHHHCCCCEEEECCCCCCCCCCCCHHHCC T ss_conf 70379999869886899639988266898958809 No 5 >COG2088 SpoVG Uncharacterized protein, involved in the regulation of septum location [Cell envelope biogenesis, outer membrane] Probab=18.26 E-value=33 Score=16.75 Aligned_cols=35 Identities=34% Similarity=0.595 Sum_probs=27.5 Q ss_pred EEEEEECCCHHHHHHCCCCHHHCCCCCHHHHCCCCCCCC Q ss_conf 333432010221110024001057862232018620046 Q 537021.9.peg.3 38 SFLVKLSSRRVAKSSRDGLVKDINTPDKQQTKNPITSSV 76 (79) Q Consensus 38 sflvklssrrvakssrdglvkdintpdkqqtknpitssv 76 (79) ...|...||| .+||-.+||-.|-.+++.+-|..+| T Consensus 42 GlfVAMPSrr----t~dgEFrDI~HPI~~~~R~kIq~aV 76 (95) T COG2088 42 GLFVAMPSRR----TPDGEFRDIAHPINSDTREKIQDAV 76 (95) T ss_pred CEEEECCCCC----CCCCCHHHCCCCCCHHHHHHHHHHH T ss_conf 2599866765----8996310212757988999999999 No 6 >TIGR01348 PDHac_trf_long pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006256 This group of sequences are a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and percent identity (UPGMA) trees. Members contain two or three copies of the lipoyl-binding domain. Escherichia coli AceF is included in this set while mitochondrial and some other bacterial forms are excluded. dihydrolipoyllysine-residue acetyltransferase E2 component of pyruvate dehydrogenase complex; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006096 glycolysis, 0045254 pyruvate dehydrogenase complex. Probab=14.14 E-value=56 Score=15.67 Aligned_cols=12 Identities=42% Similarity=0.509 Sum_probs=9.0 Q ss_pred CCCCCEEEEECC Q ss_conf 731210233034 Q 537021.9.peg.3 25 PTTIPLVTQFSA 36 (79) Q Consensus 25 pttiplvtqfsa 36 (79) =++||.||||.- T Consensus 440 W~~iPhVT~FDk 451 (655) T TIGR01348 440 WVMIPHVTHFDK 451 (655) T ss_pred CCCCCCCCCCCC T ss_conf 534782102681 No 7 >TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 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 group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=13.35 E-value=61 Score=15.49 Aligned_cols=28 Identities=36% Similarity=0.318 Sum_probs=22.4 Q ss_pred HCCCCHHHCCCCCHHHHCCCCCCCCCCC Q ss_conf 0024001057862232018620046459 Q 537021.9.peg.3 52 SRDGLVKDINTPDKQQTKNPITSSVPII 79 (79) Q Consensus 52 srdglvkdintpdkqqtknpitssvpii 79 (79) .+=||+|-|+-=|-.+-+.=.|-.||.| T Consensus 38 G~iGL~kAidrFD~~~g~~F~tyAVPtI 65 (229) T TIGR02980 38 GTIGLVKAIDRFDPSYGVKFSTYAVPTI 65 (229) T ss_pred HHHHHHHHHHHHCHHCCCCCCCCCCCCE T ss_conf 8888887775301111698664104602 No 8 >COG1274 PckA Phosphoenolpyruvate carboxykinase (GTP) [Energy production and conversion] Probab=13.27 E-value=78 Score=14.94 Aligned_cols=29 Identities=38% Similarity=0.518 Sum_probs=15.9 Q ss_pred ECCCCCCCEEEEECCCE---EE-EEECCCHHHH Q ss_conf 15873121023303413---33-4320102211 Q 537021.9.peg.3 22 FSRPTTIPLVTQFSARS---FL-VKLSSRRVAK 50 (79) Q Consensus 22 fsrpttiplvtqfsars---fl-vklssrrvak 50 (79) --|++|+|||+|--.-. |+ .-++|.+.|. T Consensus 421 gRr~~TvPlV~EA~~W~HGV~mGA~m~Se~TAA 453 (608) T COG1274 421 GRRPTTVPLVTEAFDWEHGVFMGATMGSETTAA 453 (608) T ss_pred CCCCCCCCCEEEECCCCCCEEEEECCCCCHHHH T ss_conf 767765672456035555526640324313445 No 9 >TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor; InterPro: IPR006548 These sequences represent the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human . ELAV stands for the Drosophila Embryonic lethal abnormalvisual protein . ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (IPR006546 from INTERPRO). ; GO: 0003723 RNA binding. Probab=12.47 E-value=96 Score=14.51 Aligned_cols=22 Identities=50% Similarity=0.838 Sum_probs=14.9 Q ss_pred CCCCCCCCCCCCCCCEEEEEECCCCC Q ss_conf 74236473556866302586158731 Q 537021.9.peg.3 2 NSLRGIRPSNLSPTSTTTVSFSRPTT 27 (79) Q Consensus 2 nslrgirpsnlsptstttvsfsrptt 27 (79) |+|-|.|--| -|--|||.||-- T Consensus 76 n~LNGLRLQn----KTIKVSyARPSs 97 (436) T TIGR01661 76 NSLNGLRLQN----KTIKVSYARPSS 97 (436) T ss_pred HHHCCCCCCC----CEEEEEECCCCH T ss_conf 8732300013----605776305881 No 10 >KOG2965 consensus Probab=8.97 E-value=1.2e+02 Score=14.07 Aligned_cols=14 Identities=50% Similarity=0.688 Sum_probs=11.2 Q ss_pred HHCCCCCHHHHCCC Q ss_conf 10578622320186 Q 537021.9.peg.3 58 KDINTPDKQQTKNP 71 (79) Q Consensus 58 kdintpdkqqtknp 71 (79) .||||||...++|- T Consensus 138 aDinTp~ts~SgNL 151 (318) T KOG2965 138 ADINTPDTSPSGNL 151 (318) T ss_pred CCCCCCCCCCCCCC T ss_conf 65689888998872 Done!