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!