Query 537021.9.peg.1080_1 Match_columns 110 No_of_seqs 50 out of 52 Neff 3.6 Searched_HMMs 39220 Date Wed May 25 08:31:38 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_1080.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam03237 Terminase_6 Terminas 92.8 0.22 5.5E-06 29.7 4.6 47 1-58 3-49 (380) 2 COG3892 Uncharacterized protei 79.6 1.3 3.3E-05 25.1 2.1 21 9-30 186-206 (310) 3 pfam09863 DUF2090 Uncharacteri 75.8 2 5E-05 24.1 2.2 25 6-31 190-214 (310) 4 PRK13775 formimidoylglutamase; 65.0 1.6 4.2E-05 24.6 -0.2 41 25-65 10-58 (328) 5 KOG2199 consensus 64.8 2.1 5.3E-05 23.9 0.3 29 20-52 243-271 (462) 6 COG3411 Ferredoxin [Energy pro 55.7 11 0.00028 19.7 2.7 35 36-70 24-59 (64) 7 TIGR01290 nifB nitrogenase cof 55.4 4.1 0.0001 22.2 0.5 12 23-34 152-164 (461) 8 TIGR02713 allophanate_hyd allo 46.0 6.2 0.00016 21.2 0.1 38 56-104 79-118 (582) 9 TIGR03435 Soli_TIGR03435 Solib 37.1 17 0.00042 18.7 1.2 40 18-60 50-89 (237) 10 pfam10244 MRP-L51 Mitochondria 26.7 25 0.00064 17.6 0.7 35 54-88 13-48 (94) 11 KOG0033 consensus 23.7 37 0.00095 16.6 1.1 45 25-69 181-238 (355) 12 pfam00910 RNA_helicase RNA hel 22.4 74 0.0019 14.9 2.5 36 4-41 7-56 (105) 13 TIGR02812 fadR_gamma fatty aci 22.2 43 0.0011 16.3 1.2 14 43-56 41-54 (275) 14 PRK10528 multifunctional acyl- 20.2 42 0.0011 16.3 0.8 25 32-56 39-63 (191) 15 TIGR00441 gmhA phosphoheptose 20.1 61 0.0016 15.3 1.6 23 7-36 48-70 (186) No 1 >pfam03237 Terminase_6 Terminase-like family. This family represents a group of terminase proteins. Probab=92.76 E-value=0.22 Score=29.67 Aligned_cols=47 Identities=28% Similarity=0.242 Sum_probs=36.5 Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEECCCCEEEEECCCCHHHHHHHHHHHC Q ss_conf 9521021247889999998638998501754555772799941453257876566650 Q 537021.9.peg.1 1 MAGNQLGKTLAGAAEAAMHLSGCYPSWWRGYRFLQPIVMVAGSVTYELTRDGIQRLLL 58 (110) Q Consensus 1 mAgNr~GKT~~ga~E~A~HlTG~YP~WW~G~RF~~Pi~aWa~g~t~E~tRDivQ~~Ll 58 (110) |+|.|.|||++.+.++.+|+...-+. ..+..+.|..+.|++..+.+. T Consensus 3 ~ggr~~GKT~~~~~~~~~~a~~~~~~-----------~~~i~~~t~~~~~~~~~~~~~ 49 (380) T pfam03237 3 LGSRQSGKTFAFAREALRHALGNGPK-----------NQIILSASKAQARLEFKKGII 49 (380) T ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCC-----------CEEEEECCHHHHHHHHHHHHH T ss_conf 26452528399999999999858997-----------289997999999999999999 No 2 >COG3892 Uncharacterized protein conserved in bacteria [Function unknown] Probab=79.63 E-value=1.3 Score=25.13 Aligned_cols=21 Identities=43% Similarity=0.953 Sum_probs=14.8 Q ss_pred HHHHHHHHHHHHHCCCCCCCCC Q ss_conf 4788999999863899850175 Q 537021.9.peg.1 9 TLAGAAEAAMHLSGCYPSWWRG 30 (110) Q Consensus 9 T~~ga~E~A~HlTG~YP~WW~G 30 (110) |+.-+.|--|.| |.|||||+= T Consensus 186 t~~Raier~Y~l-Gv~PDWWKL 206 (310) T COG3892 186 TVPRAIERFYNL-GVYPDWWKL 206 (310) T ss_pred HHHHHHHHHHHC-CCCCCCCCC T ss_conf 899999999973-778640127 No 3 >pfam09863 DUF2090 Uncharacterized protein conserved in bacteria (DUF2090). This domain, found in various prokaryotic carbohydrate kinases, has no known function. Probab=75.80 E-value=2 Score=24.08 Aligned_cols=25 Identities=32% Similarity=0.559 Sum_probs=18.5 Q ss_pred CCHHHHHHHHHHHHHHCCCCCCCCCE Q ss_conf 21247889999998638998501754 Q 537021.9.peg.1 6 LGKTLAGAAEAAMHLSGCYPSWWRGY 31 (110) Q Consensus 6 ~GKT~~ga~E~A~HlTG~YP~WW~G~ 31 (110) -..|+..+++--|-| |.|||||+=- T Consensus 190 ~~~~~~~~i~r~Y~l-GI~PDWWKLe 214 (310) T pfam09863 190 DDDTVARAIRRFYNL-GIKPDWWKLE 214 (310) T ss_pred CHHHHHHHHHHHHHC-CCCCCEEECC T ss_conf 868999999999976-9998635458 No 4 >PRK13775 formimidoylglutamase; Provisional Probab=64.95 E-value=1.6 Score=24.55 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=34.1 Q ss_pred CCCCCCE--------EECCCCEEEEECCCCHHHHHHHHHHHCCCCCCCC Q ss_conf 8501754--------5557727999414532578765666504646853 Q 537021.9.peg.1 25 PSWWRGY--------RFLQPIVMVAGSVTYELTRDGIQRLLLGEPMSPD 65 (110) Q Consensus 25 P~WW~G~--------RF~~Pi~aWa~g~t~E~tRDivQ~~LlG~~~~~~ 65 (110) |+||+|| ||-..++.--......+.-+.++-.|||-|.|.+ T Consensus 10 ~~~w~gr~dd~~~~~r~~~~~~~~~l~~~~~~~~~~~dvailG~p~D~G 58 (328) T PRK13775 10 TSYYHGGIDDDLYTAKWGMVMTFLDLNDSSLTPFEGTHFALIGFKSDKG 58 (328) T ss_pred HHHCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCEEEECCCCCCC T ss_conf 3540777677654413056367521477446756799999982276667 No 5 >KOG2199 consensus Probab=64.81 E-value=2.1 Score=23.95 Aligned_cols=29 Identities=28% Similarity=0.439 Sum_probs=16.2 Q ss_pred HHCCCCCCCCCEEECCCCEEEEECCCCHHHHHH Q ss_conf 638998501754555772799941453257876 Q 537021.9.peg.1 20 LSGCYPSWWRGYRFLQPIVMVAGSVTYELTRDG 52 (110) Q Consensus 20 lTG~YP~WW~G~RF~~Pi~aWa~g~t~E~tRDi 52 (110) |---||+||+|.--.- + -.=.||-.|+|+ T Consensus 243 Ld~s~~~WWKG~~~~~-~---GlFPsnfVT~~l 271 (462) T KOG2199 243 LDDSDPNWWKGENHRG-I---GLFPSNFVTADL 271 (462) T ss_pred CCCCCCCHHCCCCCCC-C---EECCHHHHHHHH T ss_conf 0467821312445786-1---005466531222 No 6 >COG3411 Ferredoxin [Energy production and conversion] Probab=55.75 E-value=11 Score=19.68 Aligned_cols=35 Identities=29% Similarity=0.232 Sum_probs=27.3 Q ss_pred CCEEEEECCCCHHHHHHHHHHHC-CCCCCCCCCCCC Q ss_conf 72799941453257876566650-464685323665 Q 537021.9.peg.1 36 PIVMVAGSVTYELTRDGIQRLLL-GEPMSPDQQGSG 70 (110) Q Consensus 36 Pi~aWa~g~t~E~tRDivQ~~Ll-G~~~~~~~~GtG 70 (110) |=..|-..++-|.-+.|+|.-|+ |+|.++.-+.++ T Consensus 24 pegvWY~~V~p~~a~rIv~~hl~~Gr~Ve~~~~~~~ 59 (64) T COG3411 24 PEGVWYTRVDPEDARRIVQSHLLGGRPVEELIYHTG 59 (64) T ss_pred CCCEEEECCCHHHHHHHHHHHHHCCCCCHHHCCCCC T ss_conf 587468216989999999999767985123001578 No 7 >TIGR01290 nifB nitrogenase cofactor biosynthesis protein NifB; InterPro: IPR005980 NifB is a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. Archaeal homologs lack most of the C-terminal region and are excluded from this model.; GO: 0009108 coenzyme biosynthetic process, 0009399 nitrogen fixation. Probab=55.44 E-value=4.1 Score=22.20 Aligned_cols=12 Identities=33% Similarity=0.692 Sum_probs=9.3 Q ss_pred CCCC-CCCCEEEC Q ss_conf 9985-01754555 Q 537021.9.peg.1 23 CYPS-WWRGYRFL 34 (110) Q Consensus 23 ~YP~-WW~G~RF~ 34 (110) -||+ ||+|+||+ T Consensus 152 IYpWv~y~G~RY~ 164 (461) T TIGR01290 152 IYPWVAYEGKRYT 164 (461) T ss_pred ECCCEEECCCCCC T ss_conf 0652332673335 No 8 >TIGR02713 allophanate_hyd allophanate hydrolase; InterPro: IPR014085 Allophanate hydrolase catalyses the second reaction in an ATP-dependent two-step degradation of urea to ammonia and C02, following the action of the biotin-containing urea carboxylase. The yeast enzyme, a fusion of allophanate hydrolase to urea carboxylase, is designated urea amidolyase.. Probab=45.96 E-value=6.2 Score=21.17 Aligned_cols=38 Identities=24% Similarity=0.473 Sum_probs=26.9 Q ss_pred HHCCCCCCCCCCCCCCCCHHHHCCCEECCC--CCCCCEEEEEEEECCCCEE Q ss_conf 650464685323665035777500145379--9997026999970588137 Q 537021.9.peg.1 56 LLLGEPMSPDQQGSGMIPANKVLNMTRRSN--IAGAYSTVTVRHLSGRDIG 104 (110) Q Consensus 56 ~LlG~~~~~~~~GtG~IP~~~I~~ttr~~G--vpnavd~v~VrH~SGg~~~ 104 (110) +++|. .|=|.|=||+.- ||.|+ ++|++|. +|+|||+|| T Consensus 79 iv~GK-TNLDQFATGLVG-------TRSPYG~vrnAf~~---~yiSGGSSS 118 (582) T TIGR02713 79 IVVGK-TNLDQFATGLVG-------TRSPYGAVRNAFDP---AYISGGSSS 118 (582) T ss_pred EEECC-CCCCHHHCCCCC-------CCCCCCCCCCCCCC---CCCCCCCHH T ss_conf 04115-475301005687-------41387546888674---558897406 No 9 >TIGR03435 Soli_TIGR03435 Solibacter paralogous family TIGR03435. This model describes a paralogous family of about 40 proteins found in Solibacter usitatus Ellin6076, one of the first three members of the Acidobacteria to be sequenced, and nowhere else. The family is well-diversified, with few pairs showing greater than 50 % pairwise identity. Two members of the family are longer, multidomain proteins with (two different) fused peptidase domains. Probab=37.13 E-value=17 Score=18.66 Aligned_cols=40 Identities=30% Similarity=0.370 Sum_probs=32.7 Q ss_pred HHHHCCCCCCCCCEEECCCCEEEEECCCCHHHHHHHHHHHCCC Q ss_conf 9863899850175455577279994145325787656665046 Q 537021.9.peg.1 18 MHLSGCYPSWWRGYRFLQPIVMVAGSVTYELTRDGIQRLLLGE 60 (110) Q Consensus 18 ~HlTG~YP~WW~G~RF~~Pi~aWa~g~t~E~tRDivQ~~LlG~ 60 (110) |+++| |+|=..-|||=--++ -.|.+.|+.|.-+|.+|--+ T Consensus 50 ~Qv~G--P~Wl~serfDI~AK~-p~g~~~~q~~~MLQ~LLaeR 89 (237) T TIGR03435 50 YQVSG--PDWLDSERFDIVAKA-PAGATREQVRLMLQTLLAER 89 (237) T ss_pred CCCCC--CCCCCCCEEEEEEEC-CCCCCHHHHHHHHHHHHHHH T ss_conf 40539--863456434179637-99999899999999999987 No 10 >pfam10244 MRP-L51 Mitochondrial ribosomal subunit. MRP-L51 is a family of small proteins from the intact 55 S mitochondrial ribosome. It has otherwise been referred to as bMRP-64. The exact function of this family is not known. Probab=26.67 E-value=25 Score=17.59 Aligned_cols=35 Identities=20% Similarity=0.214 Sum_probs=27.7 Q ss_pred HHHHCCCCCCCCCCCCCCC-CHHHHCCCEECCCCCC Q ss_conf 6665046468532366503-5777500145379999 Q 537021.9.peg.1 54 QRLLLGEPMSPDQQGSGMI-PANKVLNMTRRSNIAG 88 (110) Q Consensus 54 Q~~LlG~~~~~~~~GtG~I-P~~~I~~ttr~~Gvpn 88 (110) .+.|||..+.-+-+|.+.+ |++.|.+-.+-.|+++ T Consensus 13 krAlFGqnDyIdILGd~~~hP~~l~~~P~WLRG~~G 48 (94) T pfam10244 13 KRALFGQNDYIDILGDFKAHPKDLIYGPSWLRGWRG 48 (94) T ss_pred HHHHCCCCCCCCCCCCCCCCCHHHEECCHHHHCCCC T ss_conf 775516752003127987680765038699963772 No 11 >KOG0033 consensus Probab=23.75 E-value=37 Score=16.61 Aligned_cols=45 Identities=16% Similarity=0.130 Sum_probs=32.8 Q ss_pred CCCCCCEEECCCCEEEEECC------------CCHHHHHHHHHHHCCCCCCCC-CCCC Q ss_conf 85017545557727999414------------532578765666504646853-2366 Q 537021.9.peg.1 25 PSWWRGYRFLQPIVMVAGSV------------TYELTRDGIQRLLLGEPMSPD-QQGS 69 (110) Q Consensus 25 P~WW~G~RF~~Pi~aWa~g~------------t~E~tRDivQ~~LlG~~~~~~-~~Gt 69 (110) |+--.--++.+|+-.|++|+ ++|.+-|+-|.+.-|.++-|. +|-+ T Consensus 181 PEv~rkd~y~kpvDiW~cGViL~iLL~G~~PF~~e~~~rlye~I~~g~yd~~~~~w~~ 238 (355) T KOG0033 181 PEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYEQIKAGAYDYPSPEWDT 238 (355) T ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCC T ss_conf 7876238888961244454899999817889788748899999971566689643676 No 12 >pfam00910 RNA_helicase RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses. Probab=22.43 E-value=74 Score=14.87 Aligned_cols=36 Identities=31% Similarity=0.592 Sum_probs=22.5 Q ss_pred CCCCHHHHHHHHHHHHH---------HCCC-----CCCCCCEEECCCCEEEE Q ss_conf 10212478899999986---------3899-----85017545557727999 Q 537021.9.peg.1 4 NQLGKTLAGAAEAAMHL---------SGCY-----PSWWRGYRFLQPIVMVA 41 (110) Q Consensus 4 Nr~GKT~~ga~E~A~Hl---------TG~Y-----P~WW~G~RF~~Pi~aWa 41 (110) ..+|||...-. +|-+| ...| .+||.|++ .++++.|- T Consensus 7 ~G~GKS~~a~~-la~~~~~~~~~~~~~~~Y~~~~~~~~wdgY~-gq~vvi~D 56 (105) T pfam00910 7 PGCGKSTLAKY-LARALLDHLGLPKKDSVYSRNPDDDFWDGYT-GQPVVIID 56 (105) T ss_pred CCCCHHHHHHH-HHHHHHHHHCCCCCCCEEECCCCCCCCCCCC-CCEEEEEE T ss_conf 98988999999-9999999837787897796788776567889-98579996 No 13 >TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178 Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process. Probab=22.22 E-value=43 Score=16.25 Aligned_cols=14 Identities=43% Similarity=0.480 Sum_probs=12.9 Q ss_pred CCCCHHHHHHHHHH Q ss_conf 14532578765666 Q 537021.9.peg.1 43 SVTYELTRDGIQRL 56 (110) Q Consensus 43 g~t~E~tRDivQ~~ 56 (110) |||-=|.|.++||+ T Consensus 41 GVTRTTLREVLQRL 54 (275) T TIGR02812 41 GVTRTTLREVLQRL 54 (275) T ss_pred CCCCCHHHHHHHHH T ss_conf 76630378999887 No 14 >PRK10528 multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1; Provisional Probab=20.24 E-value=42 Score=16.29 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=18.8 Q ss_pred EECCCCEEEEECCCCHHHHHHHHHH Q ss_conf 5557727999414532578765666 Q 537021.9.peg.1 32 RFLQPIVMVAGSVTYELTRDGIQRL 56 (110) Q Consensus 32 RF~~Pi~aWa~g~t~E~tRDivQ~~ 56 (110) ++.+....--+|+|+|||.+.++|. T Consensus 39 ~l~~~~~viNaGvSGdTT~~gL~Rl 63 (191) T PRK10528 39 KWQSKTSVVNASISGDTSQQGLARL 63 (191) T ss_pred HHHHCCCEEECCCCHHHHHHHHHHH T ss_conf 9861894886687633254699998 No 15 >TIGR00441 gmhA phosphoheptose isomerase; InterPro: IPR004515 Phosphoheptose isomerase is involved in lipopolysaccharide biosynthesis, and more specifically in the synthesis of glyceromannoheptose 7-phosphate. It may also have a role in virulence in Haemophilus ducreyi.; GO: 0008968 phosphoheptose isomerase activity, 0009244 lipopolysaccharide core region biosynthetic process, 0005737 cytoplasm. Probab=20.11 E-value=61 Score=15.33 Aligned_cols=23 Identities=30% Similarity=0.496 Sum_probs=19.5 Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCEEECCC Q ss_conf 124788999999863899850175455577 Q 537021.9.peg.1 7 GKTLAGAAEAAMHLSGCYPSWWRGYRFLQP 36 (110) Q Consensus 7 GKT~~ga~E~A~HlTG~YP~WW~G~RF~~P 36 (110) |-|.|-|+-.|--||||| |++|| T Consensus 48 GgSaadAqHFAaEl~GRf-------~~eR~ 70 (186) T TIGR00441 48 GGSAADAQHFAAELVGRF-------KLERP 70 (186) T ss_pred CCCHHHHHHHHHHHHCCC-------CCCCC T ss_conf 504335888999871640-------00267 Done!