Query gi|254781080|ref|YP_003065493.1| hypothetical protein CLIBASIA_04910 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 85 No_of_seqs 100 out of 205 Neff 3.6 Searched_HMMs 39220 Date Mon May 30 04:07:07 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781080.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK13694 hypothetical protein; 100.0 2.7E-33 6.8E-38 234.0 11.1 81 2-82 4-84 (84) 2 pfam10073 DUF2312 Uncharacteri 100.0 1.2E-31 3.1E-36 223.4 10.7 74 8-81 1-74 (74) 3 COG3750 Uncharacterized protei 100.0 1.5E-30 3.8E-35 216.5 10.5 82 1-82 4-85 (85) 4 pfam07862 Nif11 Nitrogen fixat 81.8 2.5 6.4E-05 24.0 4.2 42 8-49 1-44 (49) 5 pfam00038 Filament Intermediat 66.9 13 0.00033 19.4 6.0 51 10-60 10-62 (312) 6 PRK02249 DNA primase large sub 62.3 16 0.0004 18.9 6.3 57 29-85 195-259 (333) 7 pfam11126 Phage_DsbA Transcrip 62.2 16 0.00041 18.9 7.2 54 19-78 11-66 (69) 8 pfam02787 CPSase_L_D3 Carbamoy 59.7 16 0.00041 18.9 4.1 59 15-83 38-99 (122) 9 pfam07889 DUF1664 Protein of u 58.0 19 0.00048 18.4 5.8 52 6-57 59-114 (126) 10 COG0178 UvrA Excinuclease ATPa 44.4 13 0.00033 19.5 1.6 21 29-49 699-722 (935) 11 COG3040 Blc Bacterial lipocali 40.5 15 0.00038 19.1 1.4 21 31-51 146-166 (174) 12 PRK10098 hypothetical protein; 39.9 36 0.00092 16.6 4.1 56 2-57 1-56 (350) 13 PHA02244 ATPase-like protein 35.8 42 0.0011 16.2 3.9 42 15-56 5-46 (383) 14 COG1392 Phosphate transport re 29.0 54 0.0014 15.5 5.7 48 10-57 146-195 (217) 15 PRK00349 uvrA excinuclease ABC 26.2 38 0.00097 16.5 1.6 19 30-48 708-729 (944) 16 pfam11572 DUF3234 Protein of u 25.7 44 0.0011 16.1 1.8 18 66-83 55-72 (102) 17 pfam10910 DUF2744 Protein of u 25.3 63 0.0016 15.1 2.6 21 64-85 103-123 (125) 18 TIGR02760 TraI_TIGR conjugativ 24.6 65 0.0017 15.0 2.9 49 5-53 261-333 (2193) 19 COG0373 HemA Glutamyl-tRNA red 23.9 67 0.0017 14.9 4.1 28 29-56 112-139 (414) 20 pfam05201 GlutR_N Glutamyl-tRN 22.4 71 0.0018 14.7 4.3 29 28-56 108-136 (150) 21 COG4472 Uncharacterized protei 21.8 74 0.0019 14.7 5.2 52 25-80 15-85 (88) 22 TIGR00630 uvra excinuclease AB 21.7 35 0.0009 16.7 0.7 19 30-48 738-759 (956) 23 COG5113 UFD2 Ubiquitin fusion 21.5 66 0.0017 14.9 2.1 30 10-39 824-853 (929) 24 cd04787 HTH_HMRTR_unk Helix-Tu 21.0 76 0.0019 14.6 4.1 34 39-72 51-84 (133) 25 pfam09840 DUF2067 Uncharacteri 20.9 77 0.002 14.5 5.2 43 25-68 116-162 (190) 26 PRK07093 para-aminobenzoate sy 20.2 79 0.002 14.4 2.8 25 60-84 165-189 (322) No 1 >PRK13694 hypothetical protein; Provisional Probab=100.00 E-value=2.7e-33 Score=234.04 Aligned_cols=81 Identities=54% Similarity=0.931 Sum_probs=78.8 Q ss_pred CCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 41243100899999999999999999999999999999987589879999999999618999999999999999998598 Q gi|254781080|r 2 IDNIQNVTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALGM 81 (85) Q Consensus 2 ~~~~~~va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALGm 81 (85) .+++++|++++||||||||||||+||++|++|||+|||||||+|||||+||+||++||+|+++|+|+|+||++|++|||| T Consensus 4 ~~~~~~va~~~Lr~fIERIErLeeEkk~i~~dikeVyaEAK~~GfD~K~mR~Iv~lRk~d~~er~E~ealLdlY~~ALGm 83 (84) T PRK13694 4 DDDAEVVAKEQLRAYIERIERLEEEKKTISDDIKDVYAEAKGNGFDVKAMRTIIRLRKKDDDERAEQEAILELYMDALGM 83 (84) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 56302545999999999999999999989998999999988678868999999999838886898899999999998477 Q ss_pred C Q ss_conf 8 Q gi|254781080|r 82 L 82 (85) Q Consensus 82 ~ 82 (85) + T Consensus 84 ~ 84 (84) T PRK13694 84 I 84 (84) T ss_pred C T ss_conf 9 No 2 >pfam10073 DUF2312 Uncharacterized protein conserved in bacteria (DUF2312). Members of this family of hypothetical bacterial proteins have no known function. Probab=99.97 E-value=1.2e-31 Score=223.43 Aligned_cols=74 Identities=58% Similarity=0.932 Sum_probs=73.1 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 00899999999999999999999999999999987589879999999999618999999999999999998598 Q gi|254781080|r 8 VTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALGM 81 (85) Q Consensus 8 va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALGm 81 (85) |++++||||||||||||+||++|++|||||||||||+|||||+||+||++||+|+++|+|+|+||++|++|||| T Consensus 1 va~~~Lr~fIERIErLeeEkk~i~~dikeVyaEAK~~GfD~K~mR~ii~lRk~d~~er~E~e~ll~~Y~~ALGm 74 (74) T pfam10073 1 VAADQLRQFIERIERLEEEKKDIADDIKDVYAEAKGNGFDTKALRQIIKLRKMDKDERAEQEAILELYKAALGM 74 (74) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 93888999999999899999979998999999987578869999999999818887898799999999987187 No 3 >COG3750 Uncharacterized protein conserved in bacteria [Function unknown] Probab=99.97 E-value=1.5e-30 Score=216.50 Aligned_cols=82 Identities=55% Similarity=0.895 Sum_probs=79.7 Q ss_pred CCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC Q ss_conf 94124310089999999999999999999999999999998758987999999999961899999999999999999859 Q gi|254781080|r 1 MIDNIQNVTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALG 80 (85) Q Consensus 1 ~~~~~~~va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALG 80 (85) .|+++.+++++|||+|||||||||+||++|++||||||+||||+|||+|++|+||++||+|.++|+|++++|++|+.||| T Consensus 4 ~t~~s~tva~~QLrafIerIERlEeEk~~i~~dikdvy~eakg~GFDvKa~r~iirlrK~D~~er~EedAildlY~~aLg 83 (85) T COG3750 4 ITSTSQTVAAGQLRAFIERIERLEEEKKTIADDIKDVYAEAKGHGFDVKAVRTIIRLRKLDKAERQEEDAILDLYMDALG 83 (85) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 35789999999999999999999999999988899999997637861999999999996038888888899999999854 Q ss_pred CC Q ss_conf 88 Q gi|254781080|r 81 ML 82 (85) Q Consensus 81 m~ 82 (85) |. T Consensus 84 ~~ 85 (85) T COG3750 84 MI 85 (85) T ss_pred CC T ss_conf 79 No 4 >pfam07862 Nif11 Nitrogen fixation protein of unknown function. This domain is found in the Cyanobacteria, and may be involved in nitrogen fixation, but no role has been assigned. Probab=81.80 E-value=2.5 Score=24.01 Aligned_cols=42 Identities=21% Similarity=0.504 Sum_probs=33.0 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHCCCCHH Q ss_conf 0089999999999999999999999--99999999875898799 Q gi|254781080|r 8 VTQDQLRTFIERLERLEEEKKLLTE--NIKDIYGEAKATGFDVK 49 (85) Q Consensus 8 va~~~Lr~~IERIErLeeEkk~i~~--dikdVyaEAK~~GfD~K 49 (85) .+.++|+.|++++..=..=...+.. +.-+|-+=|+..||+.- T Consensus 1 MS~e~l~~Fl~~~~~d~~l~~~l~~~~~~~~vi~lA~~~Gf~~t 44 (49) T pfam07862 1 MSEEQLKAFLEKVKSDPSLREQLKACSDAEEVVALAKEAGFEFT 44 (49) T ss_pred CCHHHHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHCCCCCC T ss_conf 98999999999985399999999875999999999999599867 No 5 >pfam00038 Filament Intermediate filament protein. Probab=66.86 E-value=13 Score=19.43 Aligned_cols=51 Identities=25% Similarity=0.460 Sum_probs=38.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH--HHHHHHHHC Q ss_conf 899999999999999999999999999999987589879999--999999618 Q gi|254781080|r 10 QDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAI--KKILSLRKK 60 (85) Q Consensus 10 ~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~l--r~IiklRk~ 60 (85) .++|-+||+++-.||.+-+.+..+|.....-....+-+++.+ ..+-.+|+. T Consensus 10 N~Rla~YiekVr~LE~~N~~Le~~i~~~~~~~~~~~~~~~~~ye~el~~lr~~ 62 (312) T pfam00038 10 NDRLASYIDKVRFLEQQNKELEAKIEELRQKKSAEPSRLYSLYEQEIRELRKQ 62 (312) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 99999999999999998999999999997076999998288899999999999 No 6 >PRK02249 DNA primase large subunit; Validated Probab=62.34 E-value=16 Score=18.90 Aligned_cols=57 Identities=26% Similarity=0.307 Sum_probs=39.5 Q ss_pred HHHHHHHHHHHHHHH--------CCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 999999999999875--------898799999999996189999999999999999985988679 Q gi|254781080|r 29 LLTENIKDIYGEAKA--------TGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALGMLKDE 85 (85) Q Consensus 29 ~i~~dikdVyaEAK~--------~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALGm~~~~ 85 (85) ...+.|++.|++-.. .|-.|--|+.+|.--+.+.+---..--.|.+|+..+||..|+ T Consensus 195 ~~~~~i~~~~~~~~~~~~~~~~~~~~~PPCmk~~i~~l~~G~Nl~H~~Rf~Lasfl~~iG~~~d~ 259 (333) T PRK02249 195 PLLEEIREEYEKRKLETEFGEVTPGAFPPCMKALLSALQAGENLPHTARFAITSFLHNIGMDVDE 259 (333) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHH T ss_conf 99999999999743103234226778980799999998669987717899999999976998899 No 7 >pfam11126 Phage_DsbA Transcriptional regulator DsbA. DsbA is a double stranded binding protein found in bacteriophage T4 which is involved in transcriptional regulation. DsbA, along with other viral proteins, interacts with the host RNA polymerase core enzyme enabling initiation of transcription. DsbA acts as an enhancer protein of late genes in vitro. The protein consists of mainly alpha helices. Probab=62.17 E-value=16 Score=18.88 Aligned_cols=54 Identities=22% Similarity=0.343 Sum_probs=34.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCC-HH-HHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999875898799999999996189-99-999999999999998 Q gi|254781080|r 19 RLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSLRKKD-EK-QWMEEEQILDVYLRA 78 (85) Q Consensus 19 RIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~IiklRk~d-~~-er~E~e~iLd~Y~~A 78 (85) +||...+-.|+|.+..|+= -|.|+|...+.+++--++ .. .-+|.+-+.++|-.. T Consensus 11 ~ies~~e~iKdI~~~AK~E------~GvdgK~fnkl~klYHkq~R~~feae~~ev~elYd~i 66 (69) T pfam11126 11 QIESYGELIKEIKNRAKEE------LGVDGKMFNKLFKLYHKQEREQFEAENDEVVELYDQI 66 (69) T ss_pred HHHHHHHHHHHHHHHHHHH------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9998998999999999998------3878899999999998865899998788899999998 No 8 >pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. Probab=59.74 E-value=16 Score=18.87 Aligned_cols=59 Identities=27% Similarity=0.376 Sum_probs=36.2 Q ss_pred HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 99999999999999999---9999999998758987999999999961899999999999999999859886 Q gi|254781080|r 15 TFIERLERLEEEKKLLT---ENIKDIYGEAKATGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALGMLK 83 (85) Q Consensus 15 ~~IERIErLeeEkk~i~---~dikdVyaEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALGm~~ 83 (85) =|+++|+++-+--+.|. .--++.+-+||..||--+-+-++. ..+..+ .--++..+|+.| T Consensus 38 wFL~~i~~Iv~~e~~l~~~~~~~~~~l~~aK~~GFSD~~IA~l~---~~~e~~-------Ir~~R~~~~i~P 99 (122) T pfam02787 38 WFLEKIKEIVELEKELKKGDPLSDDLLLKAKKLGFSDAQIAKLL---GVTEEE-------VRKLRKELGIRP 99 (122) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHH---CCCHHH-------HHHHHHHCCCCC T ss_conf 99999999999999998548999999999999499989999883---986999-------999999879912 No 9 >pfam07889 DUF1664 Protein of unknown function (DUF1664). The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long. Probab=57.98 E-value=19 Score=18.42 Aligned_cols=52 Identities=25% Similarity=0.351 Sum_probs=39.4 Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCHHHHHHHHHH Q ss_conf 31008999999999999999999999999999999875----89879999999999 Q gi|254781080|r 6 QNVTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKA----TGFDVKAIKKILSL 57 (85) Q Consensus 6 ~~va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~----~GfD~K~lr~Iikl 57 (85) -..+.-+|-+.|+++-.=-+|-++|+..+++=-.|+++ -|||++.++++|.- T Consensus 59 l~~tKrhLsqRI~~vd~kld~~~eis~~i~~eV~e~~~~~~~i~~D~~~v~~~v~~ 114 (126) T pfam07889 59 IAATKKHLSQRIDNLDDKLDEQKEISESTRDEVTEIREDLSNIGEDVKSVQQAVEG 114 (126) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999998873532199999999999999999996499887699999999998 No 10 >COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair] Probab=44.38 E-value=13 Score=19.45 Aligned_cols=21 Identities=29% Similarity=0.613 Sum_probs=16.5 Q ss_pred HHHHHHHHHHH---HHHHCCCCHH Q ss_conf 99999999999---9875898799 Q gi|254781080|r 29 LLTENIKDIYG---EAKATGFDVK 49 (85) Q Consensus 29 ~i~~dikdVya---EAK~~GfD~K 49 (85) .+.++|++.|| |||.+||.+- T Consensus 699 g~Fd~IR~lFA~tpeAK~rGyk~g 722 (935) T COG0178 699 GVFDDIRELFAGTPEAKARGYKPG 722 (935) T ss_pred CCHHHHHHHHHHCHHHHHCCCCCC T ss_conf 243789999820939897399865 No 11 >COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane] Probab=40.48 E-value=15 Score=19.07 Aligned_cols=21 Identities=38% Similarity=0.600 Sum_probs=16.6 Q ss_pred HHHHHHHHHHHHHCCCCHHHH Q ss_conf 999999999987589879999 Q gi|254781080|r 31 TENIKDIYGEAKATGFDVKAI 51 (85) Q Consensus 31 ~~dikdVyaEAK~~GfD~K~l 51 (85) .+..+...++||..|||+..+ T Consensus 146 ~~~~~~ml~~ak~~Gfdv~~l 166 (174) T COG3040 146 QETLKRMLEIAKRRGFDVSKL 166 (174) T ss_pred HHHHHHHHHHHHHCCCCCCEE T ss_conf 899999999999718774236 No 12 >PRK10098 hypothetical protein; Provisional Probab=39.90 E-value=36 Score=16.62 Aligned_cols=56 Identities=18% Similarity=0.257 Sum_probs=42.3 Q ss_pred CCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 41243100899999999999999999999999999999987589879999999999 Q gi|254781080|r 2 IDNIQNVTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSL 57 (85) Q Consensus 2 ~~~~~~va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~Iikl 57 (85) |++...++.++|++|+.++=.---=-..-+..+-|+.-+|--+|.+..=+..+... T Consensus 1 m~~~~ri~~~~l~~~~~~~~~~~G~~~~~A~~vA~~Lv~adl~G~~SHGv~rl~~Y 56 (350) T PRK10098 1 MESGHRIDAQTLHSFVQALWRQAGSEEREAKLVADHLVAANLAGHDSHGVGMIPSY 56 (350) T ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH T ss_conf 98767438999999999999985999999999999999998288604439899999 No 13 >PHA02244 ATPase-like protein Probab=35.84 E-value=42 Score=16.22 Aligned_cols=42 Identities=31% Similarity=0.415 Sum_probs=35.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 999999999999999999999999998758987999999999 Q gi|254781080|r 15 TFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILS 56 (85) Q Consensus 15 ~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~Iik 56 (85) .-||+.|||-|..-.-.-|..|-..|-.|+-|.-.++-.|+. T Consensus 5 dsie~lerlveqqmettkdladklgeknsnpyeqaiid~i~~ 46 (383) T PHA02244 5 DSIEGLERLVEQQMETTKDLADKLGEKNSNPYEQAIIDAIRE 46 (383) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 578999999999888889999984334699278999999998 No 14 >COG1392 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism] Probab=29.04 E-value=54 Score=15.51 Aligned_cols=48 Identities=23% Similarity=0.265 Sum_probs=36.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHH Q ss_conf 899999999999999999999999999999987589--879999999999 Q gi|254781080|r 10 QDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATG--FDVKAIKKILSL 57 (85) Q Consensus 10 ~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~G--fD~K~lr~Iikl 57 (85) ..++..++..|+++|.+-..+....-...-...... .+.-.+++|+.. T Consensus 146 ~~~~~~i~~eI~~~E~e~D~i~~~l~k~Lf~~e~~~~~~~~~~~~~i~~~ 195 (217) T COG1392 146 ADRLLEIIKEIEALEHECDDIQRELLKKLFSLETEINPIDVIILKEIIEK 195 (217) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 78899999999998887149999999999723245125899999999999 No 15 >PRK00349 uvrA excinuclease ABC subunit A; Reviewed Probab=26.18 E-value=38 Score=16.48 Aligned_cols=19 Identities=32% Similarity=0.719 Sum_probs=9.2 Q ss_pred HHHHHHHHHH---HHHHCCCCH Q ss_conf 9999999999---987589879 Q gi|254781080|r 30 LTENIKDIYG---EAKATGFDV 48 (85) Q Consensus 30 i~~dikdVya---EAK~~GfD~ 48 (85) +.++|+..|| +||.+||.+ T Consensus 708 ~~d~IR~lFA~~~~ak~rg~~~ 729 (944) T PRK00349 708 VFDPIRELFAGTPEAKARGYKP 729 (944) T ss_pred CHHHHHHHHHCCHHHHHHCCCC T ss_conf 5799999984194879709997 No 16 >pfam11572 DUF3234 Protein of unknown function (DUF3234). This bacterial family of proteins has no known function. Some members in this family of proteins are annotated as TTHA0547 however this cannot be confirmed. Probab=25.75 E-value=44 Score=16.08 Aligned_cols=18 Identities=44% Similarity=0.868 Sum_probs=14.7 Q ss_pred HHHHHHHHHHHHHHCCCC Q ss_conf 999999999999859886 Q gi|254781080|r 66 MEEEQILDVYLRALGMLK 83 (85) Q Consensus 66 ~E~e~iLd~Y~~ALGm~~ 83 (85) .|--++-+.|+.||||+. T Consensus 55 LE~~ALKEafL~ALG~L~ 72 (102) T pfam11572 55 LESRALKEAFLRALGMLQ 72 (102) T ss_pred HHHHHHHHHHHHHHHHCC T ss_conf 457888999999975404 No 17 >pfam10910 DUF2744 Protein of unknown function (DUF2744). This is a viral family of proteins with unknown function. Probab=25.28 E-value=63 Score=15.08 Aligned_cols=21 Identities=33% Similarity=0.550 Sum_probs=16.9 Q ss_pred HHHHHHHHHHHHHHHHCCCCCC Q ss_conf 9999999999999985988679 Q gi|254781080|r 64 QWMEEEQILDVYLRALGMLKDE 85 (85) Q Consensus 64 er~E~e~iLd~Y~~ALGm~~~~ 85 (85) ..+|++++|+.|+ .||+++++ T Consensus 103 t~qe~~a~l~q~r-~lg~i~d~ 123 (125) T pfam10910 103 TQQEQRAQLEQYR-ELGLIPDE 123 (125) T ss_pred CCHHHHHHHHHHH-HHCCCCCC T ss_conf 3698999999999-83766778 No 18 >TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI; InterPro: IPR014129 This entry represents TraI, which is a component of the relaxosome complex. In the process of conjugative plasmid transfer the relaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein .. Probab=24.58 E-value=65 Score=15.00 Aligned_cols=49 Identities=27% Similarity=0.398 Sum_probs=30.8 Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHH------------------------HHHHHHHHHHHHHHCCCCHHHHHH Q ss_conf 4310089999999999999999999------------------------999999999998758987999999 Q gi|254781080|r 5 IQNVTQDQLRTFIERLERLEEEKKL------------------------LTENIKDIYGEAKATGFDVKAIKK 53 (85) Q Consensus 5 ~~~va~~~Lr~~IERIErLeeEkk~------------------------i~~dikdVyaEAK~~GfD~K~lr~ 53 (85) +.||+-.-|.+|=.|=+.+++.-.. -..-..+...++|+.|||+..+.+ T Consensus 261 I~GvPe~~~~afS~R~~qI~~~~~E~G~~sakard~AAl~TR~~K~~~d~~~l~~~W~~~~K~~GFD~~~~v~ 333 (2193) T TIGR02760 261 IEGVPEEVLTAFSKRRQQIDEAVKEKGTSSAKARDVAALDTRKSKTYIDDETLMEKWQQEIKDLGFDISALVA 333 (2193) T ss_pred CCCCCHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 4778745776530178999997310376118899998863276875058789989999998644888899999 No 19 >COG0373 HemA Glutamyl-tRNA reductase [Coenzyme metabolism] Probab=23.93 E-value=67 Score=14.92 Aligned_cols=28 Identities=21% Similarity=0.425 Sum_probs=18.0 Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 9999999999998758987999999999 Q gi|254781080|r 29 LLTENIKDIYGEAKATGFDVKAIKKILS 56 (85) Q Consensus 29 ~i~~dikdVyaEAK~~GfD~K~lr~Iik 56 (85) .|..++|+-|+.|+.+|+-.+.+..+.. T Consensus 112 QILGQVK~Ay~~a~~~g~~g~~L~~lFq 139 (414) T COG0373 112 QILGQVKDAYAKAQENGTLGKVLNRLFQ 139 (414) T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 9999999999999981985289999999 No 20 >pfam05201 GlutR_N Glutamyl-tRNAGlu reductase, N-terminal domain. Probab=22.41 E-value=71 Score=14.74 Aligned_cols=29 Identities=17% Similarity=0.337 Sum_probs=25.1 Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 99999999999998758987999999999 Q gi|254781080|r 28 KLLTENIKDIYGEAKATGFDVKAIKKILS 56 (85) Q Consensus 28 k~i~~dikdVyaEAK~~GfD~K~lr~Iik 56 (85) ..|..++|+-|..|+..|+-.+.|..++. T Consensus 108 ~qIlgQvK~A~~~a~~~g~~g~~L~~lf~ 136 (150) T pfam05201 108 PQILGQVKEAYELAREAGTVGKILNRLFQ 136 (150) T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 89999999999999982984489999999 No 21 >COG4472 Uncharacterized protein conserved in bacteria [Function unknown] Probab=21.77 E-value=74 Score=14.65 Aligned_cols=52 Identities=27% Similarity=0.624 Sum_probs=37.8 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH-------------------HHHHCCHHHHHHHHHHHHHHHHHHC Q ss_conf 9999999999999999875898799999999-------------------9961899999999999999999859 Q gi|254781080|r 25 EEKKLLTENIKDIYGEAKATGFDVKAIKKIL-------------------SLRKKDEKQWMEEEQILDVYLRALG 80 (85) Q Consensus 25 eEkk~i~~dikdVyaEAK~~GfD~K~lr~Ii-------------------klRk~d~~er~E~e~iLd~Y~~ALG 80 (85) ..++++.+-..+||.--+..||.| +.||| .+||.+.++.-| .++-.|+.--| T Consensus 15 ~~~~~v~e~L~~VY~sL~ekGYNp--iNQiVGYllSGDPaYIpr~ndARn~IRk~eRDeIvE--Elvk~YLk~~~ 85 (88) T COG4472 15 SDKKDVKETLNDVYNSLEEKGYNP--INQIVGYLLSGDPAYIPRYNDARNQIRKLERDEIVE--ELVKYYLKGNG 85 (88) T ss_pred CHHHHHHHHHHHHHHHHHHCCCCH--HHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHH--HHHHHHHHHCC T ss_conf 708899999999999998727872--877884401489644676210899999874889999--99999985157 No 22 >TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex. Probab=21.65 E-value=35 Score=16.70 Aligned_cols=19 Identities=32% Similarity=0.751 Sum_probs=11.8 Q ss_pred HHHHHHHHHH---HHHHCCCCH Q ss_conf 9999999999---987589879 Q gi|254781080|r 30 LTENIKDIYG---EAKATGFDV 48 (85) Q Consensus 30 i~~dikdVya---EAK~~GfD~ 48 (85) +.++||+.|| |||.+||.+ T Consensus 738 vFd~IR~LFA~~PeAk~RGY~~ 759 (956) T TIGR00630 738 VFDEIRELFAETPEAKARGYKP 759 (956) T ss_pred CCHHHHHHHHCCCHHHHCCCCC T ss_conf 4305777640585378738899 No 23 >COG5113 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones] Probab=21.55 E-value=66 Score=14.94 Aligned_cols=30 Identities=30% Similarity=0.544 Sum_probs=16.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 899999999999999999999999999999 Q gi|254781080|r 10 QDQLRTFIERLERLEEEKKLLTENIKDIYG 39 (85) Q Consensus 10 ~~~Lr~~IERIErLeeEkk~i~~dikdVya 39 (85) -+.||+||.|.|..+--++.=.+|.-||-. T Consensus 824 IE~l~~f~nr~E~~r~~ea~EeED~GDvPD 853 (929) T COG5113 824 IEELRSFINRLEKVRVIEAVEEEDMGDVPD 853 (929) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCH T ss_conf 999999999998989887522332168956 No 24 >cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c Probab=21.01 E-value=76 Score=14.55 Aligned_cols=34 Identities=29% Similarity=0.394 Sum_probs=22.4 Q ss_pred HHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHH Q ss_conf 9987589879999999999618999999999999 Q gi|254781080|r 39 GEAKATGFDVKAIKKILSLRKKDEKQWMEEEQIL 72 (85) Q Consensus 39 aEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iL 72 (85) ..++..||..+-||+++.++..++....+-..+| T Consensus 51 ~~~r~~G~sL~eIr~ll~l~~~~~~~~~~~~~ll 84 (133) T cd04787 51 LSARQLGFSLKDIKEILSHADQGESPCPMVRRLI 84 (133) T ss_pred HHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHH T ss_conf 9999869999999999988737999789999999 No 25 >pfam09840 DUF2067 Uncharacterized protein conserved in archaea (DUF2067). This domain, found in various archaeal proteins, has no known function. Probab=20.90 E-value=77 Score=14.54 Aligned_cols=43 Identities=26% Similarity=0.380 Sum_probs=28.4 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH----HHCCHHHHHHH Q ss_conf 999999999999999987589879999999999----61899999999 Q gi|254781080|r 25 EEKKLLTENIKDIYGEAKATGFDVKAIKKILSL----RKKDEKQWMEE 68 (85) Q Consensus 25 eEkk~i~~dikdVyaEAK~~GfD~K~lr~Iikl----Rk~d~~er~E~ 68 (85) +|.-.+...+.++|+|+...-.-++ +|.+|.. ..+||++.-|. T Consensus 116 eev~e~~~~L~eiy~ei~~~~lt~~-~k~vv~~~s~~~g~~~~evie~ 162 (190) T pfam09840 116 EEVVEVARELSEIYKELRFQPLTTK-AKRVVVAASYATGKDPDDAIEE 162 (190) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHH-HHHHHHEEHHHHCCCHHHHHHH T ss_conf 9999999999999999854766765-6645311034618998999999 No 26 >PRK07093 para-aminobenzoate synthase component I; Validated Probab=20.18 E-value=79 Score=14.44 Aligned_cols=25 Identities=32% Similarity=0.546 Sum_probs=22.7 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 8999999999999999998598867 Q gi|254781080|r 60 KDEKQWMEEEQILDVYLRALGMLKD 84 (85) Q Consensus 60 ~d~~er~E~e~iLd~Y~~ALGm~~~ 84 (85) .|+-+++|+-+|.|+-+.-||+.++ T Consensus 165 ~d~Ke~aEh~MIVDL~RNDL~~va~ 189 (322) T PRK07093 165 NDEKEFAEHATIVDLMRNDLSMVAT 189 (322) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 2938789999999999868772387 Done!