Query gi|254780763|ref|YP_003065176.1| hypothetical protein CLIBASIA_03260 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 107 No_of_seqs 107 out of 1265 Neff 6.1 Searched_HMMs 39220 Date Sun May 29 18:50:15 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780763.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK00153 hypothetical protein; 100.0 1.8E-32 4.5E-37 228.1 15.4 105 1-107 3-107 (107) 2 COG0718 Uncharacterized protei 100.0 1.9E-29 4.7E-34 208.9 14.4 102 1-104 4-105 (105) 3 PRK03762 hypothetical protein; 100.0 2.1E-28 5.4E-33 202.2 14.4 94 3-98 2-95 (97) 4 PRK00587 hypothetical protein; 99.9 2.6E-26 6.8E-31 188.9 13.8 98 3-103 2-99 (99) 5 TIGR00103 TIGR00103 conserved 99.9 3E-26 7.6E-31 188.6 12.1 101 3-103 12-112 (112) 6 pfam02575 DUF149 Uncharacteriz 99.9 2.3E-24 5.9E-29 176.6 13.0 92 8-100 1-92 (92) 7 PRK00587 hypothetical protein; 94.9 0.28 7.1E-06 30.1 8.5 90 1-97 3-99 (99) 8 PRK00153 hypothetical protein; 91.0 0.63 1.6E-05 27.9 5.4 93 9-107 4-103 (107) 9 KOG3675 consensus 64.9 7.6 0.00019 21.0 3.2 52 21-72 266-317 (417) 10 pfam11576 DUF3236 Protein of u 63.2 14 0.00035 19.4 4.2 49 32-82 103-151 (154) 11 TIGR01352 tonB_Cterm TonB fami 56.0 21 0.00053 18.3 4.5 42 34-79 13-54 (81) 12 pfam10437 Lip_prot_lig_C Bacte 41.6 35 0.00088 16.9 4.9 52 31-82 10-68 (85) 13 TIGR00389 glyS_dimeric glycyl- 35.1 30 0.00076 17.3 2.3 50 9-63 407-457 (606) 14 TIGR01202 bchC Chlorophyll syn 32.6 23 0.00058 18.0 1.3 15 93-107 46-60 (325) 15 pfam07472 PA-IIL Fucose-bindin 32.2 35 0.0009 16.8 2.3 28 32-59 50-77 (107) 16 TIGR01506 ribC_arch riboflavin 31.1 46 0.0012 16.1 2.7 58 36-99 79-142 (152) 17 COG2968 Uncharacterized conser 30.4 52 0.0013 15.7 7.1 64 27-94 112-190 (243) 18 PRK10718 hypothetical protein; 28.6 56 0.0014 15.5 3.0 49 30-79 85-134 (191) 19 COG4572 ChaB Putative cation t 28.2 51 0.0013 15.8 2.5 24 59-82 13-36 (76) 20 PRK05886 yajC preprotein trans 27.6 58 0.0015 15.4 5.2 53 7-60 21-73 (108) 21 pfam05958 tRNA_U5-meth_tr tRNA 27.4 29 0.00075 17.3 1.2 52 9-60 181-233 (353) 22 TIGR02063 RNase_R ribonuclease 27.3 59 0.0015 15.4 5.8 72 2-81 419-490 (755) 23 PRK03822 lplA lipoate-protein 26.6 61 0.0015 15.3 8.5 56 29-84 255-317 (338) 24 COG1422 Predicted membrane pro 26.2 61 0.0016 15.3 3.1 20 9-28 72-91 (201) 25 PRK13259 regulatory protein Sp 26.2 61 0.0016 15.3 3.4 28 60-87 65-92 (94) 26 pfam08714 Fae Formaldehyde-act 26.1 62 0.0016 15.2 4.0 38 43-83 101-138 (160) 27 TIGR01377 soxA_mon sarcosine o 24.9 31 0.00078 17.2 0.9 33 22-54 168-201 (401) 28 pfam10991 DUF2815 Protein of u 24.3 67 0.0017 15.0 3.7 41 59-107 36-76 (181) 29 pfam08345 YscJ_FliF_C Flagella 24.2 58 0.0015 15.4 2.2 40 36-75 91-145 (162) 30 COG0858 RbfA Ribosome-binding 23.7 69 0.0017 15.0 8.5 77 6-89 6-83 (118) 31 PHA00431 internal virion prote 23.4 69 0.0018 14.9 5.4 58 25-84 658-715 (749) 32 pfam07830 PP2C_C Protein serin 22.8 71 0.0018 14.9 3.6 51 53-105 12-68 (81) 33 COG0810 TonB Periplasmic prote 22.4 73 0.0019 14.8 4.0 42 34-79 179-220 (244) 34 TIGR03422 mito_frataxin fratax 21.6 75 0.0019 14.7 4.1 38 12-49 11-48 (97) 35 TIGR00537 hemK_rel_arch methyl 21.1 19 0.00048 18.5 -0.8 34 27-60 23-58 (183) 36 PRK05031 tRNA (uracil-5-)-meth 20.4 68 0.0017 15.0 1.9 50 10-59 192-242 (363) No 1 >PRK00153 hypothetical protein; Validated Probab=100.00 E-value=1.8e-32 Score=228.11 Aligned_cols=105 Identities=43% Similarity=0.736 Sum_probs=103.5 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 92179999999999999999999985308999976984999996483074688647882910068999999999999999 Q gi|254780763|r 1 MSNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHK 80 (107) Q Consensus 1 M~nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~ 80 (107) |+||++||+|||+||++|+++|++|++.+|+|+|+||+|+||+||+++|++|+|||++++++|+++|||+|++|+|+|++ T Consensus 3 m~nm~~mmkqaq~mq~~~~~~q~el~~~~v~~~sg~glV~V~~nG~~~v~~i~Id~~ll~~~d~e~LedlI~~A~N~A~~ 82 (107) T PRK00153 3 MGNMANLMKQAQQMQEKMQKMQEELANKEVTGTAGGGLVTVTMTGKKEVVRVKIDPSVVDPEDVEMLEDLVAAAFNDALR 82 (107) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEEEECCCEEEEEEECHHHCCCCCHHHHHHHHHHHHHHHHH T ss_conf 43599999999999999999999983758999987985999995495699999888986941599999999999999999 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 999999999999744899899999998 Q gi|254780763|r 81 KIEDLVATKTQEITEGLPIPPGLKFPF 107 (107) Q Consensus 81 k~~~~~~~~m~~~tggl~lp~g~~lPf 107 (107) ++++.++++|+++|||| +||||+ || T Consensus 83 ka~~~~~~~m~~~tgg~-~~PG~~-p~ 107 (107) T PRK00153 83 KADETTQEKMGALTGGL-LPPGFK-PF 107 (107) T ss_pred HHHHHHHHHHHHHHCCC-CCCCCC-CC T ss_conf 99999999999984798-999999-98 No 2 >COG0718 Uncharacterized protein conserved in bacteria [Function unknown] Probab=99.97 E-value=1.9e-29 Score=208.92 Aligned_cols=102 Identities=46% Similarity=0.734 Sum_probs=99.3 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 92179999999999999999999985308999976984999996483074688647882910068999999999999999 Q gi|254780763|r 1 MSNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHK 80 (107) Q Consensus 1 M~nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~ 80 (107) |+||+.|++|||+||++|+++|++|++.+|+|+||||+|+|++||+++|++|+|||++++|+|+|+|||||++|+|+|.+ T Consensus 4 ~~~~~~l~kqaqqmQ~~~~~~Q~ela~~ev~g~aggGlVtV~~~G~~ev~~v~Idp~l~dpeD~E~LeDLi~aA~ndA~~ 83 (105) T COG0718 4 MMDMQKLMKQAQQMQKKMQKMQEELAQKEVTGKAGGGLVTVTINGKGEVKSVEIDPSLLDPEDKEMLEDLILAAFNDAKK 83 (105) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEECCCCEEEEEEECCCCEEEEEECHHHCCCCCHHHHHHHHHHHHHHHHH T ss_conf 13099999999999999999999998527765227847999994796478887287875964188999999999999999 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 999999999999744899899999 Q gi|254780763|r 81 KIEDLVATKTQEITEGLPIPPGLK 104 (107) Q Consensus 81 k~~~~~~~~m~~~tggl~lp~g~~ 104 (107) ++++..+++|+++|+||+ | ||+ T Consensus 84 kv~e~~~e~m~~~t~gm~-P-G~~ 105 (105) T COG0718 84 KVEETRKEKMGALTGGMP-P-GFK 105 (105) T ss_pred HHHHHHHHHHHHHHCCCC-C-CCC T ss_conf 999999999998645489-9-999 No 3 >PRK03762 hypothetical protein; Provisional Probab=99.96 E-value=2.1e-28 Score=202.23 Aligned_cols=94 Identities=31% Similarity=0.453 Sum_probs=92.3 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 17999999999999999999998530899997698499999648307468864788291006899999999999999999 Q gi|254780763|r 3 NIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKI 82 (107) Q Consensus 3 nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~ 82 (107) ||++||+|||+||++|+++|++|++.+|+|+||||+|+|++||+++|++|+|||+++ +|+|+|||||++|+|+|++++ T Consensus 2 d~~~mmkqaq~mQ~km~~~Qeel~~~~v~g~sGGGlVkV~~nGk~ev~~i~IDp~l~--eD~emLeDLI~aA~NdA~~k~ 79 (97) T PRK03762 2 DFSKMGEMLEQMQEKAKQLEEENANTEFTAKSGGGLVSVSANGKGEIIDISIDDSLL--EDKESLQILLISAINDVLKMV 79 (97) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEEEECCCEEEEEEECHHHC--CCHHHHHHHHHHHHHHHHHHH T ss_conf 889999999999999999999984879999974967999995573089999887880--768799999999999999999 Q ss_pred HHHHHHHHHHHHCCCC Q ss_conf 9999999999744899 Q gi|254780763|r 83 EDLVATKTQEITEGLP 98 (107) Q Consensus 83 ~~~~~~~m~~~tggl~ 98 (107) ++.++++|+++||||+ T Consensus 80 ~~~~~~~m~~~tgGmg 95 (97) T PRK03762 80 EENRKNLAFNMLGGFG 95 (97) T ss_pred HHHHHHHHHHHHCCCC T ss_conf 9999999998757788 No 4 >PRK00587 hypothetical protein; Provisional Probab=99.94 E-value=2.6e-26 Score=188.90 Aligned_cols=98 Identities=18% Similarity=0.218 Sum_probs=93.4 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 17999999999999999999998530899997698499999648307468864788291006899999999999999999 Q gi|254780763|r 3 NIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKI 82 (107) Q Consensus 3 nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~ 82 (107) ||++||+|||+||++|.+.|++|++.+|++++ ||+|+|++||+++|++|+|||++++|+|+|+|||||++|+|+|++++ T Consensus 2 Nm~~mmkQaqkMQ~~m~~~Qeel~~~~~~~s~-gG~V~v~~nG~~ei~~i~I~pe~VDPeD~EmLeDLi~aAvNeAl~~v 80 (99) T PRK00587 2 NFQKLAQQLKKMQNTMEKKQKEFEEKEFDFDY-KKYILIKIKGNLNIEKIEINKELIDPEDKETLQDMLREAINEAISIT 80 (99) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEC-CCEEEEEEECCEEEEEEEECHHCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 88999999999999999999999737888855-98799999678469998727001694218899999999999999999 Q ss_pred HHHHHHHHHHHHCCCCCCCCC Q ss_conf 999999999974489989999 Q gi|254780763|r 83 EDLVATKTQEITEGLPIPPGL 103 (107) Q Consensus 83 ~~~~~~~m~~~tggl~lp~g~ 103 (107) ++...+.|++.++++ |+|| T Consensus 81 ~~~~~~~m~~~m~~~--tG~f 99 (99) T PRK00587 81 CKERDAIMNSTIPKG--TGLF 99 (99) T ss_pred HHHHHHHHHHHCCCC--CCCC T ss_conf 999999998663788--8999 No 5 >TIGR00103 TIGR00103 conserved hypothetical protein TIGR00103; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta . YbaB is co-transcribed with recR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.. Probab=99.94 E-value=3e-26 Score=188.56 Aligned_cols=101 Identities=43% Similarity=0.656 Sum_probs=99.9 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 17999999999999999999998530899997698499999648307468864788291006899999999999999999 Q gi|254780763|r 3 NIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKI 82 (107) Q Consensus 3 nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~ 82 (107) |+.+||+|||+||.+++.+|+|++..+|+|.||+|+|+|+++|++++++|.|||++++++|+++||++|.+|+|+|++++ T Consensus 12 ~l~~~m~~a~~~q~~~~~l~eE~~~~~~~gksG~GlV~v~~~G~~~~~~~~Id~~l~d~~D~~~Le~~i~~A~NdA~~~v 91 (112) T TIGR00103 12 NLGELMKQAQKVQEKMKKLQEEIAKLEVTGKSGAGLVTVTINGNLELKSIEIDPSLLDPEDKEALEDLITEALNDAVKKV 91 (112) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHEECCCCCCCEEEEEEECCCCCEEEECCHHHCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 79999999999999899999888721316423773578886368652021035533286664889999999999999999 Q ss_pred HHHHHHHHHHHHCCCCCCCCC Q ss_conf 999999999974489989999 Q gi|254780763|r 83 EDLVATKTQEITEGLPIPPGL 103 (107) Q Consensus 83 ~~~~~~~m~~~tggl~lp~g~ 103 (107) ++..+++|..++.+||+|||| T Consensus 92 ~e~~~~kM~~~~~~l~~~PGl 112 (112) T TIGR00103 92 KEKYKEKMALVTKGLPLVPGL 112 (112) T ss_pred HHHHHHHHHHHHHHCCCCCCC T ss_conf 999988899999752789899 No 6 >pfam02575 DUF149 Uncharacterized BCR, YbaB family COG0718. Probab=99.92 E-value=2.3e-24 Score=176.58 Aligned_cols=92 Identities=45% Similarity=0.688 Sum_probs=89.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999853089999769849999964830746886478829100689999999999999999999999 Q gi|254780763|r 8 VGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIEDLVA 87 (107) Q Consensus 8 lkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~~~~ 87 (107) |+|||+||++|+++|++|++.+|+|+|++|+|+|++||+++|++|+|||++++ +|+++|+|+|++|||+|++++++.++ T Consensus 1 ~~qaq~mq~~~~~~q~el~~~~~~~~s~~g~V~v~~~G~~~v~~i~Id~~l~~-~d~e~Ledli~~A~n~A~~~a~~~~~ 79 (92) T pfam02575 1 MKQAQQMQEKMEKAQEELANKEVEGTSGGGLVKVTVNGKGEVKDVEIDPELLD-EDKEMLEDLIVAAINDALKKAEELAK 79 (92) T ss_pred CHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEEECCCCEEEEEEECHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 95899999999999999727499999889839999826847999999889963-88999999999999999999999999 Q ss_pred HHHHHHHCCCCCC Q ss_conf 9999974489989 Q gi|254780763|r 88 TKTQEITEGLPIP 100 (107) Q Consensus 88 ~~m~~~tggl~lp 100 (107) ++|+++||||++| T Consensus 80 ~~m~~~~gg~~~p 92 (92) T pfam02575 80 EEMGKLTGGLNLP 92 (92) T ss_pred HHHHHHHCCCCCC T ss_conf 9999983699999 No 7 >PRK00587 hypothetical protein; Provisional Probab=94.92 E-value=0.28 Score=30.14 Aligned_cols=90 Identities=14% Similarity=0.145 Sum_probs=57.2 Q ss_pred CCCHHHHHHHHH----HHHHHHHHHHHHHH---HEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHH Q ss_conf 921799999999----99999999999985---30899997698499999648307468864788291006899999999 Q gi|254780763|r 1 MSNIMKMVGQFK----EIQGKMEKMKESIT---SLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIA 73 (107) Q Consensus 1 M~nm~~llkqaq----~mq~~m~~~q~eL~---~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~ 73 (107) |.+|..-.++.| +.|+.+.+. ++. .--|++..-|..--+.++=+-++++=+ |++.| .+.+-..|-. T Consensus 3 m~~mmkQaqkMQ~~m~~~Qeel~~~--~~~~s~gG~V~v~~nG~~ei~~i~I~pe~VDPe-D~EmL----eDLi~aAvNe 75 (99) T PRK00587 3 FQKLAQQLKKMQNTMEKKQKEFEEK--EFDFDYKKYILIKIKGNLNIEKIEINKELIDPE-DKETL----QDMLREAINE 75 (99) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC--EEEEECCCEEEEEEECCEEEEEEEECHHCCCCC-CHHHH----HHHHHHHHHH T ss_conf 8999999999999999999999737--888855987999996784699987270016942-18899----9999999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 999999999999999999974489 Q gi|254780763|r 74 AHSDAHKKIEDLVATKTQEITEGL 97 (107) Q Consensus 74 A~N~A~~k~~~~~~~~m~~~tggl 97 (107) |+..+-++.++.+.+.|+++|||+ T Consensus 76 Al~~v~~~~~~~m~~~m~~~tG~f 99 (99) T PRK00587 76 AISITCKERDAIMNSTIPKGTGLF 99 (99) T ss_pred HHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 999999999999986637888999 No 8 >PRK00153 hypothetical protein; Validated Probab=90.95 E-value=0.63 Score=27.87 Aligned_cols=93 Identities=15% Similarity=0.171 Sum_probs=63.8 Q ss_pred HHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHH--HCC-CCHHHHH----HHHHHHHHHHHHHH Q ss_conf 9999999999999999853089999769849999964830746886478--829-1006899----99999999999999 Q gi|254780763|r 9 GQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRS--LLF-EDNVEIL----EDLIIAAHSDAHKK 81 (107) Q Consensus 9 kqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~--~l~-~~d~e~L----edli~~A~N~A~~k 81 (107) +..++|-++++++|+++++..-+-.. .+|+.+-.+..+.|.++-. +++ .-|.+.| .+.+-..+-.|+.+ T Consensus 4 ~nm~~mmkqaq~mq~~~~~~q~el~~----~~v~~~sg~glV~V~~nG~~~v~~i~Id~~ll~~~d~e~LedlI~~A~N~ 79 (107) T PRK00153 4 GNMANLMKQAQQMQEKMQKMQEELAN----KEVTGTAGGGLVTVTMTGKKEVVRVKIDPSVVDPEDVEMLEDLVAAAFND 79 (107) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHC----CEEEEEECCCEEEEEEECCCEEEEEEECHHHCCCCCHHHHHHHHHHHHHH T ss_conf 35999999999999999999999837----58999987985999995495699999888986941599999999999999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 99999999999744899899999998 Q gi|254780763|r 82 IEDLVATKTQEITEGLPIPPGLKFPF 107 (107) Q Consensus 82 ~~~~~~~~m~~~tggl~lp~g~~lPf 107 (107) +-+.+++.+.+-... +.+||++|- T Consensus 80 A~~ka~~~~~~~m~~--~tgg~~~PG 103 (107) T PRK00153 80 ALRKADETTQEKMGA--LTGGLLPPG 103 (107) T ss_pred HHHHHHHHHHHHHHH--HHCCCCCCC T ss_conf 999999999999999--847989999 No 9 >KOG3675 consensus Probab=64.88 E-value=7.6 Score=21.02 Aligned_cols=52 Identities=23% Similarity=0.280 Sum_probs=42.3 Q ss_pred HHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHH Q ss_conf 9999853089999769849999964830746886478829100689999999 Q gi|254780763|r 21 MKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLII 72 (107) Q Consensus 21 ~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~ 72 (107) ++.++--+.|--++|.|+|+++.|-...=..|++|.+.++......|++-+. T Consensus 266 ~~ARfvi~kv~lEageglvkie~T~g~Dd~~vrLDrSkI~svG~pal~~FL~ 317 (417) T KOG3675 266 MRARFVIMKVLLEAGEGLVKIEPTTGSDDARVRLDRSKIDSVGRPALEDFLR 317 (417) T ss_pred HHHHHHHEEHHHHHCCCEEEEEECCCCCCEEEEECHHHHHHCCCHHHHHHHH T ss_conf 3201001012677558827861047886447882166553047177999999 No 10 >pfam11576 DUF3236 Protein of unknown function (DUF3236). This family of proteins with unknown function appears to be restricted to Methanobacteria. Probab=63.17 E-value=14 Score=19.42 Aligned_cols=49 Identities=18% Similarity=0.310 Sum_probs=40.5 Q ss_pred EEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 997698499999648307468864788291006899999999999999999 Q gi|254780763|r 32 GNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKI 82 (107) Q Consensus 32 g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~ 82 (107) |--|.|-.-|.|++++.++.-.++|+-+= .++.+++.+..-.++|++++ T Consensus 103 GvPGSGSmLvimD~kgRiLTaslSPs~ii--Hk~~ie~~v~~E~~eAL~ri 151 (154) T pfam11576 103 GVPGSGSMLVIMDSKGRILTAALSPSHVI--HKKSIEEAVELELEEALERI 151 (154) T ss_pred CCCCCCCEEEEECCCCCEEEECCCCHHHH--HCCCHHHHHHHHHHHHHHHH T ss_conf 58987637999838876875137912643--00449999999999999983 No 11 >TIGR01352 tonB_Cterm TonB family C-terminal domain; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria . Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins . The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores . An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin . To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane. ; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space. Probab=56.02 E-value=21 Score=18.28 Aligned_cols=42 Identities=19% Similarity=0.283 Sum_probs=31.6 Q ss_pred ECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHH Q ss_conf 7698499999648307468864788291006899999999999999 Q gi|254780763|r 34 AGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAH 79 (107) Q Consensus 34 sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~ 79 (107) .|-=.|+++++-+|.|.+++|..+ .....|....+.|+..+- T Consensus 13 ~G~V~v~~~v~~~G~v~~~~v~~S----sg~~~lD~~Al~a~~~~~ 54 (81) T TIGR01352 13 EGTVVVRFTVDASGRVTSVRVLKS----SGNRALDRAALEAVRKAR 54 (81) T ss_pred CCEEEEEEEECCCCCEEEEEEECC----CCCHHHHHHHHHHHHHCC T ss_conf 656899998689983557888305----798788799999998500 No 12 >pfam10437 Lip_prot_lig_C Bacterial lipoate protein ligase C-terminus. This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB pfam03099, further upstream. This C-terminal domain is more stable than the BPL_LipA_LipB and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues. Probab=41.59 E-value=35 Score=16.86 Aligned_cols=52 Identities=27% Similarity=0.330 Sum_probs=39.7 Q ss_pred EEEECCCEEEEEEE-CCCCEEEEEECHHHCCCCHHHHHHHHHH------HHHHHHHHHH Q ss_conf 99976984999996-4830746886478829100689999999------9999999999 Q gi|254780763|r 31 EGNAGGGMVSVRIN-GKNMLTGVKIDRSLLFEDNVEILEDLII------AAHSDAHKKI 82 (107) Q Consensus 31 ~g~sg~g~V~V~~~-G~~~i~~i~Id~~~l~~~d~e~Ledli~------~A~N~A~~k~ 82 (107) +..-.+|.|.+.++ =++.|++++|--+++.+.|.+.|+..+. +++.+++... T Consensus 10 ~~rf~~G~ve~~l~V~~G~I~~iki~gDf~~~~~i~~le~~L~G~~y~~~~i~~~L~~~ 68 (85) T pfam10437 10 DKRFPWGTIEVHLNVEKGKIKDIKIFGDFLGPGDLEELEEKLIGVKYDKEAIKKALNEI 68 (85) T ss_pred EEECCCCEEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHC T ss_conf 34748847999999738999899998456983549999998679986999999999849 No 13 >TIGR00389 glyS_dimeric glycyl-tRNA synthetase; InterPro: IPR002315 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . In eubacteria, glycyl-tRNA synthetase (6.1.1.14 from EC) is an alpha2/beta2 tetramer composed of 2 different subunits , , . In some eubacteria, in archaea and eukaryota, glycyl-tRNA synthetase is an alpha2 dimer, this family. It belongs to class IIc and is one of the most complex synthetases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha (see IPR002310 from INTERPRO) and beta subunits (see IPR002311 from INTERPRO) also lack significant sequence similarity. However, they are translated from a single mRNA , and a single chain glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain . The sequence and crystal structure of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA synthetase due to the conserved nature of the class II active site , .; GO: 0000166 nucleotide binding, 0004820 glycine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006426 glycyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=35.12 E-value=30 Score=17.28 Aligned_cols=50 Identities=20% Similarity=0.382 Sum_probs=34.7 Q ss_pred HHHHHHHHHHHHH-HHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCH Q ss_conf 9999999999999-999853089999769849999964830746886478829100 Q gi|254780763|r 9 GQFKEIQGKMEKM-KESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDN 63 (107) Q Consensus 9 kqaq~mq~~m~~~-q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d 63 (107) ++|+++..-+..+ |.+|......... +|.+++.++| ..++|+++++.=.+ T Consensus 407 kdAk~ies~L~~lse~dl~~~~~~l~~-~G~f~~~~dG----~~ve~~~~~v~i~~ 457 (606) T TIGR00389 407 KDAKKIESALENLSEDDLEEVEKELDE-EGKFIIEVDG----KEVEILKDLVEIKE 457 (606) T ss_pred CHHHHHHHHHHHCCHHHHHHHHHHHHC-CCEEEEEECC----EEEEECHHHEEEEE T ss_conf 117899999973287478999998634-9869999858----18987121242666 No 14 >TIGR01202 bchC Chlorophyll synthesis pathway, bchC; InterPro: IPR005903 Some prokaryotes, such as the purple and green sulphur bacteria, gain energy from a mode of photosynthesis that does not generate oxygen, and is inhibited by its presence , . These organisms do not include chlorophylls in their photosynthetic pigments, but instead use closely related molecules known as bacteriochlorophylls. Like chlorophylls, bacteriochlorophylls are tetrapyroles with a five-membered ring structure, differing in the side chains and hydration state of the ring structure. These alterations in structure determine what light wavelengths can be harvested by the organism . Bacteriochlorophyll a is a photosynthetic pigment found in many of the purple bacteria. It is synthesised from protoporphyrin IX in a series of reactions including magnesium-chelation, methyl transfer, ring formation, vinyl-group reduction protochlorophyllide reduction, and finally phytol addition . This entry represents 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase, the enzyme catalysing the penultimate step in light-independent bacteriochlorophyll a biosynthesis .; GO: 0016491 oxidoreductase activity, 0030494 bacteriochlorophyll biosynthetic process. Probab=32.61 E-value=23 Score=18.01 Aligned_cols=15 Identities=27% Similarity=0.625 Sum_probs=12.4 Q ss_pred HHCCCCCCCCCCCCC Q ss_conf 744899899999998 Q gi|254780763|r 93 ITEGLPIPPGLKFPF 107 (107) Q Consensus 93 ~tggl~lp~g~~lPf 107 (107) .+|-||=||||-+|| T Consensus 46 ~~G~~P~fPGmgyPl 60 (325) T TIGR01202 46 WNGLMPPFPGMGYPL 60 (325) T ss_pred HCCCCCCCCCCCCCC T ss_conf 558985347776788 No 15 >pfam07472 PA-IIL Fucose-binding lectin II (PA-IIL). In Pseudomonas aeruginosa the fucose-binding lectin II (PA-IIL) contributes to the pathogenic virulence of the bacterium. PA-IIL functions as a tetramer when binding fucose. Each monomer is comprised of a nine-stranded, antiparallel beta-sandwich arrangement and contains two calcium cations that mediate the binding of fucose in a recognition mode unique among carbohydrate-protein interactions. Probab=32.22 E-value=35 Score=16.79 Aligned_cols=28 Identities=18% Similarity=0.266 Sum_probs=21.6 Q ss_pred EEECCCEEEEEEECCCCEEEEEECHHHC Q ss_conf 9976984999996483074688647882 Q gi|254780763|r 32 GNAGGGMVSVRINGKNMLTGVKIDRSLL 59 (107) Q Consensus 32 g~sg~g~V~V~~~G~~~i~~i~Id~~~l 59 (107) -.||.|.|+|.+.++++...+.-....| T Consensus 50 l~Sg~GkVriev~~nGkps~l~s~q~~l 77 (107) T pfam07472 50 LNSGTGKVRIEVIANGKPSKLRSRQVTL 77 (107) T ss_pred EECCCCEEEEEEEECCCCCCCEEEECCC T ss_conf 8569972999998389424410011013 No 16 >TIGR01506 ribC_arch riboflavin synthase; InterPro: IPR006399 These archaeal proteins, bacterial riboflavin biosynthesis alpha chain, catalyze the final step in riboflavin biosynthesis. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain. ; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process. Probab=31.13 E-value=46 Score=16.09 Aligned_cols=58 Identities=17% Similarity=0.311 Sum_probs=42.9 Q ss_pred CCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH-----HH-HHHHHCCCCC Q ss_conf 9849999964830746886478829100689999999999999999999999-----99-9997448998 Q gi|254780763|r 36 GGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIEDLVA-----TK-TQEITEGLPI 99 (107) Q Consensus 36 ~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~~~~-----~~-m~~~tggl~l 99 (107) =|||-|.+=-+..|++|+|-++ ..+|+ +.|-+-|.|.|-+-++.... .+ +.+.+| +++ T Consensus 79 ~GLi~vqlmTnk~vidVtvHED--Eaedp---eeL~~~A~nRaReHa~Nl~~ll~~p~raL~k~AG-~Gl 142 (152) T TIGR01506 79 VGLIIVQLMTNKHVIDVTVHED--EAEDP---EELKVVAENRAREHARNLVALLVEPDRALVKEAG-MGL 142 (152) T ss_pred HHHHHHHHHCCCEEEEEEEECC--CCCCH---HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCC-CCC T ss_conf 8886543210878888875358--66786---7889887455668999999986078357554206-877 No 17 >COG2968 Uncharacterized conserved protein [Function unknown] Probab=30.36 E-value=52 Score=15.72 Aligned_cols=64 Identities=20% Similarity=0.264 Sum_probs=46.9 Q ss_pred HEEEEEEECCCEEEEEEE---------------CCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 308999976984999996---------------48307468864788291006899999999999999999999999999 Q gi|254780763|r 27 SLEAEGNAGGGMVSVRIN---------------GKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIEDLVATKTQ 91 (107) Q Consensus 27 ~~~v~g~sg~g~V~V~~~---------------G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~~~~~~m~ 91 (107) ..+++|..+..-|.|++. |--+|-+|.+. ++.+ ....++...+|+-||..|++...+.-.- T Consensus 112 ~~~ltGY~asn~v~V~v~dl~klg~ilD~av~~Ganqi~gisf~---~~d~-~a~~~~Ar~~Av~dA~~kA~~lA~a~gv 187 (243) T COG2968 112 EPELTGYRASNTVEVTVRDLDKLGELLDEAVKAGANQINGISFG---VDDP-EAAVQQARKAAVADAIAKAQALASALGV 187 (243) T ss_pred CCEEEEEEEEEEEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEE---ECCH-HHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 83489998542699998126678799999997575545864675---3887-9999999999999999999999986187 Q ss_pred HHH Q ss_conf 974 Q gi|254780763|r 92 EIT 94 (107) Q Consensus 92 ~~t 94 (107) ++. T Consensus 188 ~l~ 190 (243) T COG2968 188 KLG 190 (243) T ss_pred CCC T ss_conf 423 No 18 >PRK10718 hypothetical protein; Provisional Probab=28.58 E-value=56 Score=15.53 Aligned_cols=49 Identities=18% Similarity=0.108 Sum_probs=30.5 Q ss_pred EEEEECCCEEEEEEECC-CCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHH Q ss_conf 99997698499999648-307468864788291006899999999999999 Q gi|254780763|r 30 AEGNAGGGMVSVRINGK-NMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAH 79 (107) Q Consensus 30 v~g~sg~g~V~V~~~G~-~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~ 79 (107) |++-. ++.|+++++|+ ++|.+|++.++-+...-.-.+-...-+-|.+|. T Consensus 85 fqA~k-~d~V~lvi~G~kgtV~rI~V~D~~i~t~wG~~IGtpFs~lY~KAf 134 (191) T PRK10718 85 FEAMK-GDQVAMVINGQQGTVSRIDVLDSDIPTAWGVKIGTPFSDLYSKAF 134 (191) T ss_pred EEECC-CCEEEEEEECCCCEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHH T ss_conf 85417-881899996688639999985555441125403771688777663 No 19 >COG4572 ChaB Putative cation transport regulator [General function prediction only] Probab=28.22 E-value=51 Score=15.78 Aligned_cols=24 Identities=17% Similarity=0.113 Sum_probs=18.8 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 291006899999999999999999 Q gi|254780763|r 59 LFEDNVEILEDLIIAAHSDAHKKI 82 (107) Q Consensus 59 l~~~d~e~Ledli~~A~N~A~~k~ 82 (107) +..--++.++|++.+|||-|++.- T Consensus 13 vr~~lp~haqdiy~~afnsA~e~y 36 (76) T COG4572 13 VRHQLPSHAQDIYKAAFNSAWEQY 36 (76) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999917999999999999887663 No 20 >PRK05886 yajC preprotein translocase subunit YajC; Validated Probab=27.61 E-value=58 Score=15.42 Aligned_cols=53 Identities=8% Similarity=0.088 Sum_probs=35.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCC Q ss_conf 999999999999999999853089999769849999964830746886478829 Q gi|254780763|r 7 MVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLF 60 (107) Q Consensus 7 llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~ 60 (107) |++..|+-|++.+++|..|..-.-...++| +.-.+..-.-+...++|.|-..- T Consensus 21 ~iRpQkKrqk~~~~m~~sL~~Gd~VvT~~G-l~GtV~~v~dd~v~lEiApGv~v 73 (108) T PRK05886 21 ASRRQRKAMQATIDLHESLQPGDRVHTTSG-LQATIVGITDDTVDLEIAPGVVT 73 (108) T ss_pred HCCHHHHHHHHHHHHHHHCCCCCEEEECCC-CEEEEEEECCCEEEEEECCCCEE T ss_conf 316899999999999983689998997898-28999997188799997699589 No 21 >pfam05958 tRNA_U5-meth_tr tRNA (Uracil-5-)-methyltransferase. This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity. Probab=27.40 E-value=29 Score=17.30 Aligned_cols=52 Identities=10% Similarity=0.024 Sum_probs=36.5 Q ss_pred HHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECC-CCEEEEEECHHHCC Q ss_conf 99999999999999998530899997698499999648-30746886478829 Q gi|254780763|r 9 GQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGK-NMLTGVKIDRSLLF 60 (107) Q Consensus 9 kqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~-~~i~~i~Id~~~l~ 60 (107) .++++|.+.+.+.=..-....++..||-|.++..+..+ .+|..|+|+++++. T Consensus 181 ~~~~~l~~~a~~~~~~~~~~vlDlYcG~Gtfsl~lA~~~~~V~GvE~~~~AV~ 233 (353) T pfam05958 181 AVNIKMLEWACEVTQGSKGDLLELYCGNGNFSLALAQNFRRVLATEIAKPSVN 233 (353) T ss_pred HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCEEEEEECCHHHHH T ss_conf 99999999999986268995899846888888999864787999962599999 No 22 >TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity. Probab=27.30 E-value=59 Score=15.39 Aligned_cols=72 Identities=8% Similarity=0.197 Sum_probs=59.2 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 21799999999999999999999853089999769849999964830746886478829100689999999999999999 Q gi|254780763|r 2 SNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKK 81 (107) Q Consensus 2 ~nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k 81 (107) .+|.++++.+.++.+-+.+..++=..+.|+-+= ++|+++=+|++++|.+-..-.. --++|+.-++| |.|... T Consensus 419 ~~~~~~l~~~~~L~~~L~~~R~~rG~IdFd~~E----~k~ilDe~G~~~~I~~~~R~~A---~klIEefM~~A-Ne~vA~ 490 (755) T TIGR02063 419 APLKEMLKNLEELYKILRKKRKKRGAIDFDSKE----AKIILDENGKPIDIVPRERGDA---HKLIEEFMIVA-NETVAE 490 (755) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC----CEEEECCCCEEEEEEEEECCCC---CHHHHHHHHHH-HHHHHH T ss_conf 115777998999999999877651881237764----1799878842899898413332---22368889999-999999 No 23 >PRK03822 lplA lipoate-protein ligase A; Provisional Probab=26.58 E-value=61 Score=15.31 Aligned_cols=56 Identities=16% Similarity=0.070 Sum_probs=45.5 Q ss_pred EEEEEECCCEEEEEEEC-CCCEEEEEECHHHCCCCHHHHHHHHH------HHHHHHHHHHHHH Q ss_conf 89999769849999964-83074688647882910068999999------9999999999999 Q gi|254780763|r 29 EAEGNAGGGMVSVRING-KNMLTGVKIDRSLLFEDNVEILEDLI------IAAHSDAHKKIED 84 (107) Q Consensus 29 ~v~g~sg~g~V~V~~~G-~~~i~~i~Id~~~l~~~d~e~Ledli------~~A~N~A~~k~~~ 84 (107) +.+..-..|.|.+-++- ++.|++++|--+++.+.+.+.|+..+ ..|+.++++...- T Consensus 255 ~~~~rf~~G~ve~~l~V~~G~I~~~ki~gDff~~~~i~~le~~L~G~~y~~~~i~~~l~~l~~ 317 (338) T PRK03822 255 LLDERFTWGGVELHFDVEKGHITRAQIFTDSLNPAPLEALAGRLQGCLYRADALQQECEALIV 317 (338) T ss_pred EEEEECCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 533553673699999982898989999866899425999999856997789999999998764 No 24 >COG1422 Predicted membrane protein [Function unknown] Probab=26.24 E-value=61 Score=15.27 Aligned_cols=20 Identities=20% Similarity=0.386 Sum_probs=10.0 Q ss_pred HHHHHHHHHHHHHHHHHHHE Q ss_conf 99999999999999998530 Q gi|254780763|r 9 GQFKEIQGKMEKMKESITSL 28 (107) Q Consensus 9 kqaq~mq~~m~~~q~eL~~~ 28 (107) ++.+++|+.|++.|++.++. T Consensus 72 ekm~~~qk~m~efq~e~~eA 91 (201) T COG1422 72 EKMKELQKMMKEFQKEFREA 91 (201) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999 No 25 >PRK13259 regulatory protein SpoVG; Reviewed Probab=26.24 E-value=61 Score=15.27 Aligned_cols=28 Identities=18% Similarity=0.127 Sum_probs=21.6 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9100689999999999999999999999 Q gi|254780763|r 60 FEDNVEILEDLIIAAHSDAHKKIEDLVA 87 (107) Q Consensus 60 ~~~d~e~Ledli~~A~N~A~~k~~~~~~ 87 (107) +++=.+.|++.|+.||++++.+..+... T Consensus 65 t~e~R~~i~~aVl~aY~e~le~~~e~~~ 92 (94) T PRK13259 65 NSDTREKIQDAILKEYEREGELEEEEEE 92 (94) T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCHHHC T ss_conf 9899999999999999987734713340 No 26 >pfam08714 Fae Formaldehyde-activating enzyme (Fae). Formaldehyde-activating enzyme is an enzyme required for energy metabolism and formaldehyde detoxification. It catalyses the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin. Probab=26.08 E-value=62 Score=15.25 Aligned_cols=38 Identities=16% Similarity=0.052 Sum_probs=28.4 Q ss_pred EECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 96483074688647882910068999999999999999999 Q gi|254780763|r 43 INGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIE 83 (107) Q Consensus 43 ~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~ 83 (107) .+--.-|.+|.|+|++. |...|.+.=-+|...|++++- T Consensus 101 a~dl~iiv~V~i~p~a~---D~~kiy~~Ny~ATk~AI~rAm 138 (160) T pfam08714 101 ADDLVIIVSVFIHPEAL---DDKKIYRYNYEATKLAIKRAM 138 (160) T ss_pred HCCEEEEEEEECCCCCC---CHHHHHHHHHHHHHHHHHHHH T ss_conf 03479999997183303---689999999999999999998 No 27 >TIGR01377 soxA_mon sarcosine oxidase, monomeric form; InterPro: IPR006281 This set of sequences describe the alpha subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate . Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the monomeric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process. Probab=24.92 E-value=31 Score=17.19 Aligned_cols=33 Identities=12% Similarity=0.310 Sum_probs=23.7 Q ss_pred HHHHHHEEEEEEECCCEEEEEEEC-CCCEEEEEE Q ss_conf 999853089999769849999964-830746886 Q gi|254780763|r 22 KESITSLEAEGNAGGGMVSVRING-KNMLTGVKI 54 (107) Q Consensus 22 q~eL~~~~v~g~sg~g~V~V~~~G-~~~i~~i~I 54 (107) .+.+.+++.+|+||+++|+|+.+. +++-+++-| T Consensus 168 ~~kV~~i~~~GesGe~~vt~kt~~~sy~a~~lvv 201 (401) T TIGR01377 168 GTKVVEIKPDGESGELLVTVKTTKDSYQAKKLVV 201 (401) T ss_pred CCEEEEEEECCCCCCCEEEEEEECCEEECCEEEE T ss_conf 8603665426767895489997277032135789 No 28 >pfam10991 DUF2815 Protein of unknown function (DUF2815). This is a phage related family of proteins with unknown function. Probab=24.29 E-value=67 Score=15.04 Aligned_cols=41 Identities=29% Similarity=0.298 Sum_probs=21.7 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 2910068999999999999999999999999999744899899999998 Q gi|254780763|r 59 LFEDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGLPIPPGLKFPF 107 (107) Q Consensus 59 l~~~d~e~Ledli~~A~N~A~~k~~~~~~~~m~~~tggl~lp~g~~lPf 107 (107) +.+.|..+ +.+|+.|++.+.+....+ +.. |-.+|+.+++|+ T Consensus 36 ipK~d~~t-----i~~I~~AI~~a~~~~~~~--k~~-g~~~~~~~k~pl 76 (181) T pfam10991 36 IPKSDTET-----IKAIKAAIKAAAEEGWGK--KAD-GKKIPATLKTPL 76 (181) T ss_pred ECCCCHHH-----HHHHHHHHHHHHHHHHHH--HCC-CCCCCCCCCCCC T ss_conf 85798899-----999999999999875410--035-772576565631 No 29 >pfam08345 YscJ_FliF_C Flagellar M-ring protein C-terminal. This domain is found in bacterial flagellar M-ring (FliF) proteins together with the YscJ/FliF domain (pfam01514). Probab=24.17 E-value=58 Score=15.41 Aligned_cols=40 Identities=13% Similarity=0.172 Sum_probs=21.3 Q ss_pred CCEEEEEEECCCCEEEEEE----CH-----------HHCCCCHHHHHHHHHHHHH Q ss_conf 9849999964830746886----47-----------8829100689999999999 Q gi|254780763|r 36 GGMVSVRINGKNMLTGVKI----DR-----------SLLFEDNVEILEDLIIAAH 75 (107) Q Consensus 36 ~g~V~V~~~G~~~i~~i~I----d~-----------~~l~~~d~e~Ledli~~A~ 75 (107) +..++.+...-+.|.++.+ |. .-++++..+.|++||..|+ T Consensus 91 ~~~~~~~~~~~G~I~rlsvaV~vd~~~~~~~~~~~~~~~s~ee~~~i~~lV~~Ai 145 (162) T pfam08345 91 SRTVRHTVQAPGKIKRLSVAVVVDGVYVVADGKAAYVPRSPEELAQIEALVKSAV 145 (162) T ss_pred CCEEEEEECCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC T ss_conf 7489999818981777899999856423677853346679999999999999960 No 30 >COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis] Probab=23.70 E-value=69 Score=14.97 Aligned_cols=77 Identities=16% Similarity=0.107 Sum_probs=51.4 Q ss_pred HHHHHHHHHHHHHH-HHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999-99999853089999769849999964830746886478829100689999999999999999999 Q gi|254780763|r 6 KMVGQFKEIQGKME-KMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIED 84 (107) Q Consensus 6 ~llkqaq~mq~~m~-~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~ 84 (107) -..+-++++|..+. -+|.++..-.+..-. ...|.++++...-.|.+++=- ++ +.-.+-+++|+|.|-.-.+. T Consensus 6 R~~rv~e~i~~~l~~il~~eikDprl~~~~---Vt~V~vS~Dl~~A~Vyvt~l~---~~-~~~~~~~~~~L~~A~g~ir~ 78 (118) T COG0858 6 RAKRVAEQIQKELAEILQREIKDPRLGLVT---VTDVEVSKDLSHAKVYVTVLG---DE-ESSKAEILAALNKAKGFIRS 78 (118) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCEE---EEEEEECCCCCEEEEEEEECC---CC-HHHHHHHHHHHHHHHHHHHH T ss_conf 889999999999999999875497768668---889998799755899996267---74-22289999999996999999 Q ss_pred HHHHH Q ss_conf 99999 Q gi|254780763|r 85 LVATK 89 (107) Q Consensus 85 ~~~~~ 89 (107) ..... T Consensus 79 ~l~~~ 83 (118) T COG0858 79 ELGKR 83 (118) T ss_pred HHHHH T ss_conf 99985 No 31 >PHA00431 internal virion protein C Probab=23.40 E-value=69 Score=14.93 Aligned_cols=58 Identities=21% Similarity=0.236 Sum_probs=41.8 Q ss_pred HHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 853089999769849999964830746886478829100689999999999999999999 Q gi|254780763|r 25 ITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIED 84 (107) Q Consensus 25 L~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~ 84 (107) +.+...+....||-| +.++-.+. +.|.+|++++...=.+.-+.+--+|.+.|++.+.+ T Consensus 658 v~n~ql~~~~qgg~I-~lmd~TG~-Vrvr~d~ell~~~y~e~Q~~~~e~a~e~alkd~nk 715 (749) T PHA00431 658 VTNKQLTVYTQGGSI-YLMDTTGQ-VRVRYDKELLSKVYRENQQKLAEEAREKALKDVNK 715 (749) T ss_pred CCCCEEEEEECCCEE-EEECCCCC-EEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 436625888449738-99738884-68997799999999999999999999999863101 No 32 >pfam07830 PP2C_C Protein serine/threonine phosphatase 2C, C-terminal domain. Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain. Probab=22.85 E-value=71 Score=14.86 Aligned_cols=51 Identities=12% Similarity=0.245 Sum_probs=30.8 Q ss_pred EECHHHCCCCHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHC-CC-CCCCCCCC Q ss_conf 86478829100689999999999999999999----99999999744-89-98999999 Q gi|254780763|r 53 KIDRSLLFEDNVEILEDLIIAAHSDAHKKIED----LVATKTQEITE-GL-PIPPGLKF 105 (107) Q Consensus 53 ~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~----~~~~~m~~~tg-gl-~lp~g~~l 105 (107) +.+++++..+ .-|+..|..-+.+.+++... .-..-|..+.. ++ +||||-.| T Consensus 12 kv~~EAv~kE--~eLd~~le~~v~Eii~~~~~~~~~dl~~vm~~La~e~Ip~LPPGGGl 68 (81) T pfam07830 12 KVSEEAVKKE--AELDKYLEQRVEEIIEKSSEDGVPDLLHVMKTLASEDIPGLPPGGGL 68 (81) T ss_pred CCCHHHHHHH--HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCH T ss_conf 9999999999--99999999999999997254575229999999875578999999469 No 33 >COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane] Probab=22.39 E-value=73 Score=14.80 Aligned_cols=42 Identities=19% Similarity=0.205 Sum_probs=31.3 Q ss_pred ECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHH Q ss_conf 7698499999648307468864788291006899999999999999 Q gi|254780763|r 34 AGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAH 79 (107) Q Consensus 34 sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~ 79 (107) .|-=.|+++++-+|.|.+++|-.+ .....|....+.|++.+. T Consensus 179 ~G~V~V~f~i~~~G~v~~v~v~~S----Sg~~~lD~aal~air~~~ 220 (244) T COG0810 179 EGTVKVKFTIDPDGNVTNVRVLKS----SGSPALDRAALEAIRKWR 220 (244) T ss_pred CCEEEEEEEECCCCCEEEEEEEEC----CCCHHHHHHHHHHHHHHC T ss_conf 406999999899997845788623----896788899999999725 No 34 >TIGR03422 mito_frataxin frataxin. Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately. Probab=21.58 E-value=75 Score=14.70 Aligned_cols=38 Identities=16% Similarity=0.318 Sum_probs=26.0 Q ss_pred HHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCE Q ss_conf 99999999999998530899997698499999648307 Q gi|254780763|r 12 KEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNML 49 (107) Q Consensus 12 q~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i 49 (107) ..+...+.+..+......++....+|.+++++.+.+++ T Consensus 11 ~~ie~~le~~~d~~~~~d~D~~~~~gvLti~~~~~~~~ 48 (97) T TIGR03422 11 DHLLDKLEELGESRPDLDFDVEYSSGVLTLELPSVGTY 48 (97) T ss_pred HHHHHHHHHHHCCCCCCCEEEECCCCEEEEEECCCCEE T ss_conf 99999999752214565621133698799998899789 No 35 >TIGR00537 hemK_rel_arch methylase, putative; InterPro: IPR004557 These proteins exhibit homology to the Saccharomyces cerevisiae (yeast) ORF YDR140w (FYV9). No known function has been described for this yeast ORF though the null mutant is viable and exhibits K1 killer toxin hypersensitivity. Members of this entry are weakly related to the yeast ORF YNL063w which is a putative S-adenosyl-methionine-dependent methyltransferase . Members of this entry are found in archaeal, bacterial and eukaryotic lineages.; GO: 0008168 methyltransferase activity. Probab=21.08 E-value=19 Score=18.53 Aligned_cols=34 Identities=24% Similarity=0.290 Sum_probs=30.3 Q ss_pred HEEEEEEECCCEEEEEEECCCC--EEEEEECHHHCC Q ss_conf 3089999769849999964830--746886478829 Q gi|254780763|r 27 SLEAEGNAGGGMVSVRINGKNM--LTGVKIDRSLLF 60 (107) Q Consensus 27 ~~~v~g~sg~g~V~V~~~G~~~--i~~i~Id~~~l~ 60 (107) ....|.-+|-|+|.+-+.+++. |+.+.|+|-+.. T Consensus 23 deVlEiG~GtGlvair~~~Kg~k~i~~tDinP~Avk 58 (183) T TIGR00537 23 DEVLEIGAGTGLVAIRLKEKGKKKILTTDINPFAVK 58 (183) T ss_pred CEEEEEECCHHHHHHHHHCCCCCEEEEEECCHHHHH T ss_conf 528997168048999985158820788636879999 No 36 >PRK05031 tRNA (uracil-5-)-methyltransferase; Validated Probab=20.42 E-value=68 Score=14.98 Aligned_cols=50 Identities=8% Similarity=0.043 Sum_probs=30.9 Q ss_pred HHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECC-CCEEEEEECHHHC Q ss_conf 9999999999999998530899997698499999648-3074688647882 Q gi|254780763|r 10 QFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGK-NMLTGVKIDRSLL 59 (107) Q Consensus 10 qaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~-~~i~~i~Id~~~l 59 (107) ++++|-+.+.+.=..-....++..||-|.++..+... .+|..|+|+++.+ T Consensus 192 ~~e~l~~~a~~~~~~~~~~vlDLYcG~Gtfsl~LA~~~~~V~gVE~~~~aV 242 (363) T PRK05031 192 VNEKMLEWALDATKGSKGDLLELYCGNGNFTLALARNFRRVLATEISKPSV 242 (363) T ss_pred HHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCEEEEEECCHHHH T ss_conf 999999999997613898289860586642699886268799995389999 Done!