Query gi|254780138|ref|YP_003064551.1| ABC transporter [Candidatus Liberibacter asiaticus str. psy62] Match_columns 373 No_of_seqs 186 out of 1048 Neff 6.2 Searched_HMMs 39220 Date Sun May 22 12:36:25 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780138.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR00056 TIGR00056 conserved 100.0 0 0 532.2 29.0 264 110-373 6-275 (275) 2 COG0767 Ttg2B ABC-type transpo 100.0 0 0 506.1 31.7 262 105-373 6-267 (267) 3 pfam02405 DUF140 Domain of unk 100.0 0 0 473.1 29.2 215 154-368 1-215 (215) 4 cd06844 STAS Sulphate Transpor 98.3 3E-06 7.7E-11 62.4 7.9 85 3-88 6-93 (100) 5 cd07043 STAS_anti-anti-sigma_f 98.3 5E-06 1.3E-10 60.9 7.6 84 3-88 6-92 (99) 6 COG3113 Predicted NTP binding 98.2 3.4E-06 8.5E-11 62.1 6.4 80 7-89 12-94 (99) 7 pfam01740 STAS STAS domain. Th 98.1 2.7E-05 7E-10 55.7 8.2 86 3-89 7-95 (106) 8 TIGR02886 spore_II_AA anti-sig 97.7 7.7E-06 2E-10 59.6 0.8 86 3-89 6-94 (106) 9 COG1366 SpoIIAA Anti-anti-sigm 97.6 0.00041 1E-08 47.5 7.6 83 7-90 15-100 (117) 10 cd07042 STAS_SulP_like_sulfate 97.4 0.001 2.6E-08 44.7 7.3 87 2-88 6-95 (107) 11 cd07041 STAS_RsbR_RsbS_like Su 96.7 0.011 2.9E-07 37.4 7.7 82 4-86 9-93 (109) 12 TIGR00377 ant_ant_sig anti-ant 96.0 0.023 5.7E-07 35.3 6.1 87 3-89 10-99 (109) 13 PRK10782 DL-methionine transpo 79.1 4.2 0.00011 19.3 5.9 51 238-288 117-175 (217) 14 COG0795 Predicted permeases [G 76.3 5.1 0.00013 18.8 13.4 23 248-270 336-358 (364) 15 COG4591 LolE ABC-type transpor 69.5 7.2 0.00018 17.7 12.5 96 234-334 295-398 (408) 16 pfam03739 YjgP_YjgQ Predicted 69.2 7.3 0.00019 17.6 12.7 21 165-185 274-294 (353) 17 KOG0236 consensus 68.5 7.6 0.00019 17.5 7.4 67 125-191 111-188 (665) 18 COG5439 Uncharacterized conser 58.3 9.8 0.00025 16.7 2.8 53 9-63 17-72 (112) 19 COG4215 ArtQ ABC-type arginine 54.5 13 0.00033 15.8 11.6 125 130-268 24-156 (230) 20 pfam02687 FtsX Predicted perme 48.7 16 0.00041 15.2 12.5 97 230-331 72-168 (174) 21 PRK11146 outer membrane-specif 47.4 17 0.00043 15.1 12.2 96 234-334 293-402 (412) 22 TIGR01253 thiP thiamine/thiami 42.9 19 0.0005 14.6 3.0 22 304-325 446-467 (519) 23 PRK08456 flagellar motor prote 41.4 20 0.00052 14.5 6.4 57 157-219 142-198 (257) 24 TIGR02182 GRXB Glutaredoxin, G 40.7 7.1 0.00018 17.7 -0.2 14 44-57 108-121 (212) 25 pfam09838 DUF2065 Uncharacteri 40.4 21 0.00054 14.4 2.9 33 152-184 22-54 (57) 26 KOG2927 consensus 39.3 22 0.00056 14.3 3.1 50 184-234 215-268 (372) 27 pfam05197 TRIC TRIC channel. T 39.3 22 0.00056 14.3 4.1 35 268-302 15-49 (197) 28 COG4177 LivM ABC-type branched 39.2 22 0.00056 14.3 6.6 69 212-298 170-238 (314) 29 COG1079 Uncharacterized ABC-ty 38.8 22 0.00057 14.2 4.6 88 235-333 170-262 (304) 30 TIGR00815 sulP sulfate permeas 38.1 23 0.00059 14.1 2.9 21 201-221 307-327 (638) 31 PRK13108 prolipoprotein diacyl 37.9 23 0.00059 14.1 2.3 22 212-233 133-154 (460) 32 PRK10814 outer membrane-specif 37.0 24 0.00061 14.0 13.4 97 234-335 290-390 (396) 33 pfam11964 DUF3478 Protein of u 36.6 24 0.00062 14.0 7.5 84 2-86 8-94 (118) 34 pfam04123 DUF373 Domain of unk 35.8 25 0.00063 13.9 8.3 29 176-204 184-213 (344) 35 TIGR03004 ectoine_ehuC ectoine 34.0 26 0.00068 13.7 11.1 116 209-327 77-200 (216) 36 PRK08124 flagellar motor prote 33.0 27 0.0007 13.6 6.3 58 157-220 143-200 (263) 37 PRK08990 flagellar motor prote 31.9 29 0.00073 13.5 6.3 62 156-223 138-199 (253) 38 COG1291 MotA Flagellar motor c 31.6 29 0.00074 13.4 5.4 63 158-226 144-206 (266) 39 PRK11301 livM leucine/isoleuci 31.5 29 0.00074 13.4 4.7 52 236-299 292-343 (416) 40 pfam08566 Pam17 Mitochondrial 28.9 32 0.00081 13.1 6.1 50 238-299 62-113 (174) 41 PRK00965 tetrahydromethanopter 27.9 33 0.00085 13.0 2.2 29 66-94 25-56 (108) 42 COG1987 FliQ Flagellar biosynt 26.9 34 0.00088 12.9 9.7 66 155-221 8-75 (89) 43 PRK06926 flagellar motor prote 26.9 35 0.00088 12.9 6.3 47 159-211 149-195 (272) 44 pfam04710 Pellino Pellino. Pel 26.7 7.5 0.00019 17.6 -2.0 64 1-64 181-256 (416) 45 pfam03683 UPF0175 Uncharacteri 26.5 14 0.00037 15.6 -0.6 36 218-254 29-64 (76) 46 PRK11123 arginine transporter 26.4 35 0.0009 12.8 16.6 126 142-273 33-168 (238) 47 pfam08496 Peptidase_S49_N Pept 26.4 35 0.0009 12.8 4.1 14 70-83 43-56 (154) 48 PRK09109 motC flagellar motor 25.5 36 0.00093 12.7 6.2 58 157-220 142-199 (246) 49 TIGR00780 ccoN cytochrome c ox 25.5 36 0.00093 12.7 3.9 98 158-282 7-112 (485) 50 COG2239 MgtE Mg/Co/Ni transpor 25.4 37 0.00093 12.7 8.5 130 168-334 287-418 (451) 51 pfam07297 DPM2 Dolichol phosph 24.1 39 0.00098 12.6 3.0 34 250-283 37-70 (80) 52 COG2120 Uncharacterized protei 23.5 22 0.00056 14.3 -0.1 11 58-68 101-111 (237) 53 KOG3944 consensus 23.3 39 0.00099 12.5 1.2 23 307-329 235-257 (291) 54 PRK06743 flagellar motor prote 23.0 40 0.001 12.4 6.4 57 157-219 139-195 (254) 55 pfam01312 Bac_export_2 FlhB Hr 22.8 41 0.001 12.4 16.2 35 292-326 123-157 (343) 56 PRK10535 macrolide transporter 22.2 42 0.0011 12.3 13.6 94 226-329 532-633 (648) 57 KOG0539 consensus 22.0 34 0.00087 12.9 0.7 40 254-293 137-182 (240) 58 pfam03095 PTPA Phosphotyrosyl 21.8 43 0.0011 12.3 8.1 109 41-149 5-125 (298) 59 COG2011 AbcD ABC-type metal io 21.7 43 0.0011 12.2 3.9 105 163-293 66-185 (222) 60 TIGR01389 recQ ATP-dependent D 21.4 37 0.00095 12.6 0.8 13 74-86 146-158 (607) 61 COG3763 Uncharacterized protei 20.7 45 0.0011 12.1 3.9 21 269-289 8-28 (71) 62 COG4062 MtrB Tetrahydromethano 20.5 45 0.0012 12.1 3.0 33 66-98 25-60 (108) No 1 >TIGR00056 TIGR00056 conserved hypothetical protein; InterPro: IPR003453 This domain has no known function nor do any of the proteins that possess it. The aligned region is approximately 150 amino acids long.. Probab=100.00 E-value=0 Score=532.18 Aligned_cols=264 Identities=35% Similarity=0.540 Sum_probs=244.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8999859999999999999999999999999997402678----872899999999983776999999999999999999 Q gi|254780138|r 110 LHYHIGKKIVKFINDSCSQAHILGLVISNTGEFCASSYKF----KGFLLSLIRQMYYVGVSGVPVVILISFVTGAVIAQQ 185 (373) Q Consensus 110 ~~~~iG~~~~~~~~~~~~~~~f~G~~~~~~~~~~~~~~~~----r~~~~~~~~q~~~~G~~alpiv~l~~~~~G~v~a~q 185 (373) ...++|+...+..+.....+.+.|........-..++++. ..+...+++|++..|++|+||+.++++++|+|+++| T Consensus 6 ~~~~L~k~~~~~~ntfl~Af~l~g~~~F~~~~g~~~~r~~kyikqf~~~~~~~ql~~vG~~s~~i~l~t~~~iG~v~alQ 85 (275) T TIGR00056 6 LIAKLGKEIIETGNTFLRAFLLTGLMLFQLLKGKPNIRKHKYIKQFPLSALLKQLNTVGVESLPIILVTSLFIGMVIALQ 85 (275) T ss_pred HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 26533336789999999999999999999973787765413000121018999998888999999999999999999999 Q ss_pred HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 99987542756689999999999998999999999996457899999999875001344442786899999999999999 Q gi|254780138|r 186 GAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRILISPRIWALII 265 (373) Q Consensus 186 ~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i 265 (373) +|.+|++|||+..+|+++++++.|||||++||+++|||+|||+|||||+||+||||||||+|++||++|||.||++|+++ T Consensus 86 ~a~~l~~fgA~~~~g~~vals~~RELgPvltal~~AGRvgSa~TA~IG~MriTEqlDAL~~m~~~P~~~LV~PR~lA~~i 165 (275) T TIGR00056 86 GALQLIAFGAETSIGGLVALSLLRELGPVLTALVVAGRVGSAFTAEIGLMRITEQLDALEMMAVNPVEFLVLPRVLACVI 165 (275) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 99999971742589999999998889999999999998788988875134566687788862458266577889999998 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHH--HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH Q ss_conf 9999999999999999999999861139899999999861699--99999999999999999998317704559865899 Q gi|254780138|r 266 SLPLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFHSTATLA--NIFTGLIKAPFMACAIGIVAMKEGFAVGVHSNSLG 343 (373) Q Consensus 266 ~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~~~~~~~--d~~~~~~K~~~fg~~i~~i~c~~Gl~~~~~a~~VG 343 (373) ++|+|+++++++|++||++++...+|++...||+++++.++.| |+..|++|+++||++|++||||+||.++|++|||| T Consensus 166 ~~PlLt~L~~~~gi~GG~~~~~~~~gi~~~~f~~~~~~~v~~w~~D~~~G~~Ka~fFGv~Ia~igc~~Gf~t~g~~~g~G 245 (275) T TIGR00056 166 MLPLLTVLSLVAGILGGAFIASSLLGIGSESFWSKMQNAVEKWNYDIFAGLVKAVFFGVAIAIIGCYYGFTTKGGTEGVG 245 (275) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHHHHHHHHHCCCCCCCCCCCHH T ss_conf 88899999999998614987887751440467887622211104421441135789999999999732654458866313 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 999999999999999999999999985089 Q gi|254780138|r 344 KKVTTCVVQSISIVIIIDSLFAIFYFAIGI 373 (373) Q Consensus 344 ~att~aVV~si~~ii~~d~~~~~~~~~~gi 373 (373) ++||+|||+|+.+|++.|++||.++.++|+ T Consensus 246 ~~TT~sVVts~l~I~~lDf~ls~i~f~LG~ 275 (275) T TIGR00056 246 RSTTRSVVTSLLAILILDFVLSAIMFQLGI 275 (275) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 789999999999999999999999985079 No 2 >COG0767 Ttg2B ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism] Probab=100.00 E-value=0 Score=506.09 Aligned_cols=262 Identities=39% Similarity=0.611 Sum_probs=248.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 13665899985999999999999999999999999999740267887289999999998377699999999999999999 Q gi|254780138|r 105 NSFKNLHYHIGKKIVKFINDSCSQAHILGLVISNTGEFCASSYKFKGFLLSLIRQMYYVGVSGVPVVILISFVTGAVIAQ 184 (373) Q Consensus 105 ~~~~~~~~~iG~~~~~~~~~~~~~~~f~G~~~~~~~~~~~~~~~~r~~~~~~~~q~~~~G~~alpiv~l~~~~~G~v~a~ 184 (373) +...+.+.++|+.+.+..++.+....|+|..+.. .++.+.+|+++.+|+++.|.+|+||+.++++++|+++++ T Consensus 6 ~~~~~~~~~~g~~~~~~~~~~g~~~~~~~~~l~~-------~~~~~~~~~~~~~q~~~vg~~sl~Iv~~~~~~vG~vla~ 78 (267) T COG0767 6 PRLIALLRRLGKALLKTLRSLGRAFLFLGNALRG-------LFREPFRPRELVRQLYFVGVGSLPIVALTSLFVGAVLAL 78 (267) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 1389999999898999999999999999999998-------402436689999999998600379999999999999999 Q ss_pred HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 99998754275668999999999999899999999999645789999999987500134444278689999999999999 Q gi|254780138|r 185 QGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRILISPRIWALI 264 (373) Q Consensus 185 q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~ 264 (373) |++.||.+|||+.+++++++++.+||+||++|++++|||+|||+|||||+||+||||||||+||+||++|||.||++|++ T Consensus 79 qg~~~L~~fGAe~~~g~lval~~~RElgPvlTal~~AGr~gSa~tAeIG~MritEEIDAlevmgidPi~~LV~PRvlA~~ 158 (267) T COG0767 79 QGYTQLRDFGAEDFSGFLVALSLLRELGPVLTALVVAGRVGSAITAEIGAMRITEEIDALEVMGIDPISRLVAPRVLAGV 158 (267) T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHH T ss_conf 99999998089999999999999999878999999985338899999812669889999998577943888788899999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHH Q ss_conf 99999999999999999999999861139899999999861699999999999999999999983177045598658999 Q gi|254780138|r 265 ISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFHSTATLANIFTGLIKAPFMACAIGIVAMKEGFAVGVHSNSLGK 344 (373) Q Consensus 265 i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~~~~~~~d~~~~~~K~~~fg~~i~~i~c~~Gl~~~~~a~~VG~ 344 (373) +++|+|+.+++.+|++||+++++..+|+++..|++++++.++++|++.|++|+++||++|++|+||+||+++|++|+||+ T Consensus 159 i~~plL~~l~~~~gi~GG~~v~~~~~gi~~g~f~~~l~~~v~~~dv~~g~iKa~~fg~ii~li~cy~G~~~~gg~~gvG~ 238 (267) T COG0767 159 IVLPLLTALADAAGILGGYLVAVFLLGISPGAFLSRLQTFVGPEDVLIGLIKAPVFGVIIGLIGCYYGYTVGGGPEGVGR 238 (267) T ss_pred HHHHHHHHHHHHHHHHHHHHHEEEECCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCEECCCCCCHHHH T ss_conf 99999999999999850250014441798689999998625899999999999999999999996647102899552737 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 99999999999999999999999985089 Q gi|254780138|r 345 KVTTCVVQSISIVIIIDSLFAIFYFAIGI 373 (373) Q Consensus 345 att~aVV~si~~ii~~d~~~~~~~~~~gi 373 (373) +||+|||.|+++|++.|++++.+++..|+ T Consensus 239 att~sVV~s~~~v~~~d~v~t~~~~~~~~ 267 (267) T COG0767 239 ATTRSVVTSILVVIVLDFVLTALMFGVGI 267 (267) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 76589999999999999999999845689 No 3 >pfam02405 DUF140 Domain of unknown function DUF140. This domain has no known function nor do any of the proteins that possess it. The aligned region is approximately 150 amino acids long. Probab=100.00 E-value=0 Score=473.08 Aligned_cols=215 Identities=40% Similarity=0.689 Sum_probs=212.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999983776999999999999999999999875427566899999999999989999999999964578999999 Q gi|254780138|r 154 LSLIRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIG 233 (373) Q Consensus 154 ~~~~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG 233 (373) +++++|++++|++|+|++.++++++|+++++|++.+|++||++.+++++++++++||+||++||+++|||+||++||||| T Consensus 1 ~~~~~Q~~~~G~~sl~iv~~~~~~~G~v~~~q~~~~l~~~G~~~~ig~~~~~~~vRElgP~ltalilagR~Gsa~aAElG 80 (215) T pfam02405 1 REILRQIYFVGVGSLPIVALTAFFIGAVLALQGAYQLRQFGAESFVGALVALSLVRELGPVLTALLVAGRVGSAITAELG 80 (215) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 97899999998849999999999999999999999999849189999999999999998999999999987139999998 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHH Q ss_conf 99875001344442786899999999999999999999999999999999999986113989999999986169999999 Q gi|254780138|r 234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFHSTATLANIFTG 313 (373) Q Consensus 234 ~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~~~~~~~d~~~~ 313 (373) +||+||||||||+||+||++|||+||++|+++++|+|++++++++++|||++++..+|++++.|++++.+.++++|++.+ T Consensus 81 tM~v~eeIDAL~~mgi~P~~yLv~PRvlA~~i~~p~L~i~~~~~~~~gG~l~~~~~~~i~~~~f~~~~~~~~~~~Dl~~~ 160 (215) T pfam02405 81 TMRVTEEIDALEVMGIDPIRYLVLPRVLAGVIALPLLTIIADLVGILGGYLVAVVVLGISPGAFLHSFQSFVDPTDVLVG 160 (215) T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHH T ss_conf 72698899999984899247765989999999999999999999999999999997699999999999997789999999 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999983177045598658999999999999999999999999999 Q gi|254780138|r 314 LIKAPFMACAIGIVAMKEGFAVGVHSNSLGKKVTTCVVQSISIVIIIDSLFAIFY 368 (373) Q Consensus 314 ~~K~~~fg~~i~~i~c~~Gl~~~~~a~~VG~att~aVV~si~~ii~~d~~~~~~~ 368 (373) ++|+++||++|++++||+||++++|+++||++||+|||+|+++|++.|++++.+| T Consensus 161 l~K~~vFG~~I~~i~c~~Gl~~~~ga~~VG~att~aVV~s~~~I~~~d~~~s~l~ 215 (215) T pfam02405 161 LIKAVVFGLIIALIGCYYGLTAKGGAEGVGRATTRAVVTSIVAIIVLDFVLTALF 215 (215) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999996568157999748879999999999999999999999879 No 4 >cd06844 STAS Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation. Probab=98.32 E-value=3e-06 Score=62.43 Aligned_cols=85 Identities=15% Similarity=0.329 Sum_probs=72.8 Q ss_pred CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHH Q ss_conf 5882799984035635522007999986431167880899701051521299999999997---5187643158991269 Q gi|254780138|r 3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIE 79 (373) Q Consensus 3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~ 79 (373) .|+.++++++|+.+..+...+.+++...+.+. ..+.+++|+|+++++||+|.-.|....+ ..+.+....+.+|..+ T Consensus 6 ~d~~lVv~l~GelD~~ta~~lr~~l~~~i~~~-~~~~iVvDls~v~f~DSsGl~~Ll~~~k~~~~~Gg~l~l~~~~p~V~ 84 (100) T cd06844 6 VDDYWVVRLEGELDHHSVEQFKEELLHNITNV-AGKTIVIDISALEFMDSSGTGVLLERSRLAEAVGGQFVLTGISPAVR 84 (100) T ss_pred ECCEEEEEEEEEECHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCEEECHHHHHHHHHHHHHHHHCCCEEEEECCCHHHH T ss_conf 99999999779983888999999999999738-99789998768818847899999999999996699899983998999 Q ss_pred HHHHHHHHH Q ss_conf 999988642 Q gi|254780138|r 80 QLFSLISFT 88 (373) Q Consensus 80 ~Ll~Ll~~~ 88 (373) +++++.... T Consensus 85 ~vf~~tGld 93 (100) T cd06844 85 ITLTESGLD 93 (100) T ss_pred HHHHHHCCC T ss_conf 999994868 No 5 >cd07043 STAS_anti-anti-sigma_factors Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response). The STAS domain is also found in the C- terminal region of sulphate transporters and stressosomes. Probab=98.25 E-value=5e-06 Score=60.94 Aligned_cols=84 Identities=20% Similarity=0.404 Sum_probs=71.3 Q ss_pred CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHH---CCCCCCCCCCCHHHH Q ss_conf 58827999840356355220079999864311678808997010515212999999999975---187643158991269 Q gi|254780138|r 3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFMEK---YHGKIKLQGVSTHIE 79 (373) Q Consensus 3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~~---~~~~~~~~~l~~~~~ 79 (373) +++..++++.|+++..+...+.+.+.+..... .+.+++|+++++++||+|...|..+.+. .+.+....+.++..+ T Consensus 6 ~~~~~vi~l~G~ld~~~~~~~~~~~~~~~~~~--~~~vilDls~v~~idSsgl~~L~~~~~~~~~~~~~l~l~~~~~~v~ 83 (99) T cd07043 6 RGGVLVVRLSGELDAATAPELREALEELLAEG--PRRLVLDLSGVTFIDSSGLGVLLGAYKRARAAGGRLVLVNVSPAVR 83 (99) T ss_pred ECCEEEEEEEEEEEHHHHHHHHHHHHHHHHCC--CCEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHHH T ss_conf 89999999999985642899999999999769--9789998858876206899999999999872799199990998999 Q ss_pred HHHHHHHHH Q ss_conf 999988642 Q gi|254780138|r 80 QLFSLISFT 88 (373) Q Consensus 80 ~Ll~Ll~~~ 88 (373) +++++.... T Consensus 84 ~il~~~gl~ 92 (99) T cd07043 84 RVLELTGLD 92 (99) T ss_pred HHHHHCCCC T ss_conf 999981988 No 6 >COG3113 Predicted NTP binding protein (contains STAS domain) [General function prediction only] Probab=98.24 E-value=3.4e-06 Score=62.13 Aligned_cols=80 Identities=16% Similarity=0.354 Sum_probs=65.2 Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHCCC---CCCCCCCCHHHHHHHH Q ss_conf 7999840356355220079999864311678808997010515212999999999975187---6431589912699999 Q gi|254780138|r 7 TVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFMEKYHG---KIKLQGVSTHIEQLFS 83 (373) Q Consensus 7 ~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~~~~~---~~~~~~l~~~~~~Ll~ 83 (373) -++.++|+.+-+++.++|....+.+.+ .+.+++|++++.+.||+|.++|.++.+.++. ...+++.|+..+.|.+ T Consensus 12 ~tL~LsGeL~r~tl~~lw~~r~~~~~~---~~~~~idLs~v~rvDSaglALL~~~~~~~k~~g~~~~L~~~p~~L~tLa~ 88 (99) T COG3113 12 DTLVLSGELDRDTLLPLWSQREAQLKQ---LDTVRIDLSGVSRVDSAGLALLLHLIRLAKKQGNAVTLTGVPEQLRTLAE 88 (99) T ss_pred CEEEEECCCCHHHHHHHHHHHHHHCCC---CCEEEEEHHHCCEECHHHHHHHHHHHHHHHHHCCEEEEECCCHHHHHHHH T ss_conf 829995135487789999999986365---67589874344220227899999999999870880278637499999999 Q ss_pred HHHHHH Q ss_conf 886422 Q gi|254780138|r 84 LISFTH 89 (373) Q Consensus 84 Ll~~~~ 89 (373) +++..+ T Consensus 89 Ly~l~~ 94 (99) T COG3113 89 LYNLSD 94 (99) T ss_pred HHCCHH T ss_conf 969665 No 7 >pfam01740 STAS STAS domain. The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. Probab=98.06 E-value=2.7e-05 Score=55.72 Aligned_cols=86 Identities=19% Similarity=0.320 Sum_probs=71.1 Q ss_pred CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHH Q ss_conf 5882799984035635522007999986431167880899701051521299999999997---5187643158991269 Q gi|254780138|r 3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIE 79 (373) Q Consensus 3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~ 79 (373) .+|..++++.|+++..+...+.+.+.+.+... +.+.+++|+++++++||+|+..|.++.+ +.+.+..+.++++..+ T Consensus 7 ~~gv~vi~l~G~Ld~~~a~~~~~~l~~~~~~~-~~~~vvlD~~~v~~iDssgl~~l~~~~~~~~~~g~~l~l~~~~~~v~ 85 (106) T pfam01740 7 IPGILILRLDGPLDFANAEAFRERLLRAIEEG-EIRHVILDLSGVPFIDSSGLGALLELYKELRRRGVELVLVGPSPEVR 85 (106) T ss_pred ECCEEEEEEEEEEEHHHHHHHHHHHHHHHHCC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCCHHHH T ss_conf 69999999676897889999999999998658-99789999708988890299999999999997699099976998999 Q ss_pred HHHHHHHHHH Q ss_conf 9999886422 Q gi|254780138|r 80 QLFSLISFTH 89 (373) Q Consensus 80 ~Ll~Ll~~~~ 89 (373) +.++...... T Consensus 86 ~~l~~~gl~~ 95 (106) T pfam01740 86 RTLEKTGLDD 95 (106) T ss_pred HHHHHHCCCC T ss_conf 9999809986 No 8 >TIGR02886 spore_II_AA anti-sigma F factor antagonist; InterPro: IPR014237 This represents the anti-sigma F factor antagonist, also known as stage II sporulation protein AA. This protein is universally conserved in the endospore-forming bacteria, all of which belong to the Firmcutes.; GO: 0045152 antisigma factor binding, 0006355 regulation of transcription DNA-dependent, 0030435 sporulation. Probab=97.74 E-value=7.7e-06 Score=59.57 Aligned_cols=86 Identities=19% Similarity=0.387 Sum_probs=73.4 Q ss_pred CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHH-HH--HHHCCCCCCCCCCCHHHH Q ss_conf 588279998403563552200799998643116788089970105152129999999-99--975187643158991269 Q gi|254780138|r 3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIM-YF--MEKYHGKIKLQGVSTHIE 79 (373) Q Consensus 3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~-~l--~~~~~~~~~~~~l~~~~~ 79 (373) .++.++++++|..|.++...+..+....+.+. +-+.+++|+++|+++||||.-.+. |. .+..+++...++.+|..+ T Consensus 6 ~~~~L~Vrl~GELDHH~aE~~R~~i~~~i~~~-~~~~~ilnL~~vtFMDSSGlGVilGRYK~i~~~gG~v~v~~v~p~vk 84 (106) T TIGR02886 6 KGDVLIVRLSGELDHHTAEEVRRKIDDAIERR-PIKHLILNLKNVTFMDSSGLGVILGRYKKIKQEGGEVIVCNVSPAVK 84 (106) T ss_pred ECCEEEEEEEECCCHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCCEEEECCCCEEEEEEEEEEECCCEEEEECCCCCCE T ss_conf 18889999861004467899999999898507-98368986277647865122101110357730688898972993110 Q ss_pred HHHHHHHHHH Q ss_conf 9999886422 Q gi|254780138|r 80 QLFSLISFTH 89 (373) Q Consensus 80 ~Ll~Ll~~~~ 89 (373) +++++--... T Consensus 85 r~felSGlFk 94 (106) T TIGR02886 85 RVFELSGLFK 94 (106) T ss_pred EEEECCCCCC T ss_conf 0011148750 No 9 >COG1366 SpoIIAA Anti-anti-sigma regulatory factor (antagonist of anti-sigma factor) [Signal transduction mechanisms] Probab=97.58 E-value=0.00041 Score=47.51 Aligned_cols=83 Identities=14% Similarity=0.331 Sum_probs=67.6 Q ss_pred EEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHHHHHH Q ss_conf 799984035635522007999986431167880899701051521299999999997---51876431589912699999 Q gi|254780138|r 7 TVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIEQLFS 83 (373) Q Consensus 7 ~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~~Ll~ 83 (373) .++.+.|+.+..+...+.+.+.+..... ..+.+++|+++++++||+|+-.|....+ ..+.+..+.+.+|+.++.+. T Consensus 15 ~vl~l~G~lD~~~a~~~~e~~~~~~~~~-~~~~ivIDls~v~~~dS~gl~~L~~~~~~~~~~g~~~~l~~i~p~v~~~~~ 93 (117) T COG1366 15 LVLPLIGELDAARAPALKETLLEVIAAS-GARGLVIDLSGVDFMDSAGLGVLVALLKSARLRGVELVLVGIQPEVARTLE 93 (117) T ss_pred EEEEEEEEEEHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCCEECCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHH T ss_conf 8999554871888999999999999746-997799988888774545899999999999866994899929999999999 Q ss_pred HHHHHHH Q ss_conf 8864222 Q gi|254780138|r 84 LISFTHR 90 (373) Q Consensus 84 Ll~~~~~ 90 (373) +...... T Consensus 94 ~~gl~~~ 100 (117) T COG1366 94 LTGLDKS 100 (117) T ss_pred HHCCCCE T ss_conf 9397412 No 10 >cd07042 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. Probab=97.35 E-value=0.001 Score=44.69 Aligned_cols=87 Identities=18% Similarity=0.306 Sum_probs=70.2 Q ss_pred CCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHH---CCCCCCCCCCCHHH Q ss_conf 858827999840356355220079999864311678808997010515212999999999975---18764315899126 Q gi|254780138|r 2 SENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFMEK---YHGKIKLQGVSTHI 78 (373) Q Consensus 2 s~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~~---~~~~~~~~~l~~~~ 78 (373) ..++..++++.|+..-.+...+.+++.+.....+..+.+++|++++..+|++|+..|.++.+. .+.+..+.++++.. T Consensus 6 ~~~~v~i~~~~g~LfF~~~~~~~~~i~~~~~~~~~~~~vvld~~~v~~iD~s~~~~L~~~~~~~~~~g~~l~~~~~~~~~ 85 (107) T cd07042 6 EPPGVLIYRIDGPLFFGNAEYFKDRLLRLVDEDPPLKVVILDLSAVNFIDSTAAEALEELVKDLRKRGVELYLAGLNPQV 85 (107) T ss_pred CCCCEEEEEECCEEEEEEHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHH T ss_conf 68988999956706761799999999998715899729999984998547599999999999999779999998098799 Q ss_pred HHHHHHHHHH Q ss_conf 9999988642 Q gi|254780138|r 79 EQLFSLISFT 88 (373) Q Consensus 79 ~~Ll~Ll~~~ 88 (373) .+.++..... T Consensus 86 ~~~l~~~g~~ 95 (107) T cd07042 86 RELLERAGLL 95 (107) T ss_pred HHHHHHCCCH T ss_conf 9999986997 No 11 >cd07041 STAS_RsbR_RsbS_like Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors. Probab=96.69 E-value=0.011 Score=37.39 Aligned_cols=82 Identities=17% Similarity=0.384 Sum_probs=69.0 Q ss_pred CCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHHH Q ss_conf 882799984035635522007999986431167880899701051521299999999997---51876431589912699 Q gi|254780138|r 4 NGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIEQ 80 (373) Q Consensus 4 dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~~ 80 (373) +|.+++-+-|+.+......+.+++...+.+. +.+.+.+|+|++..+|+..+-.|.++.+ -.+.+.-..|.+|+..+ T Consensus 9 ~~vlvlPliG~ld~~r~~~l~e~ll~~i~~~-~~~~viiDlsGv~~iD~~~~~~L~~l~~~~~LlG~~~il~Gi~P~vA~ 87 (109) T cd07041 9 DGVLVLPLIGDLDDERAEQLQERLLEAISRR-RARGVIIDLTGVPVIDSAVARHLLRLARALRLLGARTILTGIRPEVAQ 87 (109) T ss_pred CCEEEEEEEEEECHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHH T ss_conf 9889998689885999999999999999972-988999974588637789999999999999963986999943999999 Q ss_pred HHHHHH Q ss_conf 999886 Q gi|254780138|r 81 LFSLIS 86 (373) Q Consensus 81 Ll~Ll~ 86 (373) -+--.. T Consensus 88 ~lv~~g 93 (109) T cd07041 88 TLVELG 93 (109) T ss_pred HHHHHC T ss_conf 999929 No 12 >TIGR00377 ant_ant_sig anti-anti-sigma factor; InterPro: IPR003658 An anti-sigma factor antagonist is an anti-anti-sigma factor, which relieves inhibition of sigma factor activity by the anti-sigma factor. Examples include the Bacillus subtilis SpoIIAA protein, which, in its phosphorylated form, acts as an anti-anti-sigma factor to relieve SpoIIAB inhibition of sigma F; and the anti-sigma B factor antagonist, RsbV, which counteracts the RsbW-mediated inhibition of sigma B by binding to RsbW.; GO: 0045152 antisigma factor binding, 0006355 regulation of transcription DNA-dependent. Probab=96.03 E-value=0.023 Score=35.26 Aligned_cols=87 Identities=15% Similarity=0.365 Sum_probs=69.6 Q ss_pred CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHH Q ss_conf 5882799984035635522007999986431167880899701051521299999999997---5187643158991269 Q gi|254780138|r 3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIE 79 (373) Q Consensus 3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~ 79 (373) .++..+++++|+.+..+.+...+.+.....+......+.+|+.+++++|++|...+....+ +.+.+....+..+... T Consensus 10 ~~~~~~~~~~g~~d~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (109) T TIGR00377 10 QGGVLVVRLSGELDAHTAPALRELLTPLAERGTGIRPIVLDLEGLEFMDSSGLGVLLGLYKQVKRNGGELVLVGLSPRVA 89 (109) T ss_pred CCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCHHHH T ss_conf 37556887425323301688999988876215776514775056431110037999999888751786079960766788 Q ss_pred HHHHHHHHHH Q ss_conf 9999886422 Q gi|254780138|r 80 QLFSLISFTH 89 (373) Q Consensus 80 ~Ll~Ll~~~~ 89 (373) +.++...... T Consensus 90 ~~~~~~gl~~ 99 (109) T TIGR00377 90 RLLEITGLLD 99 (109) T ss_pred HHHHHHCCCC T ss_conf 8998713100 No 13 >PRK10782 DL-methionine transporter permease subunit; Provisional Probab=79.08 E-value=4.2 Score=19.28 Aligned_cols=51 Identities=22% Similarity=0.196 Sum_probs=30.5 Q ss_pred HHHHHHHHHHCCCHHHHH---HHH----HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 500134444278689999---999----99999999-9999999999999999999998 Q gi|254780138|r 238 NEEIDAIRTMGLDFVRIL---ISP----RIWALIIS-LPLLTILANFSAIIGASIVIWK 288 (373) Q Consensus 238 ~eeidAL~~~Gi~p~~~L---v~P----Rv~A~~i~-~p~L~~~~~~~~i~gg~~~~~~ 288 (373) .+|+||-++||.+|.+.+ ++| +++..... .-.+.-++.+.|+.|+.-.... T Consensus 117 ~g~~EAa~alG~s~~q~i~~viLPqAlp~ii~~~~~~~i~~i~~tsl~g~IG~ggLG~~ 175 (217) T PRK10782 117 TGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMGGAVGAGGLGQI 175 (217) T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH T ss_conf 87999999839898899485107921999999999999999999999999810478999 No 14 >COG0795 Predicted permeases [General function prediction only] Probab=76.31 E-value=5.1 Score=18.75 Aligned_cols=23 Identities=26% Similarity=0.141 Sum_probs=10.8 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 78689999999999999999999 Q gi|254780138|r 248 GLDFVRILISPRIWALIISLPLL 270 (373) Q Consensus 248 Gi~p~~~Lv~PRv~A~~i~~p~L 270 (373) .++|+--...|-+++..+..-++ T Consensus 336 ~l~p~~a~~~p~~v~l~~~~~l~ 358 (364) T COG0795 336 KLPPFLAAWLPNLVFLALGLWLL 358 (364) T ss_pred CCCHHHHHHHHHHHHHHHHHHHH T ss_conf 82279999999999999999999 No 15 >COG4591 LolE ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane] Probab=69.54 E-value=7.2 Score=17.68 Aligned_cols=96 Identities=13% Similarity=0.123 Sum_probs=65.0 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCHHHH----HHHHHHHC Q ss_conf 9987500134444278689999999999999999999999999999999999998611----398999----99999861 Q gi|254780138|r 234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYD----IPFAVF----FSRFHSTA 305 (373) Q Consensus 234 ~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~----i~~~~f----~~~~~~~~ 305 (373) .|.=+.||.-||+||.+|-+-.-.== .---.+.+++.+.|..-|++++...-. +++..+ .+.++..+ T Consensus 295 V~ek~~eIAILrtmGa~~~~I~~iFl-----~~G~~iG~iG~llG~iLG~~~~~~i~~~~~~~~~~~~~~~~~~~lP~~~ 369 (408) T COG4591 295 VKEKTREIAILRAMGASPSHIMRIFL-----LQGLIIGLIGALLGVILGVLLALNLNSIIIFIEPLLGHTFGISTLPIEL 369 (408) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCEE T ss_conf 66455578999982998678999999-----9989999999999999999999998778740565344100112477350 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 69999999999999999999998317704 Q gi|254780138|r 306 TLANIFTGLIKAPFMACAIGIVAMKEGFA 334 (373) Q Consensus 306 ~~~d~~~~~~K~~~fg~~i~~i~c~~Gl~ 334 (373) ++.|++...+=+++..++-++...++.-+ T Consensus 370 ~~~di~~v~~~al~ls~lAtlyPA~rAsk 398 (408) T COG4591 370 SLLDVVLVLVFALLLSLLATLYPARRASK 398 (408) T ss_pred EHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 09999999999999999999978888866 No 16 >pfam03739 YjgP_YjgQ Predicted permease YjgP/YjgQ family. Members of this family are predicted integral membrane proteins of unknown function. They are about 350 amino acids long and contain about 6 transmembrane regions. They are predicted to be permeases although there is no verification of this. Probab=69.15 E-value=7.3 Score=17.62 Aligned_cols=21 Identities=10% Similarity=0.112 Sum_probs=13.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 776999999999999999999 Q gi|254780138|r 165 VSGVPVVILISFVTGAVIAQQ 185 (373) Q Consensus 165 ~~alpiv~l~~~~~G~v~a~q 185 (373) --+.|+..+...++|+-++.. T Consensus 274 r~~~pl~~l~l~ll~~~l~~~ 294 (353) T pfam03739 274 RLALPLSCLVLALLALPLGLG 294 (353) T ss_pred HHHHHHHHHHHHHHHHHHHHC T ss_conf 999899999999999998316 No 17 >KOG0236 consensus Probab=68.47 E-value=7.6 Score=17.53 Aligned_cols=67 Identities=12% Similarity=0.061 Sum_probs=35.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH-HHH-----HHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999997402678872899-999-----999983-----776999999999999999999999875 Q gi|254780138|r 125 SCSQAHILGLVISNTGEFCASSYKFKGFLLS-LIR-----QMYYVG-----VSGVPVVILISFVTGAVIAQQGAFQLS 191 (373) Q Consensus 125 ~~~~~~f~G~~~~~~~~~~~~~~~~r~~~~~-~~~-----q~~~~G-----~~alpiv~l~~~~~G~v~a~q~~~~l~ 191 (373) .+-+..|++-..+.+....++..-.....-. .+. ..+..+ ..++-+...++|+.|.+-...|..+|. T Consensus 111 yGLYssf~~~~iY~~fGtsr~isiG~~av~sLmv~~~v~~~v~~~~~~~~~~~~i~va~~lt~l~Giiq~~mG~lrLG 188 (665) T KOG0236 111 YGLYSSFFPPLIYAIFGTSRHVSIGPFAVVSLMVGTVVSQVVLSEAPSNDIATTIQVATTLTFLTGIIQLILGLLRLG 188 (665) T ss_pred HHHHHHHHHHHHHEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 988988887888357067875563589999999988898876303566674236799999999999999999998235 No 18 >COG5439 Uncharacterized conserved protein [Function unknown] Probab=58.35 E-value=9.8 Score=16.73 Aligned_cols=53 Identities=13% Similarity=0.267 Sum_probs=36.6 Q ss_pred EEEECCCCHHH---HHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 99840356355---22007999986431167880899701051521299999999997 Q gi|254780138|r 9 FRFAGNWKSPE---ISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME 63 (373) Q Consensus 9 L~LsGdWTl~~---l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~ 63 (373) +-+.|-..+.+ +.++-.-....++.. ..+.++|+.+++.+.|+|.-+|..+-- T Consensus 17 iyFdG~mRL~s~eayaPIm~l~~~~L~a~--ps~mtinL~gL~FLNSSGInlLakfti 72 (112) T COG5439 17 IYFDGFMRLESMEAYAPIMNLMLEILSAD--PSEMTINLEGLEFLNSSGINLLAKFTI 72 (112) T ss_pred EEEEEEEECCCCCCCCHHHHHHHHHHHCC--HHHHEEECCCCEEECCCCHHHHHHHHH T ss_conf 47743775054401063999999998549--177288023313402214578876634 No 19 >COG4215 ArtQ ABC-type arginine transport system, permease component [Amino acid transport and metabolism] Probab=54.46 E-value=13 Score=15.85 Aligned_cols=125 Identities=24% Similarity=0.340 Sum_probs=78.4 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH Q ss_conf 999999999999974026788728999999999837769999999-9999999999999987542756689999999999 Q gi|254780138|r 130 HILGLVISNTGEFCASSYKFKGFLLSLIRQMYYVGVSGVPVVILI-SFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQL 208 (373) Q Consensus 130 ~f~G~~~~~~~~~~~~~~~~r~~~~~~~~q~~~~G~~alpiv~l~-~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~ 208 (373) ..+-..+..+.-+..+..+.| +-.....+|-+=++.+|=..++ -++.|.-..++.... -++...+ -. T Consensus 24 sl~lgl~lGl~~A~~kls~~r--~lr~~~~~YtTv~RGvPELl~illiyfG~~~lL~~~~~--~~~~~g~--------~~ 91 (230) T COG4215 24 SLILGLLLGLLGALGKLSKNR--LLRLLGNVYTTVIRGVPELLLILLIYFGGQILLNTLAD--VTGALGV--------GF 91 (230) T ss_pred HHHHHHHHHHHHHHHHHCCCH--HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH--HHCCCCC--------CC T ss_conf 999999999999999866660--67897543535542671999999999830999999998--7301477--------74 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHHHH--HHHHHHHHHHCCCHHH---HHHHHHHHHHHHHHH Q ss_conf 998999999999996457899999--99987--5001344442786899---999999999999999 Q gi|254780138|r 209 REIGVLLTAVMIAGRSGSAIVAEI--GSMKI--NEEIDAIRTMGLDFVR---ILISPRIWALIISLP 268 (373) Q Consensus 209 RElgPlltaii~agR~gsa~aAei--G~M~v--~eeidAL~~~Gi~p~~---~Lv~PRv~A~~i~~p 268 (373) -|+.|..++++.-|=.=+|+++|- |.-+. .+|++|=+.+|.+|-+ ++++|-++- .++| T Consensus 92 idi~~FvaGviaL~~i~gAYatEt~RGA~~AVp~GQ~EAa~AlGms~~~~frrI~lPqm~R--~ALP 156 (230) T COG4215 92 IDISPFVAGVIALGLIFGAYATETLRGAFKAVPKGQIEAARALGLSRSQTFRRIVLPQMWR--HALP 156 (230) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH--HHCC T ss_conf 5567499999999999999989999999972896518899980998768899999888999--8278 No 20 >pfam02687 FtsX Predicted permease. This is a family of predicted permeases and hypothetical transmembrane proteins. The lipoprotein-releasing system transmembrane protein lolC from Buchnera aphidicola has been shown to transport lipids targeted to the outer membrane across the inner membrane. Both lolC and an ATP-binding cassette transporter-like protein from Streptococcus cristatus have been shown to require ATP. Probab=48.75 E-value=16 Score=15.25 Aligned_cols=97 Identities=11% Similarity=0.079 Sum_probs=51.1 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHH Q ss_conf 99999987500134444278689999999999999999999999999999999999998611398999999998616999 Q gi|254780138|r 230 AEIGSMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFHSTATLAN 309 (373) Q Consensus 230 AeiG~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~~~~~~~d 309 (373) --.-.++-++|+--|+++|.++-+-.-.--.-++. ..+.+...|+..|+...+.....-.........-.+++.+ T Consensus 72 ~~~~i~~r~~ei~ilka~G~~~~~i~~~~~~e~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 146 (174) T pfam02687 72 LSISIAERRREIGILKALGASKKQIFKLLLLEALL-----LGLIGSLLGLLLGFLLAYLLSSAIGYFSGFSLPLVIDPIV 146 (174) T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHH T ss_conf 99999999999999999299999999999999999-----9999999999999999999999999861434340018999 Q ss_pred HHHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999999999999999998317 Q gi|254780138|r 310 IFTGLIKAPFMACAIGIVAMKE 331 (373) Q Consensus 310 ~~~~~~K~~~fg~~i~~i~c~~ 331 (373) ++..++=..+..++.+..+.++ T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~ 168 (174) T pfam02687 147 ILLVLLLILLIALLASLLPARR 168 (174) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999 No 21 >PRK11146 outer membrane-specific lipoprotein transporter subunit LolE; Provisional Probab=47.39 E-value=17 Score=15.10 Aligned_cols=96 Identities=11% Similarity=0.089 Sum_probs=62.8 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HC---CCHHH-HHH Q ss_conf 99875001344442786899999999999999999999999999999999999986----------11---39899-999 Q gi|254780138|r 234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKY----------YD---IPFAV-FFS 299 (373) Q Consensus 234 ~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~----------~~---i~~~~-f~~ 299 (373) .+.=+.||--|++||.++-+-.-. .+.-.-++.+.+.++|++-|.+.+... .+ .++.. |.+ T Consensus 293 V~eK~reIgiLkalG~~~~~I~~i-----Fl~eg~~ig~~G~~~G~~lG~~l~~~l~~~~~~~~~~~~~~~~~~~iy~i~ 367 (412) T PRK11146 293 VKDKSGDIAILRTLGAKDGLIRAI-----FVWYGLLAGLKGSLIGVVIGVVVSLNLTPIIKGIEKLIGHQFLSGDIYFID 367 (412) T ss_pred HHHHHHHHHHHHHHCCCHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEC T ss_conf 998887999999948998899999-----999999999999999999999999999999999999837555897520120 Q ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 99986169999999999999999999998317704 Q gi|254780138|r 300 RFHSTATLANIFTGLIKAPFMACAIGIVAMKEGFA 334 (373) Q Consensus 300 ~~~~~~~~~d~~~~~~K~~~fg~~i~~i~c~~Gl~ 334 (373) .++..+++.|+....+-+.+.+++.++...++--+ T Consensus 368 ~lP~~i~~~~v~~i~~~~~i~~~las~~PA~rAa~ 402 (412) T PRK11146 368 FLPSELHWLDVAYVLVTALLLSLLASWYPARRASK 402 (412) T ss_pred CCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 35517139999999999999999999999999978 No 22 >TIGR01253 thiP thiamine/thiamine pyrophosphate ABC transporter, permease protein; InterPro: IPR005947 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). This entry represents thiamine ABC transporter, permease protein in bacteria, believed to be involved in the specific translocation of thiamine and its phosphoesters across the inner membrane. The protein belongs to the larger ABC transport system. It has been experimentally demonstrated that mutants in the various steps in the de novo synthesis of thiamine and its biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP). Thiamine pyrophosphate (TPP)1 is a required cofactor synthesized de novo in Salmonella typhimurium. The primary role for TPP is in central metabolism as an electron carrier and nucleophile for such enzymes as pyruvate dehydrogenase (1.2.4.1 from EC), acetolactate synthase (4.1.3.18 from EC), and -ketoglutarate dehydrogenase (1.2.4.2 from EC). Despite its importance in cellular physiology, neither the de novo biosynthetic pathway nor the salvage systems for thiamine are fully understood in any organism.; GO: 0005215 transporter activity, 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=42.91 E-value=19 Score=14.64 Aligned_cols=22 Identities=18% Similarity=0.099 Sum_probs=10.7 Q ss_pred HCCHHHHHHHHHHHHHHHHHHH Q ss_conf 6169999999999999999999 Q gi|254780138|r 304 TATLANIFTGLIKAPFMACAIG 325 (373) Q Consensus 304 ~~~~~d~~~~~~K~~~fg~~i~ 325 (373) .++++.+-.-+-.+..||.+.+ T Consensus 446 ~~E~~~L~~PL~~AlAl~~~LS 467 (519) T TIGR01253 446 LVELKALKAPLAYALALALVLS 467 (519) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 8879998779999999999985 No 23 >PRK08456 flagellar motor protein MotA; Validated Probab=41.44 E-value=20 Score=14.49 Aligned_cols=57 Identities=11% Similarity=-0.006 Sum_probs=36.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999837769999999999999999999998754275668999999999999899999999 Q gi|254780138|r 157 IRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVM 219 (373) Q Consensus 157 ~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii 219 (373) -..+++.-.+..|-..+++.++|+|..++... -..-+|..++.+++--+-=++.|=+ T Consensus 142 ~~~~~~~~~~~aPafGmiGtvlGLI~~l~~l~------dp~~iG~~mA~ALvtTfyGvllAn~ 198 (257) T PRK08456 142 AAHYWITAGETCPTMGLVGAVMGLMLALQLLD------NPAEMAAGIAGAFTATVTGIMGSYA 198 (257) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 36899999987458879999999999998069------9999998999999999999999999 No 24 >TIGR02182 GRXB Glutaredoxin, GrxB family; InterPro: IPR011901 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This family includes the highly abundant Escherichia coli GrxB (Grx2) glutaredoxin which is notably longer than either GrxA or GrxC. Unlike the other two E. coli glutaredoxins, GrxB appears to be unable to reduce ribonucleotide reductase , and may have more to do with resistance to redox stress .; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity. Probab=40.68 E-value=7.1 Score=17.73 Aligned_cols=14 Identities=21% Similarity=0.107 Sum_probs=5.7 Q ss_pred ECCCHHHHHHHHHH Q ss_conf 01051521299999 Q gi|254780138|r 44 LSAITEIDTIGAEL 57 (373) Q Consensus 44 ls~i~~lDTAGA~l 57 (373) ..++..+=|--|.- T Consensus 108 k~~l~EFAT~~A~~ 121 (212) T TIGR02182 108 KLDLPEFATQSARK 121 (212) T ss_pred CCCCCCCCCHHHHH T ss_conf 16886567688999 No 25 >pfam09838 DUF2065 Uncharacterized protein conserved in bacteria (DUF2065). This domain, found in various prokaryotic proteins, has no known function. Probab=40.39 E-value=21 Score=14.38 Aligned_cols=33 Identities=15% Similarity=0.165 Sum_probs=29.7 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 289999999998377699999999999999999 Q gi|254780138|r 152 FLLSLIRQMYYVGVSGVPVVILISFVTGAVIAQ 184 (373) Q Consensus 152 ~~~~~~~q~~~~G~~alpiv~l~~~~~G~v~a~ 184 (373) .|++..+|+.+.-.+.+-++.+.+..+|.++.+ T Consensus 22 ~~r~~l~~l~~~~~~~LR~~Gl~~m~~G~~ll~ 54 (57) T pfam09838 22 AWRRMLLQLAQLPDRQLRLIGLVSMLLGLVLLW 54 (57) T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999819872699995999999999872 No 26 >KOG2927 consensus Probab=39.32 E-value=22 Score=14.27 Aligned_cols=50 Identities=26% Similarity=0.386 Sum_probs=38.1 Q ss_pred HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHH Q ss_conf 9999987542756689999999999998999999999996457----89999999 Q gi|254780138|r 184 QQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGS----AIVAEIGS 234 (373) Q Consensus 184 ~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gs----a~aAeiG~ 234 (373) -|+.+.+.- |+..+++.+++++++|=+.=.+|.++.-|+.|- ..+++.|. T Consensus 215 R~gvyY~si-g~~gfl~~IlvLaIvRlILF~I~~il~~g~~g~W~FPNL~eDvGf 268 (372) T KOG2927 215 RQGVYYLSI-GAGGFLAFILVLAIVRLILFGITWILTGGKHGFWLFPNLTEDVGF 268 (372) T ss_pred HCCEEEEEC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHH T ss_conf 422113440-315999999999999999999999973787725753625654437 No 27 >pfam05197 TRIC TRIC channel. TRIC (trimeric intracellular cation) channels are differentially expressed in intracellular stores in animal cell types. TRIC subtypes contain three proposed transmembrane segments, and form homo-trimers with a bullet-like structure. Electrophysiological measurements with purified TRIC preparations identify a monovalent cation-selective channel. Probab=39.26 E-value=22 Score=14.26 Aligned_cols=35 Identities=17% Similarity=0.133 Sum_probs=15.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH Q ss_conf 99999999999999999999861139899999999 Q gi|254780138|r 268 PLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFH 302 (373) Q Consensus 268 p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~ 302 (373) |+=+.++.+...+||.+.+.+.+|-++-.++++.. T Consensus 15 P~a~Wls~ML~cFaG~iL~~llLGep~l~pl~n~~ 49 (197) T pfam05197 15 PLACWLSAMLMCFGGAILSSFLLGEPPIAPLKNTT 49 (197) T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCH T ss_conf 78999999999942899888780785245660860 No 28 >COG4177 LivM ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism] Probab=39.23 E-value=22 Score=14.26 Aligned_cols=69 Identities=25% Similarity=0.332 Sum_probs=44.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999645789999999987500134444278689999999999999999999999999999999999998611 Q gi|254780138|r 212 GVLLTAVMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYD 291 (373) Q Consensus 212 gPlltaii~agR~gsa~aAeiG~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~ 291 (373) .-+++.-++-.|.|-++.| ++|.=++-|.||+||..|- +.|.+++ +.+.|+-| .+.+..... T Consensus 170 ~~~~~~~l~~S~~Gr~l~A------iRedE~~a~alG~n~~~~K----l~aF~is-------a~~AGiAG-aL~a~~~~~ 231 (314) T COG4177 170 TLLVLERLVRSPFGRALRA------IREDEIAARALGINVTRYK----LLAFVIS-------AAIAGIAG-ALYALYLGF 231 (314) T ss_pred HHHHHHHHHCCCCCHHHHH------HCCCHHHHHHCCCCHHHHH----HHHHHHH-------HHHHHHHH-HHHHHHHCE T ss_conf 9999999864970336866------6157899998599889999----9999999-------99999999-999998150 Q ss_pred CCHHHHH Q ss_conf 3989999 Q gi|254780138|r 292 IPFAVFF 298 (373) Q Consensus 292 i~~~~f~ 298 (373) ++|..|. T Consensus 232 v~p~~f~ 238 (314) T COG4177 232 VSPESFS 238 (314) T ss_pred ECCHHCC T ss_conf 3800253 No 29 >COG1079 Uncharacterized ABC-type transport system, permease component [General function prediction only] Probab=38.80 E-value=22 Score=14.22 Aligned_cols=88 Identities=15% Similarity=0.157 Sum_probs=56.6 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-----CHHHHHHHHHHHCCHHH Q ss_conf 9875001344442786899999999999999999999999999999999999986113-----98999999998616999 Q gi|254780138|r 235 MKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDI-----PFAVFFSRFHSTATLAN 309 (373) Q Consensus 235 M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i-----~~~~f~~~~~~~~~~~d 309 (373) +-+.|.=+|.++||+|..+| |..|.++. +...|+-|+|+.-...... .-.-|+.--......|+ T Consensus 170 ravGE~P~aad~~Gi~V~r~----R~~av~~s-------G~laGlaGa~Lsl~~~~~f~~~m~aGrGfIAlA~~ifa~W~ 238 (304) T COG1079 170 RAVGENPAAADAMGINVYRY----RYLAVLVS-------GALAGLAGAYLSLAYSGQFVEGMTAGRGFIALAAVIFARWR 238 (304) T ss_pred EEECCCHHHHHHCCCCHHHH----HHHHHHHH-------HHHHHHHHHHEEEEECCCCCCCCCCCCHHHHHHHHHHHCCC T ss_conf 98269826788679875678----89999999-------99987535213555045644466677219999999994787 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 999999999999999999831770 Q gi|254780138|r 310 IFTGLIKAPFMACAIGIVAMKEGF 333 (373) Q Consensus 310 ~~~~~~K~~~fg~~i~~i~c~~Gl 333 (373) -+..+.-+.+||+.-++----|.+ T Consensus 239 Pl~~~~~allFg~~~~l~~~~q~~ 262 (304) T COG1079 239 PLGALVAALLFGFFEALAIQLQAL 262 (304) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 399999999999999999886124 No 30 >TIGR00815 sulP sulfate permease; InterPro: IPR001902 A number of proteins involved in the transport of sulphate across a membrane as well as some yet uncharacterised proteins have been shown , to be evolutionary related. These proteins are: Neurospora crassa sulphate permease II (gene cys-14). Yeast sulphate permeases (genes SUL1 and SUL2). Rat sulphate anion transporter 1 (SAT-1). Mammalian DTDST, a probable sulphate transporter which, in human, is involved in the genetic disease, diastrophic dysplasia (DTD). Sulphate transporters 1, 2 and 3 from the legume Stylosanthes hamata. Human pendrin (gene PDS), which is involved in a number of hearing loss genetic diseases. Human protein DRA (Down-Regulated in Adenoma). Soybean early nodulin 70. Escherichia coli hypothetical protein ychM. Caenorhabditis elegans hypothetical protein F41D9.5. These proteins are highly hydrophobic and seem to contain about 12 transmembrane domains. ; GO: 0008271 secondary active sulfate transmembrane transporter activity, 0008272 sulfate transport, 0016020 membrane. Probab=38.08 E-value=23 Score=14.14 Aligned_cols=21 Identities=10% Similarity=0.167 Sum_probs=9.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999989999999999 Q gi|254780138|r 201 DLMSILQLREIGVLLTAVMIA 221 (373) Q Consensus 201 ~~~~~~~~RElgPlltaii~a 221 (373) ++++..+..-++++..+.... T Consensus 307 e~~~~G~~n~~~~~f~~~~~~ 327 (638) T TIGR00815 307 ELVALGIANILGSFFGCYPAT 327 (638) T ss_pred HHHHHHHHHHHHHHHHHHHHH T ss_conf 123431366654555577777 No 31 >PRK13108 prolipoprotein diacylglyceryl transferase; Reviewed Probab=37.87 E-value=23 Score=14.12 Aligned_cols=22 Identities=18% Similarity=0.122 Sum_probs=11.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999964578999999 Q gi|254780138|r 212 GVLLTAVMIAGRSGSAIVAEIG 233 (373) Q Consensus 212 gPlltaii~agR~gsa~aAeiG 233 (373) +|-+--=--.||-|.=|.-|+= T Consensus 133 APgllLAQAIGRwGNFFNQELy 154 (460) T PRK13108 133 APGVVLAQAIGRLGNYFNQELY 154 (460) T ss_pred HHHHHHHHHHCHHHHHHCHHHC T ss_conf 3567999984404643051223 No 32 >PRK10814 outer membrane-specific lipoprotein transporter subunit LolC; Provisional Probab=37.02 E-value=24 Score=14.03 Aligned_cols=97 Identities=10% Similarity=0.027 Sum_probs=64.1 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----HHHHHHHHHHHCCHHH Q ss_conf 998750013444427868999999999999999999999999999999999999861139----8999999998616999 Q gi|254780138|r 234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIP----FAVFFSRFHSTATLAN 309 (373) Q Consensus 234 ~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~----~~~f~~~~~~~~~~~d 309 (373) .+.=+.||--|++||.++-+-.-.=-+-++ ++.+.+.++|+.-|.+.+.....+. ...+...++..+++.| T Consensus 290 V~eK~~eI~iL~alGa~~~~I~~iFl~~g~-----~ig~~G~~~G~~lG~~l~~~~~~~~~~~~~~~~~~~~Pv~i~~~~ 364 (396) T PRK10814 290 VMEKQGEVAILQTQGLTPRQIMMVFMVQGA-----SAGIIGALLGAALGALLASQLNNLMPIIGVLLDGAALPVAIEPLQ 364 (396) T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHH T ss_conf 997776899999838993559999999999-----999999999999999999999999854323236643568952999 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 99999999999999999983177045 Q gi|254780138|r 310 IFTGLIKAPFMACAIGIVAMKEGFAV 335 (373) Q Consensus 310 ~~~~~~K~~~fg~~i~~i~c~~Gl~~ 335 (373) ++...+-+.+.+++-++...++--+. T Consensus 365 v~~v~~~~~~i~~la~~~PA~~Aa~l 390 (396) T PRK10814 365 VIVIALVAMAIALLSTLYPSWRAAAT 390 (396) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99999999999999999999999587 No 33 >pfam11964 DUF3478 Protein of unknown function (DUF3478). This family of proteins is functionally uncharacterized. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. Probab=36.63 E-value=24 Score=13.99 Aligned_cols=84 Identities=11% Similarity=0.126 Sum_probs=52.0 Q ss_pred CCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHCCC---CCCCCCCCHHH Q ss_conf 858827999840356355220079999864311678808997010515212999999999975187---64315899126 Q gi|254780138|r 2 SENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFMEKYHG---KIKLQGVSTHI 78 (373) Q Consensus 2 s~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~~~~~---~~~~~~l~~~~ 78 (373) .+++...++++|..|...+..+.+.+...++.+.+ -++.+|+.+...|+-..+|==.++-.++.. ++..++-+.=. T Consensus 8 ~~~~v~~~~v~G~lt~~D~~~l~~~l~~~l~~~~~-i~ll~~~~~f~G~~~~a~~ed~k~~~~h~~~~~riAiV~d~~W~ 86 (118) T pfam11964 8 PDDNVLAFKVSGKLTHEDYEVLIPALEAKLEEHGK-VRLLIDLDDFEGWELGALWEDLKLGLKHLKDFDRIAIVGDKKWL 86 (118) T ss_pred CCCCEEEEEEEEEECHHHHHHHHHHHHHHHHHCCC-EEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECHHHH T ss_conf 99998999995168899999999999999974796-58999945788998889999999877655045489999185999 Q ss_pred HHHHHHHH Q ss_conf 99999886 Q gi|254780138|r 79 EQLFSLIS 86 (373) Q Consensus 79 ~~Ll~Ll~ 86 (373) +.+.++.. T Consensus 87 ~~~~~~~~ 94 (118) T pfam11964 87 EWAAKLFG 94 (118) T ss_pred HHHHHHHH T ss_conf 99999985 No 34 >pfam04123 DUF373 Domain of unknown function (DUF373). Archaeal domain of unknown function. Predicted to be an integral membrane protein with six transmembrane regions. Probab=35.78 E-value=25 Score=13.90 Aligned_cols=29 Identities=24% Similarity=0.549 Sum_probs=14.2 Q ss_pred HHHHHHHHHHHHHHHHH-HCHHHHHHHHHH Q ss_conf 99999999999998754-275668999999 Q gi|254780138|r 176 FVTGAVIAQQGAFQLSQ-FGAEIFSIDLMS 204 (373) Q Consensus 176 ~~~G~v~a~q~~~~l~~-fGa~~~v~~~~~ 204 (373) ..+|.+...-|.+.|-+ ||.+.++..... T Consensus 184 ~~~~~i~~~lG~y~l~kG~gid~~~~~~~~ 213 (344) T pfam04123 184 YALGVILLILGLYLLYRGFGLDDFLRELLK 213 (344) T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHH T ss_conf 799999999999999997379999999999 No 35 >TIGR03004 ectoine_ehuC ectoine/hydroxyectoine ABC transporter, permease protein EhuC; InterPro: IPR014342 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). Members of this entry are presumed to act as permease subunits of ectoine ABC transporters. Operons containing this gene also contain other genes of the ABC transporter and are typically found next to either ectoine utilization or ectoine biosynthesis operons. Permease subunits EhuC and EhuD are homologues.. Probab=33.98 E-value=26 Score=13.70 Aligned_cols=116 Identities=26% Similarity=0.236 Sum_probs=72.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHHH--HHHHHHHHHHHCCCHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 998999999999996457899999--9998--7500134444278689999---99999999999999999999999999 Q gi|254780138|r 209 REIGVLLTAVMIAGRSGSAIVAEI--GSMK--INEEIDAIRTMGLDFVRIL---ISPRIWALIISLPLLTILANFSAIIG 281 (373) Q Consensus 209 RElgPlltaii~agR~gsa~aAei--G~M~--v~eeidAL~~~Gi~p~~~L---v~PRv~A~~i~~p~L~~~~~~~~i~g 281 (373) -|+.|+-+|++.-|-.--||.||| |..| -.||.+|=+.+...|++.+ ++|- |++.|||.-+=.+.= -+=+ T Consensus 77 l~l~P~t~gv~~Lglh~GaYGAEivRGA~~sv~~~Q~EAc~ALNftrfq~~rrI~LPQ--Al~~mmp~fgNlaIE-lLK~ 153 (216) T TIGR03004 77 LELDPLTVGVLALGLHVGAYGAEIVRGAVKSVSKEQLEACIALNFTRFQALRRIVLPQ--ALVEMMPAFGNLAIE-LLKL 153 (216) T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH--HHHHHCCCCCHHHHH-HHHH T ss_conf 4025189999999973265016888888997436589999984153677998763267--999743866158999-9987 Q ss_pred HHHHHHHH-HCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999986-11398999999998616999999999999999999999 Q gi|254780138|r 282 ASIVIWKY-YDIPFAVFFSRFHSTATLANIFTGLIKAPFMACAIGIV 327 (373) Q Consensus 282 g~~~~~~~-~~i~~~~f~~~~~~~~~~~d~~~~~~K~~~fg~~i~~i 327 (373) ..+|+-.. -|++|..---+-...=+..-+...+.-=.+++.+|.++ T Consensus 154 tslVSLIslaDltF~Aq~~r~~T~~tl~~fa~~LL~YFvMa~~i~l~ 200 (216) T TIGR03004 154 TSLVSLISLADLTFRAQSVRALTLDTLKVFALILLLYFVMALIISLA 200 (216) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89999999986769999999841002799999999999999999999 No 36 >PRK08124 flagellar motor protein MotA; Validated Probab=32.98 E-value=27 Score=13.59 Aligned_cols=58 Identities=10% Similarity=0.015 Sum_probs=36.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999998377699999999999999999999987542756689999999999998999999999 Q gi|254780138|r 157 IRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMI 220 (373) Q Consensus 157 ~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~ 220 (373) -..+++.--+..|-..+++.++|+|..++.. +-..-+|..++.+++--+-=++.|=++ T Consensus 143 ~~~v~~~~~~~aPafGmiGtvlGLI~~L~~l------~dp~~iG~~mA~ALvtT~yGvllAn~~ 200 (263) T PRK08124 143 GAAIFTQAGTYAPTLGVLGAVIGLIAALGNL------NDIEKLGHAISAAFVATLLGIFTGYVL 200 (263) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 1479999998736775999999999998725------999999988999999999999999999 No 37 >PRK08990 flagellar motor protein PomA; Reviewed Probab=31.92 E-value=29 Score=13.48 Aligned_cols=62 Identities=15% Similarity=-0.013 Sum_probs=39.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999998377699999999999999999999987542756689999999999998999999999996 Q gi|254780138|r 156 LIRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGR 223 (373) Q Consensus 156 ~~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR 223 (373) ....+++.--+..|-..+++.++|+|..++.. +-..-+|..++.+++--+-=++.|=++.+- T Consensus 138 ~~~~v~~~~g~~aPafGmiGTviGLI~mL~~l------~dp~~iG~~mA~ALvtTlYGillAnl~~~P 199 (253) T PRK08990 138 TGIGIFRAFGDVAPAMGMIGTLIGLVAMLSNM------DDPKSIGPAMAVALLTTLYGAVLANMVAIP 199 (253) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 86789999998716887999999999999806------999999988899999999999999999999 No 38 >COG1291 MotA Flagellar motor component [Cell motility and secretion] Probab=31.58 E-value=29 Score=13.44 Aligned_cols=63 Identities=11% Similarity=0.021 Sum_probs=36.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999998377699999999999999999999987542756689999999999998999999999996457 Q gi|254780138|r 158 RQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGS 226 (373) Q Consensus 158 ~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gs 226 (373) .+....--++.|-..+++..+|+|.+++.... ..-+|..++.+++--+--.+.|-.+.+-.++ T Consensus 144 a~~~~~~g~~aPa~GivgaV~GlI~~l~~l~~------p~~LG~~iA~Alv~T~~Gi~~ay~~~~P~a~ 206 (266) T COG1291 144 AHAFTTAGDYAPAFGIVGAVMGLIHALGNLDD------PAELGALIAAALVGTLYGIFLAYGLFGPLAN 206 (266) T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCC------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999988458266699999999999882799------7888889999999999999999897868899 No 39 >PRK11301 livM leucine/isoleucine/valine transporter permease subunit; Provisional Probab=31.46 E-value=29 Score=13.43 Aligned_cols=52 Identities=23% Similarity=0.251 Sum_probs=35.5 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 8750013444427868999999999999999999999999999999999999861139899999 Q gi|254780138|r 236 KINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFS 299 (373) Q Consensus 236 ~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~ 299 (373) -++|.=||-|.||+|+.+|- +.|.+++ +.+.|+- |.+.++...-++|+.|-- T Consensus 292 AIRedE~AA~alGInv~r~K----L~AFals-------A~~AGlA-GaLyA~~~g~IsP~~F~~ 343 (416) T PRK11301 292 ALREDEIACRSLGLNPTRIK----LSAFTIG-------AAFAGFA-GTFFAARQGFVSPESFTF 343 (416) T ss_pred HHHCCHHHHHHCCCCHHHHH----HHHHHHH-------HHHHHHH-HHHHHHHCCEECCCCCCH T ss_conf 99627999998597769999----9999999-------9999999-999998816348330659 No 40 >pfam08566 Pam17 Mitochondrial import protein Pam17. The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins. Probab=28.92 E-value=32 Score=13.14 Aligned_cols=50 Identities=22% Similarity=0.163 Sum_probs=24.8 Q ss_pred HHHHHH--HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 500134--44427868999999999999999999999999999999999999861139899999 Q gi|254780138|r 238 NEEIDA--IRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFS 299 (373) Q Consensus 238 ~eeidA--L~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~ 299 (373) +.|+|+ -..||+||+-.+. +.++.+..+|.+.|=.+......+....+.. T Consensus 62 ~~~~D~~~~~I~GlDP~~~~g------------~~~~a~~~~G~L~GP~iG~~vf~l~~r~~~~ 113 (174) T pfam08566 62 TLEIDSPTQQIMGLDPFMVLG------------LATIACGALGWLLGPFIGNAVFRLLNRSQLK 113 (174) T ss_pred CCCCCCCCCCCCCCCHHHHHH------------HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH T ss_conf 433354203013858899999------------9999974255751636789999997377888 No 41 >PRK00965 tetrahydromethanopterin S-methyltransferase subunit B; Provisional Probab=27.87 E-value=33 Score=13.01 Aligned_cols=29 Identities=7% Similarity=0.036 Sum_probs=10.1 Q ss_pred CCCCCCCCCCH---HHHHHHHHHHHHHHHCCC Q ss_conf 87643158991---269999988642220112 Q gi|254780138|r 66 HGKIKLQGVST---HIEQLFSLISFTHRKKIK 94 (373) Q Consensus 66 ~~~~~~~~l~~---~~~~Ll~Ll~~~~~~~~~ 94 (373) +.+.-..++.| +..+|-+..+...+...| T Consensus 25 ~~dvi~~s~~PI~e~i~kLe~~addL~nsLdP 56 (108) T PRK00965 25 REDVIVVDMDPVEEEINKLEAIADDLENSLDP 56 (108) T ss_pred CCCEEEEECHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 58759985047899999999999999864599 No 42 >COG1987 FliQ Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion] Probab=26.92 E-value=34 Score=12.90 Aligned_cols=66 Identities=17% Similarity=0.263 Sum_probs=35.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCHHHHHHHHHHHHHH-HHHHHHHHHHHHH Q ss_conf 99999999837769999999999999999-9999987542756689999999999-9989999999999 Q gi|254780138|r 155 SLIRQMYYVGVSGVPVVILISFVTGAVIA-QQGAFQLSQFGAEIFSIDLMSILQL-REIGVLLTAVMIA 221 (373) Q Consensus 155 ~~~~q~~~~G~~alpiv~l~~~~~G~v~a-~q~~~~l~~fGa~~~v~~~~~~~~~-RElgPlltaii~a 221 (373) ++.++....+.-....+.+.++.+|.+++ +|...|.++-- -.|++.++++..+ -=+||-+...++. T Consensus 8 ~i~~~ai~~~L~l~~P~ll~alvvGLvIsifQA~TQIqEqT-LsFiPKIiai~~~l~~~gpWm~~~l~d 75 (89) T COG1987 8 DIGQEAIWLVLMLSAPVLLVALVVGLVISIFQAATQIQEQT-LSFIPKIIAVFLVLILLGPWMLNQLLD 75 (89) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999989999999999999999999999999-985998999999999975899999999 No 43 >PRK06926 flagellar motor protein MotP; Reviewed Probab=26.88 E-value=35 Score=12.89 Aligned_cols=47 Identities=13% Similarity=0.086 Sum_probs=26.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH Q ss_conf 99998377699999999999999999999987542756689999999999998 Q gi|254780138|r 159 QMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREI 211 (373) Q Consensus 159 q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~REl 211 (373) .+++.--+..|-..+++.++|+|..++.. +...-+|..++.+++--+ T Consensus 149 ~~~~~~g~~aPafGmiGTviGLI~mL~~l------~dp~~iG~~mAvALvtTl 195 (272) T PRK06926 149 RLFEKAGEFAPAWGMIGTLVGLVLMLKNL------NDPHTLGPNMAVALLTTL 195 (272) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHH T ss_conf 99999998725887999999999998816------999999888899999999 No 44 >pfam04710 Pellino Pellino. Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase. Probab=26.69 E-value=7.5 Score=17.56 Aligned_cols=64 Identities=19% Similarity=0.261 Sum_probs=37.5 Q ss_pred CCCCCEEEEEEECCCCHHHHHHHHHHHH--------HHHHHCCCCCEEEEE----ECCCHHHHHHHHHHHHHHHHH Q ss_conf 9858827999840356355220079999--------864311678808997----010515212999999999975 Q gi|254780138|r 1 MSENGITVFRFAGNWKSPEISEIADDVV--------MAINKSIQSDSAIVD----LSAITEIDTIGAELIMYFMEK 64 (373) Q Consensus 1 ~s~dG~~vL~LsGdWTl~~l~~l~~~l~--------~~L~~~~~~~~i~iD----ls~i~~lDTAGA~lL~~l~~~ 64 (373) |+.+|.++++-.|.|+-.+.+..|+++. +.-.+..+..+.+=| +.+=+-+|=+||.+|||.... T Consensus 181 LTTNGVLimhP~~~f~~~s~pgvWrEvSVcG~Vy~lResRSaq~~G~~ve~e~NiL~DGtLIDLCGaTLlWRsa~g 256 (416) T pfam04710 181 LTTNGVLVMHPRGGFTEDSKPGVWREISVCGDVYTLRETRSAQQPGKLVEEETNVLQDGTLIDLCGATLLWRTADG 256 (416) T ss_pred CCCCCEEEECCCCCCCCCCCCCEEEEEEECCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEECCCCEEEEECCCC T ss_conf 4216659973688887788886458998777054540134545787302488870145647030531578733453 No 45 >pfam03683 UPF0175 Uncharacterized protein family (UPF0175). This family contains small proteins of unknown function. Probab=26.49 E-value=14 Score=15.58 Aligned_cols=36 Identities=17% Similarity=0.202 Sum_probs=27.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH Q ss_conf 9999964578999999998750013444427868999 Q gi|254780138|r 218 VMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRI 254 (373) Q Consensus 218 ii~agR~gsa~aAeiG~M~v~eeidAL~~~Gi~p~~~ 254 (373) +---|+...+-||||..|...|=++-|.-.||+ +.| T Consensus 29 lY~~g~iS~gkAaelag~s~~eF~~~L~~~~I~-~~y 64 (76) T pfam03683 29 LYERGKISLGKAAELAGMSRWEFLELLARRGIP-RHY 64 (76) T ss_pred HHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC-CCC T ss_conf 998498489999999799999999999987999-889 No 46 >PRK11123 arginine transporter permease subunit ArtQ; Provisional Probab=26.39 E-value=35 Score=12.83 Aligned_cols=126 Identities=14% Similarity=0.141 Sum_probs=70.4 Q ss_pred HHHHCCCCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCHHH--HHHHHHHHHHHHHHHHHHHHH Q ss_conf 974026788728999999999837769999-99999999999999999875427566--899999999999989999999 Q gi|254780138|r 142 FCASSYKFKGFLLSLIRQMYYVGVSGVPVV-ILISFVTGAVIAQQGAFQLSQFGAEI--FSIDLMSILQLREIGVLLTAV 218 (373) Q Consensus 142 ~~~~~~~~r~~~~~~~~q~~~~G~~alpiv-~l~~~~~G~v~a~q~~~~l~~fGa~~--~v~~~~~~~~~RElgPlltai 218 (373) .+.+..+.| +-......|-.=.+..|.. .+.-+..|.-.-+... -..++... .......-..--++.|..+|+ T Consensus 33 a~~r~s~~~--~l~~~~~~yv~~~RgtP~lv~l~~~yfg~p~l~~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~f~~av 108 (238) T PRK11123 33 AVWESAKWR--PVAWPGTALVTLLRGLPEILVVLFIYFGSSQLLLTL--SDGFTLNLGFVQIPVQMDIENFEVSPFLCGV 108 (238) T ss_pred HHHHHCCCH--HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH--HHHHCCCCHHHHHHHHCCCCCCCCCHHHHHH T ss_conf 999988868--899999999999916759999999999528988763--1000001001110100121345646999999 Q ss_pred HHHHHHHHHHHHHH---HHHHH-HHHHHHHHHHCCCHHH---HHHHHHHHHHHHHHHHHHHH Q ss_conf 99996457899999---99987-5001344442786899---99999999999999999999 Q gi|254780138|r 219 MIAGRSGSAIVAEI---GSMKI-NEEIDAIRTMGLDFVR---ILISPRIWALIISLPLLTIL 273 (373) Q Consensus 219 i~agR~gsa~aAei---G~M~v-~eeidAL~~~Gi~p~~---~Lv~PRv~A~~i~~p~L~~~ 273 (373) +.-+=..+|+.||+ |-..| .+|.||=+++|.++.+ +.++|-. .-.++|-++-. T Consensus 109 ial~l~~~Ay~aEi~R~gi~sVp~GQ~EAa~alGms~~q~~r~IilPQa--~r~~lP~l~n~ 168 (238) T PRK11123 109 IALSLLYAAYASQTLRGALKAVPVGQWESGQALGLSKSAIFFRLVMPQM--WRHALPGLGNQ 168 (238) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHH--HHHHHHHHHHH T ss_conf 9999999999999999999839999999999849899999999998999--99997389999 No 47 >pfam08496 Peptidase_S49_N Peptidase family S49 N-terminal. This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Probab=26.38 E-value=35 Score=12.83 Aligned_cols=14 Identities=7% Similarity=0.226 Sum_probs=4.9 Q ss_pred CCCCCCHHHHHHHH Q ss_conf 31589912699999 Q gi|254780138|r 70 KLQGVSTHIEQLFS 83 (373) Q Consensus 70 ~~~~l~~~~~~Ll~ 83 (373) +..++++.++++-+ T Consensus 43 ~v~~Lne~y~~~~~ 56 (154) T pfam08496 43 EITDLNEEYKDLKE 56 (154) T ss_pred EEEEHHHHHHHHHH T ss_conf 98567999999999 No 48 >PRK09109 motC flagellar motor protein; Reviewed Probab=25.54 E-value=36 Score=12.73 Aligned_cols=58 Identities=10% Similarity=0.039 Sum_probs=37.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999998377699999999999999999999987542756689999999999998999999999 Q gi|254780138|r 157 IRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMI 220 (373) Q Consensus 157 ~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~ 220 (373) -..+++.-.+..|-..+++.++|+|..++.- +-..-+|..++.+++--+-=++.|=++ T Consensus 142 ~~~~~~~~g~~aPafGmiGtviGLI~mL~~l------~dp~~lG~~mA~ALvtT~yGv~lAn~v 199 (246) T PRK09109 142 AAKVFESMGGYAPTIGIIGAVMGLIHVMENL------ADPSQLGSGIAVAFVATIYGVASANLL 199 (246) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7789999998726764999999999998806------999999988799999999999999999 No 49 >TIGR00780 ccoN cytochrome c oxidase, cbb3-type, subunit I; InterPro: IPR004677 This family represents the largest subunit, I, of the ccb3-type cytochrome c oxidase 1.9.3.1 from EC, with two protohemes and copper. It shows strong homology to subunits of other types of cytochrome oxidases. Species with this type, all from the proteobacteria so far, include Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Rhodobacter sphaeroides, Rhizobium leguminosarum, and others.; GO: 0004129 cytochrome-c oxidase activity, 0006118 electron transport, 0045278 plasma membrane respiratory chain complex IV. Probab=25.53 E-value=36 Score=12.73 Aligned_cols=98 Identities=17% Similarity=0.153 Sum_probs=46.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999837769999999999999999999998754275668999999-99999989999999999964578999999998 Q gi|254780138|r 158 RQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMS-ILQLREIGVLLTAVMIAGRSGSAIVAEIGSMK 236 (373) Q Consensus 158 ~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~-~~~~RElgPlltaii~agR~gsa~aAeiG~M~ 236 (373) +.+-+.++-+.-.-.++++|+|+|+|+|.+.---++ .|+.. ....=.|=||=|.=++=|=.| T Consensus 7 d~vvr~f~ia~v~wGiVGmLvGvv~Af~L~fPaLnl------S~I~~~y~~FGrLRPLHTnAVIfaFgg----------- 69 (485) T TIGR00780 7 DSVVRLFLIATVVWGIVGMLVGVVVAFQLSFPALNL------SDIAGEYGIFGRLRPLHTNAVIFAFGG----------- 69 (485) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC------HHCCCCCCCCCCCCCCCHHHHHHHHHC----------- T ss_conf 899987877434321677899999999860564560------113565235786686502366653222----------- Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH Q ss_conf 750013444427868999999999999999-------9999999999999999 Q gi|254780138|r 237 INEEIDAIRTMGLDFVRILISPRIWALIIS-------LPLLTILANFSAIIGA 282 (373) Q Consensus 237 v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~-------~p~L~~~~~~~~i~gg 282 (373) .|+=.-.|=|.-|++-.+.. .|.++++.-.+=|.-| T Consensus 70 ----------~GliatsyYvvQRvlkiT~~~rlfgg~~~~f~FWgw~~~ivla 112 (485) T TIGR00780 70 ----------GGLIATSYYVVQRVLKITYAQRLFGGIVGLFVFWGWQILIVLA 112 (485) T ss_pred ----------CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf ----------2155446676565766511135111368999989999999999 No 50 >COG2239 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism] Probab=25.43 E-value=37 Score=12.72 Aligned_cols=130 Identities=15% Similarity=0.204 Sum_probs=57.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999987542756689999999999998999999999996457899999999875001344442 Q gi|254780138|r 168 VPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIGSMKINEEIDAIRTM 247 (373) Q Consensus 168 lpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG~M~v~eeidAL~~~ 247 (373) |.+..+.+++.|-++... +.-+..+++++.+ =|++++ +|..-.+|.-|+. |.||.+= T Consensus 287 Llvll~~~~~ta~vi~~F----------e~~l~~~vaLa~f---iPlv~g------~gGN~GsQ~~tvi----vRaLa~~ 343 (451) T COG2239 287 LLVLLVTATLTASVIGLF----------EDTLEQLVALAAF---IPLVAG------MGGNAGTQAATVI----VRALALG 343 (451) T ss_pred HHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHH---HHEEEC------CCCCHHHHHHHHH----HHHHCCC T ss_conf 999999898899999999----------9779999999988---601006------8876999999999----9753103 Q ss_pred CCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH Q ss_conf 78689999-9999999999999999999999999999-999986113989999999986169999999999999999999 Q gi|254780138|r 248 GLDFVRIL-ISPRIWALIISLPLLTILANFSAIIGAS-IVIWKYYDIPFAVFFSRFHSTATLANIFTGLIKAPFMACAIG 325 (373) Q Consensus 248 Gi~p~~~L-v~PRv~A~~i~~p~L~~~~~~~~i~gg~-~~~~~~~~i~~~~f~~~~~~~~~~~d~~~~~~K~~~fg~~i~ 325 (373) -+++.... +++|=+..- ...+.+.|...|. +.+++..+. ....+-..-+...++-+...|.++. T Consensus 344 ~i~~~~~~~vl~rE~~vG------~~~G~vl~~~~~~~~~~~~~~~~--------~l~~~v~~al~~~~~~A~l~G~~iP 409 (451) T COG2239 344 EISLKNVFRVLLKELGVG------LLLGLVLAIIIGLRVPAWLYGGL--------LLGLIVALALLLNILFAALVGVLIP 409 (451) T ss_pred CCCCCCHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHCCC--------HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 063200999989999999------99999999999999899992662--------3899999999999999999853388 Q ss_pred HHHHCCCCC Q ss_conf 998317704 Q gi|254780138|r 326 IVAMKEGFA 334 (373) Q Consensus 326 ~i~c~~Gl~ 334 (373) ++--..|+- T Consensus 410 ~ll~kl~~D 418 (451) T COG2239 410 ILLKKLGLD 418 (451) T ss_pred HHHHHCCCC T ss_conf 999874999 No 51 >pfam07297 DPM2 Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2). This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2. Probab=24.14 E-value=39 Score=12.55 Aligned_cols=34 Identities=18% Similarity=0.196 Sum_probs=17.5 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6899999999999999999999999999999999 Q gi|254780138|r 250 DFVRILISPRIWALIISLPLLTILANFSAIIGAS 283 (373) Q Consensus 250 ~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~ 283 (373) +|++-+..||-.|..+-.-++.+....+|.+-|+ T Consensus 37 h~~~~~FlpReyAi~iP~~l~v~~~~~vg~Fig~ 70 (80) T pfam07297 37 HVIHSFFLPREYAIRIPVIAGLLLLLFVGSFIGV 70 (80) T ss_pred CHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 6698817858899998999999999999988441 No 52 >COG2120 Uncharacterized proteins, LmbE homologs [Function unknown] Probab=23.46 E-value=22 Score=14.28 Aligned_cols=11 Identities=0% Similarity=0.253 Sum_probs=4.6 Q ss_pred HHHHHHHCCCC Q ss_conf 99999751876 Q gi|254780138|r 58 IMYFMEKYHGK 68 (373) Q Consensus 58 L~~l~~~~~~~ 68 (373) |.++.++.+.+ T Consensus 101 L~~ii~~~~P~ 111 (237) T COG2120 101 LVAIIRRLRPD 111 (237) T ss_pred HHHHHHHCCCC T ss_conf 99999853997 No 53 >KOG3944 consensus Probab=23.31 E-value=39 Score=12.54 Aligned_cols=23 Identities=13% Similarity=0.037 Sum_probs=16.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999983 Q gi|254780138|r 307 LANIFTGLIKAPFMACAIGIVAM 329 (373) Q Consensus 307 ~~d~~~~~~K~~~fg~~i~~i~c 329 (373) +.+=+..+.-+.+||-+....+| T Consensus 235 pf~plEn~~cavffGgi~d~~s~ 257 (291) T KOG3944 235 PFAPLENLLCAVFFGGIWDASSC 257 (291) T ss_pred CCHHHHHHHHHHHHCCCCCCHHH T ss_conf 53236667589986444763034 No 54 >PRK06743 flagellar motor protein MotP; Reviewed Probab=23.05 E-value=40 Score=12.41 Aligned_cols=57 Identities=16% Similarity=-0.048 Sum_probs=36.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999837769999999999999999999998754275668999999999999899999999 Q gi|254780138|r 157 IRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVM 219 (373) Q Consensus 157 ~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii 219 (373) -..+++.--+.-|-..+++.++|+|..++.. +-..-+|..++.+++--+-=++.|=+ T Consensus 139 ~~~v~~~~g~~APafGmiGTviGLI~mL~~l------~dp~~iG~~mAvAlvtTlYG~~lAnl 195 (254) T PRK06743 139 GAALLDKIGDFAPAWGMIGTLIGLIIMLQNL------QDTSQIGTGMAVAMLTTLYGSVLANM 195 (254) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8999999997643788999999999998726------99999989999999999999999999 No 55 >pfam01312 Bac_export_2 FlhB HrpN YscU SpaS Family. This family includes the following members: FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system. The peptides exported are quite diverse. Probab=22.81 E-value=41 Score=12.38 Aligned_cols=35 Identities=14% Similarity=0.153 Sum_probs=22.5 Q ss_pred CCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 39899999999861699999999999999999999 Q gi|254780138|r 292 IPFAVFFSRFHSTATLANIFTGLIKAPFMACAIGI 326 (373) Q Consensus 292 i~~~~f~~~~~~~~~~~d~~~~~~K~~~fg~~i~~ 326 (373) ++|-.=+.++.+.=++.++.-+++|-.+.|.+... T Consensus 123 lNPi~GlKriFS~~~LvEl~KsllKv~li~~v~~~ 157 (343) T pfam01312 123 INPIKGLKRIFSARSLVELLKSILKVVAVGLIFYF 157 (343) T ss_pred CCHHHCHHCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 68744422003777899999999999999999999 No 56 >PRK10535 macrolide transporter ATP-binding /permease protein; Provisional Probab=22.17 E-value=42 Score=12.30 Aligned_cols=94 Identities=16% Similarity=0.251 Sum_probs=49.5 Q ss_pred HHHHHHHHHHHH--------HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH Q ss_conf 789999999987--------500134444278689999999999999999999999999999999999998611398999 Q gi|254780138|r 226 SAIVAEIGSMKI--------NEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVF 297 (373) Q Consensus 226 sa~aAeiG~M~v--------~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f 297 (373) |-+.+-||-|.+ |.||==.+++|-.+-+-+.. + ++=..+|++++.++|+..|++.+....- | T Consensus 532 SLlVggIGImNIMlvSVtERTrEIGIRKAlGA~~~dI~~q--F---L~Ea~~l~~iGGiiGi~lg~~i~~~i~~-----~ 601 (648) T PRK10535 532 SLVVGGIGVMNIMLVSVTERTREIGIRMAVGARASDVLQQ--F---LIEAVLVCLVGGALGISLSLLIAFTLQL-----F 601 (648) T ss_pred HHHHHHHHHHHHHEEEHHHHHHHHHHHHHHCCCHHHHHHH--H---HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----H T ss_conf 9999999999673220178888999999838988899999--9---9999999999999999999999999998-----5 Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999861699999999999999999999983 Q gi|254780138|r 298 FSRFHSTATLANIFTGLIKAPFMACAIGIVAM 329 (373) Q Consensus 298 ~~~~~~~~~~~d~~~~~~K~~~fg~~i~~i~c 329 (373) +......++++.+..++.=+.+.|++-++... T Consensus 602 l~~~~~~~~~~~i~~a~~~s~~iGvlfGlyPA 633 (648) T PRK10535 602 LPGWEIGFSPLALLSAFLCSTVTGILFGWLPA 633 (648) T ss_pred CCCCCEECCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 66771426889999999999999999999999 No 57 >KOG0539 consensus Probab=22.02 E-value=34 Score=12.92 Aligned_cols=40 Identities=23% Similarity=0.322 Sum_probs=29.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHCCC Q ss_conf 99999999999999999999999------99999999999861139 Q gi|254780138|r 254 ILISPRIWALIISLPLLTILANF------SAIIGASIVIWKYYDIP 293 (373) Q Consensus 254 ~Lv~PRv~A~~i~~p~L~~~~~~------~~i~gg~~~~~~~~~i~ 293 (373) .||.|-+.+.+++.|.-.++..+ .++++|.+.....+|++ T Consensus 137 RLVfPP~~~~il~~pfy~~~~~vl~~~~~~a~faG~l~GYV~YDmt 182 (240) T KOG0539 137 RLVFPPTPFAILAAPFYLILSLVLPHPVAPAGFAGGLLGYVCYDMT 182 (240) T ss_pred EEECCCCHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHH T ss_conf 2736882189999999999998637503243431201321354454 No 58 >pfam03095 PTPA Phosphotyrosyl phosphate activator (PTPA) protein. Phosphotyrosyl phosphatase activator (PTPA) proteins stimulate the phosphotyrosyl phosphatase (PTPase) activity of the dimeric form of protein phosphatase 2A (PP2A). PTPase activity in PP2A (in vitro) is relatively low when compared to the better recognized phosphoserine/ threonine protein phosphorylase activity. The specific biological role of PTPA is unknown, Basal expression of PTPA depends on the activity of a ubiquitous transcription factor, Yin Yang 1 (YY1). The tumour suppressor protein p53 can inhibit PTPA expression through an unknown mechanism that negatively controls YY1. Probab=21.84 E-value=43 Score=12.25 Aligned_cols=109 Identities=8% Similarity=0.076 Sum_probs=65.4 Q ss_pred EEEECCCHHHHHHHHHH-----HHHHHHHCCC-C-CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC-CCC--CHHHHHH Q ss_conf 99701051521299999-----9999975187-6-43158991269999988642220112456533-543--1136658 Q gi|254780138|r 41 IVDLSAITEIDTIGAEL-----IMYFMEKYHG-K-IKLQGVSTHIEQLFSLISFTHRKKIKNQKPQR-SFF--YNSFKNL 110 (373) Q Consensus 41 ~iDls~i~~lDTAGA~l-----L~~l~~~~~~-~-~~~~~l~~~~~~Ll~Ll~~~~~~~~~~~~~~~-~~~--~~~~~~~ 110 (373) +.+.++++.|-.+-|.. +.++.+...+ + -.....++..++++++++...+-..+.||.+. +.+ -..++.| T Consensus 5 I~~~~D~~~f~~S~ay~~i~~fI~~l~~sv~g~~~~~~~~~s~~i~~l~~il~~l~~~i~e~PP~~~~~~RFGN~afR~w 84 (298) T pfam03095 5 ILSPSDLELFLRSQAYYDILAFIQKLSDSVQGKPISDTFPISPAVRKLLEILDKLDALIDETPPLDQNPSRFGNKAFRDW 84 (298) T ss_pred CCCHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHH T ss_conf 37777898885379999999999999998538868988888989999999999999999858998898766687789999 Q ss_pred HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHCCCC Q ss_conf 99985999999999999--9999999999999997402678 Q gi|254780138|r 111 HYHIGKKIVKFINDSCS--QAHILGLVISNTGEFCASSYKF 149 (373) Q Consensus 111 ~~~iG~~~~~~~~~~~~--~~~f~G~~~~~~~~~~~~~~~~ 149 (373) ..++-+.+..+.++... .-..+-|....+.+.+.++.|. T Consensus 85 ~~~l~~~~~~ll~~~l~~~~~~~~~EL~~Yl~~SFGn~~Ri 125 (298) T pfam03095 85 HDKLEERAPSLLSELLPSSKDEAINELSYYLLNSFGNRTRI 125 (298) T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCC T ss_conf 99999989999998658304658999999998675987005 No 59 >COG2011 AbcD ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism] Probab=21.65 E-value=43 Score=12.23 Aligned_cols=105 Identities=20% Similarity=0.213 Sum_probs=59.7 Q ss_pred HHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 83776999999999999999-------99999987542756689999999999998999999999996457899999999 Q gi|254780138|r 163 VGVSGVPVVILISFVTGAVI-------AQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIGSM 235 (373) Q Consensus 163 ~G~~alpiv~l~~~~~G~v~-------a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG~M 235 (373) .-.+|+|.+.++-.++-..- .-..+..--..||--|...++-. -+||.- T Consensus 66 Ni~Rs~PFiILlv~liP~Tr~ivGTsiG~~AAivPL~i~a~PF~ARlve~-aL~EVd----------------------- 121 (222) T COG2011 66 NILRSIPFIILLVALIPLTRLIVGTSIGTTAAIVPLTIGAAPFVARLVES-ALREVD----------------------- 121 (222) T ss_pred HHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH-HHHHCC----------------------- T ss_conf 98751209999999998899997265253047741678888899999999-997447----------------------- Q ss_pred HHHHHHHHHHHHCCCHHHHHH-------HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 875001344442786899999-------999999-9999999999999999999999999861139 Q gi|254780138|r 236 KINEEIDAIRTMGLDFVRILI-------SPRIWA-LIISLPLLTILANFSAIIGASIVIWKYYDIP 293 (373) Q Consensus 236 ~v~eeidAL~~~Gi~p~~~Lv-------~PRv~A-~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~ 293 (373) .+-|+|=+.||.+|.+-.- .|-++. .++..-.|.-|+.+.|..||--..+...-.. T Consensus 122 --~GvIEAA~amGAs~~~II~kVlLpEa~p~li~g~Tvt~I~LIg~SAMAGaIGgGGLGdlAiryG 185 (222) T COG2011 122 --KGVIEAAQAMGASPWQIIRKVLLPEALPGLVSGITVTLISLIGYSAMAGAIGGGGLGDLAIRYG 185 (222) T ss_pred --CCHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH T ss_conf --2589999984998888878732621367899889999999980888830226673369999987 No 60 >TIGR01389 recQ ATP-dependent DNA helicase RecQ; InterPro: IPR006293 The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase. A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0004003 ATP-dependent DNA helicase activity, 0006310 DNA recombination, 0009432 SOS response. Probab=21.40 E-value=37 Score=12.65 Aligned_cols=13 Identities=15% Similarity=0.105 Sum_probs=4.7 Q ss_pred CCHHHHHHHHHHH Q ss_conf 9912699999886 Q gi|254780138|r 74 VSTHIEQLFSLIS 86 (373) Q Consensus 74 l~~~~~~Ll~Ll~ 86 (373) ++|++++|-.+.+ T Consensus 146 FRPeY~~L~~l~~ 158 (607) T TIGR01389 146 FRPEYRRLGELAE 158 (607) T ss_pred CCHHHHHHHHHHH T ss_conf 7565899999998 No 61 >COG3763 Uncharacterized protein conserved in bacteria [Function unknown] Probab=20.65 E-value=45 Score=12.09 Aligned_cols=21 Identities=33% Similarity=0.506 Sum_probs=14.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999986 Q gi|254780138|r 269 LLTILANFSAIIGASIVIWKY 289 (373) Q Consensus 269 ~L~~~~~~~~i~gg~~~~~~~ 289 (373) ++.+++-++|++||+.++.-. T Consensus 8 l~ivl~ll~G~~~G~fiark~ 28 (71) T COG3763 8 LLIVLALLAGLIGGFFIARKQ 28 (71) T ss_pred HHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999 No 62 >COG4062 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme metabolism] Probab=20.52 E-value=45 Score=12.07 Aligned_cols=33 Identities=18% Similarity=0.124 Sum_probs=14.5 Q ss_pred CCCCCCCCCCHHHHH---HHHHHHHHHHHCCCCCCC Q ss_conf 876431589912699---999886422201124565 Q gi|254780138|r 66 HGKIKLQGVSTHIEQ---LFSLISFTHRKKIKNQKP 98 (373) Q Consensus 66 ~~~~~~~~l~~~~~~---Ll~Ll~~~~~~~~~~~~~ 98 (373) ..+....+.+|-.++ |-.+.+...+...|..+| T Consensus 25 ~edvi~ldv~pi~Eqi~kLe~~vddl~~sldPstp~ 60 (108) T COG4062 25 FEDVIFLDVDPIEEQIKKLETLVDDLENSLDPSTPP 60 (108) T ss_pred CCCEEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 575489964179999999999999999635999998 Done!