Query gi|254780224|ref|YP_003064637.1| hypothetical protein CLIBASIA_00545 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 382 No_of_seqs 178 out of 252 Neff 6.5 Searched_HMMs 39220 Date Mon May 23 19:59:09 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780224.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG5330 Uncharacterized protei 100.0 0 0 373.8 32.7 356 1-363 7-362 (364) 2 pfam10098 DUF2336 Uncharacteri 100.0 0 0 373.6 28.5 238 86-323 1-239 (263) 3 COG5330 Uncharacterized protei 98.6 6.1E-06 1.5E-10 54.5 15.7 236 40-305 6-284 (364) 4 PRK09687 hypothetical protein; 96.7 0.042 1.1E-06 30.8 17.0 55 4-67 26-80 (280) 5 pfam10098 DUF2336 Uncharacteri 96.6 0.047 1.2E-06 30.5 21.0 220 44-304 15-238 (263) 6 KOG2025 consensus 91.2 0.9 2.3E-05 22.7 8.9 46 133-180 174-219 (892) 7 pfam01816 LRV Leucine rich rep 80.8 1.1 2.8E-05 22.2 2.1 25 56-84 2-26 (26) 8 PRK13800 putative oxidoreducta 67.8 7.2 0.00018 17.1 11.5 41 46-86 626-668 (894) 9 TIGR02160 PA_CoA_Oxy5 phenylac 52.2 9.9 0.00025 16.2 2.0 132 101-246 112-243 (371) 10 KOG2023 consensus 48.0 16 0.0004 15.0 8.7 117 2-127 175-292 (885) 11 PRK05686 fliG flagellar motor 46.9 16 0.00042 14.9 21.2 257 45-340 27-319 (337) 12 pfam09339 HTH_IclR IclR helix- 45.0 18 0.00045 14.7 2.7 34 253-286 8-41 (52) 13 pfam09904 DUF2131 Uncharacteri 41.1 16 0.0004 15.0 1.6 22 293-314 2-23 (67) 14 cd00020 ARM Armadillo/beta-cat 37.9 23 0.00058 14.0 13.5 97 2-115 8-109 (120) 15 TIGR02812 fadR_gamma fatty aci 33.6 24 0.00062 13.8 1.6 32 258-289 90-121 (275) 16 pfam01602 Adaptin_N Adaptin N 32.5 28 0.00071 13.5 7.1 62 1-67 79-140 (534) 17 KOG1240 consensus 28.7 32 0.00082 13.1 5.1 68 2-69 463-536 (1431) 18 TIGR01691 enolase-ppase 2,3-di 26.3 34 0.00086 13.0 1.3 86 274-373 91-179 (240) 19 TIGR02944 suf_reg_Xantho FeS a 24.2 39 0.00099 12.6 3.1 34 253-286 15-48 (130) 20 cd01392 HTH_LacI Helix-turn-he 24.0 39 0.001 12.6 5.5 43 268-324 2-44 (52) 21 smart00346 HTH_ICLR helix_turn 23.8 39 0.001 12.5 2.7 39 283-321 14-52 (91) 22 TIGR02431 pcaR_pcaU beta-ketoa 23.5 40 0.001 12.5 2.2 19 318-336 50-68 (252) 23 pfam02985 HEAT HEAT repeat. Th 23.3 40 0.001 12.5 2.9 22 45-66 4-25 (31) 24 COG1414 IclR Transcriptional r 22.4 42 0.0011 12.4 2.8 59 261-325 127-187 (246) 25 PRK09834 DNA-binding transcrip 21.4 44 0.0011 12.2 2.7 53 266-323 142-194 (264) No 1 >COG5330 Uncharacterized protein conserved in bacteria [Function unknown] Probab=100.00 E-value=0 Score=373.76 Aligned_cols=356 Identities=26% Similarity=0.328 Sum_probs=337.6 Q ss_pred CHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHC Q ss_conf 95899999841799789999999999996357899899999999999985196989999999982148789889999870 Q gi|254780224|r 1 MSVQSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALS 80 (382) Q Consensus 1 miv~~fl~~~~~a~~~~Ra~~a~~l~r~~~~~~l~~~er~~a~~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA 80 (382) |+++.|++|.+++++++|..+++.+++.+++++++-.|+..++++++.|++|+++.||+.+|+.|++|+.+|+.|+.+|+ T Consensus 7 ~~~~~~i~~~~~a~~~eR~~~A~~l~~~~~~~~~sr~d~~~~~~l~~~Ll~d~s~~vrr~lA~aL~~~~~~Pr~l~~~La 86 (364) T COG5330 7 STDQDLIRLLEEASSGERALAARVLAFASLQRPLSREDMRQFEDLARPLLDDSSEEVRRELAAALAQCETAPRALARALA 86 (364) T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHH T ss_conf 46999999844798368999999988888537521778999999999986086588999999998718767799999884 Q ss_pred CCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHH Q ss_conf 89778999999738589989999999549999999986299999899999984398999999860899846946799999 Q gi|254780224|r 81 EDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIV 160 (382) Q Consensus 81 ~D~~~vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~AIA~R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv 160 (382) +|+++|+.|+|.+||+|+|+||++|++++|+.|+.+||+|+++|+.|+++|++.|+.+++..++.|++|.+++.++..+. T Consensus 87 ~d~~~IAapll~rSpal~d~dLv~i~~~~G~~h~raIarR~~ls~~v~~~Lv~~g~~~~~~~~~~n~~A~~~~~al~~~~ 166 (364) T COG5330 87 EDPISIAAPLLIRSPALTDDDLVDIARRQGPAHARAIARRPSLSPLVIDALVERGDEEEVLVLLENDAAPLSPYALQRVA 166 (364) T ss_pred CCCHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCHHHHHHHH T ss_conf 59766767899718677837899999964889999998456888689999998077123310233545766788998876 Q ss_pred HHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 98178989999986246899899999999867999997852158998999999998888786432015677346999999 Q gi|254780224|r 161 ERFCHDASIRNLLSLRTDLSLKARYLLMKSVCNVLSQSKIVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVD 240 (382) Q Consensus 161 ~ra~~~~~l~~~L~~R~dLp~~~~~~L~~~vs~~lr~~l~~r~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~ 240 (382) ++++.++.++..++.|..+|.+.+..++.++++.+++.++....+++.+...+...++++.+........+..+. .++. T Consensus 167 d~~a~~~~~~~~~~~r~~lp~~~~~~~~~~~~~~~~~~~l~~~~~~~~r~~~l~~~a~~~~a~~~~aa~ad~~~~-~~~~ 245 (364) T COG5330 167 DRAAAEPALRQAAVDREALPLRARIELAARVGERLRDSILVKAQISEARAAELVRFARERAAILFAAALADALDI-RFVA 245 (364) T ss_pred HHHCCCHHHHHHHHCHHHCCHHHHHHHHHHHHHHHHCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCH-HHHH T ss_conf 420147667786203342452579999999887763365044135777799999987322578877750673124-7899 Q ss_pred HHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC Q ss_conf 99865899989999989819947999999998299989999997179917999999962999889999999999998402 Q gi|254780224|r 241 LLHDDGQLTPALLIYAIMIGAIDFVSVILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELA 320 (382) Q Consensus 241 ~L~~~g~Lt~~lllral~~G~~~~f~~aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~ 320 (382) +++..++++|+++..++|+|.+.||++++..++|+|...++.|+.+.+.+++..+|+.+|++++++-.|.+++. + T Consensus 246 ~~r~~~~~s~~~L~~aL~~~~~~~~~aalv~~ag~p~~~~r~i~~~~r~~al~~i~~~~~l~~rV~~~f~a~~~-----~ 320 (364) T COG5330 246 ALRIMLSLSPALLAAALRSLGLSFFEAALVDLAGLPSHRVRRIGRGGRPHALRAILRTAALDERVRSWFRADAL-----E 320 (364) T ss_pred HHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHH-----H T ss_conf 99997247889999999738987148999986278721279986033179999987522540789999997634-----3 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH Q ss_conf 6676531788999999999973025788200899999853168 Q gi|254780224|r 321 VGSTVMEPGIIAEKLLERMRKRNISGLPAGELLEMVERIYLDV 363 (382) Q Consensus 321 ~~~~~~~~~~~~~~~~er~~~~~~~~~~~~~l~~ll~r~~~~~ 363 (382) +++..+.+..+...++.++.+.. ...+..+.-+..++..... T Consensus 321 ~~~~~~~r~s~~a~~~~r~~r~s-~~aa~~~~~~~~r~~~~a~ 362 (364) T COG5330 321 LRDHAMARASALAEALARFPRDS-DEAAVDELSAPVRKLDLAA 362 (364) T ss_pred CCCCHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHHHHHH T ss_conf 14424444654458886046762-5778998997767765542 No 2 >pfam10098 DUF2336 Uncharacterized protein conserved in bacteria (DUF2336). Members of this family of hypothetical bacterial proteins have no known function. Probab=100.00 E-value=0 Score=373.58 Aligned_cols=238 Identities=28% Similarity=0.406 Sum_probs=232.8 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCC Q ss_conf 99999973858998999999954999999998629999989999998439899999986089984694679999998178 Q gi|254780224|r 86 VSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCH 165 (382) Q Consensus 86 vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~AIA~R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~ 165 (382) ||+|||++||+|+|+||++|+++++++|+++||+|++||+.|+|+|+++||.+|+..|+.|+||.||+.+|+++++|+++ T Consensus 1 VA~PvL~~S~~Lsd~DLi~ia~~~~~~h~~AIA~R~~ls~~VtdaLve~gd~~vv~~Ll~N~gA~is~~~~~~lv~ra~~ 80 (263) T pfam10098 1 VAGPVLERSPVLSDADLIEIARTGGQEHLLAIARRPDLSEAVTDALVERGDREVVRRLLRNPGARFSEAGLERLVERAAD 80 (263) T ss_pred CCHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHCC T ss_conf 97677724999998999999996899999997778989989999999728889999987299981786789999998765 Q ss_pred CHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 989999986246899899999999867999997852158-9989999999988887864320156773469999999986 Q gi|254780224|r 166 DASIRNLLSLRTDLSLKARYLLMKSVCNVLSQSKIVQKS-ITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHD 244 (382) Q Consensus 166 ~~~l~~~L~~R~dLp~~~~~~L~~~vs~~lr~~l~~r~~-l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~ 244 (382) ++.++.+|+.|+|||++++++|++++++.++++++.+++ ++++.++.+..+++++++...+....++++++.+|++|+. T Consensus 81 ~~~l~~~L~~R~dLp~~~~~~L~~~vs~~lr~~l~~~~~~~~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~~v~~l~~ 160 (263) T pfam10098 81 DAALREALGARPDLPADVRRRLLAKVSEALRAKLLARAAPLSAERIQRAVREAAERAAADLAADSRDFAEAKRLVRHLRA 160 (263) T ss_pred CHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 68899988556469999999999996799999999834556899999999999998750001234325679999999987 Q ss_pred CCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC Q ss_conf 5899989999989819947999999998299989999997179917999999962999889999999999998402667 Q gi|254780224|r 245 DGQLTPALLIYAIMIGAIDFVSVILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGS 323 (382) Q Consensus 245 ~g~Lt~~lllral~~G~~~~f~~aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~ 323 (382) +|+||+++|++++|+|+++||.++|+.|+|+|+.+|++||+++++++|.++||++|||+.+|++|+.++..|+++..+. T Consensus 161 ~g~L~~~~l~r~l~~g~~~~~~~ala~l~gi~~~~v~~il~~~~~~~l~~l~kaaGL~~~~~~~~~~a~~~~~~~~~~~ 239 (263) T pfam10098 161 RGRLTEALLLRAALSGRLEEFAAALAELSGLPVETVRRLLHDGRGEGLAALCKAAGLSWATFAALLAARDGWRRIAPSD 239 (263) T ss_pred CCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHH T ss_conf 5899999999999859978999999988693999999998379956999999985989999999999866322498778 No 3 >COG5330 Uncharacterized protein conserved in bacteria [Function unknown] Probab=98.62 E-value=6.1e-06 Score=54.52 Aligned_cols=236 Identities=16% Similarity=0.114 Sum_probs=121.4 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHC Q ss_conf 99999999985196989999999982148789889999870897789999997385899899999995499999999862 Q gi|254780224|r 40 DSLVLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALSEDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVAS 119 (382) Q Consensus 40 ~~a~~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA~D~~~vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~AIA~ 119 (382) +...+-+..++.+++..-|.-+|..++.+...++ +-+..-++..++..|.+..+......++..........++..+.. T Consensus 6 ~~~~~~~i~~~~~a~~~eR~~~A~~l~~~~~~~~-~sr~d~~~~~~l~~~Ll~d~s~~vrr~lA~aL~~~~~~Pr~l~~~ 84 (364) T COG5330 6 QSTDQDLIRLLEEASSGERALAARVLAFASLQRP-LSREDMRQFEDLARPLLDDSSEEVRRELAAALAQCETAPRALARA 84 (364) T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHH T ss_conf 6469999998447983689999999888885375-217789999999999860865889999999987187677999998 Q ss_pred CCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHH--------- Q ss_conf 99999899999984398999999860899846946799999981789899999862468998999999998--------- Q gi|254780224|r 120 RHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLSLKARYLLMKS--------- 190 (382) Q Consensus 120 R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp~~~~~~L~~~--------- 190 (382) ....|..|++.|.. |. -.+++.-+-.++.+ +.+.-...++.|+++++.+...|... T Consensus 85 La~d~~~IAapll~------------rS-pal~d~dLv~i~~~--~G~~h~raIarR~~ls~~v~~~Lv~~g~~~~~~~~ 149 (364) T COG5330 85 LAEDPISIAAPLLI------------RS-PALTDDDLVDIARR--QGPAHARAIARRPSLSPLVIDALVERGDEEEVLVL 149 (364) T ss_pred HHCCCHHHHHHHHH------------CC-CCCCHHHHHHHHHH--CCHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCC T ss_conf 84597667678997------------18-67783789999996--48899999984568886899999980771233102 Q ss_pred ----------------HH-----HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCC Q ss_conf ----------------67-----999997852158998999999998888786432015677346999999998658999 Q gi|254780224|r 191 ----------------VC-----NVLSQSKIVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHDDGQLT 249 (382) Q Consensus 191 ----------------vs-----~~lr~~l~~r~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~~g~Lt 249 (382) .. ..+++....++.++............++..-..... +.-+..+ T Consensus 150 ~~n~~A~~~~~al~~~~d~~a~~~~~~~~~~~r~~lp~~~~~~~~~~~~~~~~~~~l~~--------------~~~~~~r 215 (364) T COG5330 150 LENDAAPLSPYALQRVADRAAAEPALRQAAVDREALPLRARIELAARVGERLRDSILVK--------------AQISEAR 215 (364) T ss_pred CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHCHHHCCHHHHHHHHHHHHHHHHCCCHHH--------------HCCCHHH T ss_conf 33545766788998876420147667786203342452579999999887763365044--------------1357777 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHCCCHHHH-------------HHHHHCCCCHHHHHHHHHCCCCHHH Q ss_conf 8999998981994799999999829998999-------------9997179917999999962999889 Q gi|254780224|r 250 PALLIYAIMIGAIDFVSVILANIAEYSTDRV-------------YSILSTGGFHVICALYELVGLSPEI 305 (382) Q Consensus 250 ~~lllral~~G~~~~f~~aLA~lsgi~~~~v-------------~~ll~d~~~~~l~aL~~aaGLp~~~ 305 (382) ...++++.+.++..+|.++++.-.+...... ..+-+.+.+....++|+-+|+|... T Consensus 216 ~~~l~~~a~~~~a~~~~aa~ad~~~~~~~~~~r~~~~~s~~~L~~aL~~~~~~~~~aalv~~ag~p~~~ 284 (364) T COG5330 216 AAELVRFARERAAILFAAALADALDIRFVAALRIMLSLSPALLAAALRSLGLSFFEAALVDLAGLPSHR 284 (364) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHCCCCCHH T ss_conf 999999873225788777506731247899999972478899999997389871489999862787212 No 4 >PRK09687 hypothetical protein; Provisional Probab=96.65 E-value=0.042 Score=30.85 Aligned_cols=55 Identities=16% Similarity=0.056 Sum_probs=23.7 Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 9999984179978999999999999635789989999999999998519698999999998214 Q gi|254780224|r 4 QSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIAL 67 (382) Q Consensus 4 ~~fl~~~~~a~~~~Ra~~a~~l~r~~~~~~l~~~er~~a~~iL~~L~~d~~~~vR~alA~~La~ 67 (382) .+++++.+...+..|-.++..|.. ..+ ..+-..+..|+.|.++.||..-+..|.+ T Consensus 26 ~~Li~lL~D~n~~VR~~AA~aLg~--ig~-------~~a~~~li~llkd~n~~VR~~Aa~ALGq 80 (280) T PRK09687 26 NELFRLLDDHNSLKRISSARVLQL--RGG-------QEAFRLAVELCSSKNYIERDLGAFILSQ 80 (280) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHC--CCC-------HHHHHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 889998726988889999999880--484-------6699999998737878899999999984 No 5 >pfam10098 DUF2336 Uncharacterized protein conserved in bacteria (DUF2336). Members of this family of hypothetical bacterial proteins have no known function. Probab=96.58 E-value=0.047 Score=30.55 Aligned_cols=220 Identities=15% Similarity=0.072 Sum_probs=133.6 Q ss_pred HHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCHH-HHHHHHH-HCCCCCHHHHHHHHH--CCCHHHHHHHHC Q ss_conf 999998519698999999998214878988999987089778-9999997-385899899999995--499999999862 Q gi|254780224|r 44 LAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALSEDHPD-VSGTIIL-HSPVLKDNDLVDLIG--RGNKLTSIFVAS 119 (382) Q Consensus 44 ~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA~D~~~-vA~pvL~-~Sp~L~d~dLv~ia~--~~~~~~~~AIA~ 119 (382) +-|..++...++.-+.++|.+ ++.+..|...|+.--+. +...++. ..-.|++.-+..++. ..++..+..+.. T Consensus 15 ~DLi~ia~~~~~~h~~AIA~R----~~ls~~VtdaLve~gd~~vv~~Ll~N~gA~is~~~~~~lv~ra~~~~~l~~~L~~ 90 (263) T pfam10098 15 ADLIEIARTGGQEHLLAIARR----PDLSEAVTDALVERGDREVVRRLLRNPGARFSEAGLERLVERAADDAALREALGA 90 (263) T ss_pred HHHHHHHHHCCHHHHHHHHCC----CCCCHHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHC T ss_conf 999999996899999997778----9899899999997288899999872999817867899999987656889998855 Q ss_pred CCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 99999899999984398999999860899846946799999981789899999862468998999999998679999978 Q gi|254780224|r 120 RHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLSLKARYLLMKSVCNVLSQSK 199 (382) Q Consensus 120 R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp~~~~~~L~~~vs~~lr~~l 199 (382) |+++|+.+...|...-...+...++. ....+.......++............ ..+.+ ..-...+...+ T Consensus 91 R~dLp~~~~~~L~~~vs~~lr~~l~~-~~~~~~~~~~~~~~~~a~~~a~~~~~-----~~~~~------~~~~~~~v~~l 158 (263) T pfam10098 91 RPDLPADVRRRLLAKVSEALRAKLLA-RAAPLSAERIQRAVREAAERAAADLA-----ADSRD------FAEAKRLVRHL 158 (263) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHHC-----CCCCC------HHHHHHHHHHH T ss_conf 64699999999999967999999998-34556899999999999998750001-----23432------56799999999 Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCHHH Q ss_conf 52158998999999998888786432015677346999999998658999899999898199479999999982999899 Q gi|254780224|r 200 IVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHDDGQLTPALLIYAIMIGAIDFVSVILANIAEYSTDR 279 (382) Q Consensus 200 ~~r~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~~g~Lt~~lllral~~G~~~~f~~aLA~lsgi~~~~ 279 (382) ..+..+++..+.+.+.. +. ...+...+-.-..+....+-+.+.++... -...+..-+|+|... T Consensus 159 ~~~g~L~~~~l~r~l~~-------------g~---~~~~~~ala~l~gi~~~~v~~il~~~~~~-~l~~l~kaaGL~~~~ 221 (263) T pfam10098 159 RARGRLTEALLLRAALS-------------GR---LEEFAAALAELSGLPVETVRRLLHDGRGE-GLAALCKAAGLSWAT 221 (263) T ss_pred HHCCCCCHHHHHHHHHC-------------CC---HHHHHHHHHHHHCCCHHHHHHHHHCCCCH-HHHHHHHHCCCCHHH T ss_conf 87589999999999985-------------99---78999999988693999999998379956-999999985989999 Q ss_pred HHHHHHCCCCHHHHHHHHHCCCCHH Q ss_conf 9999717991799999996299988 Q gi|254780224|r 280 VYSILSTGGFHVICALYELVGLSPE 304 (382) Q Consensus 280 v~~ll~d~~~~~l~aL~~aaGLp~~ 304 (382) ...++. +.+..-+++.. T Consensus 222 ~~~~~~--------a~~~~~~~~~~ 238 (263) T pfam10098 222 FAALLA--------ARDGWRRIAPS 238 (263) T ss_pred HHHHHH--------HHHHHCCCCHH T ss_conf 999999--------86632249877 No 6 >KOG2025 consensus Probab=91.22 E-value=0.9 Score=22.68 Aligned_cols=46 Identities=26% Similarity=0.114 Sum_probs=26.9 Q ss_pred HCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCC Q ss_conf 439899999986089984694679999998178989999986246899 Q gi|254780224|r 133 ETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLS 180 (382) Q Consensus 133 e~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp 180 (382) -+..++|.++.+.|- ..+..++..+++|+.|....-..|+.-.=|| T Consensus 174 nDps~EVRraaLsnI--~vdnsTlp~IveRarDV~~anRrlvY~r~lp 219 (892) T KOG2025 174 NDPSDEVRRAALSNI--SVDNSTLPCIVERARDVSGANRRLVYERCLP 219 (892) T ss_pred CCCCHHHHHHHHHHC--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 399589999999860--7787755168887500679999999999876 No 7 >pfam01816 LRV Leucine rich repeat variant. The function of this repeat is unknown. It has an unusual structure of two helices. One is an alpha helix, the other is the much rarer 3-10 helix. Probab=80.84 E-value=1.1 Score=22.16 Aligned_cols=25 Identities=28% Similarity=0.389 Sum_probs=18.4 Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHCCCCH Q ss_conf 99999999821487898899998708977 Q gi|254780224|r 56 RVRLSLARAIALSDTAPKHVVLALSEDHP 84 (382) Q Consensus 56 ~vR~alA~~La~~~~aP~~vi~~LA~D~~ 84 (382) .||..+|.+ |++|.+.+..|+.|++ T Consensus 2 ~VR~~vA~r----p~lp~~~L~~L~~Dpd 26 (26) T pfam01816 2 EVRAAVARR----PDLPPEALERLAHDPD 26 (26) T ss_pred HHHHHHHCC----CCCCHHHHHHHCCCCC T ss_conf 177776528----9999899998513989 No 8 >PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional Probab=67.84 E-value=7.2 Score=17.10 Aligned_cols=41 Identities=24% Similarity=0.325 Sum_probs=17.8 Q ss_pred HHHHHCCCCHHHHHHHHHHHCCC--CCCCHHHHHHHCCCCHHH Q ss_conf 99985196989999999982148--789889999870897789 Q gi|254780224|r 46 MMHLLDDPSSRVRLSLARAIALS--DTAPKHVVLALSEDHPDV 86 (382) Q Consensus 46 L~~L~~d~~~~vR~alA~~La~~--~~aP~~vi~~LA~D~~~v 86 (382) |.-.++||+|.||+.....|... |.+-+.++..|+....+| T Consensus 626 ~~~~L~Dpdp~VRr~Av~~Lte~~pp~~~p~l~~al~D~~~~V 668 (894) T PRK13800 626 LAPYLADPDPGVRRTAVAVLTEHTPDGYAPALLDALGDDAAAV 668 (894) T ss_pred HHHHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHH T ss_conf 6554269974788999999860489861679999853998789 No 9 >TIGR02160 PA_CoA_Oxy5 phenylacetate-CoA oxygenase/reductase, PaaK subunit; InterPro: IPR011884 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA . . Probab=52.22 E-value=9.9 Score=16.24 Aligned_cols=132 Identities=11% Similarity=0.086 Sum_probs=101.9 Q ss_pred HHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCC Q ss_conf 99999954999999998629999989999998439899999986089984694679999998178989999986246899 Q gi|254780224|r 101 DLVDLIGRGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLS 180 (382) Q Consensus 101 dLv~ia~~~~~~~~~AIA~R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp 180 (382) |-..|+...++.|..|||.-..+.|-++-+ ...|+.||.+.|.- --..|-.++--+++.|..-.|.= T Consensus 112 daetiaqeaG~~hyvavAAGSGITP~lai~---------~tvLa~~p~S~ftL----vY~Nr~~~~vMFa~~L~DLKd~y 178 (371) T TIGR02160 112 DAETIAQEAGAGHYVAVAAGSGITPILAIA---------KTVLAAEPKSTFTL----VYGNRRSASVMFAEELADLKDKY 178 (371) T ss_pred HHHHHHHHHCCCCEEEEEECCCCHHHHHHH---------HHHHCCCCCCEEEE----EECCCCCCCHHHHHHHHHHHCCH T ss_conf 256888860689689998178705899999---------98740699520899----96178887277899898763120 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC Q ss_conf 899999999867999997852158998999999998888786432015677346999999998658 Q gi|254780224|r 181 LKARYLLMKSVCNVLSQSKIVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHDDG 246 (382) Q Consensus 181 ~~~~~~L~~~vs~~lr~~l~~r~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~~g 246 (382) +. |-.|+...|..-+...+-+.-|+.+++..+.......-..+.|--.+..+-+..--..|...| T Consensus 179 p~-Rf~l~~vlSrE~~~~~ll~GRlD~ekl~~L~~~li~~~~~deaFlCGP~~mv~~~~~~L~a~G 243 (371) T TIGR02160 179 PQ-RFALLHVLSREEREAPLLSGRLDGEKLRALLDSLIDVDEVDEAFLCGPAAMVDDAEDALKALG 243 (371) T ss_pred HH-HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHCCEEEECCCHHHHHHHHHHHHHCC T ss_conf 45-789986631211136410242278999988532002100240011185899999999997268 No 10 >KOG2023 consensus Probab=47.97 E-value=16 Score=15.00 Aligned_cols=117 Identities=15% Similarity=0.159 Sum_probs=71.8 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHC Q ss_conf 5899999841799789999999999996-357899899999999999985196989999999982148789889999870 Q gi|254780224|r 2 SVQSFIKWAKNAKLQERISIARILGRTW-CMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALS 80 (382) Q Consensus 2 iv~~fl~~~~~a~~~~Ra~~a~~l~r~~-~~~~l~~~er~~a~~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA 80 (382) ++-.|+...++.+|--|..+..-+-.-. ....--......+-+.+..|+.|.++.||+-+-..|.-.-+.- .-+|. T Consensus 175 mipkfl~f~~h~spkiRs~A~~cvNq~i~~~~qal~~~iD~Fle~lFalanD~~~eVRk~vC~alv~Llevr---~dkl~ 251 (885) T KOG2023 175 MIPKFLQFFKHPSPKIRSHAVGCVNQFIIIQTQALYVHIDKFLEILFALANDEDPEVRKNVCRALVFLLEVR---PDKLV 251 (885) T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHEEECCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHC---HHHCC T ss_conf 679999987289836789987202220233728899999999999999806998889999999999999836---77413 Q ss_pred CCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCHHH Q ss_conf 89778999999738589989999999549999999986299999899 Q gi|254780224|r 81 EDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVASRHKLSHVV 127 (382) Q Consensus 81 ~D~~~vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~AIA~R~~ls~~V 127 (382) -.-..|..-+|.+...-.+. |.+- .-+-+.++|..| ++..| T Consensus 252 phl~~IveyML~~tqd~dE~--VALE---ACEFwla~aeqp-i~~~~ 292 (885) T KOG2023 252 PHLDNIVEYMLQRTQDVDEN--VALE---ACEFWLALAEQP-ICKEV 292 (885) T ss_pred CCHHHHHHHHHHHCCCCCHH--HHHH---HHHHHHHHHCCC-CCHHH T ss_conf 22578999999970586545--7899---999999985076-73888 No 11 >PRK05686 fliG flagellar motor switch protein G; Validated Probab=46.92 E-value=16 Score=14.90 Aligned_cols=257 Identities=12% Similarity=0.120 Sum_probs=132.5 Q ss_pred HHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCHH--------------HHHHHHHHCCCCCHHHHHHHHH--- Q ss_conf 99998519698999999998214878988999987089778--------------9999997385899899999995--- Q gi|254780224|r 45 AMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALSEDHPD--------------VSGTIILHSPVLKDNDLVDLIG--- 107 (382) Q Consensus 45 iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA~D~~~--------------vA~pvL~~Sp~L~d~dLv~ia~--- 107 (382) .-..++..-++.--+.++...+.....|++.+.....+-.. .+.-+|. ..|+++-.-.|.. T Consensus 27 ~Aa~vlk~L~~~Ei~~i~~~m~~l~~i~~~~~~~Vl~EF~~~~~~~~~~~~g~~~~~~~~L~--~alg~~~a~~il~~i~ 104 (337) T PRK05686 27 AAAKVLKHLTPDEVQKLSAAMANLRNVSPEQVEAVLEEFEDEFEAGAYILMGGIDYARRLLE--KALGEEKANSILERIL 104 (337) T ss_pred HHHHHHHCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH--HHCCHHHHHHHHHHHC T ss_conf 79999863999999999999975699899999999999999998247767773899999999--8359899999998621 Q ss_pred -CCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHH Q ss_conf -4999999998629999989999998439899999986089984694679999998178989999986246899899999 Q gi|254780224|r 108 -RGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLSLKARYL 186 (382) Q Consensus 108 -~~~~~~~~AIA~R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp~~~~~~ 186 (382) ...... ...=.++++.+...+...-.+.++..++.+ ||++.+-. T Consensus 105 ~~~~~~~---~~~L~~~dp~~La~~L~~EhPQtiAlILs~--------------------------------L~~~~AA~ 149 (337) T PRK05686 105 ESLQTSG---FDFLRKMDPQQLANFIRNEHPQTIALILSY--------------------------------LDPDQAAE 149 (337) T ss_pred CCCCCCH---HHHHHCCCHHHHHHHHHCCCHHHHHHHHHH--------------------------------CCHHHHHH T ss_conf 5665876---899865999999999872485899999980--------------------------------99999999 Q ss_pred HHHHHHHHHHHHHHHC----CCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCH Q ss_conf 9998679999978521----589989999999988887864320156773469999999986589998999998981994 Q gi|254780224|r 187 LMKSVCNVLSQSKIVQ----KSITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHDDGQLTPALLIYAIMIGAI 262 (382) Q Consensus 187 L~~~vs~~lr~~l~~r----~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~~g~Lt~~lllral~~G~~ 262 (382) ++...++.++..++.| ..++++....+..--.....................+.-|+...+-+..-++..+...+- T Consensus 150 VL~~Lp~~~~~eVi~RiA~l~~v~p~~v~~ie~~L~~~~~~~~~~~~~~~~G~~~vA~ILN~~~~~~~~~il~~L~~~dp 229 (337) T PRK05686 150 ILSLLPEELRADVMMRIATLEGVQPEALKELEEVLEKKLSSMANADRTKMGGVKTVAEILNNLDRQTEKTIMESLEEEDP 229 (337) T ss_pred HHHHCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCH T ss_conf 99869999999999998677899999999999999999743554223445539999999874764689999999987589 Q ss_pred HHHHH------HHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHH------HHHCCCCCC--CCH Q ss_conf 79999------9999829998999999717991799999996299988999999999999------840266765--317 Q gi|254780224|r 263 DFVSV------ILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIW------RELAVGSTV--MEP 328 (382) Q Consensus 263 ~~f~~------aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~------r~~~~~~~~--~~~ 328 (382) ++... .+-.+..++...+..++..-...-+...+| |-+..+-..|+..++-+ .++++.|.. .+. T Consensus 230 ~la~~Ir~~mF~Fedi~~l~~~~l~~ll~~v~~~~l~~ALK--ga~~~~~~~il~nmS~R~a~~l~eel~~~gpv~~~dv 307 (337) T PRK05686 230 ELAEKIKDLMFVFEDLVDLDDRAIQRLLREVDNDDLALALK--GADEELREKFLSNMSKRAAEMLREDLEALGPVRLSDV 307 (337) T ss_pred HHHHHHHHHHEEHHHHHCCCHHHHHHHHHHCCHHHHHHHHC--CCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHH T ss_conf 99999998812299774779999999998489999999877--8989999999986289999999999986399878999 Q ss_pred HHHHHHHHHHHH Q ss_conf 889999999999 Q gi|254780224|r 329 GIIAEKLLERMR 340 (382) Q Consensus 329 ~~~~~~~~er~~ 340 (382) ..-++..+..+. T Consensus 308 e~Aq~~Iv~~~r 319 (337) T PRK05686 308 EEAQKKIVQIAR 319 (337) T ss_pred HHHHHHHHHHHH T ss_conf 999999999999 No 12 >pfam09339 HTH_IclR IclR helix-turn-helix domain. Probab=45.05 E-value=18 Score=14.72 Aligned_cols=34 Identities=12% Similarity=0.083 Sum_probs=16.8 Q ss_pred HHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHC Q ss_conf 9998981994799999999829998999999717 Q gi|254780224|r 253 LIYAIMIGAIDFVSVILANIAEYSTDRVYSILST 286 (382) Q Consensus 253 llral~~G~~~~f~~aLA~lsgi~~~~v~~ll~d 286 (382) |+.++...+-..-...|+..+|+|..++.+++.. T Consensus 8 iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~t 41 (52) T pfam09339 8 ILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQT 41 (52) T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 9999862899989999999989199999999999 No 13 >pfam09904 DUF2131 Uncharacterized protein conserved in bacteria (DUF2131). This domain, found in various hypothetical prokaryotic proteins, has no known function. Probab=41.11 E-value=16 Score=14.99 Aligned_cols=22 Identities=27% Similarity=0.300 Sum_probs=18.6 Q ss_pred HHHHHHCCCCHHHHHHHHHHHH Q ss_conf 9999962999889999999999 Q gi|254780224|r 293 CALYELVGLSPEISEIFVEATM 314 (382) Q Consensus 293 ~aL~~aaGLp~~~~~af~~A~~ 314 (382) ..|.+.+|+|++|.+.-.+|+. T Consensus 2 P~L~~~TGmPRRT~QDti~AL~ 23 (67) T pfam09904 2 PALMELTGMPRRTAQDTIAALA 23 (67) T ss_pred CHHHHHHCCCHHHHHHHHHHHC T ss_conf 1066531897337899998600 No 14 >cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model. Probab=37.87 E-value=23 Score=14.03 Aligned_cols=97 Identities=13% Similarity=0.102 Sum_probs=55.0 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHH-----HHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHH Q ss_conf 58999998417997899999999999963578998999999-----9999998519698999999998214878988999 Q gi|254780224|r 2 SVQSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSL-----VLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVV 76 (382) Q Consensus 2 iv~~fl~~~~~a~~~~Ra~~a~~l~r~~~~~~l~~~er~~a-----~~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi 76 (382) .|+.++++.++..++.+..++..|...... +++.+... -..|..|+.+.++.++...+.. + T Consensus 8 ~i~~Lv~lL~~~~~~~~~~A~~aL~~l~~~---~~~~~~~i~~~g~i~~Lv~lL~~~~~~v~~~a~~a-----------L 73 (120) T cd00020 8 GLPALVSLLSSSDENVQREAAWALSNLSAG---NNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWA-----------L 73 (120) T ss_pred CHHHHHHHHCCCCHHHHHHHHHHHHHHHCC---CHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHH-----------H T ss_conf 899999988599999999999999998328---99989999985869999998746980599999999-----------9 Q ss_pred HHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHH Q ss_conf 987089778999999738589989999999549999999 Q gi|254780224|r 77 LALSEDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSI 115 (382) Q Consensus 77 ~~LA~D~~~vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~ 115 (382) ..|+.+.+.....+... -. -.-|+.+..++++..+. T Consensus 74 ~nla~~~~~~~~~~~~~-g~--i~~Lv~ll~~~~~~v~~ 109 (120) T cd00020 74 RNLAAGPEDNKLIVLEA-GG--VPKLVNLLDSSNEDIQK 109 (120) T ss_pred HHHHCCCHHHHHHHHHC-CC--HHHHHHHHCCCCHHHHH T ss_conf 99826989999999987-99--98999988589989999 No 15 >TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178 Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process. Probab=33.65 E-value=24 Score=13.84 Aligned_cols=32 Identities=6% Similarity=-0.019 Sum_probs=14.4 Q ss_pred HCCCHHHHHHHHHHHHCCCHHHHHHHHHCCCC Q ss_conf 81994799999999829998999999717991 Q gi|254780224|r 258 MIGAIDFVSVILANIAEYSTDRVYSILSTGGF 289 (382) Q Consensus 258 ~~G~~~~f~~aLA~lsgi~~~~v~~ll~d~~~ 289 (382) .++-...+.-.||..|+|+.-.++..+-.... T Consensus 90 ~~~~P~l~dnLLSARTnIS~IYir~A~K~np~ 121 (275) T TIGR02812 90 GESVPSLIDNLLSARTNISAIYIRAAFKNNPE 121 (275) T ss_pred CCCCCHHHHHHHHHHHCCCHHHHHHHHHCCHH T ss_conf 77770799999977641377889998622835 No 16 >pfam01602 Adaptin_N Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles. Probab=32.45 E-value=28 Score=13.49 Aligned_cols=62 Identities=23% Similarity=0.162 Sum_probs=33.2 Q ss_pred CHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC Q ss_conf 9589999984179978999999999999635789989999999999998519698999999998214 Q gi|254780224|r 1 MSVQSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIAL 67 (382) Q Consensus 1 miv~~fl~~~~~a~~~~Ra~~a~~l~r~~~~~~l~~~er~~a~~iL~~L~~d~~~~vR~alA~~La~ 67 (382) |+|+.|.+=.++..+..|+-+.+.++.. .+++-.......+..++.|+++.||+..+-.+.. T Consensus 79 L~intl~kDl~s~n~~ir~lALr~ls~i-----~~~~l~~~l~~~i~~~l~d~~p~VRk~A~l~~~k 140 (534) T pfam01602 79 LTTNTIKKDLQSPNPLIRGLALRTLSCI-----RVPELAEDLAPDIKKLLVDPNPYVRKKAALAILK 140 (534) T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH T ss_conf 9999999876999787899999998737-----9799999999999998679978999999999999 No 17 >KOG1240 consensus Probab=28.73 E-value=32 Score=13.10 Aligned_cols=68 Identities=16% Similarity=0.253 Sum_probs=50.4 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHH----HHHHHHCC-CCHHHHHHHHHHHCCCC Q ss_conf 5899999841799789999999999996-357899899999999----99998519-69899999999821487 Q gi|254780224|r 2 SVQSFIKWAKNAKLQERISIARILGRTW-CMEELLDQEKDSLVL----AMMHLLDD-PSSRVRLSLARAIALSD 69 (382) Q Consensus 2 iv~~fl~~~~~a~~~~Ra~~a~~l~r~~-~~~~l~~~er~~a~~----iL~~L~~d-~~~~vR~alA~~La~~~ 69 (382) |+-.|+.+.+...+..|+.+...|++.. ...+.++.+-.++-+ -|..|+.| ....||.+-|..|+... T Consensus 463 VlPY~v~l~~Ds~a~Vra~Al~Tlt~~L~~Vr~~~~~daniF~eYlfP~L~~l~~d~~~~~vRiayAsnla~LA 536 (1431) T KOG1240 463 VLPYFVHLLMDSEADVRATALETLTELLALVRDIPPSDANIFPEYLFPHLNHLLNDSSAQIVRIAYASNLAQLA 536 (1431) T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEHHHHHHHHHHHH T ss_conf 67778877528637889999999999986455788410413076650446764125763001366875599999 No 18 >TIGR01691 enolase-ppase 2,3-diketo-5-methylthio-1-phosphopentane phosphatase; InterPro: IPR010041 This family of proteins are annotated as either enolase-phosphatases or putative enolase-phosphatases. The methionine salvage pathway converts the methylthioribose moiety of 5'-(methylthio)-adenosine to methionine via a series of biochemical steps in a wide variety of organisms. One enzyme active in this pathway is a bifunctional enolase-phosphatase called E-1 that promotes oxidative cleavage of the synthetic substrate 2,3-diketo-1-phosphohexane to 2-keto-pentanoate; it has been purified from the Gram-negative bacterium Klebsiella pneumoniae . The unusual metabolite 2,3-diketo-5-methylthio-1-phosphopentane is oxidatively cleaved to yield formate (from C-1), 2-keto-4-methylthiobutyrate (the transamination product of methionine), and 3-methylthiopropionate by E-1. The native enzyme is a monomeric protein of M(r) 27,000 requiring magnesium ion as a cofactor . The cloning and analysis of E-1 from Klebsiella oxytoca has been reported . . Probab=26.35 E-value=34 Score=12.96 Aligned_cols=86 Identities=20% Similarity=0.243 Sum_probs=58.2 Q ss_pred CCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH-HHHHHHHHHHHCCCCCCCHH Q ss_conf 99989999997179917999999962999889999999999998402667653178899-99999999730257882008 Q gi|254780224|r 274 EYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGSTVMEPGIIA-EKLLERMRKRNISGLPAGEL 352 (382) Q Consensus 274 gi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~~~~~~~~~~-~~~~er~~~~~~~~~~~~~l 352 (382) -.|..++.-+++..| |..--|...+||....|+..|+..+..=..=-.+++. |.|+ ++++..|+| T Consensus 91 ~tplK~lQG~iW~~G-------Y~~g~L~~hlYpDV~pAl~~w~~~Gl~~~vYSSGSvaAQKLl-------Fghs~~GdL 156 (240) T TIGR01691 91 ATPLKTLQGLIWRQG-------YEDGELTAHLYPDVPPALEAWKKAGLRLYVYSSGSVAAQKLL-------FGHSDAGDL 156 (240) T ss_pred HHHHHHHHHHHHHHC-------CCCCCCCCCCCCCHHHHHHHHHHCCCEEEEECCCCHHHHHHH-------HHCCCCCCC T ss_conf 125567634565400-------458850124465547899999874987998704417777766-------530533430 Q ss_pred HHHHH-HHHHHH-HHHHHHHHHH Q ss_conf 99999-853168-8999999999 Q gi|254780224|r 353 LEMVE-RIYLDV-NRRFVRSMAT 373 (382) Q Consensus 353 ~~ll~-r~~~~~-~r~~ar~~a~ 373 (382) ..+++ .|++.. .++|+.+|-+ T Consensus 157 ~~lf~~YFDt~vG~K~e~~SY~~ 179 (240) T TIGR01691 157 TPLFSGYFDTLVGAKKEAQSYKK 179 (240) T ss_pred HHHHHHHHHCCCCCCHHHHHHHH T ss_conf 45543231001477302256899 No 19 >TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.. Probab=24.21 E-value=39 Score=12.60 Aligned_cols=34 Identities=18% Similarity=0.146 Sum_probs=25.8 Q ss_pred HHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHC Q ss_conf 9998981994799999999829998999999717 Q gi|254780224|r 253 LIYAIMIGAIDFVSVILANIAEYSTDRVYSILST 286 (382) Q Consensus 253 llral~~G~~~~f~~aLA~lsgi~~~~v~~ll~d 286 (382) +...+..+.-.|-.+-||+.+|+..++|+++|.. T Consensus 15 l~~lA~~~~~~ySAA~lA~~tgL~~pTvsK~Lk~ 48 (130) T TIGR02944 15 LTVLAQADEQTYSAAELAEQTGLEAPTVSKILKA 48 (130) T ss_pred HHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHH T ss_conf 9998528997006888786459886047899887 No 20 >cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre Probab=23.95 E-value=39 Score=12.56 Aligned_cols=43 Identities=26% Similarity=0.213 Sum_probs=31.9 Q ss_pred HHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 999982999899999971799179999999629998899999999999984026676 Q gi|254780224|r 268 ILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGST 324 (382) Q Consensus 268 aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~~ 324 (382) -+|..+|++..+|.+.|.+.. |+...+-..++.++ .+++|... T Consensus 2 diA~~~gvS~~TVSr~ln~~~-----------~Vs~~tr~~I~~~~---~elgY~~~ 44 (52) T cd01392 2 DIARAAGVSVATVSRVLNGKP-----------RVSEETRERVLAAA---EELGYRPN 44 (52) T ss_pred HHHHHHCCCHHHHHHHHCCCC-----------CCCHHHHHHHHHHH---HHHCCCCC T ss_conf 288887859999999987989-----------89999999999999---99888979 No 21 >smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation. Probab=23.81 E-value=39 Score=12.55 Aligned_cols=39 Identities=15% Similarity=0.130 Sum_probs=27.1 Q ss_pred HHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC Q ss_conf 971799179999999629998899999999999984026 Q gi|254780224|r 283 ILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAV 321 (382) Q Consensus 283 ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~ 321 (382) +-..+++..+.-+++..|+|..+.--++..+..+.=+.. T Consensus 14 l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~~G~l~~ 52 (91) T smart00346 14 LAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91) T ss_pred HHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE T ss_conf 972899989999999989099999999999998899688 No 22 >TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process. Probab=23.47 E-value=40 Score=12.51 Aligned_cols=19 Identities=16% Similarity=0.029 Sum_probs=6.3 Q ss_pred HHCCCCCCCCHHHHHHHHH Q ss_conf 4026676531788999999 Q gi|254780224|r 318 ELAVGSTVMEPGIIAEKLL 336 (382) Q Consensus 318 ~~~~~~~~~~~~~~~~~~~ 336 (382) +++|...++....+.-|++ T Consensus 50 ~LGY~~~Dg~~F~LTPrvL 68 (252) T TIGR02431 50 ELGYVESDGRLFWLTPRVL 68 (252) T ss_pred HHCCEECCCCCEECCHHHH T ss_conf 6230421798331024677 No 23 >pfam02985 HEAT HEAT repeat. The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514). Probab=23.32 E-value=40 Score=12.49 Aligned_cols=22 Identities=36% Similarity=0.641 Sum_probs=14.2 Q ss_pred HHHHHHCCCCHHHHHHHHHHHC Q ss_conf 9999851969899999999821 Q gi|254780224|r 45 AMMHLLDDPSSRVRLSLARAIA 66 (382) Q Consensus 45 iL~~L~~d~~~~vR~alA~~La 66 (382) .+..++.|+++.||.+.++.+. T Consensus 4 ~l~~~~~d~~~~VR~~a~~~l~ 25 (31) T pfam02985 4 LLLELLNDPDPEVREAAAEALG 25 (31) T ss_pred HHHHHHCCCCHHHHHHHHHHHH T ss_conf 9999965998799999999988 No 24 >COG1414 IclR Transcriptional regulator [Transcription] Probab=22.41 E-value=42 Score=12.38 Aligned_cols=59 Identities=10% Similarity=0.000 Sum_probs=32.8 Q ss_pred CHHHH--HHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 94799--999999829998999999717991799999996299988999999999999840266765 Q gi|254780224|r 261 AIDFV--SVILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGSTV 325 (382) Q Consensus 261 ~~~~f--~~aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~~~ 325 (382) +++.+ ....+.|+.+|...+..++...... ..+.-.....+.+...+...|+.+|.-.. T Consensus 127 rlPl~~tA~Gk~lLA~l~~~e~~~~~~~~~~~------~~t~~t~~~~~~l~~el~~iR~~Gya~~~ 187 (246) T COG1414 127 RLPLYATASGKALLAFLPEEEREALLEEEELR------PFTPRTITDPEALLEELAEIRARGYAVDD 187 (246) T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC------CCCCCCCCCHHHHHHHHHHHHHCCEEEEC T ss_conf 34687788999999369989999997511345------78998757999999999999955989764 No 25 >PRK09834 DNA-binding transcriptional activator MhpR; Provisional Probab=21.39 E-value=44 Score=12.25 Aligned_cols=53 Identities=9% Similarity=-0.156 Sum_probs=26.6 Q ss_pred HHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC Q ss_conf 9999998299989999997179917999999962999889999999999998402667 Q gi|254780224|r 266 SVILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGS 323 (382) Q Consensus 266 ~~aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~ 323 (382) ...-+.|+.+|+.....++........ ...-+...-..+...+...|+.+|.- T Consensus 142 A~GkalLA~l~~~~~~~~l~~~~~~~~-----~~~~~~~~~~~l~~~L~~iR~~GyA~ 194 (264) T PRK09834 142 AAGRAYLAFCPEEEREALLELLRRRPG-----DEDQLARDPARLQAMLARTRKRGYGQ 194 (264) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHCCCC-----CCCCCCCCHHHHHHHHHHHHHCCEEE T ss_conf 679999836999999999986541678-----88876688999999999999678999 Done!