RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780701|ref|YP_003065114.1| putative two-component sensor histidine kinase transcriptional regulatory protein [Candidatus Liberibacter asiaticus str. psy62] (495 letters) >gnl|CDD|163083 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS. This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072). Length = 968 Score = 162 bits (411), Expect = 2e-40 Identities = 92/242 (38%), Positives = 134/242 (55%), Gaps = 8/242 (3%) Query: 236 DETRKRAEEENLAKSRFLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIH 295 + R AEE N AKS FLA+MSHE+RTPLN ILG +EL L ++ ++Y+ I+ Sbjct: 451 AKARAEAEEANRAKSAFLATMSHEIRTPLNGILG---TLELLGDTGLTSQ-QQQYLQVIN 506 Query: 296 RSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKID 355 RSG+ LL+++N+ILD S+IEAG +S L ++ + ++ RAQ K I++ I Sbjct: 507 RSGESLLDILNDILDYSKIEAGHLSISPRPFDLNALLDDVHHLMVSRAQLKGIQLRLNIP 566 Query: 356 PSLSSVW-ADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAE 414 L + W D +RQV++NL+ NA+KFT G V + V ++D G GIAE Sbjct: 567 EQLPNWWQGDGPRIRQVLINLVGNAIKFTD-RGSVVLRVSLNDDSSLLFEVEDTGCGIAE 625 Query: 415 GEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAILPN 474 E T+ +F Q +S G GLGL I+Q ++ G+ + S+L G LP Sbjct: 626 EEQATLFDAFTQADGRRRSG--GTGLGLAISQRLVEAMDGELGVESELGVGSCFWFTLPL 683 Query: 475 TR 476 TR Sbjct: 684 TR 685 >gnl|CDD|185245 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional. Length = 921 Score = 157 bits (399), Expect = 6e-39 Identities = 80/241 (33%), Positives = 122/241 (50%), Gaps = 15/241 (6%) Query: 236 DETRKRAEEENLAKSRFLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDI- 294 E ++RAE+ N KS L ++SHE+RTPLN +LG +EL PL E + D Sbjct: 385 AEAKQRAEQANKRKSEHLTTISHEIRTPLNGVLG---ALELLQNTPLTAEQMD--LADTA 439 Query: 295 HRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKI 354 + LL +IN +LD SRIE+G+ LS +L+ ++ + ++ +Q AQ K++ + + Sbjct: 440 RQCTLSLLAIINNLLDFSRIESGQMTLSLEETALLPLLDQAMLTIQGPAQSKSLTLRTFV 499 Query: 355 DPSLSSVWA-DEKGMRQVILNLLSNAVKFTAIGG-RVHVTVGWTSGRGQYISIKDNGPGI 412 + D +RQ+++NLL NAVKFT GG R+ V + +++D G GI Sbjct: 500 GAHVPLYLHLDSLRLRQILVNLLGNAVKFTETGGIRLRV---KRHEQQLCFTVEDTGCGI 556 Query: 413 AEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAIL 472 + + T F Q QG GLGL IA S+ GG+ + S G +L Sbjct: 557 DIQQQQQIFTPFYQADTHS----QGTGLGLTIASSLAKMMGGELTLFSTPGVGSCFSLVL 612 Query: 473 P 473 P Sbjct: 613 P 613 >gnl|CDD|182968 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional. Length = 919 Score = 150 bits (382), Expect = 6e-37 Identities = 90/244 (36%), Positives = 133/244 (54%), Gaps = 17/244 (6%) Query: 227 ELEVAKSLSDETRKRAEEENLAKSRFLASMSHELRTPLNAILGFSEVIELETMGPLNNET 286 EL++AK KRA+E KS FLA+MSHELRTPLN ++GF+ L+T PL T Sbjct: 278 ELDLAK-------KRAQEAARIKSEFLANMSHELRTPLNGVIGFTRQT-LKT--PLTP-T 326 Query: 287 YKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEK 346 ++Y+ I RS +LL +IN+ILD S++EAG+ L SL + + E + +L A EK Sbjct: 327 QRDYLQTIERSANNLLAIINDILDFSKLEAGKLVLENIPFSLRETLDEVVTLLAHSAHEK 386 Query: 347 NIEIFQKIDPSL-SSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYIS- 404 +E+ IDP + +V D ++Q+I NL+ NA+KFT G + + V + + Sbjct: 387 GLELTLNIDPDVPDNVIGDPLRLQQIITNLVGNAIKFTESGN-IDILVELRALSNTKVQL 445 Query: 405 ---IKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSK 461 I+D G GI+E + + +F Q +I G GLGL I Q ++ GG S+ Sbjct: 446 EVQIRDTGIGISERQQSQLFQAFRQADASISRRHGGTGLGLVITQKLVNEMGGDISFHSQ 505 Query: 462 LREG 465 G Sbjct: 506 PNRG 509 >gnl|CDD|163090 TIGR02966, phoR_proteo, phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154). Length = 333 Score = 129 bits (326), Expect = 2e-30 Identities = 71/230 (30%), Positives = 117/230 (50%), Gaps = 20/230 (8%) Query: 245 ENLAKSR--FLASMSHELRTPLNAILGFSEVIELETM---GPLNNETYKEYIGDIHRSGQ 299 L + R F+A++SHELRTPL + G+ LET+ + E + + + Q Sbjct: 108 RRLEQMRRDFVANVSHELRTPLTVLRGY-----LETLADGPDEDPEEWNRALEIMLEQSQ 162 Query: 300 HLLNLINEILDLSRIEAGRYELSESAI---SLIDIVRECIIMLQLRAQEKNIEIFQKIDP 356 + +L+ ++L LSR+E+ L + + +L+D +R+ + +Q KN +I +ID Sbjct: 163 RMQSLVEDLLTLSRLESAASPLEDEPVDMPALLDHLRD---EAEALSQGKNHQITFEIDG 219 Query: 357 SLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTS-GRGQYISIKDNGPGIAEG 415 + V DE +R NL+SNA+K+T GG +TV W G G S+ D G GIA Sbjct: 220 GV-DVLGDEDELRSAFSNLVSNAIKYTPEGG--TITVRWRRDGGGAEFSVTDTGIGIAPE 276 Query: 416 EIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREG 465 +P + F + + G GLGL I + +++ H + I S+L +G Sbjct: 277 HLPRLTERFYRVDKSRSRDTGGTGLGLAIVKHVLSRHHARLEIESELGKG 326 >gnl|CDD|182956 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional. Length = 779 Score = 120 bits (304), Expect = 7e-28 Identities = 82/258 (31%), Positives = 132/258 (51%), Gaps = 17/258 (6%) Query: 239 RKRAEE--ENLA--KSRFLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDI 294 RKR ++ E + K+ F++++SHELRTPLN I+G S I L+T L E K Y+ I Sbjct: 269 RKRYQDALEKASRDKTTFISTISHELRTPLNGIVGLSR-ILLDT--ELTAEQRK-YLKTI 324 Query: 295 HRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKI 354 H S L N+ N+I+D+ ++E + +L I D + + + L+A++K + + Sbjct: 325 HVSAITLGNIFNDIIDMDKMERRKLQLDNQPIDFTDFLADLENLSGLQAEQKGLRFDLEP 384 Query: 355 DPSL-SSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIA 413 L V D +RQ++ NL+SNAVKFT GG V V V + G ++D+G GI Sbjct: 385 LLPLPHKVITDGTRLRQILWNLISNAVKFTQQGG-VTVRVRYEEGDMLTFEVEDSGIGIP 443 Query: 414 EGEIPTVLTSFGQ--GSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREG----VE 467 E E+ + + Q S K A G G+GL +++ + GG + S+ +G + Sbjct: 444 EDELDKIFAMYYQVKDSHGGKPA-TGTGIGLAVSKRLAQAMGGDITVTSEEGKGSCFTLT 502 Query: 468 VIAILPNTRVLNFIPEDN 485 + A V + ED+ Sbjct: 503 IHAPAVAEEVEDAFDEDD 520 >gnl|CDD|183148 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional. Length = 914 Score = 118 bits (296), Expect = 5e-27 Identities = 85/266 (31%), Positives = 130/266 (48%), Gaps = 18/266 (6%) Query: 208 FKSNVKILSCQAEK-DDLI----AELEVAKSLSDETRKRAEEENLAKSRFLASMSHELRT 262 F+SNV L+ E+ + AEL+ + R AE+ + AKS FLA+MSHE+RT Sbjct: 398 FRSNVHALNRHREQLAAQVKARTAELQELVIEHRQARAEAEKASQAKSAFLAAMSHEIRT 457 Query: 263 PLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYE-- 320 PL ILG +L P N ++ + I SG+ LL ++N+ILD S IEAG Sbjct: 458 PLYGILG---TAQLLADNPALNA-QRDDLRAITDSGESLLTILNDILDYSAIEAGGKNVS 513 Query: 321 LSESAISLIDIVRECIIMLQLRAQEKNIEIFQKIDPSL-SSVWADEKGMRQVILNLLSNA 379 +S+ ++ + ++ R + + I + I L +++ D + +RQVI NLLSNA Sbjct: 514 VSDEPFEPRPLLESTLQLMSGRVKGRPIRLATDIADDLPTALMGDPRRIRQVITNLLSNA 573 Query: 380 VKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVG 439 ++FT G V T G + ++D+G GI ++ + F Q S G G Sbjct: 574 LRFTDEG--SIVLRSRTDGEQWLVEVEDSGCGIDPAKLAEIFQPFVQVS----GKRGGTG 627 Query: 440 LGLPIAQSIMANHGGQFLIRSKLREG 465 LGL I+ + GG+ S G Sbjct: 628 LGLTISSRLAQAMGGELSATSTPEVG 653 >gnl|CDD|182962 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional. Length = 475 Score = 112 bits (282), Expect = 3e-25 Identities = 60/221 (27%), Positives = 111/221 (50%), Gaps = 10/221 (4%) Query: 255 SMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDLSRI 314 +++HEL++PL AI G +E+++ E P E + G+I L LI+ +L+L+R+ Sbjct: 262 TLTHELKSPLAAIRGAAELLQ-EDPPP---EDRARFTGNILTQSARLQQLIDRLLELARL 317 Query: 315 EAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKIDPSLSSVWADEKGMRQVILN 374 E + ++L ++ E + + +A K I + ++ P + V D +RQ + N Sbjct: 318 EQRQELEVLEPVALAALLEELVEAREAQAAAKGITL--RLRPDDARVLGDPFLLRQALGN 375 Query: 375 LLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQGSIA-IKS 433 LL NA+ F+ GG + ++ + +S++D GPGI + +P + F S+ + Sbjct: 376 LLDNAIDFSPEGGTITLSAEVDGEQVA-LSVEDQGPGIPDYALPRIFERF--YSLPRPAN 432 Query: 434 AEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAILPN 474 + GLGL + + HGG+ +R++ GV LP Sbjct: 433 GRKSTGLGLAFVREVARLHGGEVTLRNRPEGGVLATLTLPR 473 >gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional. Length = 1197 Score = 110 bits (277), Expect = 6e-25 Identities = 86/259 (33%), Positives = 128/259 (49%), Gaps = 18/259 (6%) Query: 220 EKDDLIAELEVAKSLSDETRKRAEEENLAKSRFLASMSHELRTPLNAILGFSEVIELETM 279 E DLI LEV R +A +AKS+FLA+MSHE+RTP+++I+GF +EL + Sbjct: 690 ETRDLIHALEVE-------RNKAINATVAKSQFLATMSHEIRTPISSIMGF---LELLSG 739 Query: 280 GPLNNETYKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIML 339 L+ E E I + +GQ LL LI EILD+ +IE+G Y+L + + +V+ Sbjct: 740 SGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNYQLQPQWVDIPTLVQNTCHSF 799 Query: 340 QLRAQEKNIEIF-QKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSG 398 A K+I + P V D + +QV+ NLLSNA+KFT G V +T Sbjct: 800 GAIAASKSIALSCSSTFPDHYLVKIDPQAFKQVLSNLLSNALKFTTEGA-VKITTSLGHI 858 Query: 399 RGQYISIK----DNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGG 454 + IK D+G G+++ E + + Q S + G GLGL I + ++ N G Sbjct: 859 DDNHAVIKMTIMDSGSGLSQEEQQQLFKRYSQTSAG--RQQTGSGLGLMICKELIKNMQG 916 Query: 455 QFLIRSKLREGVEVIAILP 473 + S G +P Sbjct: 917 DLSLESHPGIGTTFTITIP 935 >gnl|CDD|181772 PRK09303, PRK09303, adaptive-response sensory kinase; Validated. Length = 380 Score = 110 bits (278), Expect = 7e-25 Identities = 77/249 (30%), Positives = 122/249 (48%), Gaps = 27/249 (10%) Query: 234 LSDET-RKRAEEENL-----AKSRFLASMSHELRTPLNAILGFSEVIELETM-GPLNNET 286 LSDE R E E L K R LA ++H+LRTPL A + LET+ +E Sbjct: 130 LSDELFVLRQENETLLEQLKFKDRVLAMLAHDLRTPLTA-----ASLALETLELGQIDED 184 Query: 287 YKEYIGDIHRSGQHLLN-------LINEILDLSRIEAGRYELSESAISLIDIVRECIIML 339 + I + LI ++L++ R + + L + +E I+ L Sbjct: 185 TELKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWEALRFNPQKLDLGSLCQEVILEL 244 Query: 340 QLRAQEKNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTV-GWTSG 398 + R K++EI I L SV+AD++ +RQV+LNLL NA+K+T GG + +++ T+ Sbjct: 245 EKRWLAKSLEIQTDIPSDLPSVYADQERIRQVLLNLLDNAIKYTPEGGTITLSMLHRTTQ 304 Query: 399 RGQYISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQ--GVGLGLPIAQSIMANHGGQF 456 + Q +SI D GPGI E E + + + + E G G+GL + + I+ H GQ Sbjct: 305 KVQ-VSICDTGPGIPEEEQERIF----EDRVRLPRDEGTEGYGIGLSVCRRIVRVHYGQI 359 Query: 457 LIRSKLREG 465 + S+ +G Sbjct: 360 WVDSEPGQG 368 >gnl|CDD|183098 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional. Length = 607 Score = 110 bits (276), Expect = 1e-24 Identities = 71/248 (28%), Positives = 119/248 (47%), Gaps = 21/248 (8%) Query: 233 SLSDET-RKRAEE-----ENLAK-SRFLASMSHELRTPLNAILGFSEVIELETMGPLNNE 285 SD T RKR + E LA +A ++HE+R PL AI G+ ++ +T P Sbjct: 367 IFSDLTERKRLQRRVARQERLAALGELVAGVAHEIRNPLTAIRGYVQIWRQQTSDP---- 422 Query: 286 TYKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQE 345 +EY+ + R L +I+++L+ SR E +SL +V E + + Q + Sbjct: 423 PSQEYLSVVLREVDRLNKVIDQLLEFSRPR----ESQWQPVSLNALVEEVLQLFQTAGVQ 478 Query: 346 KNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISI 405 ++ ++D L +WAD + ++QV+LN+L NAV+ + G++ + S +SI Sbjct: 479 ARVDFETELDNELPPIWADPELLKQVLLNILINAVQAISARGKIRIRTWQYSDGQVAVSI 538 Query: 406 KDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREG 465 +DNG GI + + F + +G GLGL ++Q I+ HGG + S+ G Sbjct: 539 EDNGCGIDPELLKKIFDPF------FTTKAKGTGLGLALSQRIINAHGGDIEVESEPGVG 592 Query: 466 VEVIAILP 473 LP Sbjct: 593 TTFTLYLP 600 >gnl|CDD|182496 PRK10490, PRK10490, sensor protein KdpD; Provisional. Length = 895 Score = 103 bits (260), Expect = 9e-23 Identities = 74/253 (29%), Positives = 121/253 (47%), Gaps = 22/253 (8%) Query: 239 RKRAEEENLAKSRFLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSG 298 R +E E L + LA++SH+LRTPL + G +E++ L+ L +E + Sbjct: 655 RLASEREQLRNA-LLAALSHDLRTPLTVLFGQAEILTLD----LASEGSP-HARQASEIR 708 Query: 299 QHLLN---LINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKID 355 Q +LN L+N +LD++RI++G + L + ++L ++V + ML+ I + + Sbjct: 709 QQVLNTTRLVNNLLDMARIQSGGFNLRKEWLTLEEVVGSALQMLEPGLSGHPINL--SLP 766 Query: 356 PSLSSVWADEKGMRQVILNLLSNAVKFTA----IGGRVHVTVGWTSGRGQYISIKDNGPG 411 L+ + D +V++NLL NAVK+ IG HV G + + DNGPG Sbjct: 767 EPLTLIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHV-----EGERLQLDVWDNGPG 821 Query: 412 IAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAI 471 I G+ + F +G+ +SA GVGLGL I ++I+ HGG ++ G Sbjct: 822 IPPGQEQLIFDKFARGN--KESAIPGVGLGLAICRAIVEVHGGTIWAENRPEGGACFRVT 879 Query: 472 LPNTRVLNFIPED 484 LP Sbjct: 880 LPLETPPELEEFH 892 >gnl|CDD|182895 PRK11006, phoR, phosphate regulon sensor protein; Provisional. Length = 430 Score = 102 bits (257), Expect = 2e-22 Identities = 79/260 (30%), Positives = 125/260 (48%), Gaps = 27/260 (10%) Query: 228 LEVAKSLSDETRKRAEEENLAKSRFLASMSHELRTPLNAILGFSEVIELETM-GPLNNET 286 L VA+ D T+ E A+ F A++SHELRTPL + G+ E+++ + + G L + Sbjct: 188 LMVAR---DVTQMHQLEG--ARRNFFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKA 242 Query: 287 YKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQE- 345 R + L+ ++L LS+IEA I L + V + +ML++ +E Sbjct: 243 LHTMREQTQR----MEGLVKQLLTLSKIEAA------PTIDLNEKV-DVPMMLRVLEREA 291 Query: 346 -----KNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGW-TSGR 399 I ++D SL V+ +E +R I NL+ NAV T G H+TV W + Sbjct: 292 QTLSQGKHTITFEVDNSL-KVFGNEDQLRSAISNLVYNAVNHTPEG--THITVRWQRVPQ 348 Query: 400 GQYISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIR 459 G S++DNGPGIA IP + F + A G GLGL I + +++H + I Sbjct: 349 GAEFSVEDNGPGIAPEHIPRLTERFYRVDKARSRQTGGSGLGLAIVKHALSHHDSRLEIE 408 Query: 460 SKLREGVEVIAILPNTRVLN 479 S++ +G +LP + Sbjct: 409 SEVGKGTRFSFVLPERLIAK 428 >gnl|CDD|128669 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Length = 111 Score = 99.3 bits (248), Expect = 2e-21 Identities = 37/111 (33%), Positives = 56/111 (50%), Gaps = 2/111 (1%) Query: 363 ADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLT 422 D +RQV+ NLL NA+K+T GGR+ VT+ I+++DNGPGI ++ + Sbjct: 1 GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGDHL-EITVEDNGPGIPPEDLEKIFE 59 Query: 423 SFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAILP 473 F + G GLGL I + ++ HGG+ + S+ G LP Sbjct: 60 PFFRTD-GRSRKIGGTGLGLSIVKKLVELHGGEISVESEPGGGTTFTITLP 109 >gnl|CDD|182411 PRK10364, PRK10364, sensor protein ZraS; Provisional. Length = 457 Score = 96.8 bits (241), Expect = 1e-20 Identities = 79/318 (24%), Positives = 146/318 (45%), Gaps = 44/318 (13%) Query: 160 PYAVFLSF--FPVVVALSTQAIMSMHVLDISLAGMLATALSFFTYITYHLFKSNVKILSC 217 P A+F++F +V A + + ++ +L +LA+ L+FF Y Y Sbjct: 170 PQAIFIAFDASNLVSAQAREQRNTLIILFALATVLLASLLAFFWYRRY------------ 217 Query: 218 QAEKDDLIAELEVAKSLSDETRKRAEEENLAKSRFLASMSHELRTPLNAILGFSEVI-EL 276 L + L DE +++ E+ +A A ++HE+R PL++I G ++ E Sbjct: 218 ----------LRSRQLLQDEMKRK--EKLVALGHLAAGVAHEIRNPLSSIKGLAKYFAER 265 Query: 277 ETMGPLNNETYKEYIGDIHRSGQHLLN-LINEILDLSRIEAGRYELSESAISLIDIVREC 335 G ++ + + R LN +++E+L+L + L+ A+ L D++ Sbjct: 266 APAGGEAHQLAQVMAKEADR-----LNRVVSELLELVKPT----HLALQAVDLNDLINHS 316 Query: 336 IIMLQLRAQEKNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGW 395 + ++ A + I++ + +L + AD + QV+LNL NA++ G + VT Sbjct: 317 LQLVSQDANSREIQLRFTANDTLPEIQADPDRLTQVLLNLYLNAIQAIGQHGVISVTASE 376 Query: 396 TSGRGQYISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQ 455 SG G IS+ D+G GIA ++ + T + + +G GLGL + +I+ HGG Sbjct: 377 -SGAGVKISVTDSGKGIAADQLEAIFTPY------FTTKAEGTGLGLAVVHNIVEQHGGT 429 Query: 456 FLIRSKLREGVEVIAILP 473 + S+ +G LP Sbjct: 430 IQVASQEGKGATFTLWLP 447 >gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional. Length = 924 Score = 96.2 bits (240), Expect = 2e-20 Identities = 76/253 (30%), Positives = 128/253 (50%), Gaps = 26/253 (10%) Query: 223 DLIAELEVAKSLSDETRKRAEEENLAKSRFLASMSHELRTPLNAILGFSEVIELETMGPL 282 D+ A +++ +SL E + AE+ + +KS FLA++SHELRTPL I+G ++++ + L Sbjct: 422 DVSARVKMEESLQ-EMAQAAEQASQSKSMFLATVSHELRTPLYGIIGNLDLLQTKE---L 477 Query: 283 NNETYKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLR 342 + + ++ S LL +I++ILD S+IE+ + ++ S +++ Sbjct: 478 PKGVDR-LVTAMNNSSSLLLKIISDILDFSKIESEQLKIEPREFSPREVINHITANYLPL 536 Query: 343 AQEKNIEIFQKIDPSL-SSVWADEKGMRQVILNLLSNAVKFTAIGGRV-HVTVGWTSGRG 400 +K + ++ I+P + ++ D ++QVI NLLSNA+KFT G V HV V G Sbjct: 537 VVKKRLGLYCFIEPDVPVALNGDPMRLQQVISNLLSNAIKFTDTGCIVLHVRV-----DG 591 Query: 401 QY--ISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMA-------- 450 Y ++D G GI E+ + F Q ++ QG GLGL I + ++ Sbjct: 592 DYLSFRVRDTGVGIPAKEVVRLFDPFFQVGTGVQRNFQGTGLGLAICEKLINMMDGDISV 651 Query: 451 ----NHGGQFLIR 459 G QF IR Sbjct: 652 DSEPGMGSQFTIR 664 >gnl|CDD|162333 TIGR01386, cztS_silS_copS, heavy metal sensor kinase. Members of this family contain a sensor histidine kinase domain (Pfam:PF00512) and a domain found in bacterial signal proteins (Pfam:PF00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Length = 457 Score = 95.9 bits (239), Expect = 2e-20 Identities = 70/241 (29%), Positives = 120/241 (49%), Gaps = 9/241 (3%) Query: 215 LSCQAEKDDLIAEL-EVAKSLSDETRKRAEEENLAKSRFLASMSHELRTPLNAILGFSEV 273 L + + AEL E+A+S + R E+ S+F A ++HELRTPL +LG ++V Sbjct: 207 LDQRLDPSRAPAELRELAQSF-NAMLGRLEDAFQRLSQFSADLAHELRTPLTNLLGQTQV 265 Query: 274 IELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVR 333 + P E Y+E + + L +++++L L+R + G+ L + L + Sbjct: 266 ALSQ---PRTGEEYREVLESNLEELERLSRMVSDMLFLARADNGQLALERVRLDLAAELA 322 Query: 334 ECIIMLQLRAQEKNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTV 393 + + A+E+ + I + + V D + R+ I NLLSNA++ T GG + V + Sbjct: 323 KVAEYFEPLAEERGVRIRVEGE---GLVRGDPQMFRRAISNLLSNALRHTPDGGTITVRI 379 Query: 394 GWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHG 453 S + +S+ + GPGI + + F + A ++ +G GLGL I +SIM HG Sbjct: 380 ERRSDEVR-VSVSNPGPGIPPEHLSRLFDRFYRVDPARSNSGEGTGLGLAIVRSIMEAHG 438 Query: 454 G 454 G Sbjct: 439 G 439 >gnl|CDD|184354 PRK13837, PRK13837, two-component VirA-like sensor kinase; Provisional. Length = 828 Score = 84.3 bits (209), Expect = 6e-17 Identities = 67/262 (25%), Positives = 106/262 (40%), Gaps = 41/262 (15%) Query: 236 DETRKRAEEENLAKSR------FLAS-MSHELRTPLNAILGFSEVIE--LETMGPLNNET 286 ET + A E L +R LAS ++H L AILG++E+ L Sbjct: 430 LETERDALERRLEHARRLEAVGTLASGIAHNFNNILGAILGYAEMALNKLARHSRA---- 485 Query: 287 YKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQ-E 345 YI +I +G +I++IL R + E + L ++V E I LR Sbjct: 486 -ARYIDEIISAGARARLIIDQILAFGR----KGERNTKPFDLSELVTE--IAPLLRVSLP 538 Query: 346 KNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGR------ 399 +E+ D + V + ++QV++NL SNA + GRV +++ R Sbjct: 539 PGVELDFDQDQEPAVVEGNPAELQQVLMNLCSNAAQAMDGAGRVDISLSRAKLRAPKVLS 598 Query: 400 ------GQY--ISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMAN 451 G+Y + + D G GI E +P + F + G GLGL I++ Sbjct: 599 HGVLPPGRYVLLRVSDTGAGIDEAVLPHIFEPF------FTTRAGGTGLGLATVHGIVSA 652 Query: 452 HGGQFLIRSKLREGVEVIAILP 473 H G ++S + G LP Sbjct: 653 HAGYIDVQSTVGRGTRFDVYLP 674 >gnl|CDD|128670 smart00388, HisKA, His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases. Length = 66 Score = 80.7 bits (200), Expect = 9e-16 Identities = 39/70 (55%), Positives = 50/70 (71%), Gaps = 4/70 (5%) Query: 248 AKSRFLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINE 307 AK FLA++SHELRTPL AI G+ E++E L+ E +EY+ I RS + LL LIN+ Sbjct: 1 AKREFLANLSHELRTPLTAIRGYLELLE---DTELSEEQ-REYLETILRSAERLLRLIND 56 Query: 308 ILDLSRIEAG 317 +LDLSRIEAG Sbjct: 57 LLDLSRIEAG 66 >gnl|CDD|181882 PRK09467, envZ, osmolarity sensor protein; Provisional. Length = 435 Score = 76.5 bits (189), Expect = 2e-14 Identities = 58/226 (25%), Positives = 96/226 (42%), Gaps = 31/226 (13%) Query: 253 LASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYI-GDIHRSGQHLLNLINEILD- 310 +A +SH+LRTPL I +E M + E I DI N I++ Sbjct: 233 MAGVSHDLRTPLTRIRLATE------MMSEEDGYLAESINKDIEEC--------NAIIEQ 278 Query: 311 -LSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIE--IFQKIDPSLSSVWADEKG 367 + + G+ E+ L ++ E I A E E I + P V + Sbjct: 279 FIDYLRTGQ-EMPMEMADLNALLGEVI------AAESGYEREIETALQPGPIEVPMNPIA 331 Query: 368 MRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQG 427 +++ + NL+ NA ++ G + V+ G R + ++D+GPGI ++ + F +G Sbjct: 332 IKRALANLVVNAARYG--NGWIKVSSGTEGKRA-WFQVEDDGPGIPPEQLKHLFQPFTRG 388 Query: 428 SIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAILP 473 A S G GLGL I + I+ H G+ + + G+ A LP Sbjct: 389 DSARGS--SGTGLGLAIVKRIVDQHNGKVELGNSEEGGLSARAWLP 432 >gnl|CDD|182583 PRK10604, PRK10604, sensor protein RstB; Provisional. Length = 433 Score = 72.7 bits (179), Expect = 2e-13 Identities = 59/205 (28%), Positives = 90/205 (43%), Gaps = 16/205 (7%) Query: 257 SHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDLSRIEA 316 +HELRTPL L + LE +N + E ++R L LI E+L +R++ Sbjct: 220 AHELRTPL-VRLRY----RLEM---SDNLSAAESQA-LNRDIGQLEALIEELLTYARLDR 270 Query: 317 GRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKIDPSLSSVWA-DEKGMRQVILNL 375 + EL S L + + +Q EK + + P A D + M +V+ NL Sbjct: 271 PQNELHLSEPDLPAWLSTHLADIQAVTPEKTVRLDT---PHQGDYGALDMRLMERVLDNL 327 Query: 376 LSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAE 435 L+NA+++ RV V++ G + ++D+GPGI E V F + + A Sbjct: 328 LNNALRYA--HSRVRVSL-LLDGNQACLIVEDDGPGIPPEERERVFEPFVRLDPSRDRAT 384 Query: 436 QGVGLGLPIAQSIMANHGGQFLIRS 460 G GLGL I SI GG Sbjct: 385 GGCGLGLAIVHSIALAMGGSVNCDE 409 >gnl|CDD|182101 PRK09835, PRK09835, sensor kinase CusS; Provisional. Length = 482 Score = 71.0 bits (174), Expect = 6e-13 Identities = 55/233 (23%), Positives = 106/233 (45%), Gaps = 23/233 (9%) Query: 249 KSRFLASMSHELRTPLNAILGFSEVI--------ELETMGPLNNETYKEYIGDIHRSGQH 300 +S F A ++HE+RTP+ ++ +E+ ELE + N E Sbjct: 262 QSNFSADIAHEIRTPITNLITQTEIALSQSRSQKELEDVLYSNLEEL-----------TR 310 Query: 301 LLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKIDPSLSS 360 + +++++L L++ + + + + L D V + + A+E+ +E+ + Sbjct: 311 MAKMVSDMLFLAQADNNQLIPEKKMLDLADEVGKVFDFFEAWAEERGVEL--RFVGDPCQ 368 Query: 361 VWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTV 420 V D +R+ I NLLSNA+++T G + V + Q + +++ G IA +P + Sbjct: 369 VAGDPLMLRRAISNLLSNALRYTPAGEAITVRCQEVDHQVQLV-VENPGTPIAPEHLPRL 427 Query: 421 LTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAILP 473 F + + + +G G+GL I +SI+ H G + S R G + LP Sbjct: 428 FDRFYRVDPSRQRKGEGSGIGLAIVKSIVVAHKGTVAVTSDAR-GTRFVISLP 479 >gnl|CDD|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase BaeS; Provisional. Length = 466 Score = 68.5 bits (168), Expect = 3e-12 Identities = 48/203 (23%), Positives = 96/203 (47%), Gaps = 7/203 (3%) Query: 252 FLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDL 311 F+A +SHELRTPL + G ELE + + E + + L L++++ L Sbjct: 243 FMADISHELRTPLAVLRG-----ELEAIQDGVRKFTPESVASLQAEVGTLTKLVDDLHQL 297 Query: 312 SRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKIDPSLSSVWADEKGMRQV 371 S + G ++ + L+ ++ + R + + + + S ++V+ D + Q+ Sbjct: 298 SLSDEGALAYRKTPVDLVPLLEVAGGAFRERFASRGLTLQLSLPDS-ATVFGDPDRLMQL 356 Query: 372 ILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQGSIAI 431 NLL N++++T GG +H++ ++ D+ PG+++ ++ + F + + Sbjct: 357 FNNLLENSLRYTDSGGSLHISAEQRDKT-LRLTFADSAPGVSDEQLQKLFERFYRTEGSR 415 Query: 432 KSAEQGVGLGLPIAQSIMANHGG 454 A G GLGL I +I+ H G Sbjct: 416 NRASGGSGLGLAICLNIVEAHNG 438 >gnl|CDD|182388 PRK10337, PRK10337, sensor protein QseC; Provisional. Length = 449 Score = 65.4 bits (160), Expect = 3e-11 Identities = 54/216 (25%), Positives = 99/216 (45%), Gaps = 33/216 (15%) Query: 251 RFLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEY-IGDIHRSGQHLLNLINEIL 309 RF + +HELR+PL A+ +EV +L ++ ++ + +H L++++L Sbjct: 239 RFTSDAAHELRSPLAALKVQTEVAQLS----DDDPQARKKALLQLHAGIDRATRLVDQLL 294 Query: 310 DLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIE---------IFQKIDPSLSS 360 LSR+++ + I L D+++ ++ + AQ+ I+ + + P L S Sbjct: 295 TLSRLDSLDNLQDVAEIPLEDLLQSAVMDIYHTAQQAGIDVRLTLNAHPVIRTGQPLLLS 354 Query: 361 VWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTV 420 + ++ NLL NA++++ G V VT+ + +++DNGPG+ P Sbjct: 355 L---------LVRNLLDNAIRYSPQGSVVDVTL-----NARNFTVRDNGPGVT----PEA 396 Query: 421 LTSFGQGSIAIKSAEQ-GVGLGLPIAQSIMANHGGQ 455 L G+ E G GLGL I + I HG Sbjct: 397 LARIGERFYRPPGQEATGSGLGLSIVRRIAKLHGMN 432 >gnl|CDD|131984 TIGR02938, nifL_nitrog, nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes. Length = 494 Score = 59.9 bits (145), Expect = 1e-09 Identities = 58/244 (23%), Positives = 98/244 (40%), Gaps = 30/244 (12%) Query: 242 AEEENLAKSR-FLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQH 300 AEEE L R L++ H L+ P+N I V++ N Sbjct: 268 AEEERLEAIRETLSAAIHRLQGPMNLISAAISVLQRRGDDAGNPA--------------- 312 Query: 301 LLNLINEILDLSR--IEAGRYELSES------AISLIDIVRECIIMLQLRAQEKNIEIFQ 352 ++ + L R +EA R + +S ++L I+R+ I + R I + Sbjct: 313 SAAMLQQALSAGREHMEALRQVIPQSPQEIVVPVNLNQILRDVITLSTPRLLAAGIVVDW 372 Query: 353 KIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGG---RVHVTVGWTSGRGQYISIKDNG 409 + +L ++ E +R + L+ NA++ I G R +G +SI D+G Sbjct: 373 QPAATLPAILGRELQLRSLFKALVDNAIEAMNIKGWKRRELSITTALNGDLIVVSILDSG 432 Query: 410 PGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVI 469 PGI + V F + + +G+GL +AQ I+A+HGG + EG +I Sbjct: 433 PGIPQDLRYKVFEPF---FTTKGGSRKHIGMGLSVAQEIVADHGGIIDLDDDYSEGCRII 489 Query: 470 AILP 473 Sbjct: 490 VEFR 493 >gnl|CDD|182947 PRK11073, glnL, nitrogen regulation protein NR(II); Provisional. Length = 348 Score = 55.5 bits (134), Expect = 3e-08 Identities = 66/256 (25%), Positives = 117/256 (45%), Gaps = 35/256 (13%) Query: 215 LSCQAEKDDLIAELEVAKSLSDETRKRAEEEN-----LAKSRFLASMSHELRTPLNAILG 269 L+ Q + +I LE+A D R+ ++E+ +A + ++HE++ PL + G Sbjct: 94 LTAQRLPEGMIL-LEMAPM--DNQRRLSQEQLQHAQQVAARDLVRGLAHEIKNPLGGLRG 150 Query: 270 FSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLI 329 +++ L P + EY I L NL++ +L R G ++ES + Sbjct: 151 AAQL--LSKALP--DPALTEYTKVIIEQADRLRNLVDRLLGPQR--PGT-HVTESIHKVA 203 Query: 330 DIVRECIIMLQLRAQEKNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVK-FTAIGGR 388 + V + ++ L + N+ + + DPSL + D + QV+LN++ NA++ GG Sbjct: 204 ERVVQ---LVSLELPD-NVRLIRDYDPSLPELAHDPDQIEQVLLNIVRNALQALGPEGGT 259 Query: 389 VHV---TVGWTSGRGQY------ISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVG 439 + + T + G+ I I+DNGPGI T+ G E G G Sbjct: 260 ITLRTRTAFQLTLHGERYRLAARIDIEDNGPGIPPHLQDTLFYPMVSGR------EGGTG 313 Query: 440 LGLPIAQSIMANHGGQ 455 LGL IA++++ H G+ Sbjct: 314 LGLSIARNLIDQHSGK 329 >gnl|CDD|182702 PRK10755, PRK10755, sensor protein BasS/PmrB; Provisional. Length = 356 Score = 54.6 bits (132), Expect = 6e-08 Identities = 58/237 (24%), Positives = 103/237 (43%), Gaps = 38/237 (16%) Query: 252 FLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDL 311 F A ++HELRTPL I + LE + ++ I + +++ + ++L L Sbjct: 140 FTADVAHELRTPLAGIR-----LHLELLEKQHHIDVAPLIARL----DQMMHTVEQLLQL 190 Query: 312 SRIE----AGRYELSESAISLIDIV-----RECIIMLQLRAQEKNIEIFQKIDPSLSSVW 362 +R +G Y+ + L++ V E ML+ R Q + + +V Sbjct: 191 ARAGQSFSSGHYQ----TVKLLEDVILPSQDELSEMLEQRQQT----LLLPESAADITVQ 242 Query: 363 ADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLT 422 D +R ++ NL+ NA +++ G + + + G ++++D GPGI E + Sbjct: 243 GDATLLRLLLRNLVENAHRYSPEGSTITIKLS-QEDGGAVLAVEDEGPGIDESKC----- 296 Query: 423 SFGQGSIAIKSAEQ---GVGLGLPIAQSIMANHGGQFLIRSKL-REGVEVIAILPNT 475 G+ S A + G+GLGL I I H GQF ++++ R G LP Sbjct: 297 --GELSKAFVRMDSRYGGIGLGLSIVSRITQLHHGQFFLQNRQERSGTRAWVWLPKA 351 >gnl|CDD|163497 TIGR03785, marine_sort_HK, proteobacterial dedicated sortase system histidine kinase. This histidine kinase protein is paired with an adjacent response regulator (TIGR03787) gene. It co-occurs with a variant sortase enzyme (TIGR03784), usually in the same gene neighborhood, in proteobacterial species most of which are marine, and with an LPXTG motif-containing sortase target conserved protein (TIGR03788). Sortases and LPXTG proteins are far more common in Gram-positive bacteria, where sortase systems mediate attachment to the cell wall or cross-linking of pilin structures. We give this predicted sensor histidine kinase the gene symbol psdS, for Proteobacterial Dedicated Sortase system Sensor histidine kinase. Length = 703 Score = 54.0 bits (130), Expect = 8e-08 Identities = 67/330 (20%), Positives = 141/330 (42%), Gaps = 40/330 (12%) Query: 170 VVVALSTQAIMSMH------VLDISLAGMLATALSFFTYITYHLFKSNVKILSCQAEK-- 221 V+ +T I ++ + ++ LA M L+ F + ++ ++ LS AE Sbjct: 388 VIAEQTTNGIRTLRNSALEKLFNVILAIMSIGTLALFGFASW--ISWRIRRLSDDAEAAI 445 Query: 222 DD---LIAELEVAKS---LSDETRKRAEEENLAK----SRFLASMS----HELRTPLNAI 267 D + + ++S + D +R A+ +A+ + +L +MS HELRTP+ A+ Sbjct: 446 DSQGRISGAIPASRSRDEIGDLSRSFAQM--VARLRQYTHYLENMSSRLSHELRTPV-AV 502 Query: 268 LGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAIS 327 + S +E + L E ++Y+ + L ++N + + +R+E Sbjct: 503 VRSS--LENLELQALEQEK-QKYLERAREGTERLSMILNNMSEATRLEQAIQSAEVEDFD 559 Query: 328 LIDIVRECIIMLQLRAQEKNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGG 387 L +++ C+ Q+ + E+ P + + Q++ L+ NA +F+ G Sbjct: 560 LSEVLSGCMQGYQMTYPPQRFELNIPETPLVMRGSPELIA--QMLDKLVDNAREFSPEDG 617 Query: 388 RVHVTVGWTSGRGQY-ISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQG--VGLGLPI 444 + V + + + +++ + GP + E + S S+ + A+ +GLGL I Sbjct: 618 LIEVGL--SQNKSHALLTVSNEGPPLPEDMGEQLFDSM--VSVRDQGAQDQPHLGLGLYI 673 Query: 445 AQSIMANHGGQFLIRSKLR-EGVEVIAILP 473 + I H G+ ++ + +GV LP Sbjct: 674 VRLIADFHQGRIQAENRQQNDGVVFRISLP 703 >gnl|CDD|163071 TIGR02916, PEP_his_kin, putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes. Length = 679 Score = 52.8 bits (127), Expect = 2e-07 Identities = 44/163 (26%), Positives = 78/163 (47%), Gaps = 11/163 (6%) Query: 311 LSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKIDPSLSSVWADEKGMRQ 370 L+++ + E + + L+D++R + RAQ E+ ID LS V AD + + + Sbjct: 528 LAQLRSKGLEEEKLCVDLVDLLRR--AIASKRAQGPRPEVS--IDTDLS-VRADRERLER 582 Query: 371 VILNLLSNAVKFTAIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQGSIA 430 V+ +L+ NA++ T GRV + V G I I+D+G G++ I L + Sbjct: 583 VLGHLVQNALEATPGEGRVAIRVERECGAA-RIEIEDSGCGMSPAFIRERLFKPFDTT-- 639 Query: 431 IKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAILP 473 K A G+G+G+ + + GG+ + S +G +LP Sbjct: 640 -KGA--GMGIGVYECRQYVEEIGGRIEVESTPGQGTIFTLVLP 679 >gnl|CDD|181885 PRK09470, cpxA, two-component sensor protein; Provisional. Length = 461 Score = 50.7 bits (122), Expect = 8e-07 Identities = 52/218 (23%), Positives = 88/218 (40%), Gaps = 39/218 (17%) Query: 251 RFLASMSHELRTPL------NAIL----GFS---EVIELETMGPLNNETYKEYIGDIHRS 297 R L+ +SHELRTPL A+L G S E IE E Sbjct: 245 RLLSDISHELRTPLTRLQLATALLRRRQGESKELERIETEA------------------- 285 Query: 298 GQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKIDPS 357 Q L ++IN++L LSR + + L + E + + A++ + P Sbjct: 286 -QRLDSMINDLLVLSRNQQ-KNHLERETFKANSLWSEVLEDAKFEAEQMGKSLTVSAPPG 343 Query: 358 LSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWT-SGRGQYISIKDNGPGIAEGE 416 + + + + N++ NA+++ + V ++ G I++ D+GPG+ E E Sbjct: 344 PWPINGNPNALASALENIVRNALRY----SHTKIEVAFSVDKDGLTITVDDDGPGVPEEE 399 Query: 417 IPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGG 454 + F + A G GLGL I ++ + H G Sbjct: 400 REQIFRPFYRVDEARDRESGGTGLGLAIVENAIQQHRG 437 >gnl|CDD|182591 PRK10618, PRK10618, phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional. Length = 894 Score = 45.3 bits (108), Expect = 3e-05 Identities = 39/198 (19%), Positives = 81/198 (40%), Gaps = 18/198 (9%) Query: 244 EENL-AKSRFLASMSHELRTPLNAILGFSEVIELETMGPLNNETYKEYIGDIHRSGQHLL 302 E+N A+ FL ++ EL+ PL ++ +L + + + L+ Sbjct: 444 EKNQQARKAFLQNIGDELKQPLQSLA--QLAAQLRQTSDEEQQQ--PELDQLAEQSDVLV 499 Query: 303 NLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKNIEIFQKIDPSLSSVW 362 L++ I L+ +E ++ + SL D++ E + + + K +++ + Sbjct: 500 RLVDNIQLLNMLETQDWKPEQELFSLQDLIDEVLPEVLPAIKRKGLQLLIHNHLKAEQLR 559 Query: 363 -ADEKGMRQVILNLLSNAVKFTAIGGRVHVTVGWTSGRGQ--YISIKDNGPGIAEGEI-- 417 D +R+++L LL+ A+ TA G++ + V I I D G G++ E+ Sbjct: 560 IGDRDALRKILLLLLNYAITTTAY-GKITLEVDQDESSPDRLTIRILDTGAGVSIKELDN 618 Query: 418 -------PTVLTSFGQGS 428 T +G+ S Sbjct: 619 LHFPFLNQTQGDRYGKAS 636 >gnl|CDD|184141 PRK13557, PRK13557, histidine kinase; Provisional. Length = 540 Score = 43.5 bits (103), Expect = 1e-04 Identities = 57/263 (21%), Positives = 99/263 (37%), Gaps = 47/263 (17%) Query: 236 DETRKRAEEENLAKSRFLASM-------SHELRTPLNAILGFSEVIELETMGPLNNETYK 288 D +R+R E+ L +++ + ++ +H+ L + G+ +VI+ Sbjct: 143 DVSRRRDAEDALRQAQKMEALGQLTGGIAHDFNNLLQVMSGYLDVIQA------ALSHPD 196 Query: 289 EYIGDIHRSGQHL-------LNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQL 341 G + RS +++ L ++L +R + L ++L +V M +L Sbjct: 197 ADRGRMARSVENIRAAAERAATLTQQLLAFAR----KQRLEGRVLNLNGLVSG---MGEL 249 Query: 342 --RAQEKNIEIFQKIDPSLSSVWADEKGMRQVILNLLSNAVKFTAIGGRVHVTV------ 393 R + I + P L + D +LN+L NA GGRV + Sbjct: 250 AERTLGDAVTIETDLAPDLWNCRIDPTQAEVALLNVLINARDAMPEGGRVTIRTRNVEIE 309 Query: 394 --------GWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIA 445 G GR I++ D G G+ + V+ F K +G GLGL + Sbjct: 310 DEDLAMYHGLPPGRYVSIAVTDTGSGMPPEILARVMDPF----FTTKEEGKGTGLGLSMV 365 Query: 446 QSIMANHGGQFLIRSKLREGVEV 468 GG I S++ EG V Sbjct: 366 YGFAKQSGGAVRIYSEVGEGTTV 388 >gnl|CDD|182952 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional. Length = 542 Score = 38.4 bits (90), Expect = 0.004 Identities = 33/107 (30%), Positives = 56/107 (52%), Gaps = 13/107 (12%) Query: 371 VILNLLSNAVKFTAIG----GRVHVTVGWTSGRGQYISIKDNGPGIAEGEIPTVLTSFGQ 426 ++ NL+ NA A+G G + V++ + +G + + D+GPGIA EI + F + Sbjct: 437 ILGNLIENA--LEAVGGEEGGEISVSLHYRNGW-LHCEVSDDGPGIAPDEIDAI---FDK 490 Query: 427 GSIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAILP 473 G + K + +GVGL L + QS+ N GG + S+ G + +P Sbjct: 491 G-YSTKGSNRGVGLYL-VKQSV-ENLGGSIAVESEPGVGTQFFVQIP 534 >gnl|CDD|182754 PRK10815, PRK10815, sensor protein PhoQ; Provisional. Length = 485 Score = 36.5 bits (85), Expect = 0.016 Identities = 36/133 (27%), Positives = 57/133 (42%), Gaps = 18/133 (13%) Query: 344 QEKNIEIFQKIDPSLSSVWADEKG-MRQVILNLLSNAVK----FTAIGGRVHVTVGWTSG 398 Q K + I I P ++ + EK +V+ N+L NA K F I R + Sbjct: 356 QRKGVNITLDISPEIT--FVGEKNDFMEVMGNVLDNACKYCLEFVEISARQ-------TD 406 Query: 399 RGQYISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQFLI 458 +I ++D+GPGI E + + F +G A + G GLGL +A+ I + G+ Sbjct: 407 EHLHIVVEDDGPGIPESKRELI---FDRGQRA-DTLRPGQGLGLSVAREITEQYEGKISA 462 Query: 459 RSKLREGVEVIAI 471 G + I Sbjct: 463 GDSPLGGARMEVI 475 >gnl|CDD|129816 TIGR00733, TIGR00733, putative oligopeptide transporter, OPT family. This protein represents a small family of integral membrane proteins from Gram-negative bacteria, a Gram-positive bacteria, and an archaeal species. Members of this family contain 15 to 18 GES predicted transmembrane regions, and this family has extensive homology to a family of yeast tetrapeptide transporters, including isp4 (Schizosaccharomyces pombe) and Opt1 (Candida albicans). EspB, an apparent equivalog from Myxococcus xanthus, shares an operon with a two component system regulatory protein, and is required for the normal timing of sporulation after the aggregation of cells. This is consistent with a role in transporting oligopeptides as signals across the membrane. Length = 591 Score = 33.3 bits (76), Expect = 0.16 Identities = 36/166 (21%), Positives = 56/166 (33%), Gaps = 45/166 (27%) Query: 55 FVLLVANIGTWFTQNPIFPMWSLITLAVYAANLSLGKKVMNSDIKIGEVYVWRIW----- 109 F + + W PI+ +LS W IW Sbjct: 206 FAMFLGGAIAWGVAIPIYTAKMGS-----PGDLSAL------------DLAWTIWSTKVR 248 Query: 110 -LLVGQIAIGLCWTLLTLVEPGT--------------------WTPEYLTIYKSATLLIA 148 + VG I + WTLL L P T E L I T L+A Sbjct: 249 YIGVGAIVVAALWTLLKLRGPIARGIKAGLEAARRRQAGEAVLRTEEDLPINIVLT-LVA 307 Query: 149 LSISALSNFMLPYAVFLSFFPVVVALSTQAIMSMHVLDISLAGMLA 194 L + L++F+L YA L + +A+ ++ + ++AG +A Sbjct: 308 LFVIPLADFLL-YAPILHNIGMAIAVMAVLMLIIGFFVAAIAGYMA 352 >gnl|CDD|162931 TIGR02578, cas_TM1811_Csm1, CRISPR-associated protein, Csm1 family. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2. A typical example is TM1811 from Thermotoga maritima. CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats. This protein family belongs to a conserved gene cluster regularly found near CRISPR repeats. Length = 648 Score = 31.2 bits (71), Expect = 0.65 Identities = 46/203 (22%), Positives = 68/203 (33%), Gaps = 33/203 (16%) Query: 196 ALSFFTYITYHLFKSNVKILSCQAEKDDLIAELEVAKSLSDETR------KRAEEENLAK 249 L L K+ VK + DDLIA E S + R EEE + Sbjct: 43 LLEVLDKKADDLLKNLVKSHHEEDYLDDLIARAERLASGLEIIDRLEAGDDREEEELGNE 102 Query: 250 SRFLASMSHELRTP--LNAILGFS---------EVIELETMGPLNNETYKEYI----GDI 294 L S ++ L GF + E + E YK + GD+ Sbjct: 103 EEPLVSPFPKIPLGNSLRNAGGFKPKYPLKSLNRAVPPENDNKASQENYKRLMEKFLGDL 162 Query: 295 ------HRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVR-ECII--MLQLRAQE 345 + LL + E L S + A S+ +SL D ++ I L +E Sbjct: 163 EKLKPSYPDKIELLLTLFEKL-WSFVPAATNGGSKPDVSLYDHLKLTAAIASALYRYLKE 221 Query: 346 KNI--EIFQKIDPSLSSVWADEK 366 N + K+D ++ W EK Sbjct: 222 NNTKDDALAKLDSAIDEDWNGEK 244 >gnl|CDD|162468 TIGR01656, Histidinol-ppas, histidinol-phosphate phosphatase family domain. This domain is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing an conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the domian modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a "capping" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3. Length = 147 Score = 30.5 bits (69), Expect = 1.1 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 11/76 (14%) Query: 414 EGEIPTVLTSFGQG-SIAIKSAEQGVGLGLPIAQSIMANHGGQFLIRSKLREGVEVIAIL 472 G +P +LT G ++ + + + G+G G A++ A +G ++ + GV V +L Sbjct: 30 PGAVPALLTLRAAGYTVVVVTNQSGIGRGYFSAEAFRAPNGR--VLELLRQLGVAVDGVL 87 Query: 473 --PNTRVLNFIPEDNH 486 P+ P DN Sbjct: 88 FCPHH------PADNC 97 >gnl|CDD|179773 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated. Length = 535 Score = 30.2 bits (69), Expect = 1.1 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 3/24 (12%) Query: 403 ISIKDNGPGIAEGEIPTVLTSFGQ 426 ++++DNGPGI EIP V FG+ Sbjct: 77 VTVEDNGPGIPPEEIPKV---FGK 97 >gnl|CDD|129363 TIGR00261, traB, pheromone shutdown-related protein TraB. traB is a plasmid encoded gene that functions in the shutdown of the peptide sex pheromone cPD1 which is produced by the plasmid free recipient cell prior to conjugative transfer in Enterococcus faecalis. Once the recipient acquires the plasmid, production of cPD1 is shut down. The gene product may play another role in the other species in the family. Length = 380 Score = 30.2 bits (68), Expect = 1.3 Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 2/64 (3%) Query: 330 DIVRECIIMLQLRAQEKNIEIFQKIDPSLSSVWADEKG--MRQVILNLLSNAVKFTAIGG 387 I E +L+ A K ++ KI P + V DE+ M +L N A+ G Sbjct: 144 KIEDEIEKLLEQDALSKIMKELSKISPKVKKVLIDERDEFMANKLLEGEGNKNIIVAVVG 203 Query: 388 RVHV 391 HV Sbjct: 204 AGHV 207 >gnl|CDD|168637 PRK06661, PRK06661, hypothetical protein; Provisional. Length = 231 Score = 29.8 bits (67), Expect = 1.7 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%) Query: 174 LSTQAIMSMHVLDISLAGMLATALSFFTYITYHLFKSNVKILSCQAEKDDLIAEL 228 T A +++ L L + AL F+ I+YH N L + L+ +L Sbjct: 95 YHTPASIAVSALKCGLLPISQWALHFYDRISYH--NYNSLALDADKQSSRLVNDL 147 >gnl|CDD|129656 TIGR00565, trpE_proteo, anthranilate synthase component I, proteobacterial subset. This enzyme resembles some other chorismate-binding enzymes, including para-aminobenzoate synthase (pabB) and isochorismate synthase. There is a fairly deep split between two sets, seen in the pattern of gaps as well as in amino acid sequence differences. This group includes proteobacteria such as E. coli and Helicobacter pylori but also the gram-positive organism Corynebacterium glutamicum. The second group includes eukaryotes, archaea, and most other bacterial lineages; sequences from the second group may resemble pabB more closely than other trpE from this group. Length = 498 Score = 29.5 bits (66), Expect = 2.0 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 3/59 (5%) Query: 429 IAIKSAEQGVGLGLPIAQSIMANHGGQFL--IRSKLREGVEVIAILPNTRVLNFIPEDN 485 + + +A + LG + ++ +GG L + + L GVE + I PN RVL F P Sbjct: 37 LLVDAALKITCLGDTVTIQALSPNGGALLQLLDAALPAGVEAV-IQPNARVLRFPPVSP 94 >gnl|CDD|163023 TIGR02794, tolA_full, TolA protein. TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. Length = 346 Score = 29.0 bits (65), Expect = 3.1 Identities = 12/32 (37%), Positives = 18/32 (56%) Query: 218 QAEKDDLIAELEVAKSLSDETRKRAEEENLAK 249 QAE++ AK ++E +K+AE E AK Sbjct: 151 QAEEEAKAKAAAEAKKKAEEAKKKAEAEAKAK 182 >gnl|CDD|152110 pfam11674, DUF3270, Protein of unknown function (DUF3270). This family of proteins with unknown function appears to be restricted to Streptococcus. Length = 90 Score = 28.9 bits (65), Expect = 3.1 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 4/49 (8%) Query: 44 SLFRVSPILPLFVLLVANIGTWFTQNPIFPMWSLITLAVYAANLSLGKK 92 ++F ++ +L F+LL + T+F FP+ I+L + KK Sbjct: 46 AVFCITTVLFSFILLSLKLTTFFA----FPLAITISLGITQLVRKGIKK 90 >gnl|CDD|181988 PRK09609, PRK09609, hypothetical protein; Provisional. Length = 312 Score = 28.9 bits (65), Expect = 3.2 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 4/83 (4%) Query: 133 TPEYLTIYKSATLLIALSISALSNFMLPYAVFLSFFPVVVALSTQAIMSM-HVLDISLAG 191 L I + ++ + + F + FL+ P+V+ A++ +V+ +S A Sbjct: 206 NKRSLMILIISGFILMIIFVIWARFFIKPKRFLTIAPIVI---FSALLEPINVILLSSAD 262 Query: 192 MLATALSFFTYITYHLFKSNVKI 214 + L F T++ H+ S +KI Sbjct: 263 AQSLGLDFDTWLFIHIITSPIKI 285 >gnl|CDD|149251 pfam08066, PMC2NT, PMC2NT (NUC016) domain. This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components. Length = 91 Score = 28.0 bits (63), Expect = 5.3 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 9/71 (12%) Query: 288 KEYIGDIHRSGQHLLNLINEILDLSRIEAGRYELSESAISLIDIVRECIIMLQLRAQEKN 347 E+ + Q LL+LIN++L + S ++ E + + N Sbjct: 24 PEFSQSLDEQSQRLLSLINDLLQS--AGSKSDIPDRSDEDDVEDQWEGV-------VDVN 74 Query: 348 IEIFQKIDPSL 358 + +K+D L Sbjct: 75 DSLLEKVDTLL 85 >gnl|CDD|184870 PRK14868, PRK14868, DNA topoisomerase VI subunit B; Provisional. Length = 795 Score = 28.2 bits (63), Expect = 5.4 Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 15/51 (29%) Query: 399 RGQY--ISIKDNGPGIAEGEIPTVL-------------TSFGQGSIAIKSA 434 G Y + ++DNGPGI + +IP V S GQ I I +A Sbjct: 78 VGDYYRLVVEDNGPGITKEQIPKVFGKLLYGSRFHAREQSRGQQGIGISAA 128 >gnl|CDD|182850 PRK10935, PRK10935, nitrate/nitrite sensor protein NarQ; Provisional. Length = 565 Score = 27.9 bits (63), Expect = 5.9 Identities = 40/153 (26%), Positives = 59/153 (38%), Gaps = 40/153 (26%) Query: 338 ML-QLRAQEKNIEIFQKIDPSLSSVWADEKGMRQV-ILNL----LSNAVKFTAIGGRVHV 391 ML QLR Q + +I +D L S D + +QV +L + NA+K A + V Sbjct: 441 MLDQLRNQ-TDAKI--TLDCRLPSQALDAQ--QQVHLLQIIREATLNAIKH-ANASEIAV 494 Query: 392 TVGWTSGRGQY-ISIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGLGLPIAQSIM- 449 + T+ G++ +SI+D+G GI E +K E GL IM Sbjct: 495 SC-VTNPDGEHTVSIRDDGIGIGE----------------LKEPEGHYGLN------IMQ 531 Query: 450 ---ANHGGQFLIRSKLREGVEVIAILPNTRVLN 479 GG I G V P+ + Sbjct: 532 ERAERLGGTLTISQPPGGGTTVSLTFPSQQEPE 564 >gnl|CDD|163120 TIGR03055, photo_alph_chp2, putative photosynthetic complex assembly protein 2. This uncharacterized protein family was identified, by the method of partial phylogenetic profiling, as having a matching phylogenetic distribution to that of the photosynthetic reaction center of the alpha-proteobacterial type. It is nearly always encoded near other photosynthesis-related genes, including puhA. Length = 245 Score = 27.8 bits (62), Expect = 6.6 Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 17/114 (14%) Query: 108 IWLLVGQIAIGLCWTLLTLVEP---GTWTPEYLTIYK-SATLLIALSISALSNFMLPYAV 163 +W + +A G+ +LT G WT L + + SA L + L + L+ LP + Sbjct: 108 LWHEICLLACGILVLVLTWGAENQVGLWTFVVLWVMRVSAKLNLFLGVPNLNAEFLPDHL 167 Query: 164 -FLS----------FFPVVVALSTQA--IMSMHVLDISLAGMLATALSFFTYIT 204 L FP+ V L T A +M LD + A + +T Sbjct: 168 AHLKSYFRRKPMNALFPISVTLLTAALVVMIERALDAATAPHEVVGFALLATLT 221 >gnl|CDD|180427 PRK06149, PRK06149, hypothetical protein; Provisional. Length = 972 Score = 27.7 bits (62), Expect = 6.8 Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%) Query: 11 DVGLLISPTGDHLG-LEYPSKMDFDREIITLHVESLFRV 48 ++G+++ PTGDHL L+ + DRE V+ L RV Sbjct: 929 ELGVIMQPTGDHLNILKIKPPLCLDRESADFFVDMLDRV 967 >gnl|CDD|131051 TIGR01996, PTS-II-BC-sucr, PTS system, sucrose-specific IIBC component. This family is closely related to the trehalose transporting PTS IIBC enzymes and the B and C domains of each are described by subfamily-domain level TIGRFAMs models (TIGR00826 and TIGR00852, respectively). Length = 461 Score = 27.6 bits (62), Expect = 7.6 Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 2/42 (4%) Query: 58 LVANIGTWFTQNPIFPMWSLITLAVYAANLSLGKKVMNSDIK 99 L+AN T N +FP+ S+ +A A L++ K + +K Sbjct: 329 LLANTKTGG--NFLFPIASMANVAQGGAALAVFFKTKDKKLK 368 >gnl|CDD|131958 TIGR02912, sulfite_red_C, sulfite reductase, subunit C. Members of this protein family include the C subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite. Length = 314 Score = 27.5 bits (61), Expect = 7.9 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 5/48 (10%) Query: 362 WADEKGMRQVILNLLSNAVKFT---AIGGRVHVTVGWTSGRGQYISIK 406 W DE + ++ILN ++ A GG+ H +G+ R Y K Sbjct: 248 WVDEDSIVKIILNTYDYITEYIDKNAPGGKEH--IGYIVDRTGYQEFK 293 >gnl|CDD|162176 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase). Length = 488 Score = 27.5 bits (61), Expect = 8.1 Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 4/41 (9%) Query: 403 ISIKDNGPGIAEGEIPTVLTSFGQGSIA---IKS-AEQGVG 439 ++++DNGPGI E IP V GS I+S +QG+G Sbjct: 67 VTVEDNGPGIPEEYIPKVFGKMLAGSKFHRIIQSRGQQGIG 107 >gnl|CDD|106506 PRK13560, PRK13560, hypothetical protein; Provisional. Length = 807 Score = 27.3 bits (60), Expect = 10.0 Identities = 11/37 (29%), Positives = 18/37 (48%) Query: 404 SIKDNGPGIAEGEIPTVLTSFGQGSIAIKSAEQGVGL 440 ++K P A G I + G G + + A+ G+GL Sbjct: 723 ALKHAFPDGAAGNIKVEIREQGDGMVNLCVADDGIGL 759 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.321 0.137 0.396 Gapped Lambda K H 0.267 0.0668 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,927,963 Number of extensions: 520576 Number of successful extensions: 1260 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1177 Number of HSP's successfully gapped: 82 Length of query: 495 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 398 Effective length of database: 3,898,497 Effective search space: 1551601806 Effective search space used: 1551601806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (26.6 bits)