RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780903|ref|YP_003065316.1| two-component sensor histidine kinase protein [Candidatus Liberibacter asiaticus str. psy62] (766 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 = 164 bits (418), Expect = 6e-41 Identities = 94/288 (32%), Positives = 152/288 (52%), Gaps = 22/288 (7%) Query: 491 QAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVE-------KERAETANKTK 543 QA R+ + L+ L Q++ ++ EL+ N + E + AE AN+ K Sbjct: 408 QADERQVAQELQEHKESLE---QLVAQRTQELAETNERLNAEVKNHAKARAEAEEANRAK 464 Query: 544 SEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNIL 603 S FLA MSHE+RTPLN ILG E++ L S + +Y Q I+ SG+ LL+++N+IL Sbjct: 465 SAFLATMSHEIRTPLNGILGTLELLGDT---GLTS-QQQQYLQVINRSGESLLDILNDIL 520 Query: 604 EMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSEL--FFNADKRII 661 + SKIE +SI + DL ++++ L+ S AQ K I++ IP +L ++ D I Sbjct: 521 DYSKIEAGHLSISPRPFDLNALLDDVHHLMVSRAQLKGIQLRLNIPEQLPNWWQGDGPRI 580 Query: 662 KKILFPILSNSIKFTNNNGKMMIRTSKIGQ-CVIITIADTGIGIPKSALEKIGQPFEPLH 720 +++L ++ N+IKFT + G +++R S ++ + DTG GI + + F Sbjct: 581 RQVLINLVGNAIKFT-DRGSVVLRVSLNDDSSLLFEVEDTGCGIAEEEQATLFDAFTQAD 639 Query: 721 NQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTI--VTICMPQ 766 + + GG GLGLAIS L G L + S+ G G+ T+ + + Sbjct: 640 GR--RRSGGTGLGLAISQRLVEAMDGELGVESELGVGSCFWFTLPLTR 685 >gnl|CDD|182968 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional. Length = 919 Score = 148 bits (376), Expect = 5e-36 Identities = 92/278 (33%), Positives = 142/278 (51%), Gaps = 38/278 (13%) Query: 507 DLSTS--RQILER---QKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAI 561 D +TS R+ LE+ Q EL +A K+RA+ A + KSEFLA MSHELRTPLN + Sbjct: 259 DQATSDLRETLEQMEIQNVELDLA-------KKRAQEAARIKSEFLANMSHELRTPLNGV 311 Query: 562 LGFS-EVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNA 620 +GF+ + +K + + +Y Q I S +LL +IN+IL+ SK+E K+ ++ Sbjct: 312 IGFTRQTLKTPL-----TPTQRDYLQTIERSANNLLAIINDILDFSKLEAGKLVLENIPF 366 Query: 621 DLIPIINEGIRLIGSSAQSKN----IKIEKKIPSELFFNADKRIIKKILFPILSNSIKFT 676 L ++E + L+ SA K + I+ +P + D +++I+ ++ N+IKFT Sbjct: 367 SLRETLDEVVTLLAHSAHEKGLELTLNIDPDVPDNV--IGDPLRLQQIITNLVGNAIKFT 424 Query: 677 NNNGKMMIRTSKIGQC-----VIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSI---- 727 +G + I + + I DTGIGI + ++ Q F Q D SI Sbjct: 425 -ESGNIDILVELRALSNTKVQLEVQIRDTGIGISERQQSQLFQAF----RQADASISRRH 479 Query: 728 GGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 GG GLGL I+ L N GG + SQ +G+ +P Sbjct: 480 GGTGLGLVITQKLVNEMGGDISFHSQPNRGSTFWFHLP 517 >gnl|CDD|185245 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional. Length = 921 Score = 145 bits (368), Expect = 4e-35 Identities = 77/237 (32%), Positives = 133/237 (56%), Gaps = 15/237 (6%) Query: 533 KERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSG 592 K+RAE ANK KSE L +SHE+RTPLN +LG E+++ L + + + A Sbjct: 388 KQRAEQANKRKSEHLTTISHEIRTPLNGVLGALELLQN---TPL-TAEQMDLADTARQCT 443 Query: 593 QHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIE----KKI 648 LL +INN+L+ S+IE+ ++++ + L+P++++ + I AQSK++ + + Sbjct: 444 LSLLAIINNLLDFSRIESGQMTLSLEETALLPLLDQAMLTIQGPAQSKSLTLRTFVGAHV 503 Query: 649 PSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSA 708 P L ++ + +++IL +L N++KFT G + +R + Q + T+ DTG GI Sbjct: 504 PLYLHLDSLR--LRQILVNLLGNAVKFT-ETGGIRLRVKRHEQQLCFTVEDTGCGI---D 557 Query: 709 LEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 +++ Q F P + Q D G GLGL I+ +L + GG L + S G G+ ++ +P Sbjct: 558 IQQQQQIFTPFY-QADTHSQGTGLGLTIASSLAKMMGGELTLFSTPGVGSCFSLVLP 613 >gnl|CDD|182956 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional. Length = 779 Score = 128 bits (324), Expect = 5e-30 Identities = 82/260 (31%), Positives = 140/260 (53%), Gaps = 23/260 (8%) Query: 512 RQILERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKE 571 R I ER++ YQ + E A++ K+ F++ +SHELRTPLN I+G S ++ Sbjct: 264 RDITERKR---------YQ---DALEKASRDKTTFISTISHELRTPLNGIVGLSRILLDT 311 Query: 572 IFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIR 631 EL + + +Y + IH S L N+ N+I++M K+E K+ +D Q D + + Sbjct: 312 ---ELTA-EQRKYLKTIHVSAITLGNIFNDIIDMDKMERRKLQLDNQPIDFTDFLADLEN 367 Query: 632 LIGSSAQSKNIK--IEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTS-K 688 L G A+ K ++ +E +P D +++IL+ ++SN++KFT G + +R + Sbjct: 368 LSGLQAEQKGLRFDLEPLLPLPHKVITDGTRLRQILWNLISNAVKFT-QQGGVTVRVRYE 426 Query: 689 IGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYD-QSIGGFGLGLAISDALTNLHGGR 747 G + + D+GIGIP+ L+KI + + + + + G G+GLA+S L GG Sbjct: 427 EGDMLTFEVEDSGIGIPEDELDKIFAMYYQVKDSHGGKPATGTGIGLAVSKRLAQAMGGD 486 Query: 748 LKIISQEGKGT--IVTICMP 765 + + S+EGKG+ +TI P Sbjct: 487 ITVTSEEGKGSCFTLTIHAP 506 >gnl|CDD|183148 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional. Length = 914 Score = 126 bits (319), Expect = 1e-29 Identities = 77/272 (28%), Positives = 141/272 (51%), Gaps = 17/272 (6%) Query: 502 KATINDLSTSRQIL----ERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTP 557 ++ ++ L+ R+ L + + EL +++ + AE A++ KS FLA MSHE+RTP Sbjct: 399 RSNVHALNRHREQLAAQVKARTAELQELVIEHRQARAEAEKASQAKSAFLAAMSHEIRTP 458 Query: 558 LNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIE--TEKISI 615 L ILG ++++ + + I SG+ LL ++N+IL+ S IE + +S+ Sbjct: 459 LYGILGTAQLLA----DNPALNAQRDDLRAITDSGESLLTILNDILDYSAIEAGGKNVSV 514 Query: 616 DKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSEL--FFNADKRIIKKILFPILSNSI 673 + + P++ ++L+ + + I++ I +L D R I++++ +LSN++ Sbjct: 515 SDEPFEPRPLLESTLQLMSGRVKGRPIRLATDIADDLPTALMGDPRRIRQVITNLLSNAL 574 Query: 674 KFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLG 733 +FT + G +++R+ G+ ++ + D+G GI + L +I QPF Q GG GLG Sbjct: 575 RFT-DEGSIVLRSRTDGEQWLVEVEDSGCGIDPAKLAEIFQPFV----QVSGKRGGTGLG 629 Query: 734 LAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 L IS L GG L S G+ + +P Sbjct: 630 LTISSRLAQAMGGELSATSTPEVGSCFCLRLP 661 >gnl|CDD|128669 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Length = 111 Score = 104 bits (262), Expect = 9e-23 Identities = 42/110 (38%), Positives = 63/110 (57%), Gaps = 1/110 (0%) Query: 656 ADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQP 715 D ++++L +L N+IK+T G++ + + G + IT+ D G GIP LEKI +P Sbjct: 1 GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGDHLEITVEDNGPGIPPEDLEKIFEP 60 Query: 716 FEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 F + + IGG GLGL+I L LHGG + + S+ G GT TI +P Sbjct: 61 FFRTDGR-SRKIGGTGLGLSIVKKLVELHGGEISVESEPGGGTTFTITLP 109 >gnl|CDD|182496 PRK10490, PRK10490, sensor protein KdpD; Provisional. Length = 895 Score = 103 bits (260), Expect = 1e-22 Identities = 63/238 (26%), Positives = 118/238 (49%), Gaps = 19/238 (7%) Query: 515 LERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFG 574 LER S A+ E+E+ A LA +SH+LRTPL + G +E++ ++ Sbjct: 642 LERLTLTASEEQARLASEREQLRNA------LLAALSHDLRTPLTVLFGQAEILTLDLAS 695 Query: 575 ELGSVKYYEYAQDIHYSGQHLLN---MINNILEMSKIETEKISIDKQNADLIPIINEGIR 631 E GS + A +I Q +LN ++NN+L+M++I++ ++ K+ L ++ ++ Sbjct: 696 E-GS-PHARQASEIR---QQVLNTTRLVNNLLDMARIQSGGFNLRKEWLTLEEVVGSALQ 750 Query: 632 LIGSSAQSKNIKIEKKIPSEL-FFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIG 690 ++ I + +P L + D + +++L +L N++K+ ++ I G Sbjct: 751 MLEPGLSGHPINLS--LPEPLTLIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEG 808 Query: 691 QCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRL 748 + + + + D G GIP + I F + + +I G GLGLAI A+ +HGG + Sbjct: 809 ERLQLDVWDNGPGIPPGQEQLIFDKFARGNKE--SAIPGVGLGLAICRAIVEVHGGTI 864 >gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional. Length = 1197 Score = 103 bits (258), Expect = 2e-22 Identities = 77/243 (31%), Positives = 122/243 (50%), Gaps = 13/243 (5%) Query: 530 QVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIH 589 +VE+ +A A KS+FLA MSHE+RTP+++I+GF E++ + V+ A + Sbjct: 699 EVERNKAINATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLA---Y 755 Query: 590 YSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKI--EKK 647 +GQ LL +I IL++ KIE+ + Q D+ ++ G+ A SK+I + Sbjct: 756 ATGQSLLGLIGEILDVDKIESGNYQLQPQWVDIPTLVQNTCHSFGAIAASKSIALSCSST 815 Query: 648 IPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKI----GQCVI-ITIADTGI 702 P D + K++L +LSN++KFT G + I TS VI +TI D+G Sbjct: 816 FPDHYLVKIDPQAFKQVLSNLLSNALKFT-TEGAVKITTSLGHIDDNHAVIKMTIMDSGS 874 Query: 703 GIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTI 762 G+ + +++ + + Q+ G GLGL I L G L + S G GT TI Sbjct: 875 GLSQEEQQQLFKRYSQTSAGRQQT--GSGLGLMICKELIKNMQGDLSLESHPGIGTTFTI 932 Query: 763 CMP 765 +P Sbjct: 933 TIP 935 >gnl|CDD|183098 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional. Length = 607 Score = 100 bits (250), Expect = 2e-21 Identities = 66/227 (29%), Positives = 114/227 (50%), Gaps = 24/227 (10%) Query: 545 EFLAKMSHELRTPLNAILGFSEVIKKEIFG----ELGSVKYYEYAQDIHYSGQHLLNMIN 600 E +A ++HE+R PL AI G+ ++ +++ E SV E L +I+ Sbjct: 392 ELVAGVAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREV--------DRLNKVID 443 Query: 601 NILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSEL-FFNADKR 659 +LE S+ + Q L ++ E ++L ++ + E ++ +EL AD Sbjct: 444 QLLEFSRPRESQW----QPVSLNALVEEVLQLFQTAGVQARVDFETELDNELPPIWADPE 499 Query: 660 IIKKILFPILSNSIKFTNNNGKMMIRTSKIGQ-CVIITIADTGIGIPKSALEKIGQPFEP 718 ++K++L IL N+++ + GK+ IRT + V ++I D G GI L+KI F+P Sbjct: 500 LLKQVLLNILINAVQAISARGKIRIRTWQYSDGQVAVSIEDNGCGIDPELLKKI---FDP 556 Query: 719 LHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 + G GLGLA+S + N HGG +++ S+ G GT T+ +P Sbjct: 557 FFTTKAK---GTGLGLALSQRIINAHGGDIEVESEPGVGTTFTLYLP 600 >gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional. Length = 924 Score = 99.7 bits (249), Expect = 3e-21 Identities = 75/239 (31%), Positives = 130/239 (54%), Gaps = 21/239 (8%) Query: 536 AETANKTKSEFLAKMSHELRTPLNAILGFSEVIK-KEIFGELGSVKYYEYAQDIHYSGQH 594 AE A+++KS FLA +SHELRTPL I+G ++++ KE+ + + ++ S Sbjct: 440 AEQASQSKSMFLATVSHELRTPLYGIIGNLDLLQTKELPKGVDRL-----VTAMNNSSSL 494 Query: 595 LLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIK--------IEK 646 LL +I++IL+ SKIE+E++ I+ + +IN I ++ +K IE Sbjct: 495 LLKIISDILDFSKIESEQLKIEPREFSPREVINH----ITANYLPLVVKKRLGLYCFIEP 550 Query: 647 KIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPK 706 +P L N D +++++ +LSN+IKFT+ G +++ G + + DTG+GIP Sbjct: 551 DVPVAL--NGDPMRLQQVISNLLSNAIKFTDT-GCIVLHVRVDGDYLSFRVRDTGVGIPA 607 Query: 707 SALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 + ++ PF + ++ G GLGLAI + L N+ G + + S+ G G+ TI +P Sbjct: 608 KEVVRLFDPFFQVGTGVQRNFQGTGLGLAICEKLINMMDGDISVDSEPGMGSQFTIRIP 666 >gnl|CDD|181772 PRK09303, PRK09303, adaptive-response sensory kinase; Validated. Length = 380 Score = 99.6 bits (249), Expect = 3e-21 Identities = 68/253 (26%), Positives = 127/253 (50%), Gaps = 27/253 (10%) Query: 521 ELSIANAKYQVEKERAETANKTKSE--FLAKMSHELRTPLNAILGFSEVIKKEIFGELGS 578 L +++ + + +E + K + LA ++H+LRTPL A E ++ E Sbjct: 127 LLQLSDELFVLRQENETLLEQLKFKDRVLAMLAHDLRTPLTAASLALETLELGQIDEDTE 186 Query: 579 VKYYEYAQDIHYSGQHLL---NMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGS 635 +K Q + + L +I ++LE+ + E + + Q DL + E I + Sbjct: 187 LKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWEALRFNPQKLDLGSLCQEVILELEK 246 Query: 636 SAQSKNIKIEKKIPSEL---FFNADKRIIKKILFPILSNSIKFTNNNGK----MMIRTSK 688 +K+++I+ IPS+L + AD+ I+++L +L N+IK+T G M+ RT+ Sbjct: 247 RWLAKSLEIQTDIPSDLPSVY--ADQERIRQVLLNLLDNAIKYTPEGGTITLSMLHRTT- 303 Query: 689 IGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQY----DQSIGGFGLGLAISDALTNLH 744 Q V ++I DTG GIP+ E+I FE ++ D+ G+G+GL++ + +H Sbjct: 304 --QKVQVSICDTGPGIPEEEQERI---FE---DRVRLPRDEGTEGYGIGLSVCRRIVRVH 355 Query: 745 GGRLKIISQEGKG 757 G++ + S+ G+G Sbjct: 356 YGQIWVDSEPGQG 368 >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 = 95.4 bits (238), Expect = 5e-20 Identities = 58/221 (26%), Positives = 112/221 (50%), Gaps = 14/221 (6%) Query: 544 SEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNIL 603 +F+A +SHELRTPL + G+ E + + ++ + + Q + +++ ++L Sbjct: 115 RDFVANVSHELRTPLTVLRGYLETLADG--PDEDPEEWNRALEIMLEQSQRMQSLVEDLL 172 Query: 604 EMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKK 663 +S++E+ ++ + D+ +++ + +Q KN +I +I + D+ ++ Sbjct: 173 TLSRLESAASPLEDEPVDMPALLDHLRDEAEALSQGKNHQITFEIDGGVDVLGDEDELRS 232 Query: 664 ILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQY 723 ++SN+IK+T G + +R + G ++ DTGIGI L ++ + F Y Sbjct: 233 AFSNLVSNAIKYTPEGGTITVRWRRDGGGAEFSVTDTGIGIAPEHLPRLTERF------Y 286 Query: 724 --DQS----IGGFGLGLAISDALTNLHGGRLKIISQEGKGT 758 D+S GG GLGLAI + + H RL+I S+ GKG+ Sbjct: 287 RVDKSRSRDTGGTGLGLAIVKHVLSRHHARLEIESELGKGS 327 >gnl|CDD|182962 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional. Length = 475 Score = 87.2 bits (217), Expect = 1e-17 Identities = 53/219 (24%), Positives = 105/219 (47%), Gaps = 12/219 (5%) Query: 550 MSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIE 609 ++HEL++PL AI G +E+++ + + +I L +I+ +LE++++E Sbjct: 263 LTHELKSPLAAIRGAAELLQ----EDPPPEDRARFTGNILTQSARLQQLIDRLLELARLE 318 Query: 610 TEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPIL 669 + + L ++ E + + A +K I + + P + D ++++ L +L Sbjct: 319 QRQELEVLEPVALAALLEELVEAREAQAAAKGITLRLR-PDDARVLGDPFLLRQALGNLL 377 Query: 670 SNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPL---HNQYDQS 726 N+I F+ G + + G+ V +++ D G GIP AL +I + F L N + Sbjct: 378 DNAIDFSPEGGTITLSAEVDGEQVALSVEDQGPGIPDYALPRIFERFYSLPRPANGRKST 437 Query: 727 IGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 GLGLA + LHGG + + ++ G + T+ +P Sbjct: 438 ----GLGLAFVREVARLHGGEVTLRNRPEGGVLATLTLP 472 >gnl|CDD|182411 PRK10364, PRK10364, sensor protein ZraS; Provisional. Length = 457 Score = 86.8 bits (215), Expect = 2e-17 Identities = 62/222 (27%), Positives = 108/222 (48%), Gaps = 20/222 (9%) Query: 548 AKMSHELRTPLNAILGFSEVIKKEIFGE---LGSVKYYEYAQDIHYSGQHLLNMINNILE 604 A ++HE+R PL++I G ++ F E G + ++ AQ + L +++ +LE Sbjct: 242 AGVAHEIRNPLSSIKGLAKY-----FAERAPAGG-EAHQLAQVMAKEADRLNRVVSELLE 295 Query: 605 MSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSEL-FFNADKRIIKK 663 + K + Q DL +IN ++L+ A S+ I++ L AD + + Sbjct: 296 LVK----PTHLALQAVDLNDLINHSLQLVSQDANSREIQLRFTANDTLPEIQADPDRLTQ 351 Query: 664 ILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQY 723 +L + N+I+ +G + + S+ G V I++ D+G GI LE I P+ + Sbjct: 352 VLLNLYLNAIQAIGQHGVISVTASESGAGVKISVTDSGKGIAADQLEAIFTPYFTTKAE- 410 Query: 724 DQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 G GLGLA+ + HGG +++ SQEGKG T+ +P Sbjct: 411 -----GTGLGLAVVHNIVEQHGGTIQVASQEGKGATFTLWLP 447 >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 = 79.0 bits (195), Expect = 4e-15 Identities = 57/233 (24%), Positives = 116/233 (49%), Gaps = 25/233 (10%) Query: 534 ERAETANKTKSEFLAKMSHELRTPLNAILGFSEV-IKKEIFGELGSVKYYEYAQDIHYSG 592 R E A + S+F A ++HELRTPL +LG ++V + + GE EY +++ S Sbjct: 232 GRLEDAFQRLSQFSADLAHELRTPLTNLLGQTQVALSQPRTGE-------EY-REVLESN 283 Query: 593 QHLLN----MINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKI 648 L M++++L +++ + ++++++ DL + + A+ + ++I ++ Sbjct: 284 LEELERLSRMVSDMLFLARADNGQLALERVRLDLAAELAKVAEYFEPLAEERGVRI--RV 341 Query: 649 PSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSA 708 E D ++ ++ + +LSN+++ T + G + +R + V +++++ G GIP Sbjct: 342 EGEGLVRGDPQMFRRAISNLLSNALRHTPDGGTITVRIERRSDEVRVSVSNPGPGIPPEH 401 Query: 709 LEKIGQPFEPLH-----NQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGK 756 L ++ F+ + G GLGLAI ++ HGGR S +GK Sbjct: 402 LSRL---FDRFYRVDPARSNSGE--GTGLGLAIVRSIMEAHGGRASAESPDGK 449 >gnl|CDD|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase BaeS; Provisional. Length = 466 Score = 70.8 bits (174), Expect = 1e-12 Identities = 56/218 (25%), Positives = 102/218 (46%), Gaps = 35/218 (16%) Query: 546 FLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQD---------IHYSGQH-- 594 F+A +SHELRTPL A+L GEL E QD + S Q Sbjct: 243 FMADISHELRTPL-AVLR----------GEL------EAIQDGVRKFTPESVA-SLQAEV 284 Query: 595 --LLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSEL 652 L +++++ ++S + ++ K DL+P++ S+ + ++ +P Sbjct: 285 GTLTKLVDDLHQLSLSDEGALAYRKTPVDLVPLLEVAGGAFRERFASRGLTLQLSLPDSA 344 Query: 653 FFNADK-RIIKKILFP-ILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALE 710 D R+++ LF +L NS+++T++ G + I + + + +T AD+ G+ L+ Sbjct: 345 TVFGDPDRLMQ--LFNNLLENSLRYTDSGGSLHISAEQRDKTLRLTFADSAPGVSDEQLQ 402 Query: 711 KIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRL 748 K+ + F +++ GG GLGLAI + H GR+ Sbjct: 403 KLFERFYRTEGSRNRASGGSGLGLAICLNIVEAHNGRI 440 >gnl|CDD|128670 smart00388, HisKA, His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases. Length = 66 Score = 67.6 bits (166), Expect = 1e-11 Identities = 30/69 (43%), Positives = 44/69 (63%), Gaps = 4/69 (5%) Query: 543 KSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNI 602 K EFLA +SHELRTPL AI G+ E+++ E + EY + I S + LL +IN++ Sbjct: 2 KREFLANLSHELRTPLTAIRGYLELLEDTELSE----EQREYLETILRSAERLLRLINDL 57 Query: 603 LEMSKIETE 611 L++S+IE Sbjct: 58 LDLSRIEAG 66 >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 = 67.2 bits (164), Expect = 1e-11 Identities = 84/404 (20%), Positives = 160/404 (39%), Gaps = 48/404 (11%) Query: 361 IGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDH 420 +G+ D+TE + LE+ A + ++ A VL D R+++ N Y+K L Sbjct: 109 LGMHRDITELHRLEQVVANQKLLIESVVDAAPVAFVLLDPTGRVILDNQEYKK---LATD 165 Query: 421 VLVPGNARSIIQDAQTRPIIEYRTSDPERSQDMSKEIKL-----ADSRWLQI-NEWCTHD 474 + V A +++ + + P++ ++E + +RWL + Sbjct: 166 LRVKEPAHTVLDLLREAWREALAENWPQQLAFSNREARFDRGGGRPARWLSCTGSVIGME 225 Query: 475 GGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKE 534 + L TI D+S R+ E+++ LS A E+E Sbjct: 226 SDCADSFFCAA-----------EQPYLLLTIADISNLRE--EQERARLSALQA-LMAEEE 271 Query: 535 RAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQH 594 R E +T L+ H L+ P+N I V+++ + G+ Q +G+ Sbjct: 272 RLEAIRET----LSAAIHRLQGPMNLISAAISVLQRR-GDDAGNPASAAMLQQALSAGRE 326 Query: 595 LLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIE----KKIPS 650 + + ++ S E +L I+ + I L + I ++ +P+ Sbjct: 327 HMEALRQVIPQSPQEI------VVPVNLNQILRDVITLSTPRLLAAGIVVDWQPAATLPA 380 Query: 651 ELFFNADKRIIKKILFPILSNSIKFTNNNG----KMMIRTSKIGQCVIITIADTGIGIPK 706 L R + K L + N+I+ N G ++ I T+ G ++++I D+G GIP+ Sbjct: 381 ILGRELQLRSLFKAL---VDNAIEAMNIKGWKRRELSITTALNGDLIVVSILDSGPGIPQ 437 Query: 707 SALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKI 750 K+ FEP S G+GL+++ + HGG + + Sbjct: 438 DLRYKV---FEPFFTTKGGSRKHIGMGLSVAQEIVADHGGIIDL 478 >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 = 67.1 bits (164), Expect = 2e-11 Identities = 54/229 (23%), Positives = 111/229 (48%), Gaps = 22/229 (9%) Query: 546 FLAKMSHELRTPLNAILGFS------EVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMI 599 +++SHELRTP+ A++ S + +++E KY E A+ G L+MI Sbjct: 488 MSSRLSHELRTPV-AVVRSSLENLELQALEQE------KQKYLERAR----EGTERLSMI 536 Query: 600 -NNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIP-SELFFNAD 657 NN+ E +++E S + ++ DL +++ ++ G + E IP + L Sbjct: 537 LNNMSEATRLEQAIQSAEVEDFDLSEVLSGCMQ--GYQMTYPPQRFELNIPETPLVMRGS 594 Query: 658 KRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFE 717 +I ++L ++ N+ +F+ +G + + S+ ++T+++ G +P+ E++ Sbjct: 595 PELIAQMLDKLVDNAREFSPEDGLIEVGLSQNKSHALLTVSNEGPPLPEDMGEQLFDSMV 654 Query: 718 PLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIIS-QEGKGTIVTICMP 765 + +Q Q GLGL I + + H GR++ + Q+ G + I +P Sbjct: 655 SVRDQGAQDQPHLGLGLYIVRLIADFHQGRIQAENRQQNDGVVFRISLP 703 >gnl|CDD|182583 PRK10604, PRK10604, sensor protein RstB; Provisional. Length = 433 Score = 64.6 bits (158), Expect = 9e-11 Identities = 49/215 (22%), Positives = 98/215 (45%), Gaps = 12/215 (5%) Query: 551 SHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIET 610 +HELRTPL + E+ E ++ +DI GQ L +I +L ++++ Sbjct: 220 AHELRTPLVRLRYRLEMSDNLSAAESQALN-----RDI---GQ-LEALIEELLTYARLDR 270 Query: 611 EKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILS 670 + + DL ++ + I + K ++++ + D R+++++L +L+ Sbjct: 271 PQNELHLSEPDLPAWLSTHLADIQAVTPEKTVRLDT-PHQGDYGALDMRLMERVLDNLLN 329 Query: 671 NSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGF 730 N++++ + ++ + G + + D G GIP E++ +PF L D++ GG Sbjct: 330 NALRY--AHSRVRVSLLLDGNQACLIVEDDGPGIPPEERERVFEPFVRLDPSRDRATGGC 387 Query: 731 GLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 GLGLAI ++ GG + E G + P Sbjct: 388 GLGLAIVHSIALAMGGSVNCDESELGGARFSFSWP 422 >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 = 63.2 bits (154), Expect = 2e-10 Identities = 39/164 (23%), Positives = 81/164 (49%), Gaps = 16/164 (9%) Query: 603 LEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIK 662 L +E EK+ +D + + +R +S +++ + E I ++L AD+ ++ Sbjct: 531 LRSKGLEEEKLCVD---------LVDLLRRAIASKRAQGPRPEVSIDTDLSVRADRERLE 581 Query: 663 KILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSAL-EKIGQPFEPLHN 721 ++L ++ N+++ T G++ IR + I I D+G G+ + + E++ +PF+ Sbjct: 582 RVLGHLVQNALEATPGEGRVAIRVERECGAARIEIEDSGCGMSPAFIRERLFKPFDTTKG 641 Query: 722 QYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 G G+G+ GGR+++ S G+GTI T+ +P Sbjct: 642 A------GMGIGVYECRQYVEEIGGRIEVESTPGQGTIFTLVLP 679 >gnl|CDD|181885 PRK09470, cpxA, two-component sensor protein; Provisional. Length = 461 Score = 60.7 bits (148), Expect = 1e-09 Identities = 59/236 (25%), Positives = 99/236 (41%), Gaps = 43/236 (18%) Query: 547 LAKMSHELRTPL------NAIL----GFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLL 596 L+ +SHELRTPL A+L G S KE+ + I Q L Sbjct: 247 LSDISHELRTPLTRLQLATALLRRRQGES----KEL-------------ERIETEAQRLD 289 Query: 597 NMINNILEMSK------IETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIE-KKIP 649 +MIN++L +S+ +E E + + +E + A+ + P Sbjct: 290 SMINDLLVLSRNQQKNHLERETFKANS-------LWSEVLEDAKFEAEQMGKSLTVSAPP 342 Query: 650 SELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSAL 709 N + + L I+ N++++++ ++ K + IT+ D G G+P+ Sbjct: 343 GPWPINGNPNALASALENIVRNALRYSHTKIEVAFSVDK--DGLTITVDDDGPGVPEEER 400 Query: 710 EKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 E+I +PF + D+ GG GLGLAI + H G +K G +TI +P Sbjct: 401 EQIFRPFYRVDEARDRESGGTGLGLAIVENAIQQHRGWVKAEDSPLGGLRLTIWLP 456 >gnl|CDD|182895 PRK11006, phoR, phosphate regulon sensor protein; Provisional. Length = 430 Score = 60.8 bits (148), Expect = 1e-09 Identities = 55/239 (23%), Positives = 100/239 (41%), Gaps = 40/239 (16%) Query: 546 FLAKMSHELRTPLNAILGFSEVIK-KEIFGEL----------------GSVKYYEYAQDI 588 F A +SHELRTPL + G+ E+++ + + G L G VK I Sbjct: 207 FFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQLLTLSKI 266 Query: 589 HYSGQHLLNMINNILEMSKI-ETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKK 647 + LN ++ M ++ E E ++ + + ++ +++ G+ Q ++ Sbjct: 267 EAAPTIDLNEKVDVPMMLRVLEREAQTLSQGKHTITFEVDNSLKVFGNEDQLRSAI---- 322 Query: 648 IPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKS 707 S L +NA + T + +R ++ Q ++ D G GI Sbjct: 323 --SNLVYNA----------------VNHTPEGTHITVRWQRVPQGAEFSVEDNGPGIAPE 364 Query: 708 ALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ 766 + ++ + F + + GG GLGLAI + H RL+I S+ GKGT + +P+ Sbjct: 365 HIPRLTERFYRVDKARSRQTGGSGLGLAIVKHALSHHDSRLEIESEVGKGTRFSFVLPE 423 >gnl|CDD|181882 PRK09467, envZ, osmolarity sensor protein; Provisional. Length = 435 Score = 52.2 bits (126), Expect = 5e-07 Identities = 54/233 (23%), Positives = 99/233 (42%), Gaps = 47/233 (20%) Query: 547 LAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMS 606 +A +SH+LRTPL I +E++ +E Y + ++ +I E + Sbjct: 233 MAGVSHDLRTPLTRIRLATEMMSEE----------DGYLAE---------SINKDIEECN 273 Query: 607 KIETEKISIDKQNADLIPIINEGIR-------LIGSSAQSKNIKIEKKI-----PSELFF 654 I I+ Q D + E L+G +++ E++I P + Sbjct: 274 AI------IE-QFIDYLRTGQEMPMEMADLNALLGEVIAAES-GYEREIETALQPGPIEV 325 Query: 655 NADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQ 714 + IK+ L ++ N+ ++ N G + + + G+ + D G GIP L+ + Q Sbjct: 326 PMNPIAIKRALANLVVNAARYGN--GWIKVSSGTEGKRAWFQVEDDGPGIPPEQLKHLFQ 383 Query: 715 PFEPLHNQYDQSIG--GFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 PF + D + G G GLGLAI + + H G++++ + E G +P Sbjct: 384 PF----TRGDSARGSSGTGLGLAIVKRIVDQHNGKVELGNSEEGGLSARAWLP 432 >gnl|CDD|184354 PRK13837, PRK13837, two-component VirA-like sensor kinase; Provisional. Length = 828 Score = 51.6 bits (124), Expect = 8e-07 Identities = 50/239 (20%), Positives = 98/239 (41%), Gaps = 46/239 (19%) Query: 551 SHELRTPLNAILGFSEVIKKEIFGELGSVKYY----EYAQDIHYSGQHLLNMINNILEMS 606 +H L AILG++E+ L + + Y +I +G +I+ IL Sbjct: 458 AHNFNNILGAILGYAEM-------ALNKLARHSRAARYIDEIISAGARARLIIDQILAFG 510 Query: 607 KIETEKISIDKQNADLIPI-INEGIRLIGSS---AQSKNIKIEKKIPSE-LFFNADKRII 661 + K + P ++E + I + ++++ E + + Sbjct: 511 R---------KGERNTKPFDLSELVTEIAPLLRVSLPPGVELDFDQDQEPAVVEGNPAEL 561 Query: 662 KKILFPILSNSIKFTNNNGKMMIRTSKI---------------GQCVIITIADTGIGIPK 706 +++L + SN+ + + G++ I S+ G+ V++ ++DTG GI + Sbjct: 562 QQVLMNLCSNAAQAMDGAGRVDISLSRAKLRAPKVLSHGVLPPGRYVLLRVSDTGAGIDE 621 Query: 707 SALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 + L I +PF + GG GLGLA + + H G + + S G+GT + +P Sbjct: 622 AVLPHIFEPF------FTTRAGGTGLGLATVHGIVSAHAGYIDVQSTVGRGTRFDVYLP 674 >gnl|CDD|182591 PRK10618, PRK10618, phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional. Length = 894 Score = 51.1 bits (123), Expect = 1e-06 Identities = 55/243 (22%), Positives = 109/243 (44%), Gaps = 18/243 (7%) Query: 530 QVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIH 589 Q E E+ + A K FL + EL+ PL ++ + +++ E + Sbjct: 440 QREYEKNQQARKA---FLQNIGDELKQPLQSLAQLAAQLRQTSDEEQQQ----PELDQLA 492 Query: 590 YSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIK--IEKK 647 L+ +++NI ++ +ET+ +++ L +I+E + + + + K ++ I Sbjct: 493 EQSDVLVRLVDNIQLLNMLETQDWKPEQELFSLQDLIDEVLPEVLPAIKRKGLQLLIHNH 552 Query: 648 IPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQ---CVIITIADTGIGI 704 + +E D+ ++KIL +L+ +I T GK+ + + + I I DTG G+ Sbjct: 553 LKAEQLRIGDRDALRKILLLLLNYAIT-TTAYGKITLEVDQDESSPDRLTIRILDTGAGV 611 Query: 705 PKSALEKIGQPF--EPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTI 762 L+ + PF + ++Y + GL + + L GG L I S+EG GT +I Sbjct: 612 SIKELDNLHFPFLNQTQGDRYGK---ASGLTFFLCNQLCRKLGGHLTIKSREGLGTRYSI 668 Query: 763 CMP 765 + Sbjct: 669 HLK 671 >gnl|CDD|182388 PRK10337, PRK10337, sensor protein QseC; Provisional. Length = 449 Score = 50.8 bits (122), Expect = 1e-06 Identities = 48/236 (20%), Positives = 91/236 (38%), Gaps = 45/236 (19%) Query: 546 FLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLL--------- 596 F + +HELR+PL A+ +EV + + D + + L Sbjct: 240 FTSDAAHELRSPLAALKVQTEVA--------------QLSDDDPQARKKALLQLHAGIDR 285 Query: 597 --NMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFF 654 +++ +L +S++++ D L ++ + I +AQ I + L Sbjct: 286 ATRLVDQLLTLSRLDSLDNLQDVAEIPLEDLLQSAVMDIYHTAQQAGIDVR------LTL 339 Query: 655 NAD--KRIIKKILFPIL-----SNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKS 707 NA R + +L +L N+I+++ + + + T+ D G G+ Sbjct: 340 NAHPVIRTGQPLLLSLLVRNLLDNAIRYSPQGSVVDVTLNARN----FTVRDNGPGVTPE 395 Query: 708 ALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTIC 763 AL +IG+ F + Q G GLGL+I + LHG + + G + Sbjct: 396 ALARIGERF---YRPPGQEATGSGLGLSIVRRIAKLHGMNVSFGNAPEGGFEAKVS 448 >gnl|CDD|182101 PRK09835, PRK09835, sensor kinase CusS; Provisional. Length = 482 Score = 47.8 bits (114), Expect = 1e-05 Identities = 46/237 (19%), Positives = 112/237 (47%), Gaps = 13/237 (5%) Query: 534 ERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSG- 592 ER E +S F A ++HE+RTP+ ++ +E+ L + + +D+ YS Sbjct: 253 ERIEDVFTRQSNFSADIAHEIRTPITNLITQTEIA-------LSQSRSQKELEDVLYSNL 305 Query: 593 ---QHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIP 649 + M++++L +++ + ++ +K+ DL + + + A+ + +++ + + Sbjct: 306 EELTRMAKMVSDMLFLAQADNNQLIPEKKMLDLADEVGKVFDFFEAWAEERGVEL-RFVG 364 Query: 650 SELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSAL 709 D ++++ + +LSN++++T + +R ++ V + + + G I L Sbjct: 365 DPCQVAGDPLMLRRAISNLLSNALRYTPAGEAITVRCQEVDHQVQLVVENPGTPIAPEHL 424 Query: 710 EKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ 766 ++ F + + G G+GLAI ++ H G + + S + +GT I +P+ Sbjct: 425 PRLFDRFYRVDPSRQRKGEGSGIGLAIVKSIVVAHKGTVAVTS-DARGTRFVISLPR 480 >gnl|CDD|182947 PRK11073, glnL, nitrogen regulation protein NR(II); Provisional. Length = 348 Score = 47.4 bits (113), Expect = 1e-05 Identities = 52/228 (22%), Positives = 100/228 (43%), Gaps = 30/228 (13%) Query: 550 MSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIE 609 ++HE++ PL + G ++++ K L EY + I L N+++ +L + Sbjct: 137 LAHEIKNPLGGLRGAAQLLSKA----LPDPALTEYTKVIIEQADRLRNLVDRLLGPQRPG 192 Query: 610 TEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKI-PSELFFNADKRIIKKILFPI 668 T ++ I + E + + S N+++ + PS D I+++L I Sbjct: 193 THVT----ES---IHKVAERVVQLVSLELPDNVRLIRDYDPSLPELAHDPDQIEQVLLNI 245 Query: 669 LSNSIK-FTNNNGKMMIRTSKIGQCVI----------ITIADTGIGIPKSALEKIGQPFE 717 + N+++ G + +RT Q + I I D G GIP + + F Sbjct: 246 VRNALQALGPEGGTITLRTRTAFQLTLHGERYRLAARIDIEDNGPGIPPHLQDTL---FY 302 Query: 718 PLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP 765 P+ + + GG GLGL+I+ L + H G+++ S G T ++ +P Sbjct: 303 PMVSGRE---GGTGLGLSIARNLIDQHSGKIEFTSWPGH-TEFSVYLP 346 >gnl|CDD|182702 PRK10755, PRK10755, sensor protein BasS/PmrB; Provisional. Length = 356 Score = 46.5 bits (111), Expect = 2e-05 Identities = 28/119 (23%), Positives = 60/119 (50%), Gaps = 5/119 (4%) Query: 649 PSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSA 708 +++ D +++ +L ++ N+ +++ + I+ S+ ++ + D G GI +S Sbjct: 236 AADITVQGDATLLRLLLRNLVENAHRYSPEGSTITIKLSQEDGGAVLAVEDEGPGIDESK 295 Query: 709 LEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIIS-QEGKGTIVTICMPQ 766 ++ + F + D GG GLGL+I +T LH G+ + + QE GT + +P+ Sbjct: 296 CGELSKAFVRM----DSRYGGIGLGLSIVSRITQLHHGQFFLQNRQERSGTRAWVWLPK 350 >gnl|CDD|184141 PRK13557, PRK13557, histidine kinase; Provisional. Length = 540 Score = 45.8 bits (109), Expect = 4e-05 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 6/85 (7%) Query: 682 MMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIG-GFGLGLAISDAL 740 M G+ V I + DTG G+P L ++ PF + G G GLGL++ Sbjct: 314 AMYHGLPPGRYVSIAVTDTGSGMPPEILARVMDPFFTTKEE-----GKGTGLGLSMVYGF 368 Query: 741 TNLHGGRLKIISQEGKGTIVTICMP 765 GG ++I S+ G+GT V + P Sbjct: 369 AKQSGGAVRIYSEVGEGTTVRLYFP 393 >gnl|CDD|106506 PRK13560, PRK13560, hypothetical protein; Provisional. Length = 807 Score = 45.0 bits (106), Expect = 8e-05 Identities = 42/198 (21%), Positives = 77/198 (38%), Gaps = 21/198 (10%) Query: 329 DQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEADQRLSKAI 388 ++ H R G +I + R + G A D+TE+ E+R EA L + + Sbjct: 153 EEEGHFRCGDGR--FIDCCLRFERHAHADDQVDGFAEDITERKRAEERIDEALHFLQQLL 210 Query: 389 ECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSD-- 446 + ++ D++ ++ CN A G ++ SI A +P +Y+ +D Sbjct: 211 DNIADPAFWKDEDAKVFGCNDAACLACGFRREEII---GMSIHDFAPAQPADDYQEADAA 267 Query: 447 ---PERSQDMSKEIKLADSRW----LQINEWCTHDG------GTISVGTDITLLKHNQAQ 493 + SQ + E + D R + N D G + TDI+ + + + Sbjct: 268 KFDADGSQIIEAEFQNKDGRTRPVDVIFNH-AEFDDKENHCAGLVGAITDISGRRAAERE 326 Query: 494 LRESKRRLKATINDLSTS 511 L E + L+A I + Sbjct: 327 LLEKEDMLRAIIEAAPIA 344 Score = 30.8 bits (69), Expect = 1.2 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%) Query: 300 RAIARLIHYDNKKICEIARSV---TGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISG 356 R A +IH + + ++A V + V + +Q + + GA WI ++ R G Sbjct: 519 RMFAAIIHPADLE--QVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEG 576 Query: 357 GM-NIIGIAMDLTEKYHLEKR 376 + + GI +D++E+ H E++ Sbjct: 577 QISHFEGIVIDISERKHAEEK 597 Score = 28.9 bits (64), Expect = 4.7 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 17/69 (24%) Query: 642 IKIEKKIPSELFFNADKRIIKKILFPILSNSIKF-----TNNNGKMMIRTSKIGQCVIIT 696 + I+K IP L I+ +LSN++K N K+ IR G V + Sbjct: 704 LDIDKAIPCGL-----------IISELLSNALKHAFPDGAAGNIKVEIREQGDGM-VNLC 751 Query: 697 IADTGIGIP 705 +AD GIG+P Sbjct: 752 VADDGIGLP 760 >gnl|CDD|182070 PRK09776, PRK09776, putative diguanylate cyclase; Provisional. Length = 1092 Score = 39.3 bits (92), Expect = 0.004 Identities = 33/140 (23%), Positives = 58/140 (41%), Gaps = 9/140 (6%) Query: 264 GRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYD-NKKICEIARSVTG 322 G G+W ++ + M+E+ IP K A L D + EI ++ G Sbjct: 419 GGIGIWEWDLKPNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQG 478 Query: 323 KHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNI---IGIAMDLTEKYHLEKRYAE 379 + +L+ F + G +RA R ++ + +GI MD+TE L + + Sbjct: 479 RSPFKLE--FRIVVKDGV---RHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQ 533 Query: 380 ADQRLSKAIECTSEALVLWD 399 +RL ++ EA+V D Sbjct: 534 EKERLHITLDSIGEAVVCTD 553 >gnl|CDD|185013 PRK15053, dpiB, sensor histidine kinase DpiB; Provisional. Length = 545 Score = 35.6 bits (82), Expect = 0.054 Identities = 26/95 (27%), Positives = 46/95 (48%), Gaps = 3/95 (3%) Query: 672 SIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFG 731 S++ N + + S G V+I +AD G G+P+S +KI FE + G G Sbjct: 448 SLRSDEGNKIVELFLSDEGDDVVIEVADQGCGVPESLRDKI---FEQGVSTRADEPGEHG 504 Query: 732 LGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ 766 +GL + + GG + + + GT+ +I +P+ Sbjct: 505 IGLYLIASYVTRCGGVITLEDNDPCGTLFSIFIPK 539 >gnl|CDD|117024 pfam08447, PAS_3, PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. Length = 90 Score = 34.7 bits (80), Expect = 0.086 Identities = 18/91 (19%), Positives = 36/91 (39%), Gaps = 4/91 (4%) Query: 277 KFHLSRSMYEIMGIPYENKTLSFRAIARLIHYD--NKKICEIARSVTGKHVKQLDQIFHM 334 + S EI+G E S+ L+H + + + K + + + Sbjct: 1 IIYWSPRFEEILGYTPEELKSSYEDWLDLVHPEDRERVRRALQEFSLKKG-EPYSGEYRI 59 Query: 335 RHASGADIWIQVRAQMMRTISGG-MNIIGIA 364 R G W++ R + +R +G + +IG+A Sbjct: 60 RRKDGEYRWVEARGRPIRDENGKPVRVIGVA 90 >gnl|CDD|162393 TIGR01500, sepiapter_red, sepiapterin reductase. This model describes sepiapterin reductase, a member of the short chain dehydrogenase/reductase family. The enzyme catalyzes the last step in the biosynthesis of tetrahydrobiopterin. A similar enzyme in Bacillus cereus was isolated for its ability to convert benzil to (S)-benzoin, a property sepiapterin reductase also shares. Cutoff scores for this model are set such that benzil reductase scores between trusted and noise cutoffs. Length = 256 Score = 33.3 bits (76), Expect = 0.26 Identities = 10/36 (27%), Positives = 16/36 (44%) Query: 481 GTDITLLKHNQAQLRESKRRLKATINDLSTSRQILE 516 G+ + L N LR+ K + A + L R L+ Sbjct: 28 GSVLVLSARNDEALRQLKAEIGAERSGLRVVRVSLD 63 >gnl|CDD|182850 PRK10935, PRK10935, nitrate/nitrite sensor protein NarQ; Provisional. Length = 565 Score = 32.1 bits (74), Expect = 0.47 Identities = 21/74 (28%), Positives = 27/74 (36%), Gaps = 18/74 (24%) Query: 693 VIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIIS 752 ++I D GIGI E G H +GL + A L G L I Sbjct: 504 HTVSIRDDGIGIG-ELKEPEG------H---------YGLNIMQERA-ERLGG-TLTISQ 545 Query: 753 QEGKGTIVTICMPQ 766 G GT V++ P Sbjct: 546 PPGGGTTVSLTFPS 559 >gnl|CDD|178884 PRK00128, ipk, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional. Length = 286 Score = 32.1 bits (74), Expect = 0.51 Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 35/82 (42%) Query: 592 GQHLLNMI------NNILEMSKIETEKISIDKQNADLIPI------------------IN 627 G H + MI + LE+ K++ + I ++ N +P I Sbjct: 24 GYHEVEMIMQTIDLADRLEIEKLKEDGIVVESNNRY-VPNDERNLAYKAAKLLKERYNIK 82 Query: 628 EGIRLIGSSAQSKNIKIEKKIP 649 +G+ I I+K IP Sbjct: 83 QGVS----------ITIDKNIP 94 >gnl|CDD|128397 smart00086, PAC, Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold. Length = 43 Score = 32.2 bits (74), Expect = 0.56 Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 1/43 (2%) Query: 329 DQIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEK 370 + +R G+ IW+ V A +R G + I+G+ D+TE+ Sbjct: 1 TVEYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43 >gnl|CDD|182952 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional. Length = 542 Score = 31.0 bits (71), Expect = 1.1 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 18/80 (22%) Query: 692 CVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIG------GFGLGLAISDALTNLHG 745 + ++D G GI ++ I +D+ G GL L ++ NL G Sbjct: 467 WLHCEVSDDGPGIAPDEIDAI----------FDKGYSTKGSNRGVGLYLV-KQSVENL-G 514 Query: 746 GRLKIISQEGKGTIVTICMP 765 G + + S+ G GT + +P Sbjct: 515 GSIAVESEPGVGTQFFVQIP 534 >gnl|CDD|165248 PHA02938, PHA02938, hypothetical protein; Provisional. Length = 361 Score = 30.7 bits (69), Expect = 1.5 Identities = 13/48 (27%), Positives = 21/48 (43%) Query: 486 LLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEK 533 LL+H+ ++RE R S ++ E KT+L K + K Sbjct: 299 LLQHSIDEIRELSREKPPDSETYVVSVKLPESLKTQLDPIAEKGRTVK 346 >gnl|CDD|161776 TIGR00229, sensory_box, PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. Length = 124 Score = 30.7 bits (70), Expect = 1.6 Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 4/46 (8%) Query: 335 RHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEA 380 R G++IW++V +RT G + ++GI D+TE+ K+ EA Sbjct: 82 RRKDGSEIWVEVSVSPIRTNGGELGVVGIVRDITER----KQAEEA 123 >gnl|CDD|179626 PRK03660, PRK03660, anti-sigma F factor; Provisional. Length = 146 Score = 30.3 bits (69), Expect = 1.8 Identities = 24/96 (25%), Positives = 47/96 (48%), Gaps = 13/96 (13%) Query: 670 SNSI--KFTNN-NGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQS 726 +N+I + NN +G + I + + IT+ D G GI +E+ QP + ++S Sbjct: 49 TNAIIHGYENNPDGVVYIEVEIEEEELEITVRDEGKGIED--IEEAMQPLYTTKPELERS 106 Query: 727 IGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTI 762 G+G + ++ + +++ S+ GKGT V + Sbjct: 107 ----GMGFTVMESFMD----EVEVESEPGKGTTVRM 134 >gnl|CDD|182754 PRK10815, PRK10815, sensor protein PhoQ; Provisional. Length = 485 Score = 30.4 bits (69), Expect = 2.0 Identities = 30/116 (25%), Positives = 54/116 (46%), Gaps = 12/116 (10%) Query: 638 QSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITI 697 Q K + I I E+ F +K +++ +L N+ K+ ++ R + + + I + Sbjct: 356 QRKGVNITLDISPEITFVGEKNDFMEVMGNVLDNACKYCLEFVEISARQT--DEHLHIVV 413 Query: 698 ADTGIGIPKSALEKI---GQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKI 750 D G GIP+S E I GQ + L G GLGL+++ +T + G++ Sbjct: 414 EDDGPGIPESKRELIFDRGQRADTLRP-------GQGLGLSVAREITEQYEGKISA 462 >gnl|CDD|185452 PTZ00109, PTZ00109, DNA gyrase subunit b; Provisional. Length = 903 Score = 30.2 bits (68), Expect = 2.2 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 9/75 (12%) Query: 646 KKIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIP 705 +K P N D++ + ++LF IL NS+ I + + + I+D G GIP Sbjct: 115 RKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVV-LHKDGSVEISDNGRGIP 173 Query: 706 --------KSALEKI 712 KS LE + Sbjct: 174 CDVSEKTGKSGLETV 188 >gnl|CDD|180756 PRK06928, PRK06928, pyrroline-5-carboxylate reductase; Reviewed. Length = 277 Score = 30.1 bits (68), Expect = 2.3 Identities = 12/42 (28%), Positives = 20/42 (47%) Query: 477 TISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQ 518 T +VG +L+ H + +K RL+ T++ S I E Sbjct: 123 TSAVGVGTSLVAHAETVNEANKSRLEETLSHFSHVMTIREEN 164 >gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. Length = 852 Score = 29.5 bits (67), Expect = 3.5 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 14/85 (16%) Query: 483 DITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKY------------- 529 ++ L+ A L E + KA I + ++ +E+ + EL A + Sbjct: 442 ELAELEEEYADLEEQWKAEKAAIQGIQQIKEEIEQVRLELEQAEREGDLAKAAELQYGKL 501 Query: 530 -QVEKERAETANKTKSEFLAKMSHE 553 ++EK K E ++ E Sbjct: 502 PELEKRLQAAEAKLGEETKPRLLRE 526 >gnl|CDD|182537 PRK10547, PRK10547, chemotaxis protein CheA; Provisional. Length = 670 Score = 29.3 bits (66), Expect = 4.1 Identities = 10/21 (47%), Positives = 16/21 (76%) Query: 745 GGRLKIISQEGKGTIVTICMP 765 GG ++I S++GKGT + I +P Sbjct: 502 GGHVEIQSKQGKGTTIRILLP 522 >gnl|CDD|167649 PRK03963, PRK03963, V-type ATP synthase subunit E; Provisional. Length = 198 Score = 28.6 bits (64), Expect = 6.4 Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 13/133 (9%) Query: 490 NQAQLRESKRRLKATINDLSTSRQILERQKTELS------IANAKYQVEKERAETANKTK 543 +AQ K + +A S + IL + KT+ IANAK +V ++R + Sbjct: 24 EEAQKEAEKIKEEARKRAESKAEWILRKAKTQAELEKQRIIANAKLEVRRKRLAVQEELI 83 Query: 544 SEFLAKMSHELRT-PLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNI 602 SE L + L P + + + KE ELG K + S + L +I++ Sbjct: 84 SEVLEAVRERLAELPEDEYFETLKALTKEAVEELGEDKV------VVRSNERTLKLIDSR 137 Query: 603 LEMSKIETEKISI 615 LE + E + I Sbjct: 138 LEEIRDELGDVEI 150 >gnl|CDD|128402 smart00091, PAS, PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press). Length = 67 Score = 28.5 bits (64), Expect = 7.3 Identities = 8/42 (19%), Positives = 19/42 (45%) Query: 382 QRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLV 423 +RL +E + + + D + R++ N ++ G L+ Sbjct: 1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELI 42 >gnl|CDD|162182 TIGR01061, parC_Gpos, DNA topoisomerase IV, A subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. Length = 738 Score = 28.2 bits (63), Expect = 7.7 Identities = 12/41 (29%), Positives = 19/41 (46%) Query: 482 TDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTEL 522 TDI LK Q +L + L+ I ++L++Q E Sbjct: 427 TDIFELKEEQNELEKKIISLEQIIASEKARNKLLKKQLEEY 467 >gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. Length = 771 Score = 28.2 bits (63), Expect = 7.9 Identities = 29/186 (15%), Positives = 55/186 (29%), Gaps = 29/186 (15%) Query: 492 AQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQ---------VEKERAETANKT 542 +L ++ L+ L + E+ K EL + + +EKE E Sbjct: 518 EKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKAL 577 Query: 543 KSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNI 602 K E + + EL+ KK + +K E + + Q + N Sbjct: 578 KKE-VESIIRELKE------------KKIH--KAKEIKSIEDLVKLKETKQKIPQKPTNF 622 Query: 603 LEMSKIETEKISIDKQNADLIPI-----INEGIRLIGSSAQSKNIKIEKKIPSELFFNAD 657 + +I Q ++ I N + + ++ K P F Sbjct: 623 QADKIGDKVRIRYFGQKGKIVQILGGNKWNVTVGGMRMKVHGSELEKINKAPPPKKFKVP 682 Query: 658 KRIIKK 663 K + Sbjct: 683 KTTKPE 688 >gnl|CDD|130980 TIGR01925, spIIAB, anti-sigma F factor. This model describes the SpoIIAB anti-sigma F factor. Sigma F regulates spore development in B subtilis. SpoIIAB binds to sigma F, preventing formation of the transcription complex at the promoter. SpoIIAA (anti-anti-sigma F factor) binds to SpoIIAB to inhibit association with sigma F, however SpoIIAB can phosphorylate SpoIIAA, causing disassociation of the SpoIIAA/B complex. The SpoIIE phosphatase dephosphorylates SpoIIAA. Length = 137 Score = 28.4 bits (63), Expect = 8.1 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 10/82 (12%) Query: 677 NNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAI 736 N G + I + V IT+ D GIGI LE+ +P + ++S G+G + Sbjct: 59 NCEGVVYISATIEDHEVYITVRDEGIGI--ENLEEAREPLYTSKPELERS----GMGFTV 112 Query: 737 SDALTNLHGGRLKIISQEGKGT 758 + + + + S++ KGT Sbjct: 113 MENFMD----DVSVDSEKEKGT 130 >gnl|CDD|185272 PRK15374, PRK15374, pathogenicity island 1 effector protein SipB; Provisional. Length = 593 Score = 28.0 bits (62), Expect = 9.0 Identities = 11/37 (29%), Positives = 21/37 (56%) Query: 506 NDLSTSRQILERQKTELSIANAKYQVEKERAETANKT 542 NDL+ + E ++ E+ +A++Q E +AE N+ Sbjct: 277 NDLALFNALQEGRQAEMEKKSAEFQEETRKAEETNRI 313 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 0.319 0.133 0.374 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: 11,940,061 Number of extensions: 777325 Number of successful extensions: 1936 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1864 Number of HSP's successfully gapped: 103 Length of query: 766 Length of database: 5,994,473 Length adjustment: 101 Effective length of query: 665 Effective length of database: 3,812,065 Effective search space: 2535023225 Effective search space used: 2535023225 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: 61 (27.4 bits)