RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780450|ref|YP_003064863.1| two-component sensor histidine kinase/response regulator hybrid protein [Candidatus Liberibacter asiaticus str. psy62] (803 letters) >gnl|CDD|184141 PRK13557, PRK13557, histidine kinase; Provisional. Length = 540 Score = 280 bits (719), Expect = 9e-76 Identities = 141/405 (34%), Positives = 222/405 (54%), Gaps = 19/405 (4%) Query: 400 EITEQKALEARMAQTQKLNAVGTLAGGIAHDFNNVLTAILLSSDHLLLQSRSSDASFADL 459 +++ ++ E + Q QK+ A+G L GGIAHDFNN+L + D + DA + Sbjct: 143 DVSRRRDAEDALRQAQKMEALGQLTGGIAHDFNNLLQVMSGYLDVIQAALSHPDADRGRM 202 Query: 460 ME----IKHNANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQKLISEPPQVKL 515 I+ A RAA L +QLLAF+RKQ + VLNL ++ + + ++ + + V + Sbjct: 203 ARSVENIRAAAERAATLTQQLLAFARKQRLEGRVLNLNGLVSGMGELAERTLGD--AVTI 260 Query: 516 TVDYERDLWGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSD 575 D DLW + D +Q E L+N+ +NA A + E G +T+RTRN+ + Y Sbjct: 261 ETDLAPDLWNCRIDPTQAEVALLNVLINARDA--MPEGGRVTIRTRNVEIEDEDLAMYHG 318 Query: 576 LPTKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYILP 635 LP V + V DTG GM P+I+ ++ +PFFTTK+ G+GTGLGLS+VYG +QSGG + Sbjct: 319 LPPGRYVSIAVTDTGSGMPPEILARVMDPFFTTKEEGKGTGLGLSMVYGFAKQSGGAVRI 378 Query: 636 ESEVGKGTIFRIFLPRYVQEHTQESHYSHDIAIIPQEEPADLTGNSAIVLLVEDEDSVRR 695 SEVG+GT R++ P S + + P+ D G I L+V+D V Sbjct: 379 YSEVGEGTTVRLYFP--------ASDQAENPEQEPKARAIDRGGTETI-LIVDDRPDVAE 429 Query: 696 GSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMP-EMDGPTLLRELRKTYP 754 ++ +LE GY A +G +AL++++ VD++ +D++MP M+G L RE R+ P Sbjct: 430 LARMILEDFGYRTLVASNGREALEILDS-HPEVDLLFTDLIMPGGMNGVMLAREARRRQP 488 Query: 755 SLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHELL 799 +K + +GYAE + + ++F L+KP+ +LA V +L Sbjct: 489 KIKVLLTTGYAEASIERTDAGGSEFDILNKPYRRAELARRVRMVL 533 >gnl|CDD|184354 PRK13837, PRK13837, two-component VirA-like sensor kinase; Provisional. Length = 828 Score = 220 bits (563), Expect = 1e-57 Identities = 126/397 (31%), Positives = 195/397 (49%), Gaps = 29/397 (7%) Query: 402 TEQKALEARMAQTQKLNAVGTLAGGIAHDFNNVLTAILLSSDHLLLQSRSSDASFADLME 461 TE+ ALE R+ ++L AVGTLA GIAH+FNN+L AIL ++ L + + + E Sbjct: 432 TERDALERRLEHARRLEAVGTLASGIAHNFNNILGAILGYAEMALNKLARHSRAARYIDE 491 Query: 462 IKHNANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQKLISEPPQVKLTVDYER 521 I RA +++ Q+LAF RK +L+E++ + +++ +S PP V+L D ++ Sbjct: 492 IISAGARARLIIDQILAFGRKGERNTKPFDLSELVTEIAPLLR--VSLPPGVELDFDQDQ 549 Query: 522 DLWGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDM 581 + V+ + ++ +QVL+NLC NA A+ +G + + ++ LP Sbjct: 550 EPAVVEGNPAELQQVLMNLCSNAAQAM--DGAGRVDISLSRAKLRAPKVLSHGVLPPGRY 607 Query: 582 VLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYILPESEVGK 641 VL+ V DTG G+ ++ IFEPFFTT+ GTGLGL+ V+GI+ GYI +S VG+ Sbjct: 608 VLLRVSDTGAGIDEAVLPHIFEPFFTTR--AGGTGLGLATVHGIVSAHAGYIDVQSTVGR 665 Query: 642 GTIFRIFLPRYVQEHTQESHYSHDIAIIPQEEPADLT---GNSAIVLLVEDEDSVRRGSK 698 GT F ++LP S + + PQ G VLLVE +D+ + Sbjct: 666 GTRFDVYLPP-----------SSKVPVAPQAFFGPGPLPRGRGETVLLVEPDDATLERYE 714 Query: 699 RMLETRGYTVHE--AFSG-TDALKVMEKLQGRVDIVISDVVMPEMDGPTLLRELRKTYPS 755 L GY E FS A+ + K R D+V+ D + + + L P+ Sbjct: 715 EKLAALGY---EPVGFSTLAAAIAWISKGPERFDLVLVDDRLLDEEQAAAA--LHAAAPT 769 Query: 756 LKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLA 792 L I A S +L + L+KP S + LA Sbjct: 770 LPIILGGNSKTMALSPDL-LASVAEILAKPISSRTLA 805 >gnl|CDD|183098 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional. Length = 607 Score = 165 bits (419), Expect = 5e-41 Identities = 82/262 (31%), Positives = 133/262 (50%), Gaps = 20/262 (7%) Query: 394 AILYTVEITEQKALEARMAQTQKLNAVGTLAGGIAHDFNNVLTAILLSSDHLLLQSRSSD 453 A++ ++TE+K L+ R+A+ ++L A+G L G+AH+ N LTAI Q S Sbjct: 364 ALVIFSDLTERKRLQRRVARQERLAALGELVAGVAHEIRNPLTAIRGYVQIWR-QQTSDP 422 Query: 454 ASFADLMEIKHNANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQKLISEPPQV 513 S L + +R ++ QLL FSR + + ++L ++ + + Q + +V Sbjct: 423 PSQEYLSVVLREVDRLNKVIDQLLEFSRPRESQWQPVSLNALVEEVLQLFQTAGVQA-RV 481 Query: 514 KLTVDYERDLWGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNY 573 + + +L + D +QVL+N+ +NA AI G + +RT ++ Sbjct: 482 DFETELDNELPPIWADPELLKQVLLNILINAVQAI--SARGKIRIRTWQYSDGQVA---- 535 Query: 574 SDLPTKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYI 633 V +ED G G+ P++++KIF+PFFTTK +GTGLGL++ II GG I Sbjct: 536 ----------VSIEDNGCGIDPELLKKIFDPFFTTKA--KGTGLGLALSQRIINAHGGDI 583 Query: 634 LPESEVGKGTIFRIFLPRYVQE 655 ESE G GT F ++LP Q Sbjct: 584 EVESEPGVGTTFTLYLPINPQG 605 >gnl|CDD|182411 PRK10364, PRK10364, sensor protein ZraS; Provisional. Length = 457 Score = 129 bits (326), Expect = 2e-30 Identities = 78/247 (31%), Positives = 128/247 (51%), Gaps = 26/247 (10%) Query: 407 LEARMAQTQKLNAVGTLAGGIAHDFNNVLTAILLSSDHLLLQSR--SSDASFADLMEIKH 464 L+ M + +KL A+G LA G+AH+ N L++I + + ++ A +M K Sbjct: 224 LQDEMKRKEKLVALGHLAAGVAHEIRNPLSSIKGLAKYFAERAPAGGEAHQLAQVM-AKE 282 Query: 465 NANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGN-LRMMIQKLISEPPQVKLTVDYERDL 523 A+R +V +LL + + L ++L ++I + L+++ Q S Q++ T + L Sbjct: 283 -ADRLNRVVSELLELVKPTHLALQAVDLNDLINHSLQLVSQDANSREIQLRFTANDT--L 339 Query: 524 WGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVL 583 ++ D + QVL+NL +NA AI + G ++V + V Sbjct: 340 PEIQADPDRLTQVLLNLYLNAIQAI--GQHGVISVTASE---------------SGAGVK 382 Query: 584 VEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYILPESEVGKGT 643 + V D+G G++ D +E IF P+FTTK EGTGLGL+VV+ I+ Q GG I S+ GKG Sbjct: 383 ISVTDSGKGIAADQLEAIFTPYFTTK--AEGTGLGLAVVHNIVEQHGGTIQVASQEGKGA 440 Query: 644 IFRIFLP 650 F ++LP Sbjct: 441 TFTLWLP 447 >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 = 114 bits (287), Expect = 1e-25 Identities = 81/283 (28%), Positives = 131/283 (46%), Gaps = 41/283 (14%) Query: 529 DLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVED 588 D + QVL+NL NA I + GS+ +R + + L EVED Sbjct: 576 DGPRIRQVLINLVGNA---IKFTDRGSVVLRVSLNDDSSL--------------LFEVED 618 Query: 589 TGIGMSPDIMEKIFEPFFTT--KKVGEGTGLGLSVVYGIIRQSGGYILPESEVGKGTIFR 646 TG G++ + +F+ F ++ GTGLGL++ ++ G + ESE+G G+ F Sbjct: 619 TGCGIAEEEQATLFDAFTQADGRRRSGGTGLGLAISQRLVEAMDGELGVESELGVGSCFW 678 Query: 647 IFLPRYVQEHTQESHYSHDIAIIPQEEPADLTGNSAIVLLVEDEDSVRRGSKRMLETRGY 706 LP + ++S I + PQ VLLVED + + ++ L G+ Sbjct: 679 FTLPLTRGKPAEDSATLTVIDLPPQR-----------VLLVEDNEVNQMVAQGFLTRLGH 727 Query: 707 TVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGPTLLRELRKTYPS---LKFIFISG 763 V A SG AL+ Q D+ + D+ +P+ DG TLL++LR Y + +KFI S Sbjct: 728 KVTLAESGQSALECFH--QHAFDLALLDINLPDGDGVTLLQQLRAIYGAKNEVKFIAFSA 785 Query: 764 YAEDAFSKNLPK--DAKF-SFLSKPFSLKQLATSVHELLQSDS 803 + F++++ + A F FL+KP +QL + +L Sbjct: 786 H---VFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVILAGGK 825 >gnl|CDD|183148 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional. Length = 914 Score = 99.6 bits (248), Expect = 3e-21 Identities = 73/272 (26%), Positives = 118/272 (43%), Gaps = 37/272 (13%) Query: 499 LRMMIQKLISEPPQVKLTVDYERDL--WGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSL 556 L++M ++ P ++L D DL + D + QV+ NL NA + + GS+ Sbjct: 529 LQLMSGRVKGRP--IRLATDIADDLPTA-LMGDPRRIRQVITNLLSNA---LRFTDEGSI 582 Query: 557 TVRTRNIPSTEIHTFNYSDLPTKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTG 616 +R+R + VEVED+G G+ P + +IF+PF GTG Sbjct: 583 VLRSR---TDGEQWL------------VEVEDSGCGIDPAKLAEIFQPFVQVSGKRGGTG 627 Query: 617 LGLSVVYGIIRQSGGYILPESEVGKGTIFRIFLP-RYVQEHTQESHYSHDIAIIPQEEPA 675 LGL++ + + GG + S G+ F + LP R ++ + Sbjct: 628 LGLTISSRLAQAMGGELSATSTPEVGSCFCLRLPLRVATAPVPKT----------VNQAV 677 Query: 676 DLTGNSAIVLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDV 735 L G +LL+ED +R + ML T G V + AL+ ++ + + D Sbjct: 678 RLDGLR--LLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLQNSEP-FAAALVDF 734 Query: 736 VMPEMDGPTLLRELRKTYPSLKFIFISGYAED 767 +P+ DG TL R+L + YPSL I S + D Sbjct: 735 DLPDYDGITLARQLAQQYPSLVLIGFSAHVID 766 >gnl|CDD|128669 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Length = 111 Score = 98.5 bits (246), Expect = 6e-21 Identities = 49/127 (38%), Positives = 60/127 (47%), Gaps = 22/127 (17%) Query: 528 TDLSQFEQVLVNLCVNA-HHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEV 586 D + QVL NL NA + E G +TV D + + V Sbjct: 1 GDPDRLRQVLSNLLDNAIKYT---PEGGRITVTLE---------------RDGDHLEITV 42 Query: 587 EDTGIGMSPDIMEKIFEPFFTTKK---VGEGTGLGLSVVYGIIRQSGGYILPESEVGKGT 643 ED G G+ P+ +EKIFEPFF T GTGLGLS+V ++ GG I ESE G GT Sbjct: 43 EDNGPGIPPEDLEKIFEPFFRTDGRSRKIGGTGLGLSIVKKLVELHGGEISVESEPGGGT 102 Query: 644 IFRIFLP 650 F I LP Sbjct: 103 TFTITLP 109 >gnl|CDD|182956 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional. Length = 779 Score = 92.3 bits (230), Expect = 4e-19 Identities = 88/303 (29%), Positives = 140/303 (46%), Gaps = 49/303 (16%) Query: 503 IQKLISEPPQVKLTVDYERDL-WGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTR 561 + L +E ++ ++ L V TD ++ Q+L NL NA + + G +TVR R Sbjct: 368 LSGLQAEQKGLRFDLEPLLPLPHKVITDGTRLRQILWNLISNA---VKFTQQGGVTVRVR 424 Query: 562 NIPSTEIHTFNYSDLPTKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTK-----KVGEGTG 616 Y + DM+ EVED+GIG+ D ++KIF ++ K K GTG Sbjct: 425 -----------YEE---GDMLTFEVEDSGIGIPEDELDKIFAMYYQVKDSHGGKPATGTG 470 Query: 617 LGLSVVYGIIRQSGGYILPESEVGKGTIFRIFLPRYVQEHTQESHYSHDIAIIPQEEPAD 676 +GL+V + + GG I SE GKG+ F + + E + D Sbjct: 471 IGLAVSKRLAQAMGGDITVTSEEGKGSCFTLTIHAPAVAEEVED----------AFDEDD 520 Query: 677 LTGNSAIVLLVED-EDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDV 735 + + +LLVED E +V ++ +LE G +V A +G +AL++ + D+V+ D+ Sbjct: 521 MPLPALNILLVEDIELNVIV-ARSVLEKLGNSVDVAMTGKEALEMFD--PDEYDLVLLDI 577 Query: 736 VMPEMDGPTLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSF-------LSKPFSL 788 +P+M G + RELR+ YP + A + N+ KD K LSKP S+ Sbjct: 578 QLPDMTGLDIARELRERYPREDLPPLV-----ALTANVLKDKKEYLDAGMDDVLSKPLSV 632 Query: 789 KQL 791 L Sbjct: 633 PAL 635 >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 = 90.9 bits (226), Expect = 1e-18 Identities = 71/254 (27%), Positives = 122/254 (48%), Gaps = 41/254 (16%) Query: 404 QKALEARMAQTQKLNAVGTLAGGIAHDFNNVLT--AILLSS--DHLLLQSRSSDASFAD- 458 +A EA +A+ ++ A ++ + HD N++ ++LL + H + F D Sbjct: 460 MEASEA-LAEARQFEAFNRMSAFVVHDLKNLVAQLSLLLRNAERH------KDNPEFQDD 512 Query: 459 -LMEIKHNANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQKLISEPPQVKLTV 517 L +++ NR +++LLA R + + L + +++ LR I ++ P+ ++++ Sbjct: 513 MLETVENAVNR----MKKLLAQLRSKGLEEEKLCV-DLVDLLRRAIASKRAQGPRPEVSI 567 Query: 518 DYERDLWGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLP 577 D DL V+ D + E+VL +L NA A G + +R Sbjct: 568 D--TDL-SVRADRERLERVLGHLVQNALEAT--PGEGRVAIRVEREC------------- 609 Query: 578 TKDMVLVEVEDTGIGMSPD-IMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYILPE 636 +E+ED+G GMSP I E++F+PF TTK G G G+G+ + + GG I E Sbjct: 610 --GAARIEIEDSGCGMSPAFIRERLFKPFDTTK--GAGMGIGVYECRQYVEEIGGRIEVE 665 Query: 637 SEVGKGTIFRIFLP 650 S G+GTIF + LP Sbjct: 666 STPGQGTIFTLVLP 679 >gnl|CDD|185245 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional. Length = 921 Score = 85.5 bits (212), Expect = 5e-17 Identities = 112/473 (23%), Positives = 177/473 (37%), Gaps = 128/473 (27%) Query: 398 TVEITE--QKALEARMAQTQKLNAVGTLAGGIAHD----FNNVLTAILLSSDHLLLQSRS 451 T + E Q+A +A +++ L I+H+ N VL A+ L LQ+ Sbjct: 381 TQALAEAKQRAEQANKRKSEHLTT-------ISHEIRTPLNGVLGALEL------LQNTP 427 Query: 452 SDASFADLMEIKHNANRAA-ILVRQLLAFSRKQTMRLTV----LNLTEVIGNLRMMIQ-K 505 A DL + + ++ LL FSR ++ ++T+ L ++ + IQ Sbjct: 428 LTAEQMDLADTARQCTLSLLAIINNLLDFSRIESGQMTLSLEETALLPLLDQAMLTIQGP 487 Query: 506 LISEP--------PQVKLTVDYERDLWGVKTDLSQFEQVLVNLCVNAHHAIMLKESG--S 555 S+ V L + D + Q+LVNL NA + E+G Sbjct: 488 AQSKSLTLRTFVGAHVPLYLH---------LDSLRLRQILVNLLGNA---VKFTETGGIR 535 Query: 556 LTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGT 615 L V+ + VEDTG G+ ++IF PF+ +GT Sbjct: 536 LRVKRHE-----------------QQLCFTVEDTGCGIDIQQQQQIFTPFYQADTHSQGT 578 Query: 616 GLGLSVVYGIIRQSGGYILPESEVGKGTIFRIFLPRYVQEHT------------------ 657 GLGL++ + + GG + S G G+ F + LP + E+ Sbjct: 579 GLGLTIASSLAKMMGGELTLFSTPGVGSCFSLVLP--LNEYAPPEPLKGELSAPLALHRQ 636 Query: 658 --------QESH-----------------YSHDIAIIPQEEPADLTGN------SAIVLL 686 Q H Y II Q P + N +LL Sbjct: 637 LSAWGITCQPGHQNPALLDPELAYLPGRLYDLLQQII-QGAPNEPVINLPLQPWQLQILL 695 Query: 687 VEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGPTLL 746 V+D ++ R ML G V A SGT+AL++ Q R D+V+ D+ MP +DG Sbjct: 696 VDDVETNRDIIGMMLVELGQQVTTAASGTEALELGR--QHRFDLVLMDIRMPGLDGLETT 753 Query: 747 RELRKTY----PSLKFIFISGYA--EDAFSKNLPKDAKF-SFLSKPFSLKQLA 792 + R P + ++ A E+ + K A +L+KP +L QLA Sbjct: 754 QLWRDDPNNLDPDCMIVALTANAAPEE---IHRCKKAGMNHYLTKPVTLAQLA 803 >gnl|CDD|182947 PRK11073, glnL, nitrogen regulation protein NR(II); Provisional. Length = 348 Score = 78.2 bits (193), Expect = 7e-15 Identities = 77/265 (29%), Positives = 118/265 (44%), Gaps = 22/265 (8%) Query: 390 PEEQAILYTVEITEQKALEARMAQTQKLNAVGTLAGGIAHDFNNVLTAILLSSDHLLLQS 449 PE +L + Q+ L Q + A L G+AH+ N L L LL Sbjct: 100 PEGMILLEMAPMDNQRRLSQEQLQHAQQVAARDLVRGLAHEIKNPLGG--LRGAAQLLSK 157 Query: 450 RSSDASFADLME----IKHNANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQK 505 D + L E I A+R LV +LL R T ++ +V + ++ Sbjct: 158 ALPDPA---LTEYTKVIIEQADRLRNLVDRLLGPQRPGTH--VTESIHKVAERVVQLVS- 211 Query: 506 LISEPPQVKLTVDYERDLWGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPS 565 + P V+L DY+ L + D Q EQVL+N+ NA A + E G++T+RTR Sbjct: 212 -LELPDNVRLIRDYDPSLPELAHDPDQIEQVLLNIVRNALQA-LGPEGGTITLRTRTAFQ 269 Query: 566 TEIHTFNYSDLPTKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGI 625 +H Y + +++ED G G+ P + + +F P + ++ GTGLGLS+ + Sbjct: 270 LTLHGERY-----RLAARIDIEDNGPGIPPHLQDTLFYPMVSGRE--GGTGLGLSIARNL 322 Query: 626 IRQSGGYILPESEVGKGTIFRIFLP 650 I Q G I S G T F ++LP Sbjct: 323 IDQHSGKIEFTSWPGH-TEFSVYLP 346 >gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional. Length = 1197 Score = 77.1 bits (189), Expect = 2e-14 Identities = 83/284 (29%), Positives = 127/284 (44%), Gaps = 31/284 (10%) Query: 522 DLWGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDM 581 D + VK D F+QVL NL NA + G++ + T + H + Sbjct: 818 DHYLVKIDPQAFKQVLSNLLSNA---LKFTTEGAVKITTSLGHIDDNHA----------V 864 Query: 582 VLVEVEDTGIGMSPDIMEKIFEPFFTTK--KVGEGTGLGLSVVYGIIRQSGGYILPESEV 639 + + + D+G G+S + +++F+ + T + G+GLGL + +I+ G + ES Sbjct: 865 IKMTIMDSGSGLSQEEQQQLFKRYSQTSAGRQQTGSGLGLMICKELIKNMQGDLSLESHP 924 Query: 640 GKGTIFRIFLPRYVQEHTQESHYSHDIAIIPQEEPADLTGNSAIVLLVEDEDSVRRGSKR 699 G GT F I +P E +Q+ A P P L+ +L+ +D + R KR Sbjct: 925 GIGTTFTITIP---VEISQQVATVEAKAEQPITLPEKLS-----ILIADDHPTNRLLLKR 976 Query: 700 MLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGPTLLRELRKTYPSLKFI 759 L GY V EA G AL + D++I+DV MP MDG L R+LR+ SL Sbjct: 977 QLNLLGYDVDEATDGVQALHKVS--MQHYDLLITDVNMPNMDGFELTRKLREQNSSLP-- 1032 Query: 760 FISGYAEDAFSKNLPKDAKFSF---LSKPFSLKQLATSVHELLQ 800 I G +A + K L KP +L L T + +L Q Sbjct: 1033 -IWGLTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQLHQ 1075 >gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein AtoC; Provisional. Length = 457 Score = 72.6 bits (178), Expect = 4e-13 Identities = 39/117 (33%), Positives = 59/117 (50%), Gaps = 2/117 (1%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 +L+V+DED+VRR +G+ H A +G AL + D+V+ D+ MPEMDG Sbjct: 7 ILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFA--DIHPDVVLMDIRMPEMDGI 64 Query: 744 TLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHELLQ 800 L+E+R I ++ YAE + + F ++ KPF L +L V LQ Sbjct: 65 KALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQ 121 >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 = 71.9 bits (177), Expect = 6e-13 Identities = 82/380 (21%), Positives = 145/380 (38%), Gaps = 76/380 (20%) Query: 289 RFNRFFNNIPMAIASIDKKGRILRTNAHFLKLFPNCTEGDGTSNDIFSIVHKNE-KRKII 347 RF +P A+ +D++G+I N +L D I +++ E + Sbjct: 7 RFRAAAQALPDAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQR-ITNLIRHPEFVEYLA 65 Query: 348 AALYDANDQKSDISPIDSPHPQDENRYFRFYISATLDRSTEAP--EEQAILYTVEITEQK 405 A + P++ P P + R I AP EEQ +L ++T + Sbjct: 66 AGRFSE--------PLELPSPINSERVLEIRI---------APYGEEQKLLVARDVTRLR 108 Query: 406 ALEARMAQTQKLNAVGTLAGGIAHDFNNVLTAI-----LLSSDHLLLQSRSSDASFADLM 460 LE +M + N ++H+ LT + L+ + ++M Sbjct: 109 RLE-QMRRDFVAN--------VSHELRTPLTVLRGYLETLADGPDEDPEEWN--RALEIM 157 Query: 461 EIKHNANRAAILVRQLLAFSR----KQTMRLTVLNLTEVIGNLRMMIQKLISEPPQVKLT 516 + R LV LL SR + +++ ++ +LR + L S+ ++T Sbjct: 158 L--EQSQRMQSLVEDLLTLSRLESAASPLEDEPVDMPALLDHLRDEAEAL-SQGKNHQIT 214 Query: 517 VDYERDLWGVKTDLSQFEQVLVNLCVNA-HHAIMLKESGSLTVRTRNIPSTEIHTFNYSD 575 + + + V D + NL NA + E G++TVR R Sbjct: 215 FEIDGGVD-VLGDEDELRSAFSNLVSNAIKYT---PEGGTITVRWRR------------- 257 Query: 576 LPTKDMVLVEVEDTGIGMSPDIMEKIFEPFF--------TTKKVGEGTGLGLSVVYGIIR 627 V DTGIG++P+ + ++ E F+ T GTGLGL++V ++ Sbjct: 258 --DGGGAEFSVTDTGIGIAPEHLPRLTERFYRVDKSRSRDTG----GTGLGLAIVKHVLS 311 Query: 628 QSGGYILPESEVGKGTIFRI 647 + + ESE+GKG+ F Sbjct: 312 RHHARLEIESELGKGSTFSF 331 >gnl|CDD|182496 PRK10490, PRK10490, sensor protein KdpD; Provisional. Length = 895 Score = 71.2 bits (175), Expect = 1e-12 Identities = 73/286 (25%), Positives = 114/286 (39%), Gaps = 54/286 (18%) Query: 390 PEEQAILYTVEITEQKALE----ARMAQTQKLNAV-----GTLAGGIAHDFNNVLTAILL 440 PE+Q +L T + ALE + +L + L ++HD LT +L Sbjct: 625 PEQQRLLETFTLLIANALERLTLTASEEQARLASEREQLRNALLAALSHDLRTPLT-VLF 683 Query: 441 SSDHLLLQSRSSDASFADLMEIKH----NANRAAI-----LVRQLLAFSRKQT----MRL 487 +L +S+ S H + R + LV LL +R Q+ +R Sbjct: 684 GQAEILTLDLASEGS-------PHARQASEIRQQVLNTTRLVNNLLDMARIQSGGFNLRK 736 Query: 488 TVLNLTEVIGN-LRMMIQKLISEPPQVKLTVDYERDLWGVKTDLSQFEQVLVNLCVNAHH 546 L L EV+G+ L+M+ L P + + L + D FE+VL+NL NA Sbjct: 737 EWLTLEEVVGSALQMLEPGLSGHP----INLSLPEPLTLIHVDGPLFERVLINLLENAV- 791 Query: 547 AIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVEDTGIGMSPDIMEKIFEPFF 606 K +G+ I + + + ++V D G G+ P + IF+ F Sbjct: 792 ----KYAGAQA--EIGIDAHV----------EGERLQLDVWDNGPGIPPGQEQLIFDKFA 835 Query: 607 TTKKVGE--GTGLGLSVVYGIIRQSGGYILPESEVGKGTIFRIFLP 650 K G GLGL++ I+ GG I E+ G FR+ LP Sbjct: 836 RGNKESAIPGVGLGLAICRAIVEVHGGTIWAENRPEGGACFRVTLP 881 >gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc. Length = 463 Score = 70.9 bits (174), Expect = 1e-12 Identities = 34/118 (28%), Positives = 60/118 (50%), Gaps = 2/118 (1%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 V +V+D+ S+R ++ L GY V + L+ + + Q D++I+DV MP DG Sbjct: 1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQP--DLLITDVRMPGEDGL 58 Query: 744 TLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHELLQS 801 LL +++K +P L I ++ +++ + + F +L KPF L + T V L Sbjct: 59 DLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERALAH 116 >gnl|CDD|185070 PRK15115, PRK15115, response regulator GlrR; Provisional. Length = 444 Score = 69.5 bits (170), Expect = 3e-12 Identities = 42/123 (34%), Positives = 68/123 (55%), Gaps = 6/123 (4%) Query: 680 NSAIVLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPE 739 A +LLV+D+ + + L + GY+V A SG +AL+V+ + +VD+VISD+ M E Sbjct: 4 KPAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNR--EKVDLVISDLRMDE 61 Query: 740 MDGPTLLRELRKTYPSLKFIFIS--GYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHE 797 MDG L E++K P + I ++ G DA + + FSFL+KP L ++ + Sbjct: 62 MDGMQLFAEIQKVQPGMPVIILTAHGSIPDAVAAT--QQGVFSFLTKPVDRDALYKAIDD 119 Query: 798 LLQ 800 L+ Sbjct: 120 ALE 122 >gnl|CDD|182952 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional. Length = 542 Score = 68.4 bits (168), Expect = 6e-12 Identities = 37/115 (32%), Positives = 58/115 (50%), Gaps = 17/115 (14%) Query: 536 VLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVEDTGIGMSP 595 +L NL NA A+ +E G ++V + +Y + + EV D G G++P Sbjct: 437 ILGNLIENALEAVGGEEGGEISV-----------SLHYRN----GWLHCEVSDDGPGIAP 481 Query: 596 DIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYILPESEVGKGTIFRIFLP 650 D ++ IF+ ++TK G G+GL +V + GG I ESE G GT F + +P Sbjct: 482 DEIDAIFDKGYSTK--GSNRGVGLYLVKQSVENLGGSIAVESEPGVGTQFFVQIP 534 >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 = 68.4 bits (167), Expect = 8e-12 Identities = 80/369 (21%), Positives = 151/369 (40%), Gaps = 59/369 (15%) Query: 295 NNIPMAIASIDKKGRILRTNAHFLKLFPNCTEGDGTSNDIFSIVHKNEKRKIIAALYDAN 354 + P+A +D GR++ N + KL + ++ + ++ + + AL + Sbjct: 137 DAAPVAFVLLDPTGRVILDNQEYKKLATDLRV-KEPAHTVLDLLREAWR----EALAENW 191 Query: 355 DQKSDISPIDSPHPQDENRYFRFYI---------SATLDRSTEAPEEQAILYTV-EITEQ 404 Q+ S ++ + R R+ S D A E+ +L T+ +I+ Sbjct: 192 PQQLAFSNREARFDRGGGRPARWLSCTGSVIGMESDCADSFFCAAEQPYLLLTIADISNL 251 Query: 405 K---------ALEARMAQTQKLNAVG-TLAGGIAHDFNNVLTAILLSSDHLLLQSRSSDA 454 + AL+A MA+ ++L A+ TL+ I H + L+S+ +LQ R DA Sbjct: 252 REEQERARLSALQALMAEEERLEAIRETLSAAI-HRLQGPMN--LISAAISVLQRRGDDA 308 Query: 455 ---SFADLMEIKHNANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQKLISEPP 511 + A +++ +A R + + + Q + + V NL ++ LR +I Sbjct: 309 GNPASAAMLQQALSAGREHMEALRQVIPQSPQEIVVPV-NLNQI---LRDVITLSTPRLL 364 Query: 512 QVKLTVDYERDL---WGVKTDLSQ---FEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPS 565 + VD++ + +L F+ ++ N + + S+T Sbjct: 365 AAGIVVDWQPAATLPAILGRELQLRSLFKALVDNAIEAMNIKGWKRRELSITTALNG--- 421 Query: 566 TEIHTFNYSDLPTKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTK-KVGEGTGLGLSVVYG 624 D+++V + D+G G+ D+ K+FEPFFTTK + G+GLSV Sbjct: 422 --------------DLIVVSILDSGPGIPQDLRYKVFEPFFTTKGGSRKHIGMGLSVAQE 467 Query: 625 IIRQSGGYI 633 I+ GG I Sbjct: 468 IVADHGGII 476 >gnl|CDD|181772 PRK09303, PRK09303, adaptive-response sensory kinase; Validated. Length = 380 Score = 62.7 bits (153), Expect = 4e-10 Identities = 70/245 (28%), Positives = 99/245 (40%), Gaps = 43/245 (17%) Query: 427 IAHDFNNVLTAILLSSDHL-LLQSRSSDASFADLME--IKHNANRAAI---LVRQLLAFS 480 +AHD LTA L+ + L L Q L+E + L+ LL Sbjct: 158 LAHDLRTPLTAASLALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLLEVG 217 Query: 481 RKQTMRLTV----LNLT----EVIGNLRMMIQKLISEPPQVKLTVDYERDLWGVKTDLSQ 532 R + L L+L EVI L +++ D DL V D + Sbjct: 218 RTRWEALRFNPQKLDLGSLCQEVILELEKRWLA-----KSLEIQTDIPSDLPSVYADQER 272 Query: 533 FEQVLVNLCVNAHHAIMLK---ESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVEDT 589 QVL+NL NA +K E G++T+ + +H T V V + DT Sbjct: 273 IRQVLLNLLDNA-----IKYTPEGGTITL-------SMLHR-------TTQKVQVSICDT 313 Query: 590 GIGMSPDIMEKIFEPFFTTKKVG--EGTGLGLSVVYGIIRQSGGYILPESEVGKGTIFRI 647 G G+ + E+IFE + EG G+GLSV I+R G I +SE G+G+ F Sbjct: 314 GPGIPEEEQERIFEDRVRLPRDEGTEGYGIGLSVCRRIVRVHYGQIWVDSEPGQGSCFHF 373 Query: 648 FLPRY 652 LP Y Sbjct: 374 TLPVY 378 >gnl|CDD|182583 PRK10604, PRK10604, sensor protein RstB; Provisional. Length = 433 Score = 60.8 bits (148), Expect = 1e-09 Identities = 51/191 (26%), Positives = 85/191 (44%), Gaps = 34/191 (17%) Query: 472 LVRQLLAFSR----KQTMRLTVLNLTEVIGNLRMMIQKLISEPPQVKLTVDYERDLWGVK 527 L+ +LL ++R + + L+ +L + + + ++ V+L ++ D + Sbjct: 258 LIEELLTYARLDRPQNELHLSEPDLPAWLST-HLADIQAVTPEKTVRLDTPHQGDYGAL- 315 Query: 528 TDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVE 587 D+ E+VL NL NA L+ + S VR S L + + VE Sbjct: 316 -DMRLMERVLDNLLNNA-----LRYAHS-RVRV-------------SLLLDGNQACLIVE 355 Query: 588 DTGIGMSPDIMEKIFEPFF-----TTKKVGEGTGLGLSVVYGIIRQSGGYI-LPESEVGK 641 D G G+ P+ E++FEPF + G G GLGL++V+ I GG + ESE+G Sbjct: 356 DDGPGIPPEERERVFEPFVRLDPSRDRATG-GCGLGLAIVHSIALAMGGSVNCDESELG- 413 Query: 642 GTIFRIFLPRY 652 G F P + Sbjct: 414 GARFSFSWPVW 424 >gnl|CDD|128724 smart00448, REC, cheY-homologous receiver domain. CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues. Length = 55 Score = 55.3 bits (134), Expect = 6e-08 Identities = 19/55 (34%), Positives = 37/55 (67%), Gaps = 2/55 (3%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMP 738 +L+V+D+ +R K +LE GY V EA G +AL+++++ + D+++ D++MP Sbjct: 3 ILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLKEEK--PDLILLDIMMP 55 >gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR; Provisional. Length = 441 Score = 55.0 bits (132), Expect = 6e-08 Identities = 35/124 (28%), Positives = 64/124 (51%), Gaps = 4/124 (3%) Query: 677 LTGNSAIVLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRV-DIVISDV 735 +T ++ +L+V+D+ S + +L GY V A SG AL E+++ +V D+V+ DV Sbjct: 1 MTHDNIDILVVDDDISHCTILQALLRGWGYNVALANSGRQAL---EQVREQVFDLVLCDV 57 Query: 736 VMPEMDGPTLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSV 795 M EMDG L+E++ P++ + ++ Y+ + K +L KP L ++ Sbjct: 58 RMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATL 117 Query: 796 HELL 799 + L Sbjct: 118 EKAL 121 >gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional. Length = 924 Score = 54.2 bits (131), Expect = 1e-07 Identities = 42/142 (29%), Positives = 60/142 (42%), Gaps = 11/142 (7%) Query: 622 VYGIIRQSGGYILPESEVGKG-----TIFRIFLPRYVQEHTQESHYSHDIAIIPQEEPAD 676 +I +I E+ G T LP + + S D A Sbjct: 736 GRAVITFCRRHIGIPLEIAPGEWVHSTATPHELPALLARIYRIELESDDSANALPSTDKA 795 Query: 677 LTGNSAIVLLVEDEDSV-RRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDV 735 ++ N +++LV D+ + RR L + GY A G DAL V+ K +DIV++DV Sbjct: 796 VSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSK--NHIDIVLTDV 853 Query: 736 VMPEMDGPTL---LRELRKTYP 754 MP MDG L LR+L T P Sbjct: 854 NMPNMDGYRLTQRLRQLGLTLP 875 Score = 53.8 bits (130), Expect = 2e-07 Identities = 41/140 (29%), Positives = 62/140 (44%), Gaps = 33/140 (23%) Query: 534 EQVLVNLCVNAHHAIMLKESGS--LTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVEDTGI 591 +QV+ NL NA I ++G L VR D + V DTG+ Sbjct: 564 QQVISNLLSNA---IKFTDTGCIVLHVRVD-----------------GDYLSFRVRDTGV 603 Query: 592 GMSPDIMEKIFEPFFTTKKVG-------EGTGLGLSVVYGIIRQSGGYILPESEVGKGTI 644 G+ + ++F+PFF +VG +GTGLGL++ +I G I +SE G G+ Sbjct: 604 GIPAKEVVRLFDPFF---QVGTGVQRNFQGTGLGLAICEKLINMMDGDISVDSEPGMGSQ 660 Query: 645 FRIFLPRY-VQEHTQESHYS 663 F I +P Y Q ++ Sbjct: 661 FTIRIPLYGAQYPQKKGVEG 680 >gnl|CDD|182842 PRK10923, glnG, nitrogen regulation protein NR(I); Provisional. Length = 469 Score = 54.1 bits (130), Expect = 1e-07 Identities = 31/117 (26%), Positives = 62/117 (52%), Gaps = 2/117 (1%) Query: 683 IVLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDG 742 IV +V+D+ S+R +R L G T +G + L+ + D+++SD+ MP MDG Sbjct: 5 IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALA--SKTPDVLLSDIRMPGMDG 62 Query: 743 PTLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHELL 799 LL+++++ +P L I ++ +++ + + + F +L KPF + + V + Sbjct: 63 LALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAI 119 >gnl|CDD|185013 PRK15053, dpiB, sensor histidine kinase DpiB; Provisional. Length = 545 Score = 53.7 bits (129), Expect = 2e-07 Identities = 38/129 (29%), Positives = 61/129 (47%), Gaps = 14/129 (10%) Query: 529 DLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVED 588 D ++F ++ NL NA A + + G+ V E+ SD D V++EV D Sbjct: 429 DSTEFAAIVGNLLDNAFEASLRSDEGNKIV--------ELF---LSD--EGDDVVIEVAD 475 Query: 589 TGIGMSPDIMEKIFEPFFTTKKVGEGT-GLGLSVVYGIIRQSGGYILPESEVGKGTIFRI 647 G G+ + +KIFE +T+ G G+GL ++ + + GG I E GT+F I Sbjct: 476 QGCGVPESLRDKIFEQGVSTRADEPGEHGIGLYLIASYVTRCGGVITLEDNDPCGTLFSI 535 Query: 648 FLPRYVQEH 656 F+P+ Sbjct: 536 FIPKVKPND 544 >gnl|CDD|182968 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional. Length = 919 Score = 53.3 bits (129), Expect = 2e-07 Identities = 35/125 (28%), Positives = 62/125 (49%), Gaps = 23/125 (18%) Query: 533 FEQVLVNLCVNAHHAIMLKESGSLTVR--TRNIPSTEIHTFNYSDLPTKDMVLVEVEDTG 590 +Q++ NL NA I ESG++ + R + +T++ + V++ DTG Sbjct: 409 LQQIITNLVGNA---IKFTESGNIDILVELRALSNTKVQ------------LEVQIRDTG 453 Query: 591 IGMSPDIMEKIFEPF-----FTTKKVGEGTGLGLSVVYGIIRQSGGYILPESEVGKGTIF 645 IG+S ++F+ F +++ G GTGLGL + ++ + GG I S+ +G+ F Sbjct: 454 IGISERQQSQLFQAFRQADASISRRHG-GTGLGLVITQKLVNEMGGDISFHSQPNRGSTF 512 Query: 646 RIFLP 650 LP Sbjct: 513 WFHLP 517 Score = 30.6 bits (70), Expect = 1.6 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 2/53 (3%) Query: 700 MLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGPTLLRELRKT 752 +LE + V SG A++ ++ D+++ D+ MP MDG +R+ Sbjct: 686 LLEEQVEHVVLCDSGHQAVEQAKQRP--FDLILMDIQMPGMDGIRACELIRQL 736 >gnl|CDD|181815 PRK09390, fixJ, response regulator FixJ; Provisional. Length = 202 Score = 53.1 bits (128), Expect = 3e-07 Identities = 30/107 (28%), Positives = 52/107 (48%), Gaps = 2/107 (1%) Query: 681 SAIVLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEM 740 +V +V+D++++R +L++ G+ V S L + L R V++DV MP + Sbjct: 3 KGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGL--RFGCVVTDVRMPGI 60 Query: 741 DGPTLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFS 787 DG LLR L+ L I ++G+ + + K F+ KPF Sbjct: 61 DGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFE 107 >gnl|CDD|181897 PRK09483, PRK09483, response regulator; Provisional. Length = 217 Score = 52.0 bits (125), Expect = 6e-07 Identities = 34/103 (33%), Positives = 55/103 (53%), Gaps = 4/103 (3%) Query: 684 VLLVEDEDSVRRGSKRMLE-TRGYTV-HEAFSGTDALKVMEKLQGRVDIVISDVVMPEMD 741 VLLV+D + VR G +R+LE +G V EA G DA+K VD+V+ D+ MP + Sbjct: 4 VLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCR--TNAVDVVLMDMNMPGIG 61 Query: 742 GPTLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSK 784 G R++ + P +K I ++ + E+ + + +LSK Sbjct: 62 GLEATRKILRYTPDVKIIMLTVHTENPLPAKVMQAGAAGYLSK 104 >gnl|CDD|130454 TIGR01387, cztR_silR_copR, heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). 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. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system. Length = 218 Score = 51.0 bits (122), Expect = 1e-06 Identities = 40/120 (33%), Positives = 62/120 (51%), Gaps = 8/120 (6%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 +L+VEDE ++ L GY V A +G D L + K D++I DV++P MDG Sbjct: 1 ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLALK--DDYDLIILDVMLPGMDGW 58 Query: 744 TLLRELRKTYPSLKFIFISGYAEDAFS---KNLPKDAKFSFLSKPFSLKQLATSVHELLQ 800 +L+ LR++ +F++ A D+ + K L A +L KPFS +L V LL+ Sbjct: 59 QILQTLRRSGKQTPVLFLT--ARDSVADKVKGLDLGAD-DYLVKPFSFSELLARVRTLLR 115 >gnl|CDD|182711 PRK10766, PRK10766, DNA-binding transcriptional regulator TorR; Provisional. Length = 221 Score = 50.4 bits (121), Expect = 2e-06 Identities = 39/118 (33%), Positives = 61/118 (51%), Gaps = 7/118 (5%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 +L+VEDE R + E GYTV EA SG ++M+ VD+++ D+ +P DG Sbjct: 5 ILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQ--NQHVDLILLDINLPGEDGL 62 Query: 744 TLLRELRKTYPSLKFIFISGYAEDAFSK--NLPKDAKFSFLSKPFSLKQLATSVHELL 799 L RELR ++ I ++G D+ + L A +++KP L++L V LL Sbjct: 63 MLTRELRSR-STVGIILVTG-RTDSIDRIVGLEMGAD-DYVTKPLELRELLVRVKNLL 117 >gnl|CDD|182950 PRK11083, PRK11083, DNA-binding response regulator CreB; Provisional. Length = 228 Score = 50.3 bits (121), Expect = 2e-06 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 2/79 (2%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 +LLVEDE ++ L++ G+TV G AL + Q D+VI DV +P++ G Sbjct: 6 ILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLR--QQPPDLVILDVGLPDISGF 63 Query: 744 TLLRELRKTYPSLKFIFIS 762 L R+L +P+L IF++ Sbjct: 64 ELCRQLLAFHPALPVIFLT 82 >gnl|CDD|181966 PRK09581, pleD, response regulator PleD; Reviewed. Length = 457 Score = 50.3 bits (121), Expect = 2e-06 Identities = 29/83 (34%), Positives = 48/83 (57%), Gaps = 11/83 (13%) Query: 681 SAIVLLVEDEDSVRRGSKRMLETR----GYTVHEAFSGTDALKVMEKLQGRVDIVISDVV 736 +A +L+V+D + + ++LE + YTV A SG +A+ + E+ Q DI++ DV+ Sbjct: 2 TARILVVDDIPA----NVKLLEAKLLAEYYTVLTASSGAEAIAICEREQ--PDIILLDVM 55 Query: 737 MPEMDGPTLLRELRKTYPSLKFI 759 MP MDG + R L K+ P+ I Sbjct: 56 MPGMDGFEVCRRL-KSDPATTHI 77 >gnl|CDD|182522 PRK10529, PRK10529, DNA-binding transcriptional activator KdpE; Provisional. Length = 225 Score = 49.0 bits (117), Expect = 4e-06 Identities = 37/111 (33%), Positives = 64/111 (57%), Gaps = 9/111 (8%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALK--VMEKLQGRVDIVISDVVMPEMD 741 VL+VEDE ++RR + LE G V EA + L+ ++E + D++I D+ +P+ D Sbjct: 4 VLIVEDEQAIRRFLRTALEGDGMRVFEA----ETLQRGLLEAATRKPDLIILDLGLPDGD 59 Query: 742 GPTLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFS-FLSKPFSLKQL 791 G +R+LR+ + ++ I +S +E++ K DA +LSKPF + +L Sbjct: 60 GIEFIRDLRQ-WSAIPVIVLSARSEES-DKIAALDAGADDYLSKPFGIGEL 108 >gnl|CDD|183013 PRK11173, PRK11173, two-component response regulator; Provisional. Length = 237 Score = 49.2 bits (118), Expect = 5e-06 Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 3/80 (3%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 +L+VEDE R K + E GY V EA G + +++ + +++VI D+ +P +G Sbjct: 6 ILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--ENDINLVIMDINLPGKNGL 63 Query: 744 TLLRELRKTYPSLKFIFISG 763 L RELR+ ++ +F++G Sbjct: 64 LLARELREQ-ANVALMFLTG 82 >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 = 47.4 bits (113), Expect = 1e-05 Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 5/75 (6%) Query: 580 DMVLVEVEDTGIGMSPDIMEKIFEPFF----TTKKVGEGTGLGLSVVYGIIRQSGGYILP 635 D V V V + G G+ P+ + ++F+ F+ GEGTGLGL++V I+ GG Sbjct: 384 DEVRVSVSNPGPGIPPEHLSRLFDRFYRVDPARSNSGEGTGLGLAIVRSIMEAHGGRASA 443 Query: 636 ESEVGKGTIFRIFLP 650 ES GK T F + P Sbjct: 444 ESPDGK-TRFILRFP 457 >gnl|CDD|181885 PRK09470, cpxA, two-component sensor protein; Provisional. Length = 461 Score = 47.2 bits (113), Expect = 2e-05 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 10/62 (16%) Query: 579 KDMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGE-------GTGLGLSVVYGIIRQSGG 631 KD + + V+D G G+ + E+IF PF+ +V E GTGLGL++V I+Q G Sbjct: 381 KDGLTITVDDDGPGVPEEEREQIFRPFY---RVDEARDRESGGTGLGLAIVENAIQQHRG 437 Query: 632 YI 633 ++ Sbjct: 438 WV 439 >gnl|CDD|181882 PRK09467, envZ, osmolarity sensor protein; Provisional. Length = 435 Score = 47.2 bits (113), Expect = 2e-05 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 4/76 (5%) Query: 578 TKDMVLVEVEDTGIGMSPDIMEKIFEPFFT--TKKVGEGTGLGLSVVYGIIRQSGGYI-L 634 +VED G G+ P+ ++ +F+PF + + GTGLGL++V I+ Q G + L Sbjct: 358 EGKRAWFQVEDDGPGIPPEQLKHLFQPFTRGDSARGSSGTGLGLAIVKRIVDQHNGKVEL 417 Query: 635 PESEVGKGTIFRIFLP 650 SE G G R +LP Sbjct: 418 GNSEEG-GLSARAWLP 432 >gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW; Provisional. Length = 223 Score = 46.0 bits (109), Expect = 3e-05 Identities = 31/117 (26%), Positives = 52/117 (44%), Gaps = 3/117 (2%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 +LL+ED + + L GY + G D L + L+ ++I D+++P MDG Sbjct: 3 ILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYL--ALKDDYALIILDIMLPGMDGW 60 Query: 744 TLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHELLQ 800 +L+ LR + + + D + L A +L KPFS +L V L+ Sbjct: 61 QILQTLRTAKQTPVICLTARDSVDDRVRGLDSGAN-DYLVKPFSFSELLARVRAQLR 116 >gnl|CDD|182864 PRK10955, PRK10955, DNA-binding transcriptional regulator CpxR; Provisional. Length = 232 Score = 46.3 bits (110), Expect = 3e-05 Identities = 34/120 (28%), Positives = 61/120 (50%), Gaps = 10/120 (8%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 +LLV+D+ + K +LE G+ V A G AL + L +D+++ DV+MP+ +G Sbjct: 4 ILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDL---LDDSIDLLLLDVMMPKKNGI 60 Query: 744 TLLRELRKTYPSLKFIFISGYAED---AFSKNLPKDAKFSFLSKPFSLKQLATSVHELLQ 800 L+ELR+T+ I ++ + L D +L KPF+ ++L + +L+ Sbjct: 61 DTLKELRQTH-QTPVIMLTARGSELDRVLGLELGAD---DYLPKPFNDRELVARIRAILR 116 >gnl|CDD|170568 PRK10610, PRK10610, chemotaxis regulatory protein CheY; Provisional. Length = 129 Score = 45.7 bits (108), Expect = 4e-05 Identities = 30/68 (44%), Positives = 40/68 (58%), Gaps = 5/68 (7%) Query: 685 LLVEDEDSVRRGSKRMLETRGY-TVHEAFSGTDALKVMEKLQ-GRVDIVISDVVMPEMDG 742 L+V+D ++RR + +L+ G+ V EA G DAL KLQ G VISD MP MDG Sbjct: 9 LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALN---KLQAGGFGFVISDWNMPNMDG 65 Query: 743 PTLLRELR 750 LL+ +R Sbjct: 66 LELLKTIR 73 >gnl|CDD|185376 PRK15479, PRK15479, transcriptional regulatory protein TctD; Provisional. Length = 221 Score = 45.9 bits (109), Expect = 5e-05 Identities = 37/121 (30%), Positives = 54/121 (44%), Gaps = 10/121 (8%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQG-RVDIVISDVVMPEMDG 742 +LL ED + ++ L G+ V F D L LQ + + D+ MP MDG Sbjct: 3 LLLAEDNRELAHWLEKALVQNGFAVDCVF---DGLAADHLLQSEMYALAVLDINMPGMDG 59 Query: 743 PTLLRELRK---TYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHELL 799 +L+ LRK T P L S A+ N+ D +L KPF L++L + LL Sbjct: 60 LEVLQRLRKRGQTLPVLLLTARSAVADRVKGLNVGAD---DYLPKPFELEELDARLRALL 116 Query: 800 Q 800 + Sbjct: 117 R 117 >gnl|CDD|182652 PRK10693, PRK10693, response regulator of RpoS; Provisional. Length = 303 Score = 45.0 bits (107), Expect = 7e-05 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%) Query: 709 HEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGPTLLRELRKTYPSLKFIFIS 762 A +G DAL+++ D++I D+ MP M+G + LR + IS Sbjct: 1 VLAANGVDALELLGGF--TPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVIS 52 >gnl|CDD|182168 PRK09958, PRK09958, DNA-binding transcriptional activator EvgA; Provisional. Length = 204 Score = 44.9 bits (106), Expect = 8e-05 Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 3/101 (2%) Query: 685 LLVEDEDSVRRGSKRMLETRGYTV-HEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 ++++D + +L + E G A++ +E L+ DIVI DV +P ++G Sbjct: 4 IIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKP--DIVIIDVDIPGVNGI 61 Query: 744 TLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSK 784 +L LRK S I +S + + K+ F+SK Sbjct: 62 QVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSK 102 >gnl|CDD|182387 PRK10336, PRK10336, DNA-binding transcriptional regulator QseB; Provisional. Length = 219 Score = 43.3 bits (102), Expect = 2e-04 Identities = 34/122 (27%), Positives = 60/122 (49%), Gaps = 12/122 (9%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVH---EAFSGTDALKVMEKLQGRVDIVISDVVMPEM 740 +LL+ED+ + G K L G++V + G +AL D VI D+ +P M Sbjct: 3 ILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEAL-----YSAPYDAVILDLTLPGM 57 Query: 741 DGPTLLRELRKTYPSLKFIFISGYAEDAFSKNLP--KDAKFSFLSKPFSLKQLATSVHEL 798 DG +LRE R+ + ++ A DA ++ + + +L KPF+L ++A + L Sbjct: 58 DGRDILREWREKGQREPVLILT--ARDALAERVEGLRLGADDYLCKPFALIEVAARLEAL 115 Query: 799 LQ 800 ++ Sbjct: 116 MR 117 >gnl|CDD|182962 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional. Length = 475 Score = 43.3 bits (103), Expect = 2e-04 Identities = 50/201 (24%), Positives = 81/201 (40%), Gaps = 35/201 (17%) Query: 462 IKHNANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQKLISEP----PQVKLTV 517 I + R L+ +LL +R + R + L V L ++++L+ +T+ Sbjct: 297 ILTQSARLQQLIDRLLELARLEQ-RQELEVLEPV--ALAALLEELVEAREAQAAAKGITL 353 Query: 518 DYERDLWGVKTDLSQFEQVLVNLCVNAHHAIMLK---ESGSLTVRTRNIPSTEIHTFNYS 574 D V D Q L NL NA + E G++T+ Sbjct: 354 RLRPDDARVLGDPFLLRQALGNLLDNA-----IDFSPEGGTITLSAE------------- 395 Query: 575 DLPTKDMVLVEVEDTGIGMSPDI-MEKIFEPFFTTKKVGEG---TGLGLSVVYGIIRQSG 630 + V + VED G G+ PD + +IFE F++ + G TGLGL+ V + R G Sbjct: 396 --VDGEQVALSVEDQGPGI-PDYALPRIFERFYSLPRPANGRKSTGLGLAFVREVARLHG 452 Query: 631 GYILPESEVGKGTIFRIFLPR 651 G + + G + + LPR Sbjct: 453 GEVTLRNRPEGGVLATLTLPR 473 >gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional. Length = 216 Score = 43.5 bits (103), Expect = 2e-04 Identities = 26/91 (28%), Positives = 48/91 (52%), Gaps = 6/91 (6%) Query: 681 SAIVLLVEDEDSVRRGSKRMLET--RGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMP 738 A +LL++D +R G K+++ V EA +G +++ E L D+++ D+ MP Sbjct: 6 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESL--DPDLILLDLNMP 63 Query: 739 EMDGPTLLRELRKTYPSLKFIF--ISGYAED 767 M+G L +LR+ S + + +S + ED Sbjct: 64 GMNGLETLDKLREKSLSGRIVVFSVSNHEED 94 >gnl|CDD|182101 PRK09835, PRK09835, sensor kinase CusS; Provisional. Length = 482 Score = 43.2 bits (102), Expect = 2e-04 Identities = 56/240 (23%), Positives = 104/240 (43%), Gaps = 43/240 (17%) Query: 427 IAHDFNNVLTAILLSSDHLLLQSRS----SDASFADLMEIKHNANRAAILVRQLLAFSRK 482 IAH+ +T ++ ++ L QSRS D +++L E+ R A +V +L ++ Sbjct: 269 IAHEIRTPITNLITQTEIALSQSRSQKELEDVLYSNLEEL----TRMAKMVSDMLFLAQA 324 Query: 483 QTMRLTVLNLTEVIGNLRMMIQKLI------SEPPQVKLTVD-YERDLWGVKTDLSQFEQ 535 +L + + +L + K+ +E V+L + G D + Sbjct: 325 DNNQLI---PEKKMLDLADEVGKVFDFFEAWAEERGVELRFVGDPCQVAG---DPLMLRR 378 Query: 536 VLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVEDTGIGMSP 595 + NL NA R P+ E T + V + VE+ G ++P Sbjct: 379 AISNLLSNA---------------LRYTPAGEAITVRCQE--VDHQVQLVVENPGTPIAP 421 Query: 596 DIMEKIFEPFF----TTKKVGEGTGLGLSVVYGIIRQSGGYILPESEVGKGTIFRIFLPR 651 + + ++F+ F+ + ++ GEG+G+GL++V I+ G + S+ +GT F I LPR Sbjct: 422 EHLPRLFDRFYRVDPSRQRKGEGSGIGLAIVKSIVVAHKGTVAVTSDA-RGTRFVISLPR 480 >gnl|CDD|182537 PRK10547, PRK10547, chemotaxis protein CheA; Provisional. Length = 670 Score = 43.2 bits (102), Expect = 3e-04 Identities = 23/53 (43%), Positives = 35/53 (66%), Gaps = 3/53 (5%) Query: 601 IFEPFFTT-KKVGE--GTGLGLSVVYGIIRQSGGYILPESEVGKGTIFRIFLP 650 IF P F+T ++V + G G+G+ VV I++ GG++ +S+ GKGT RI LP Sbjct: 470 IFAPGFSTAEQVTDVSGRGVGMDVVKRNIQEMGGHVEIQSKQGKGTTIRILLP 522 >gnl|CDD|131922 TIGR02875, spore_0_A, sporulation transcription factor Spo0A. Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species. Length = 262 Score = 43.2 bits (102), Expect = 3e-04 Identities = 25/92 (27%), Positives = 51/92 (55%), Gaps = 4/92 (4%) Query: 711 AFSGTDALKVMEKLQGRVDIVISDVVMPEMDGPTLLRELRKTYPSL--KFIFISGYAEDA 768 A +G DAL+++++ Q D+V+ D++MP +DG +L +L + S + I +S + ++ Sbjct: 34 AHNGVDALELIKEQQP--DVVVLDIIMPHLDGIGVLEKLNEIELSARPRVIMLSAFGQEK 91 Query: 769 FSKNLPKDAKFSFLSKPFSLKQLATSVHELLQ 800 ++ ++ KPF L+ LA + +L Sbjct: 92 ITQRAVALGADYYVLKPFDLEILAARIRQLAW 123 >gnl|CDD|182612 PRK10643, PRK10643, DNA-binding transcriptional regulator BasR; Provisional. Length = 222 Score = 43.1 bits (102), Expect = 3e-04 Identities = 35/128 (27%), Positives = 63/128 (49%), Gaps = 13/128 (10%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 +L+VED+ + +G L+T GY A + +A ++E G +V+ D+ +P+ DG Sbjct: 3 ILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLE--SGHYSLVVLDLGLPDEDGL 60 Query: 744 TLLRELRKTYPSLKFIFISGYAEDAFS---KNLPKDAKFSFLSKPFSLKQLATSVHELL- 799 LLR R+ +L + ++ A D L A +L KPF+L++L + L+ Sbjct: 61 HLLRRWRQKKYTLPVLILT--ARDTLEDRVAGLDVGAD-DYLVKPFALEELHARIRALIR 117 Query: 800 ----QSDS 803 Q ++ Sbjct: 118 RHQGQGEN 125 >gnl|CDD|182895 PRK11006, phoR, phosphate regulon sensor protein; Provisional. Length = 430 Score = 42.7 bits (101), Expect = 4e-04 Identities = 53/195 (27%), Positives = 85/195 (43%), Gaps = 32/195 (16%) Query: 466 ANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQKLISEP-----PQVKLTVDYE 520 R LV+QLL S+ + ++L E + ++ MM++ L E + +T + + Sbjct: 250 TQRMEGLVKQLLTLSKIEAA--PTIDLNEKV-DVPMMLRVLEREAQTLSQGKHTITFEVD 306 Query: 521 RDLWGVKTDLSQFEQVLVNLCVNA-HHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPTK 579 L V + Q + NL NA +H E +TVR + +P Sbjct: 307 NSL-KVFGNEDQLRSAISNLVYNAVNHT---PEGTHITVRWQRVPQG------------- 349 Query: 580 DMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGE----GTGLGLSVVYGIIRQSGGYILP 635 VED G G++P+ + ++ E F+ K G+GLGL++V + + Sbjct: 350 --AEFSVEDNGPGIAPEHIPRLTERFYRVDKARSRQTGGSGLGLAIVKHALSHHDSRLEI 407 Query: 636 ESEVGKGTIFRIFLP 650 ESEVGKGT F LP Sbjct: 408 ESEVGKGTRFSFVLP 422 >gnl|CDD|131209 TIGR02154, PhoB, phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well. Length = 226 Score = 40.8 bits (96), Expect = 0.001 Identities = 37/124 (29%), Positives = 62/124 (50%), Gaps = 10/124 (8%) Query: 681 SAIVLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDAL-KVMEKLQGRVDIVISDVVMPE 739 + +L+VEDE ++R LE GY V EA G +AL + E+ D+++ D ++P Sbjct: 2 TRRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLINERGP---DLILLDWMLPG 58 Query: 740 MDGPTLLRELRKTYPSLKFIFI----SGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSV 795 G L R LR+ P + I I + E+ + L A +++KPFS ++L + Sbjct: 59 TSGIELCRRLRR-RPETRAIPIIMLTARGEEEDRVRGLETGAD-DYITKPFSPRELLARI 116 Query: 796 HELL 799 +L Sbjct: 117 KAVL 120 >gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB; Provisional. Length = 211 Score = 40.8 bits (96), Expect = 0.001 Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 6/87 (6%) Query: 684 VLLVEDEDSVRRGSKRMLET--RGYTVHEAFSGTDALKVMEK-LQGRVDIVISDVVMPEM 740 +LLV+D + + G K ML R V + + L+V Q DIVI D+ +P M Sbjct: 6 ILLVDDHELIINGIKNMLAPYPRYKIVGQV---DNGLEVYNACRQLEPDIVILDLGLPGM 62 Query: 741 DGPTLLRELRKTYPSLKFIFISGYAED 767 +G ++ +L + +P++ + ++ E+ Sbjct: 63 NGLDVIPQLHQRWPAMNILVLTARQEE 89 >gnl|CDD|183591 PRK12555, PRK12555, chemotaxis-specific methylesterase; Provisional. Length = 337 Score = 38.3 bits (90), Expect = 0.007 Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 8/75 (10%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHE----AFSGTDALKVMEKLQGRVDIVISDVVMPE 739 + +V D +R L HE A G A++ D+++ D+ MP Sbjct: 3 IGIVNDSPLAVEALRRALARDP--DHEVVWVATDGAQAVERCAAQ--PPDVILMDLEMPR 58 Query: 740 MDGPTLLRELRKTYP 754 MDG R + P Sbjct: 59 MDGVEATRRIMAERP 73 >gnl|CDD|128670 smart00388, HisKA, His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases. Length = 66 Score = 38.3 bits (90), Expect = 0.007 Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 1/66 (1%) Query: 419 AVGTLAGGIAHDFNNVLTAILLSSDHLLLQSRSSDASFADLMEIKHNANRAAILVRQLLA 478 A ++H+ LTAI LL + S+ L I +A R L+ LL Sbjct: 1 AKREFLANLSHELRTPLTAIRGYL-ELLEDTELSEEQREYLETILRSAERLLRLINDLLD 59 Query: 479 FSRKQT 484 SR + Sbjct: 60 LSRIEA 65 >gnl|CDD|182154 PRK09935, PRK09935, transcriptional regulator FimZ; Provisional. Length = 210 Score = 37.9 bits (88), Expect = 0.009 Identities = 25/116 (21%), Positives = 55/116 (47%), Gaps = 1/116 (0%) Query: 685 LLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGR-VDIVISDVVMPEMDGP 743 +++ D + R S +L + + D ++ L+ R VD++I D+ +P DG Sbjct: 6 VIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGF 65 Query: 744 TLLRELRKTYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHELL 799 T L+ +++ ++K +F+S +E ++ + F+SK + +V +L Sbjct: 66 TFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMIL 121 >gnl|CDD|181883 PRK09468, ompR, osmolarity response regulator; Provisional. Length = 239 Score = 38.0 bits (89), Expect = 0.010 Identities = 29/119 (24%), Positives = 58/119 (48%), Gaps = 8/119 (6%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGR--VDIVISDVVMPEMD 741 +L+V+D+ +R +R L +G+ V A + + M++L R +++ D+++P D Sbjct: 8 ILVVDDDMRLRALLERYLTEQGFQVRSAANA----EQMDRLLTRESFHLMVLDLMLPGED 63 Query: 742 GPTLLRELRKTYPSLKFIFISGYAEDAFS-KNLPKDAKFSFLSKPFSLKQLATSVHELL 799 G ++ R LR I ++ E+ L A +L KPF+ ++L + +L Sbjct: 64 GLSICRRLRSQNNPTPIIMLTAKGEEVDRIVGLEIGAD-DYLPKPFNPRELLARIRAVL 121 >gnl|CDD|179106 PRK00742, PRK00742, chemotaxis-specific methylesterase; Provisional. Length = 354 Score = 37.1 bits (87), Expect = 0.019 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 4/73 (5%) Query: 684 VLLVEDEDSVRRGSKRMLET-RGYTV-HEAFSGTDALKVMEKLQGRVDIVISDVVMPEMD 741 VL+V+D +RR +L + V A G +A + ++KL D++ DV MP MD Sbjct: 6 VLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKL--NPDVITLDVEMPVMD 63 Query: 742 GPTLLRELRKTYP 754 G L ++ + P Sbjct: 64 GLDALEKIMRLRP 76 >gnl|CDD|182665 PRK10710, PRK10710, DNA-binding transcriptional regulator BaeR; Provisional. Length = 240 Score = 37.0 bits (86), Expect = 0.021 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 2/78 (2%) Query: 674 PADLTGNSAIVLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVIS 733 + N+ +L+VEDE + + L+ Y G + L + Q D+++ Sbjct: 3 ELPIDENTPRILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVR--QTPPDLILL 60 Query: 734 DVVMPEMDGPTLLRELRK 751 D+++P DG TL RE+R+ Sbjct: 61 DLMLPGTDGLTLCREIRR 78 >gnl|CDD|117025 pfam08448, PAS_4, 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 = 110 Score = 36.6 bits (85), Expect = 0.024 Identities = 21/102 (20%), Positives = 36/102 (35%), Gaps = 12/102 (11%) Query: 166 LDHSPVGFMSADHQGKILYINATLAEWIGIDLTTFTSKS---ISIGDITAGEGLALIQAI 222 LD P D G++ Y NA AE G+ K+ + + A AL +A+ Sbjct: 1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERALRRAL 60 Query: 223 RTEPSHQKITTLDLD---------LRRIDNGHGIPVKIVHHI 255 E + L L+ L + + G + ++ Sbjct: 61 EGEEPIDFLEELLLNGEERHYELRLTPLRDPDGEVIGVLVIS 102 Score = 31.2 bits (71), Expect = 1.1 Identities = 22/116 (18%), Positives = 48/116 (41%), Gaps = 9/116 (7%) Query: 294 FNNIPMAIASIDKKGRILRTNAHFLKLFPNCTEGDG---TSNDIFSIVHKNEKRKIIAAL 350 +++P A+A +D GR+ NA +LF + T ++ ++ AL Sbjct: 1 LDSLPDALAVLDPDGRVRYANAAAAELF-GLPPEELLGKTLAELLPPED---AARLERAL 56 Query: 351 YDANDQKSDISPIDSPHPQDENRYFRFYISATLDRSTEAPEEQAILYTVEITEQKA 406 A + + I ++ E R++ ++ D E ++ + +ITE++ Sbjct: 57 RRALEGEEPIDFLEELLLNGEERHYELRLTPLRDPDGEV--IGVLVISRDITERRR 110 >gnl|CDD|163499 TIGR03787, marine_sort_RR, proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator. Length = 227 Score = 35.9 bits (83), Expect = 0.038 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 6/82 (7%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRV-DIVISDVVM-PEMD 741 + +VEDE ++R L+ +GY V A M+ + R+ D+ I D+ + E+D Sbjct: 3 IAIVEDEAAIRENYADALKRQGYQVTTYADRPSA---MQAFRQRLPDLAIIDIGLGEEID 59 Query: 742 GP-TLLRELRKTYPSLKFIFIS 762 G L ++LR +L IF++ Sbjct: 60 GGFMLCQDLRSLSATLPIIFLT 81 >gnl|CDD|179626 PRK03660, PRK03660, anti-sigma F factor; Provisional. Length = 146 Score = 35.7 bits (83), Expect = 0.045 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 6/71 (8%) Query: 578 TKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYILPES 637 ++ + + V D G G+ DI E + +P +TTK E +G+G +V+ + + + ES Sbjct: 71 EEEELEITVRDEGKGI-EDIEEAM-QPLYTTKPELERSGMGFTVMESFMDE----VEVES 124 Query: 638 EVGKGTIFRIF 648 E GKGT R+ Sbjct: 125 EPGKGTTVRMK 135 >gnl|CDD|182431 PRK10403, PRK10403, transcriptional regulator NarP; Provisional. Length = 215 Score = 35.6 bits (82), Expect = 0.049 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 4/70 (5%) Query: 684 VLLVEDEDSVRRGSKRMLET--RGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMD 741 VL+V+D +RRG +++LE V EA G A+ + +L D+++ D+ M M Sbjct: 9 VLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLD--PDVILLDLNMKGMS 66 Query: 742 GPTLLRELRK 751 G L LR+ Sbjct: 67 GLDTLNALRR 76 >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 = 35.7 bits (82), Expect = 0.055 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 6/68 (8%) Query: 580 DMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYILPESEV 639 V + V D GIG+ +E+ EP +T+K E +G+G +V+ + + +SE Sbjct: 73 HEVYITVRDEGIGIEN--LEEAREPLYTSKPELERSGMGFTVMENFMDD----VSVDSEK 126 Query: 640 GKGTIFRI 647 KGT + Sbjct: 127 EKGTKIIM 134 >gnl|CDD|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase BaeS; Provisional. Length = 466 Score = 35.0 bits (81), Expect = 0.081 Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 4/58 (6%) Query: 580 DMVLVEVEDTGIGMSPDIMEKIFEPFFTTK----KVGEGTGLGLSVVYGIIRQSGGYI 633 + + D+ G+S + ++K+FE F+ T+ + G+GLGL++ I+ G I Sbjct: 383 KTLRLTFADSAPGVSDEQLQKLFERFYRTEGSRNRASGGSGLGLAICLNIVEAHNGRI 440 >gnl|CDD|182388 PRK10337, PRK10337, sensor protein QseC; Provisional. Length = 449 Score = 34.2 bits (79), Expect = 0.14 Identities = 50/182 (27%), Positives = 79/182 (43%), Gaps = 37/182 (20%) Query: 459 LMEIKHNANRAAILVRQLLAFSRKQTMRLTVLNLTEVIGNLRMMIQKLISEPPQVKLTVD 518 L+++ +RA LV QLL SR + L L I L ++Q + Sbjct: 276 LLQLHAGIDRATRLVDQLLTLSRLDS--LDNLQDVAEI-PLEDLLQSAVM---------- 322 Query: 519 YERDLWGVKTDLSQFEQVLVNLCVNAHHAIMLKESGSLTVRTRNIPSTEIHTFNYSDLPT 578 D++ +Q + V L +NAH I + L++ RN+ I YS P Sbjct: 323 ---DIYH----TAQQAGIDVRLTLNAHPVIRTGQPLLLSLLVRNLLDNAIR---YS--PQ 370 Query: 579 KDMVLV-------EVEDTGIGMSPDIMEKIFEPFFTTKKVGE---GTGLGLSVVYGIIRQ 628 +V V V D G G++P+ + +I E F+ + G+ G+GLGLS+V I + Sbjct: 371 GSVVDVTLNARNFTVRDNGPGVTPEALARIGERFY--RPPGQEATGSGLGLSIVRRIAKL 428 Query: 629 SG 630 G Sbjct: 429 HG 430 >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 = 33.5 bits (77), Expect = 0.19 Identities = 13/40 (32%), Positives = 17/40 (42%) Query: 166 LDHSPVGFMSADHQGKILYINATLAEWIGIDLTTFTSKSI 205 L+ P G D G+ILY N E +G KS+ Sbjct: 7 LESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSL 46 Score = 32.8 bits (75), Expect = 0.36 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 1/65 (1%) Query: 289 RFNRFFNNIPMAIASIDKKGRILRTNAHFLKLFPNCTEGDGTSNDIFSIVHKNEKRKIIA 348 R ++P I +D GRIL N +L + + + ++H ++ ++ Sbjct: 2 RLRAILESLPDGIFVLDLDGRILYANPAAEELL-GYSPEELIGKSLLELIHPEDREEVQE 60 Query: 349 ALYDA 353 AL Sbjct: 61 ALQRL 65 >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 = 32.6 bits (75), Expect = 0.39 Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 6/43 (13%) Query: 152 QEKFFRELQNAIDYLDHSPVGFMSADHQGKILYINATLAEWIG 194 E+ +R + + SP + D +G ILY+N E G Sbjct: 1 SEERYRAI------FESSPDAIIVIDLEGNILYVNPAFEEIFG 37 Score = 30.7 bits (70), Expect = 1.6 Identities = 34/134 (25%), Positives = 53/134 (39%), Gaps = 25/134 (18%) Query: 28 LETIFMDSEPEGILITNERGHIIYANNAYNALTNAVWNKRTKSLESLLSRNQ-----EAS 82 IF +S P+ I++ + G+I+Y N A+ + S E L+ RN E Sbjct: 5 YRAIF-ESSPDAIIVIDLEGNILYVNPAFEEIFGY-------SAEELIGRNVLELIPEED 56 Query: 83 EALYRLINSLRLKSEG---SEEFRLMQSLNNYSQNSEPHWYRLKARVLPISLHKEKLLYA 139 R L+ E SEE R+ + + ++ V PI + +L Sbjct: 57 REEVRERIERLLEGEREPVSEERRV--------RRKDGSEIWVEVSVSPIRTNGGELGVV 108 Query: 140 WRITDITSERKDQE 153 + DIT ERK E Sbjct: 109 GIVRDIT-ERKQAE 121 Score = 29.2 bits (66), Expect = 4.9 Identities = 13/33 (39%), Positives = 18/33 (54%) Query: 289 RFNRFFNNIPMAIASIDKKGRILRTNAHFLKLF 321 R+ F + P AI ID +G IL N F ++F Sbjct: 4 RYRAIFESSPDAIIVIDLEGNILYVNPAFEEIF 36 >gnl|CDD|182702 PRK10755, PRK10755, sensor protein BasS/PmrB; Provisional. Length = 356 Score = 32.2 bits (74), Expect = 0.52 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 1/73 (1%) Query: 580 DMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIR-QSGGYILPESE 638 ++ VED G G+ ++ + F G GLGLS+V I + G + L + Sbjct: 278 GGAVLAVEDEGPGIDESKCGELSKAFVRMDSRYGGIGLGLSIVSRITQLHHGQFFLQNRQ 337 Query: 639 VGKGTIFRIFLPR 651 GT ++LP+ Sbjct: 338 ERSGTRAWVWLPK 350 >gnl|CDD|161941 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 312 Score = 32.2 bits (74), Expect = 0.57 Identities = 9/27 (33%), Positives = 14/27 (51%) Query: 583 LVEVEDTGIGMSPDIMEKIFEPFFTTK 609 L+EV D G G+ + + E T+K Sbjct: 53 LIEVSDNGSGIDKEDLPLACERHATSK 79 >gnl|CDD|178599 PLN03029, PLN03029, type-a response regulator protein; Provisional. Length = 222 Score = 31.5 bits (71), Expect = 0.76 Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 20/102 (19%) Query: 677 LTGNSAI-VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVM-------------- 721 +T S VL V+D R+ +++L+T Y V SG+ ALK + Sbjct: 3 ITTESQFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPS 62 Query: 722 ----EKLQGRVDIVISDVVMPEMDGPTLLRELRKTYPSLKFI 759 + V+++I+D MP M G LL++++++ SL+ I Sbjct: 63 VSPNSHQEVEVNLIITDYCMPGMTGYDLLKKIKES-SSLRNI 103 >gnl|CDD|132434 TIGR03393, indolpyr_decarb, indolepyruvate decarboxylase, Erwinia family. A family of closely related, thiamine pyrophosphate-dependent enzymes includes indolepyruvate decarboxylase (EC 4.1.1.74), phenylpyruvate decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC 4.1.1.1), branched-chain alpha-ketoacid decarboxylase, etc.. Members of this group of homologs may overlap in specificity. Within the larger family, this model represents a clade of bacterial indolepyruvate decarboxylases, part of a pathway for biosynthesis of the plant hormone indole-3-acetic acid. Typically, these species interact with plants, as pathogens or as beneficial, root-associated bacteria. Length = 539 Score = 31.8 bits (72), Expect = 0.77 Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 38/111 (34%) Query: 677 LTGNSAIVLLVEDEDSVRRGSKRM----LETRGYTVHEAFSGTD---------------- 716 L G+ + L +++ S+ R + L GYTV A G + Sbjct: 428 LIGDGSAQLTIQELGSMLRDKQHPIILVLNNEGYTVERAIHGAEQRYNDIALWNWTHLPQ 487 Query: 717 AL------------------KVMEKLQGRVDIVISDVVMPEMDGPTLLREL 749 AL V+EK+ + + +VV+P+ D P LL L Sbjct: 488 ALSLDPQSECWRVSEAEQLADVLEKVAAHERLSLIEVVLPKADIPPLLGAL 538 >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 = 31.6 bits (72), Expect = 0.81 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 5/73 (6%) Query: 583 LVEVEDTGIGMSPDIMEKIFEPFFT----TKKVGEGTGLGLSVVYGIIRQSGGYILPESE 638 L+ V + G + D+ E++F+ + + GLGL +V I G I E+ Sbjct: 631 LLTVSNEGPPLPEDMGEQLFDSMVSVRDQGAQDQPHLGLGLYIVRLIADFHQGRIQAENR 690 Query: 639 V-GKGTIFRIFLP 650 G +FRI LP Sbjct: 691 QQNDGVVFRISLP 703 >gnl|CDD|182754 PRK10815, PRK10815, sensor protein PhoQ; Provisional. Length = 485 Score = 31.1 bits (71), Expect = 1.3 Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 1/72 (1%) Query: 578 TKDMVLVEVEDTGIGMSPDIMEKIFEPFFTTKKVGEGTGLGLSVVYGIIRQSGGYIL-PE 636 T + + + VED G G+ E IF+ + G GLGLSV I Q G I + Sbjct: 405 TDEHLHIVVEDDGPGIPESKRELIFDRGQRADTLRPGQGLGLSVAREITEQYEGKISAGD 464 Query: 637 SEVGKGTIFRIF 648 S +G + IF Sbjct: 465 SPLGGARMEVIF 476 >gnl|CDD|182660 PRK10701, PRK10701, DNA-binding transcriptional regulator RstA; Provisional. Length = 240 Score = 30.8 bits (70), Expect = 1.6 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%) Query: 714 GTDALKVMEKLQGRVDIVISDVVMPEMDGPTLLRELRKTYP 754 G A + + Q D+V+ D+++P DG T+ R+LR + Sbjct: 34 GDRAEATILREQP--DLVLLDIMLPGKDGMTICRDLRPKWQ 72 >gnl|CDD|162672 TIGR02040, PpsR-CrtJ, transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954). Length = 442 Score = 30.2 bits (68), Expect = 2.0 Identities = 13/46 (28%), Positives = 18/46 (39%) Query: 275 NCDSGDPSGTIANMRFNRFFNNIPMAIASIDKKGRILRTNAHFLKL 320 + P G + R ++ P AI D G I N FL+L Sbjct: 239 PAGATQPVGDELSENLARLYHEAPDAIVFSDADGTIRGANEAFLEL 284 >gnl|CDD|177538 PHA03136, PHA03136, thymidine kinase; Provisional. Length = 378 Score = 30.1 bits (67), Expect = 2.2 Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 4/46 (8%) Query: 200 FTSKSISIGDITAGEGLALIQAIRTEPSHQKITTLDLD----LRRI 241 F + G + G+ +ALI I EP I +DLD RI Sbjct: 164 FPAAQFLSGALEFGDLIALISGIPDEPHGGNIVIMDLDECEHAERI 209 >gnl|CDD|179773 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated. Length = 535 Score = 29.9 bits (68), Expect = 2.5 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 14/54 (25%) Query: 579 KDMVLVEVEDTGIGMSPDIMEKIF-EPFFTTKKVGEGTGLGLSVVYGIIRQSGG 631 KD V VED G G+ P+ + K+F + + +K + +RQS G Sbjct: 72 KDHYRVTVEDNGPGIPPEEIPKVFGKLLYGSK-------------FHNLRQSRG 112 >gnl|CDD|152018 pfam11582, DUF3240, Protein of unknown function (DUF3240). This family of proteins with unknown function appears to be restricted to Proteobacteria. Length = 100 Score = 29.9 bits (68), Expect = 3.0 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 3/61 (4%) Query: 703 TRGYTVHEA--FSGTDAL-KVMEKLQGRVDIVISDVVMPEMDGPTLLRELRKTYPSLKFI 759 G+T+ A AL + E+++G D V ++V+P D LL LR Sbjct: 28 VSGFTLLPAAGHGREHALFDIAEQVRGYRDAVAVEIVLPAADLEELLAHLRAANAHTPIR 87 Query: 760 F 760 + Sbjct: 88 Y 88 >gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR; Provisional. Length = 638 Score = 29.6 bits (67), Expect = 3.0 Identities = 10/35 (28%), Positives = 20/35 (57%) Query: 172 GFMSADHQGKILYINATLAEWIGIDLTTFTSKSIS 206 G ++ D QG + ++NA A + +D T ++I+ Sbjct: 215 GVIAWDEQGNLQFLNAQAARLLRLDATASQGRAIT 249 >gnl|CDD|182591 PRK10618, PRK10618, phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional. Length = 894 Score = 29.5 bits (67), Expect = 3.5 Identities = 41/175 (23%), Positives = 70/175 (40%), Gaps = 33/175 (18%) Query: 579 KDMVLVEVEDTGIGMSPDIMEKIFEPFFT---TKKVGEGTGLGLSVVYGIIRQSGGYILP 635 D + + + DTG G+S ++ + PF + G+ +GL + + R+ GG++ Sbjct: 597 PDRLTIRILDTGAGVSIKELDNLHFPFLNQTQGDRYGKASGLTFFLCNQLCRKLGGHLTI 656 Query: 636 ESEVGKGTIFRIFLPRYVQEHTQESHYSHDIAIIPQEEPADLTGNSAIVLLVEDEDSVRR 695 +S G GT + I L + E +EE L G + ++ + +E VR+ Sbjct: 657 KSREGLGTRYSIHLK--MLAADPEV---------EEEEEKLLDGVTVLLDITSEE--VRK 703 Query: 696 GSKRMLETRG---YTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPE-MDGPTLL 746 R LE G T E + DI ++D P + TLL Sbjct: 704 IVTRQLENWGATCITPDERLISQEY-----------DIFLTD--NPSNLTASTLL 745 >gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional. Length = 254 Score = 29.4 bits (66), Expect = 4.2 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 8/56 (14%) Query: 379 ISATLDRSTEAPEEQAILYTVEITEQKALEARMAQTQKLNAVGTL-----AGGIAH 429 ++ T + EA +AI ++T + L A +A+T+ +G L A GIA+ Sbjct: 46 LAETAEH-IEAAGRRAIQIAADVTSKADLRAAVARTE--AELGALTLAVNAAGIAN 98 >gnl|CDD|184877 PRK14877, PRK14877, conjugal transfer mating pair stabilization protein TraN; Provisional. Length = 1062 Score = 28.9 bits (64), Expect = 5.5 Identities = 13/31 (41%), Positives = 19/31 (61%) Query: 185 INATLAEWIGIDLTTFTSKSISIGDITAGEG 215 +NA L +W G D T+ S S ++G+ TA G Sbjct: 721 VNAQLIKWTGGDTGTWASMSNAVGEWTASAG 751 >gnl|CDD|182771 PRK10840, PRK10840, transcriptional regulator RcsB; Provisional. Length = 216 Score = 28.6 bits (64), Expect = 5.9 Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 7/88 (7%) Query: 680 NSAIVLLVEDEDSVRRGSKRMLETRGY--TVHEAFSGTDALKVMEKLQGRVDIVISDVVM 737 N+ V++ +D V G ++ LE + V E T + + KL ++I+D+ M Sbjct: 2 NNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLD--AHVLITDLSM 59 Query: 738 P---EMDGPTLLRELRKTYPSLKFIFIS 762 P DG TL++ +++ +PSL I ++ Sbjct: 60 PGDKYGDGITLIKYIKRHFPSLSIIVLT 87 >gnl|CDD|149000 pfam07701, HNOBA, Heme NO binding associated. The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals. Length = 209 Score = 28.3 bits (64), Expect = 7.4 Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 1/47 (2%) Query: 293 FFNNIPMAIASIDKKGRILRTNAHFLKLFPNCTEGDGTSNDIFSIVH 339 F P + D+ I++ L++ P G D+F +V Sbjct: 13 FCKAFPFHLV-FDRDMEIVQAGEGLLRVLPKLLLGKKKLTDVFELVR 58 >gnl|CDD|128518 smart00222, Sec7, Sec7 domain. Domain named after the S. cerevisiae SEC7 gene product, which is required for proper protein transport through the Golgi. The domain facilitates guanine nucleotide exchange on the small GTPases, ARFs (ADP ribosylation factors). Length = 187 Score = 28.4 bits (64), Expect = 7.6 Identities = 24/124 (19%), Positives = 42/124 (33%), Gaps = 22/124 (17%) Query: 12 LLAIGSIEMTIKPK------IPLETIFMDSEPE--GILITNER------GHIIYANNAYN 57 LL+ GS++ KPK + D + L NE G + ++ +N Sbjct: 5 LLSEGSVKFNDKPKKGIDSLQEKGFLAKDDPQDVADFLSKNEGLNKKAIGDYLGEHDEFN 64 Query: 58 ALTNAVWNKRTKSLESLLSRNQEASEALYRLINSLRLKSEGSEEFRLMQ--SLNNYSQNS 115 V + + ++ +AL + S RL E + RL++ S N Sbjct: 65 ---RLVLHAFVDLFDF---SAKDLDQALREFLESFRLPGEAQKIDRLLEAFSSRYCECNP 118 Query: 116 EPHW 119 Sbjct: 119 SVFS 122 >gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed. Length = 790 Score = 28.1 bits (62), Expect = 8.3 Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 5/96 (5%) Query: 549 MLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMVLVEVEDTGI-GMSPDIMEKIFEPFFT 607 ML E +V +P+ TF DL +++ + E + SP + F+ + Sbjct: 650 MLAEELRYSVIREVLPTRRARTF---DLEVEELHTLVAEGVVVHNCSPPFKQAEFDILYG 706 Query: 608 TKKVGEGTGLGLSVVYGIIRQSGGYILPESE-VGKG 642 EG+ + + V G+IR+SG + E E +G+G Sbjct: 707 KGISREGSLIDMGVDQGLIRKSGAWFTYEGEQLGQG 742 >gnl|CDD|116029 pfam07407, Seadorna_VP6, Seadornavirus VP6 protein. This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown. Length = 420 Score = 28.1 bits (62), Expect = 8.6 Identities = 32/130 (24%), Positives = 53/130 (40%), Gaps = 6/130 (4%) Query: 548 IMLKESGSLTVRTRNIPSTEIHTFNYSDLPTKDMV-LVEVEDTGIGMSPDIMEKIFEPFF 606 L+E + + T+IH SD T D+V +E+ D IM+K+ EP Sbjct: 35 AALREENAKLKKENEALKTKIHRLE-SDWTTSDIVEKIELMDAQFDRIGKIMDKMREPML 93 Query: 607 TTKKVGEGTGLGLSVVYGIIRQSGGYILPESEVGKGTIFRIFLPRYVQEHTQESHYSHDI 666 + E G L+ V G++R SEV + + RY + T++ + I Sbjct: 94 FKRDDIELHGDLLARVEGLLRIKN----ERSEVEFDKDIQCIVGRYFSDETKQRNLEKMI 149 Query: 667 AIIPQEEPAD 676 ++ AD Sbjct: 150 KSFEYDDIAD 159 >gnl|CDD|182755 PRK10816, PRK10816, DNA-binding transcriptional regulator PhoP; Provisional. Length = 223 Score = 28.2 bits (63), Expect = 9.8 Identities = 30/123 (24%), Positives = 57/123 (46%), Gaps = 8/123 (6%) Query: 684 VLLVEDEDSVRRGSKRMLETRGYTVHEAFSGTDALKVMEKLQGRVDIVISDVVMPEMDGP 743 VL+VED +R K L+ G+ V A +A + + DI I D+ +P+ DG Sbjct: 3 VLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLN--EHLPDIAIVDLGLPDEDGL 60 Query: 744 TLLRELRK---TYPSLKFIFISGYAEDAFSKNLPKDAKFSFLSKPFSLKQLATSVHELLQ 800 +L+R R + P L + + + D +++KPF ++++ + L++ Sbjct: 61 SLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGAD---DYVTKPFHIEEVMARMQALMR 117 Query: 801 SDS 803 +S Sbjct: 118 RNS 120 >gnl|CDD|181722 PRK09243, PRK09243, nicotinate phosphoribosyltransferase; Validated. Length = 464 Score = 28.2 bits (64), Expect = 9.9 Identities = 8/33 (24%), Positives = 18/33 (54%), Gaps = 1/33 (3%) Query: 219 IQAIRTEPSHQKITTLDLDLRRIDNGHGIPVKI 251 ++ IR + ++ +L + +R+ N H PV + Sbjct: 429 LEEIR-AYAAAQLASLPEEYKRLLNPHAYPVDL 460 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 0.318 0.134 0.379 Gapped Lambda K H 0.267 0.0664 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 12,867,350 Number of extensions: 855597 Number of successful extensions: 1920 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1828 Number of HSP's successfully gapped: 108 Length of query: 803 Length of database: 5,994,473 Length adjustment: 101 Effective length of query: 702 Effective length of database: 3,812,065 Effective search space: 2676069630 Effective search space used: 2676069630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 61 (27.4 bits)