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)