BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.


Reference for composition-based statistics starting in round 2:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= gi|254780916|ref|YP_003065329.1| putative sigma-54-dependent
transcription regulator protein [Candidatus Liberibacter asiaticus
str. psy62]
         (482 letters)

Database: nr 
           14,124,377 sequences; 4,842,793,630 total letters

Searching..................................................done


Results from round 1


>gi|254780916|ref|YP_003065329.1| putative sigma-54-dependent transcription regulator protein
           [Candidatus Liberibacter asiaticus str. psy62]
 gi|254040593|gb|ACT57389.1| putative sigma-54-dependent transcription regulator protein
           [Candidatus Liberibacter asiaticus str. psy62]
          Length = 482

 Score =  976 bits (2524), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 482/482 (100%), Positives = 482/482 (100%)

Query: 1   MPRKKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSL 60
           MPRKKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSL
Sbjct: 1   MPRKKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSL 60

Query: 61  INCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSI 120
           INCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSI
Sbjct: 61  INCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSI 120

Query: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
           ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS
Sbjct: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLE 240
           RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLE
Sbjct: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLE 240

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY
Sbjct: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE
Sbjct: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ
Sbjct: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
           ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD
Sbjct: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480

Query: 481 SL 482
           SL
Sbjct: 481 SL 482


>gi|315122736|ref|YP_004063225.1| putative sigma-54-dependent transcription regulator protein
           [Candidatus Liberibacter solanacearum CLso-ZC1]
 gi|313496138|gb|ADR52737.1| putative sigma-54-dependent transcription regulator protein
           [Candidatus Liberibacter solanacearum CLso-ZC1]
          Length = 494

 Score =  558 bits (1438), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 295/496 (59%), Positives = 376/496 (75%), Gaps = 16/496 (3%)

Query: 1   MPRKKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV----SDLSTISKIQVNVI 56
           M  K+SLD  + +LIID+DDEQ  +IK+++ESYGYDVFI++V     DL  + KI+V+VI
Sbjct: 1   MHIKRSLDDRQGLLIIDQDDEQSNLIKEYMESYGYDVFIIDVLSQCPDLLVLDKIKVDVI 60

Query: 57  FLSLINCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQL 116
           FLSLIN  DDK  +L+ IV+K+P +PIIVQT  D +KIL   L +RI K F N VS++ L
Sbjct: 61  FLSLINFGDDKGKVLQTIVEKMPNIPIIVQTKHDELKILISSLQDRIPKCFFNPVSQEHL 120

Query: 117 CDSIICAL-REGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
             SI   L R+    ++E ++  LDSLIAVS  MIQV++LARKA  C IP+MI+GEFGVG
Sbjct: 121 FYSIRSILERKKNSSAEEQKYFTLDSLIAVSSEMIQVINLARKAVYCTIPVMIEGEFGVG 180

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           KK L+  IH SG RA FPF +VNCG+ DQDK+EK LFG VDLQ +NS  FLGKF+EANGG
Sbjct: 181 KKTLAHSIHASGSRASFPFVVVNCGISDQDKVEKDLFGKVDLQGENSTYFLGKFVEANGG 240

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           TI+LEEP AL L VQ +I +FIETGKIEF DSR A++LDVRLIF TEKNL  +VK+ VF 
Sbjct: 241 TILLEEPSALSLKVQRKILHFIETGKIEFDDSRNALKLDVRLIFATEKNLFQEVKNQVFS 300

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           KDLYY+IS+F   I TLRSR +DIPWL  FFL+ FC +N ++QI++S+KALS+LT Y W 
Sbjct: 301 KDLYYKISIFSCKIPTLRSRQDDIPWLARFFLKRFCLENNVQQINLSEKALSMLTHYKWT 360

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACT----CYTE---- 407
           DNVQEL+NI+LR+V+G+KDS++TED F  LL   G +E+E ++ T+ T    C  +    
Sbjct: 361 DNVQELENIILRSVVGIKDSYITEDCFTSLLFEAGNQEKEINSNTSETFDIYCMQDENNN 420

Query: 408 -GKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
             +SS+ +  ++S+ +I +I + GE+RRLSDIEKE+I LAMKLYR QMSEVARRLGIGRS
Sbjct: 421 IPQSSNYL--SISKGTIFSIDKYGEIRRLSDIEKEMIRLAMKLYREQMSEVARRLGIGRS 478

Query: 467 TLYRKIREYNIEVDSL 482
           TLYRKI+EYNIEVD+L
Sbjct: 479 TLYRKIKEYNIEVDTL 494


>gi|227823368|ref|YP_002827340.1| sigma-54 dependent DNA-binding response regulator [Sinorhizobium
           fredii NGR234]
 gi|227342369|gb|ACP26587.1| sigma-54 dependent DNA-binding response regulator [Sinorhizobium
           fredii NGR234]
          Length = 514

 Score =  292 bits (747), Expect = 9e-77,   Method: Compositional matrix adjust.
 Identities = 174/504 (34%), Positives = 282/504 (55%), Gaps = 35/504 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISK--IQVNVIFLSLINCEDDKE 68
           +L+ID D  Q +++ + +E  G+   + +   S L  + +    +NVI L L+  E +  
Sbjct: 5   ILVIDDDPVQRRLLTNMIERLGHVAHLADNGRSGLELLERKGGMINVILLDLLMPEMNGH 64

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL---- 124
             L+ + ++    P+IVQT Q  I+ +   +      F +  VS ++L  +I  AL    
Sbjct: 65  GFLEALAERGIDTPVIVQTGQGGIETVVQAMQAGAFDFLVKPVSPERLSIAIGNALKMAS 124

Query: 125 REGVVPSQENEHCA---LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           R+G V +           D +++ SPAMI+V+DLAR+A    IP++++GE GVGK+ ++R
Sbjct: 125 RDGRVKTARRPRGGAIGFDDIVSASPAMIRVLDLARRAAQSNIPVVLEGESGVGKEMVAR 184

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            I  +  RA  PF  VNCG I  + +E  LFG +    T  + +  GKF++A+GGT+ L+
Sbjct: 185 AIQAASDRASKPFVTVNCGAIPHNLVESILFGHEKGAFTGATEKHSGKFVDADGGTLFLD 244

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL VQ ++   ++ G+IE   +R   R++VRLI  T K+L+ +V+   FR+DLYY
Sbjct: 245 EIGDLPLEVQVKLLRAVQQGEIETVGARQPQRVNVRLISATNKDLINEVREGRFREDLYY 304

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISISDKALSLLTKYPWIDNVQ 359
           R++VF I I  LR R EDIP LV  F++ F  +  + Q +++S  A++LLT Y W  N++
Sbjct: 305 RLNVFPITIPALRRRKEDIPVLVRAFVERFTAEQRLNQPVTVSSGAMALLTAYDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLT----------------EDRFVLLLSREGKKEREFHTETACT 403
           +L+N + RAV+  +   LT                 DR        G + R     TA  
Sbjct: 365 QLENAIFRAVVLAEGGELTVKDFPQIATQIPGYVVADRSGFSWGEAGPERRPPAGATATV 424

Query: 404 CYTE------GKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEV 457
             +        +    + +  S+ +I ++ + GEVR+L+++E+E+I  A+K YR QMS+V
Sbjct: 425 LPSRPDIPERSEPFGPVPEGRSENAIASVDEGGEVRKLAEVEEELIRFALKFYRGQMSQV 484

Query: 458 ARRLGIGRSTLYRKIREYNIEVDS 481
           AR+LGIGRSTLYRK+++Y I+ D+
Sbjct: 485 ARKLGIGRSTLYRKLKDYGIDPDN 508


>gi|15966548|ref|NP_386901.1| putative sigma-54-dependent transcription regulator protein
           [Sinorhizobium meliloti 1021]
 gi|307300415|ref|ZP_07580195.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sinorhizobium meliloti BL225C]
 gi|307318280|ref|ZP_07597715.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sinorhizobium meliloti AK83]
 gi|15075819|emb|CAC47374.1| Putative sigma-54-dependent transcription regulator [Sinorhizobium
           meliloti 1021]
 gi|306895962|gb|EFN26713.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sinorhizobium meliloti AK83]
 gi|306904581|gb|EFN35165.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sinorhizobium meliloti BL225C]
          Length = 513

 Score =  291 bits (745), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 174/505 (34%), Positives = 286/505 (56%), Gaps = 38/505 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ-----VNVIFLSLINCEDDK 67
           +L+ID D  Q +++ + +E  G+   + + +  S +  +Q     +NVI L L+  E + 
Sbjct: 5   ILVIDDDPVQRRLLTNMIERLGHVAHLAD-NGRSGLELLQRKGGIINVILLDLLMPEMNG 63

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLC----DSIICA 123
             +L+ + ++   +P+IVQT Q  I+ +   +      F +  VS ++L     +++  A
Sbjct: 64  HGLLEALAERGIDIPVIVQTGQGGIETVVQAMQAGAFDFLVKPVSPERLSIALGNALKMA 123

Query: 124 LREGVVPSQENEH---CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            R+G V +           D +++ SPAMI+V+DLAR+A    IPI+++GE GVGK+ ++
Sbjct: 124 SRDGKVKTARRPRGGAVGFDDIVSASPAMIRVIDLARRAAQSNIPIVLEGESGVGKEMVA 183

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R I  +  RA  PF  VNCG I  + +E  LFG +    T  S +  GKF++A+GGT+ L
Sbjct: 184 RAIQAASDRAAKPFVTVNCGAIPHNLVESILFGHEKGAFTGASEKHSGKFVDADGGTLFL 243

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL VQ ++   ++ G+IE   +R   +++VRLI  T K+L+ +V+   FR+DLY
Sbjct: 244 DEIGDLPLDVQVKLLRAVQQGEIETIGARQPQKVNVRLISATNKDLITEVREGRFREDLY 303

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISISDKALSLLTKYPWIDNV 358
           YR++VF I I  LR R EDIP LV  F++ F  +  + Q +++S  A++LLT Y W  N+
Sbjct: 304 YRLNVFPITIPALRRRKEDIPVLVRAFVERFSAEQRLDQRLTVSSGAMALLTSYDWPGNI 363

Query: 359 QELKNILLRAVIGLKDSH-----------------LTEDRFVLLLSREGKKEREFHTETA 401
           ++L+N + RAV+ L D H                 +  DR  L     G + R    + A
Sbjct: 364 RQLENAIFRAVV-LADGHELTVRDFPQVATQIPGYIVADRSGLSWGEAGPERRPASGQLA 422

Query: 402 CTCYT-----EGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSE 456
                     +   S+   +   + +I ++ + GEVR+L+++E+E+I  A+K YR QMS+
Sbjct: 423 AAQADAGAREQPAHSEQTPEGRLENAIASLSEGGEVRKLAEVEEELIRFALKFYRGQMSQ 482

Query: 457 VARRLGIGRSTLYRKIREYNIEVDS 481
           VAR+LGIGRSTLYRK+++Y I+ D+
Sbjct: 483 VARKLGIGRSTLYRKLKDYGIDPDN 507


>gi|86359139|ref|YP_471031.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Rhizobium etli CFN 42]
 gi|86283241|gb|ABC92304.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Rhizobium etli CFN 42]
          Length = 513

 Score =  290 bits (743), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 178/505 (35%), Positives = 292/505 (57%), Gaps = 44/505 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQV-------NVIFLSLINCE 64
           ++L+++ D  Q +++K+ +E +G+   +V+ ++   I    V       NVI L L+  E
Sbjct: 12  QILVVEDDPVQRRLLKNAIERHGH---VVHQAENGRIGLEMVKRDSGLFNVIVLDLMMPE 68

Query: 65  DDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
                 L  + +    +P+IVQT Q  I+ +   +      F +  VS +++  SI  A+
Sbjct: 69  MTGLEFLDALHEFGTQIPVIVQTGQGGIETVVQAMRAGAFDFVVKPVSPERIATSISNAM 128

Query: 125 R--EGVVPSQENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
           +  +  V ++            D +++ SPAMI+V+DLA++A    IP++++GE GVGK+
Sbjct: 129 KLDQREVKARAGRRSRAGSVGFDDIVSASPAMIRVIDLAQRAAQSNIPVVLEGESGVGKE 188

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            ++R I   G+R+  PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT
Sbjct: 189 LVARAIQSGGERSNKPFVTVNCGAIPHNLVESILFGHEKGAFTGATERHIGKFMEADGGT 248

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           I L+E   LPL VQ ++   ++ G+IE   +R A +++VRLI  T K+L+ +VK+  FR+
Sbjct: 249 IFLDEIGDLPLEVQVKLLRAVQQGEIETVGARTAHKVNVRLISATNKDLIEEVKNGHFRE 308

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCT--KNAIKQISISDKALSLLTKYPW 354
           DLYYR++VF I I  LR R EDIP LV  F   F +  KN  ++++++  AL+LLT Y W
Sbjct: 309 DLYYRLNVFPITIPALRKRKEDIPHLVRVFADRFSSEQKNG-RRMTVNSGALALLTAYDW 367

Query: 355 IDNVQELKNILLRAVIGLKDSHLTE----------------DRFVLLLSREGKKEREFHT 398
             N+++L+N + RAV+  +   LTE                D   L+    G +  E ++
Sbjct: 368 PGNIRQLENAIFRAVVLAEGPELTEADFPQIAAQLPEYEVVDHLALVADNTGLEPDEAYS 427

Query: 399 ET--ACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSE 456
           E   A T +   + S+T     S+ +I ++   G+VR+L+D+E+E+I  A+K YR QMS+
Sbjct: 428 EEYRAPTEFHHHRLSET-----SENAIASVNPSGDVRKLADVEEELIRFALKFYRGQMSQ 482

Query: 457 VARRLGIGRSTLYRKIREYNIEVDS 481
           VAR+LGIGRSTLYRK+++Y I+ D+
Sbjct: 483 VARKLGIGRSTLYRKLKDYGIDPDN 507


>gi|150397881|ref|YP_001328348.1| two component sigma54 specific Fis family transcriptional regulator
           [Sinorhizobium medicae WSM419]
 gi|150029396|gb|ABR61513.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sinorhizobium medicae WSM419]
          Length = 549

 Score =  288 bits (737), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 172/503 (34%), Positives = 282/503 (56%), Gaps = 36/503 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ-----VNVIFLSLINCEDDK 67
           +L+ID D  Q +++ + +E  G+   + + +  S +  +Q     +NVI L L+    + 
Sbjct: 43  ILVIDDDPVQRRLLTNMIERLGHVAHLAD-NGRSGLELMQRKGGIINVILLDLLMPGMNG 101

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLC----DSIICA 123
            + L+ + ++    P+IVQT Q  I+ +   +      F +  VS ++L     +++  A
Sbjct: 102 HSFLEALAERGVDTPVIVQTGQGGIETVVQAMQAGAFDFLVKPVSPERLSIALGNALKMA 161

Query: 124 LREGVVPSQENEH---CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            R+G V +           D +++ SPAMI+V+DLAR+A    IP++++GE GVGK+ ++
Sbjct: 162 SRDGKVKTARRPRGGSVGFDDIVSASPAMIRVIDLARRAAQSNIPVVLEGESGVGKEMVA 221

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R I  +  RA  PF  VNCG I  + +E  LFG +    T  S +  GKF++A+GGT+ L
Sbjct: 222 RAIQAASDRATKPFVTVNCGAIPGNLVESILFGHEKGAFTGASEKHSGKFVDADGGTLFL 281

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL VQ ++   ++ G+IE   +R   +++VRLI  T K+L+ +V+   FR+DLY
Sbjct: 282 DEIGDLPLEVQVKLLRAVQQGEIETVGARQPQKVNVRLISATNKDLINEVREGRFREDLY 341

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISISDKALSLLTKYPWIDNV 358
           YR++VF I I  LR R EDIP LV  F++ F  +  + Q +++S+ A++LLT Y W  N+
Sbjct: 342 YRLNVFPITIPALRRRKEDIPVLVRAFVERFAAEQRLDQRLTVSNGAMALLTSYDWPGNI 401

Query: 359 QELKNILLRAVIGLKDSH-----------------LTEDRFVLLLSREGKKEREFHTETA 401
           ++L+N + RAV+ L + H                 +  DR  L     G + R      A
Sbjct: 402 RQLENAIFRAVV-LAEGHELTVRDFPQVATQIPGYIVADRTGLSWGDGGPEGRTAPDRPA 460

Query: 402 CTCYTEGKSSDTILDNLSQE---SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVA 458
                 G       D   +    +I ++ + GEVR+L+++E+E+I  A+K YR QMS+VA
Sbjct: 461 AVTADAGALETAPTDQRDERIENAIASLSEGGEVRKLAEVEEELIRFALKFYRGQMSQVA 520

Query: 459 RRLGIGRSTLYRKIREYNIEVDS 481
           R+LGIGRSTLYRK+++Y I+ D+
Sbjct: 521 RKLGIGRSTLYRKLKDYGIDPDN 543


>gi|209550871|ref|YP_002282788.1| Fis family transcriptional regulator [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536627|gb|ACI56562.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhizobium leguminosarum bv. trifolii WSM2304]
          Length = 514

 Score =  286 bits (733), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 176/503 (34%), Positives = 287/503 (57%), Gaps = 39/503 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQV-------NVIFLSLINCE 64
           ++L+++ D  Q +++K+ +E +G+   +V+ ++   I    V       NVI L L+  E
Sbjct: 12  QILVVEDDPVQRRLLKNAIERHGH---VVHQAENGRIGLEMVKRDSGLFNVIVLDLMMPE 68

Query: 65  DDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
                 L  + +    +P+IVQT Q  I+ +   +      F +  VS +++  SI  A+
Sbjct: 69  MTGLEFLDALHEFGTQIPVIVQTGQGGIETVVQAMRAGAFDFVVKPVSPERIATSISNAM 128

Query: 125 R--EGVVPSQENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
           +  +  V ++            D +++ SPAM++V+DLA++A    IP++++GE GVGK+
Sbjct: 129 KLDQREVKARAGRRSRSGSVGFDDIVSASPAMLRVIDLAQRAAQSNIPVVLEGESGVGKE 188

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            ++R I   G R+  PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT
Sbjct: 189 LVARAIQSGGDRSNKPFVTVNCGAIPHNLVESILFGHEKGAFTGATERHIGKFMEADGGT 248

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           I L+E   LPL VQ ++   ++ G+IE   +R A +++VRLI  T K+L+ +VK+  FR+
Sbjct: 249 IFLDEIGDLPLEVQVKLLRAVQQGEIETVGARTAHKVNVRLISATNKDLIEEVKNGHFRE 308

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCT--KNAIKQISISDKALSLLTKYPW 354
           DLYYR++VF I I  LR R EDIP LV  F + F +  KN  ++++++  AL+LLT Y W
Sbjct: 309 DLYYRLNVFPITIPALRKRKEDIPHLVRVFAERFSSEQKNG-RRMTVNAGALALLTAYDW 367

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
             N+++L+N + RAV+  +   LTE  F  + ++    E E     A      G   D  
Sbjct: 368 PGNIRQLENAIFRAVVLAEGPELTEGDFPQIAAQ--LPEYEVVDHLALVADNTGLDPDDS 425

Query: 415 ----------------LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVA 458
                           L  +S+ +I ++   G+VRRL+D+E+E+I  A+K YR QMS+VA
Sbjct: 426 YGEEFRASISGEVHHRLSEVSENAIASVNPAGDVRRLADVEEELIRFALKFYRGQMSQVA 485

Query: 459 RRLGIGRSTLYRKIREYNIEVDS 481
           R+LGIGRSTLYRK+++Y I+ D+
Sbjct: 486 RKLGIGRSTLYRKLKDYGIDPDN 508


>gi|190893375|ref|YP_001979917.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Rhizobium etli CIAT 652]
 gi|190698654|gb|ACE92739.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Rhizobium etli CIAT 652]
 gi|327188781|gb|EGE55975.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Rhizobium etli CNPAF512]
          Length = 513

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 175/502 (34%), Positives = 286/502 (56%), Gaps = 38/502 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQV-------NVIFLSLINCE 64
           ++L+++ D  Q +++K+ +E +G+   +V+ ++   I    V       NVI L L+  E
Sbjct: 12  QILVVEDDPVQRRLLKNAIERHGH---VVHQAENGRIGLEMVKRDSGLFNVIVLDLMMPE 68

Query: 65  DDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
                 L  + +    +P+IVQT Q  I+ +   +      F +  VS +++  SI  A+
Sbjct: 69  MTGLEFLDALHEFGTQIPVIVQTGQGGIETVVQAMRAGAFDFVVKPVSPERIATSISNAM 128

Query: 125 R--EGVVPSQENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
           +  +  V ++            D +++ SPAM++V+DLA++A    IP++++GE GVGK+
Sbjct: 129 KLDQREVKARAGRRSRSGSVGFDDIVSASPAMLRVIDLAQRAAQSNIPVVLEGESGVGKE 188

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            ++R I   G+R+  PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT
Sbjct: 189 LVARAIQSGGERSNKPFVTVNCGAIPHNLVESILFGHEKGAFTGATERHIGKFMEADGGT 248

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           I L+E   LPL VQ ++   ++ G+IE   +R A +++VRLI  T K+L+ +VK+  FR+
Sbjct: 249 IFLDEIGDLPLEVQVKLLRAVQQGEIETVGARTAHKVNVRLISATNKDLIEEVKNGHFRE 308

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCT--KNAIKQISISDKALSLLTKYPW 354
           DLYYR++VF I I  LR R EDIP LV  F   F +  KN  ++++++  AL+LLT Y W
Sbjct: 309 DLYYRLNVFPITIPALRKRKEDIPHLVRVFADRFSSEQKNG-RRMTVNSGALALLTAYDW 367

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
             N+++L+N + RAV+  +   LTE  F  + ++    E E     A      G  +D  
Sbjct: 368 PGNIRQLENAIFRAVVLAEGPELTEADFPQIAAQ--LPEYEVVDHLALVADNTGLDADEA 425

Query: 415 ---------------LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVAR 459
                          L   S  +I ++   G+VR+L+D+E+E+I  A+K YR QMS+VAR
Sbjct: 426 YSEEYRAPPEVHHHRLSEASDNAIASVNPSGDVRKLADVEEELIRFALKFYRGQMSQVAR 485

Query: 460 RLGIGRSTLYRKIREYNIEVDS 481
           +LGIGRSTLYRK+++Y I+ D+
Sbjct: 486 KLGIGRSTLYRKLKDYGIDPDN 507


>gi|241206285|ref|YP_002977381.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhizobium leguminosarum bv. trifolii WSM1325]
 gi|240860175|gb|ACS57842.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhizobium leguminosarum bv. trifolii WSM1325]
          Length = 515

 Score =  281 bits (719), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 173/503 (34%), Positives = 284/503 (56%), Gaps = 38/503 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQV-------NVIFLSLINCE 64
           ++L+++ D  Q +++K+ +E +G+   +V+ ++   I    V       NVI L L+  E
Sbjct: 12  QILVVEDDPVQRRLLKNAIERHGH---VVHQAENGRIGLEMVKRDSGLFNVIVLDLMMPE 68

Query: 65  DDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
                 L  + +    +P+IVQT Q  I+ +   +      F +  VS +++  SI  A+
Sbjct: 69  MTGLEFLDALHEFGTQIPVIVQTGQGGIETVVQAMRAGAFDFVVKPVSPERIATSISNAM 128

Query: 125 R--EGVVPSQENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
           +  +  V ++            D +++ SPAM++V+DLA++A    IP++++GE GVGK+
Sbjct: 129 KLDQREVKARAGRRSRSGSVGFDDIVSASPAMLRVIDLAQRAAQSNIPVVLEGESGVGKE 188

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            ++R I   G R+  PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT
Sbjct: 189 LVARAIQSGGDRSNKPFVTVNCGAIPHNLVESILFGHEKGAFTGATERHIGKFMEADGGT 248

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           I L+E   LPL VQ ++   ++ G+IE   +R A +++VRLI  T K+L+ +VK+  FR+
Sbjct: 249 IFLDEIGDLPLEVQVKLLRAVQQGEIETVGARTAHKVNVRLISATNKDLIEEVKNGHFRE 308

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCT--KNAIKQISISDKALSLLTKYPW 354
           DLYYR++VF I I  LR R EDIP LV  F   F +  KN  ++++++   L+LLT Y W
Sbjct: 309 DLYYRLNVFPITIPALRKRKEDIPHLVRVFADRFSSEQKNG-RRMTVNAGTLALLTAYDW 367

Query: 355 IDNVQELKNILLRAVIGLKDSHLTE----------------DRFVLLLSREGKKEREFHT 398
             N+++L+N + RAV+  +   LTE                D   L+    G      + 
Sbjct: 368 PGNIRQLENAIFRAVVLAEGPELTEADFPQIAAQLPEYDVVDHLALVADNTGLDPDNGYG 427

Query: 399 ETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVA 458
           E      + G+     L   S+ +I ++   G+VR+L+D+E+E+I  A+K YR QMS+VA
Sbjct: 428 EDFRASMS-GEVHHHRLSEASENAIASVNPAGDVRKLADVEEELIRFALKFYRGQMSQVA 486

Query: 459 RRLGIGRSTLYRKIREYNIEVDS 481
           R+LGIGRSTLYRK+++Y I+ D+
Sbjct: 487 RKLGIGRSTLYRKLKDYGIDPDN 509


>gi|116253805|ref|YP_769643.1| two-component response regulator [Rhizobium leguminosarum bv.
           viciae 3841]
 gi|115258453|emb|CAK09556.1| putative two-component response regulator with sigma 54 interacting
           domain transcriptional regulatory protein [Rhizobium
           leguminosarum bv. viciae 3841]
          Length = 494

 Score =  274 bits (701), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 171/493 (34%), Positives = 277/493 (56%), Gaps = 39/493 (7%)

Query: 22  QIKIIKDHVESYGYDVFIVNVSDLSTISKIQV-------NVIFLSLINCEDDKENILKNI 74
           Q +++K+ +E +G+   +V+ ++   I    V       NVI L L+  E      L  +
Sbjct: 2   QRRLLKNAIERHGH---VVHQAENGRIGLEMVKRDSGLFNVIVLDLMMPEMTGLEFLDAL 58

Query: 75  VDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR--EGVVPSQ 132
            +    +P+IVQT Q  I+ +   +      F +  VS +++  SI  A++  +  V ++
Sbjct: 59  HEFGTQIPVIVQTGQGGIETVVQAMRAGAFDFVVKPVSPERIATSISNAMKLDQREVKAR 118

Query: 133 ENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
                       D +++ SPAM++V+DLA++A    IP++++GE GVGK+ ++R I   G
Sbjct: 119 AGRRSRSGSVGFDDIVSASPAMLRVIDLAQRAAQSNIPVVLEGESGVGKELVARAIQSGG 178

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGTI L+E   LP
Sbjct: 179 DRSNKPFVTVNCGAIPHNLVESILFGHEKGAFTGATERHIGKFMEADGGTIFLDEIGDLP 238

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
           L VQ ++   ++ G+IE   +R A +++VRLI  T K+L+ +VK+  FR+DLYYR++VF 
Sbjct: 239 LEVQVKLLRAVQQGEIETVGARTAHKVNVRLISATNKDLIEEVKNGHFREDLYYRLNVFP 298

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCT--KNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
           I I  LR R EDIP LV  F   F +  KN  ++++++   L+LLT Y W  N+++L+N 
Sbjct: 299 ITIPALRKRKEDIPHLVRVFADRFSSEQKNG-RRMTVNAGTLALLTAYDWPGNIRQLENA 357

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI---------- 414
           + RAV+  +   LTE  F  + ++    E +     A      G   D            
Sbjct: 358 IFRAVVLAEGPELTEADFPQIAAQ--LPEYDVVDHLALVADNTGLDPDNGYGEDFRASMS 415

Query: 415 ------LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
                 L   S+ +I ++   G+VR+L+D+E+E+I  A+K YR QMS+VAR+LGIGRSTL
Sbjct: 416 GEVHHRLSEASENAIASVNPAGDVRKLADVEEELIRFALKFYRGQMSQVARKLGIGRSTL 475

Query: 469 YRKIREYNIEVDS 481
           YRK+++Y I+ D+
Sbjct: 476 YRKLKDYGIDPDN 488


>gi|332716497|ref|YP_004443963.1| sigma 54 dependent transcriptional activator [Agrobacterium sp.
           H13-3]
 gi|325063182|gb|ADY66872.1| sigma 54 dependent transcriptional activator [Agrobacterium sp.
           H13-3]
          Length = 514

 Score =  273 bits (698), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 173/503 (34%), Positives = 276/503 (54%), Gaps = 35/503 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKI--QVNVIFLSLINCEDDKE 68
           VL+ID D  Q +++K+ VE YG+   +     + L  + +   ++NV+ L L+  E D  
Sbjct: 5   VLVIDDDPVQRRLLKNAVERYGHLALLAENGRAGLELLKQYSGEINVVVLDLMMPEMDGL 64

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL---- 124
             LK + +    VP+IVQT Q  I  +   +      F +  VS +++  +I  AL    
Sbjct: 65  AFLKAVGELGTDVPVIVQTGQGGIDTVVQAMRAGAFDFVVKPVSPERIGAAISNALKLDR 124

Query: 125 REGVVPSQE---NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           RE    +     +       +++ SPAM++V++LA++A   +IP++++GE GVGK+ ++R
Sbjct: 125 REAKARTGRRGRSNAVNFTDIVSASPAMLRVIELAQRAAQSSIPVVLEGESGVGKEMVAR 184

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            I  +G RA  PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT+ L+
Sbjct: 185 AIQSAGDRANKPFITVNCGAIPHNLVESILFGHEKGAFTGATEKHVGKFMEADGGTLFLD 244

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL VQ ++   ++ G+IE   S    +++VRLI  T KNL+ +VK   FR+DLYY
Sbjct: 245 EIGDLPLDVQVKLLRAVQQGEIETVGSARVQKVNVRLISATNKNLIEEVKEGRFREDLYY 304

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISISDKALSLLTKYPWIDNVQ 359
           R++VF I I  LR R EDIP L   F + F  +  +   + +   AL+LLT Y W  N++
Sbjct: 305 RLNVFPITIPALRRRKEDIPHLARVFAERFSVEQKLPNPVGLDASALALLTAYDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRF---VLLLSREGKKEREFHTETACTCYT---------- 406
           +L+N + RAV+  +   L +  F    L L     ++    +  + +  +          
Sbjct: 365 QLENAVFRAVVLSQGEELADSDFPQIALQLPEFAGRDDAGESIRSPSGSSLKLAAYSPPP 424

Query: 407 EGKSSDTILDNLSQES---------IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEV 457
               S  ILD  S  S         I ++   G +R+L++IE+E+I  A++ YR QMS+V
Sbjct: 425 PAAESHAILDEASDISTTIYRGGNLISSMDDSGNIRKLAEIEEELIRFALRFYRGQMSQV 484

Query: 458 ARRLGIGRSTLYRKIREYNIEVD 480
           AR+LGIGRSTLYRK+++Y I+ D
Sbjct: 485 ARKLGIGRSTLYRKLKDYGIDPD 507


>gi|110635065|ref|YP_675273.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Mesorhizobium sp. BNC1]
 gi|110286049|gb|ABG64108.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Chelativorans sp. BNC1]
          Length = 505

 Score =  272 bits (696), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 168/492 (34%), Positives = 270/492 (54%), Gaps = 31/492 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLI----NC 63
           VLI+D D  Q++++   V   GY   + +  +     L+ +   ++  + L L+    N 
Sbjct: 5   VLIVDDDPVQLRLLDAAVRRLGYAPVLADGGEAALRILAEVRPEELRAVILDLMMPGMNG 64

Query: 64  EDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICA 123
            +  E + K  +D    +P+IVQT    ++     +      F +  VS ++L  ++  A
Sbjct: 65  IEVMETMRKRGID----MPVIVQTATGGVETAVAAMRAGAFDFVVKPVSPERLAAALKNA 120

Query: 124 LREGVVPSQEN-------EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
           L+   +  Q+        +  +   ++  SPAM +V+ LA++A    IPI+I+GE GVGK
Sbjct: 121 LKVEALEGQQRRKREKAPDKFSFRHIVTRSPAMEKVLRLAQRAAASDIPILIEGESGVGK 180

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGG 235
           + ++R +     R   PF  VNCG I  + +E  LFG +    T  + +  GKF+EANGG
Sbjct: 181 ELIARAVRNESARRGKPFVTVNCGAIPDNLVESILFGHEKGAFTGATEKHSGKFVEANGG 240

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T+ L+E   LPL VQ ++   ++ G+++    RG +++D+RLI  T ++LL +V+   FR
Sbjct: 241 TLFLDEIGELPLDVQVKLLRAVQEGEVDPVGRRGTVKVDIRLISATNRDLLQRVREGRFR 300

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
           +DLYYR+ VF I +  LR R +DIP LV +F+  F      + IS IS  A+ LL+ Y W
Sbjct: 301 EDLYYRLGVFPITVPPLRERRDDIPLLVQYFIAQFGDATTGRNISGISSDAIKLLSAYDW 360

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKE-------REFHTETACTCYT 406
             NV++L+N + RA++    + LT   F  + ++ EG  E       +  H E+A     
Sbjct: 361 PGNVRQLENAVFRAMVLCDGTVLTAAEFPQIRAQVEGIDEKLLADEIKPAHQESAPPPQP 420

Query: 407 EGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
           + K+S   +  L    +P IG+DG VR L ++E+E+I  A++ Y  +MSEVARRLGIGRS
Sbjct: 421 D-KASQQEMQPLHPALLPVIGEDGNVRPLEEMEREMIQFAIEHYDGRMSEVARRLGIGRS 479

Query: 467 TLYRKIREYNIE 478
           TLYRK++E  IE
Sbjct: 480 TLYRKLKEMGIE 491


>gi|163758859|ref|ZP_02165946.1| putative sigma-54-dependent transcription regulator protein
           [Hoeflea phototrophica DFL-43]
 gi|162284149|gb|EDQ34433.1| putative sigma-54-dependent transcription regulator protein
           [Hoeflea phototrophica DFL-43]
          Length = 504

 Score =  272 bits (695), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 165/497 (33%), Positives = 271/497 (54%), Gaps = 30/497 (6%)

Query: 14  LIIDKDDEQIKIIKDHVESYGY--DVFIVNVSDLSTI--SKIQVNVIFLSLINCEDDKEN 69
           +I+D D  Q +++K   E+ G+  ++F    + L  +      ++ + L L+  E     
Sbjct: 1   MIVDDDPVQRRLLKAAGEAAGHTCEMFDNGRAALERLMSDGPAIDALVLDLMMPEMGGLE 60

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL---RE 126
           +L+ +      +P+IVQT+   I+++   +      F +  VS ++L  SI  AL   R 
Sbjct: 61  VLERLTAAKSRIPVIVQTSHGGIEMVVKAMRAGAFDFVVKPVSPERLALSIANALKATRT 120

Query: 127 GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES 186
            V P   +       ++A SP+M +V+ LAR+A    IP++++GE GVGK+ ++R I   
Sbjct: 121 PVAPRARSRAAGFGGIVAASPSMDRVISLARRAAGSGIPVVLEGESGVGKEMIARAIQAE 180

Query: 187 GKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDAL 245
             R   PF  VNCG I ++ +E  LFG +    T  S + +GKF EA+GGT+ L+E   L
Sbjct: 181 SARRSKPFVTVNCGAIPENLVESILFGHEKGAFTGASERHVGKFSEADGGTLFLDEIGEL 240

Query: 246 PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF 305
           P+ VQ ++   ++ G+IE   +R   ++DVRLI  T K+L+ +VK+  FR+DLYYR++VF
Sbjct: 241 PVEVQVKLLRAVQMGEIETVGARQTQKVDVRLISATNKDLIEEVKAGRFREDLYYRLNVF 300

Query: 306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWIDNVQELKNI 364
            I++  LR R EDIP LV  F+  F ++   + I+ I   A++L+T + W  N++EL+N 
Sbjct: 301 PIHVPALRKRKEDIPQLVRHFIARFSSETLSQNITGIVPDAMALVTGHDWPGNIRELENA 360

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSR------EGKKEREFHTETACTCYTEGKSSDTILDNL 418
           + RA++      LT D F  + ++         +   F T+      +        +  L
Sbjct: 361 IHRAIVLCDGGLLTRDLFPQIEAQMPGYKLASSEMSGFETDDQSAAESGPSGGHQTMAAL 420

Query: 419 ---------------SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGI 463
                          ++ ++ A+  DGEVR +++IE+E+I  A+  Y  QMSEVARRLGI
Sbjct: 421 HDSAPTTPERQYIEPARPAVDAVSVDGEVRPIAEIEEELIRFALSFYHGQMSEVARRLGI 480

Query: 464 GRSTLYRKIREYNIEVD 480
           GRSTLYRK+++Y I+ D
Sbjct: 481 GRSTLYRKLKDYAIDPD 497


>gi|15891186|ref|NP_356858.1| sigma 54 dependent transcriptional activator [Agrobacterium
           tumefaciens str. C58]
 gi|15159542|gb|AAK89643.1| sigma 54 dependent transcriptional activator [Agrobacterium
           tumefaciens str. C58]
          Length = 513

 Score =  272 bits (695), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 173/502 (34%), Positives = 276/502 (54%), Gaps = 34/502 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKI--QVNVIFLSLINCEDDKE 68
           VL+ID D  Q +++K+ VE YG+   +     + L  + +   ++NVI L L+  E D  
Sbjct: 5   VLVIDDDPVQRRLLKNAVERYGHLALLAENGRAGLELLKQYSGEINVIVLDLMMPEMDGL 64

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR--- 125
             LK + +    VP+IVQT Q  I  +   +      F +  VS +++  +I  AL+   
Sbjct: 65  AFLKAVGELGTDVPVIVQTGQGGIDTVVQAMRAGAFDFVVKPVSPERIGAAISNALKLDR 124

Query: 126 --EGVVPSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
                   +     A++   +++ SPAM++V++LA++A   +IP++++GE GVGK+ ++R
Sbjct: 125 KEAKARTGRRGRSNAVNFTDIVSASPAMLRVIELAQRAAQSSIPVVLEGESGVGKEMVAR 184

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            I   G RA  PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT+ L+
Sbjct: 185 AIQSGGDRANKPFITVNCGAIPHNLVESILFGHEKGAFTGATEKHVGKFMEADGGTLFLD 244

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL VQ ++   ++ G+IE   S    +++VRLI  T KNL+ +VK   FR+DLYY
Sbjct: 245 EIGDLPLDVQVKLLRAVQQGEIETVGSARVQKVNVRLISATNKNLIEEVKEGRFREDLYY 304

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISISDKALSLLTKYPWIDNVQ 359
           R++VF I I  LR R EDIP L   F + F  +  +   + +   AL+LLT Y W  N++
Sbjct: 305 RLNVFPITIPALRRRKEDIPHLARVFAERFSAEQKLPNPVGLDASALALLTAYDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRF---VLLLSR-----EG----KKEREFHTETACTCYTE 407
           +L+N + RAV+  + S L++  F    L L       +G    +       + A      
Sbjct: 365 QLENAVFRAVVLSQGSELSDSDFPQIALQLPEFSNGDDGDDIIRSPSGSSLKLAAYSPPP 424

Query: 408 GKSSDTILDNLSQES---------IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVA 458
              S  +++  S  S         I +    G +R+L++IE+E+I  A++ YR QMS+VA
Sbjct: 425 AAESHAVIEEPSDISTTIYRGGNLISSTDDSGNIRKLAEIEEELIRFALRFYRGQMSQVA 484

Query: 459 RRLGIGRSTLYRKIREYNIEVD 480
           R+LGIGRSTLYRK+++Y I+ D
Sbjct: 485 RKLGIGRSTLYRKLKDYGIDPD 506


>gi|222087065|ref|YP_002545600.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Agrobacterium radiobacter K84]
 gi|221724513|gb|ACM27669.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Agrobacterium radiobacter K84]
          Length = 502

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 168/465 (36%), Positives = 256/465 (55%), Gaps = 36/465 (7%)

Query: 52  QVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLV 111
           Q+NVI L L+  E +   +L  + D    +P+IVQT Q  I+ +   +      F +  V
Sbjct: 31  QINVIVLDLMMPEMNGLELLGALSDMGTDIPVIVQTGQGGIETVVQAMRAGAFDFVVKPV 90

Query: 112 SRKQLCDSIICAL----REGVVPS---QENEHCALDSLIAVSPAMIQVVDLARKAGDCAI 164
           S +++  SI  AL    RE    +     +   + D +++ SPAM++V+DLA +A    I
Sbjct: 91  SPERIGASIANALKLDQREAKARAGRKSRSSAISFDDIVSASPAMMRVLDLAHRASQSNI 150

Query: 165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSA 223
           P++++GE GVGK+ ++R I  +  RA  PF  VNCG I  + +E  LFG +    T  + 
Sbjct: 151 PVVLEGESGVGKELVARAIQAASDRAGKPFVTVNCGAIPHNLVESILFGHEKGAFTGATE 210

Query: 224 QFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEK 283
           + +GKF+EA+GGT+ L+E   LPL VQ ++   ++ G+IE   +R A +++VRLI  T K
Sbjct: 211 RHVGKFMEADGGTLFLDEVGDLPLEVQVKLLRAVQQGEIETVGARVAQKVNVRLISATNK 270

Query: 284 NLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISIS 342
           +L+ +VK+  FR+DLYYR++VF I +  LR R EDIP L   F   F  +  +   ++IS
Sbjct: 271 DLIEEVKAGRFREDLYYRLNVFPITMPALRRRKEDIPHLARAFADRFAFEQKLGHSLAIS 330

Query: 343 DKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKEREFHTETA 401
             AL+LLT Y W  N+++L+N + RAV+  +   L E  F  + ++  G    E  T   
Sbjct: 331 HGALALLTSYDWPGNIRQLENAVFRAVVLSEGPELLETDFPQIAAQLPGYFTGEHPTLVV 390

Query: 402 CTCYTEGKSS--------------------------DTILDNLSQESIPAIGQDGEVRRL 435
               T G  S                          DT     S   I +    G+VR+L
Sbjct: 391 DNSQTYGADSVGADRFERGLRVASSEETTTSPLSIVDTSSAQASDNVIVSTDTSGDVRKL 450

Query: 436 SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
           +D+E+E+I  A+K YR QMS+VAR+LGIGRSTLYRK+++Y I+ D
Sbjct: 451 ADVEEELIRFALKFYRGQMSQVARKLGIGRSTLYRKLKDYGIDPD 495


>gi|319781623|ref|YP_004141099.1| sigma-54 factor interaction domain-containing protein
           [Mesorhizobium ciceri biovar biserrulae WSM1271]
 gi|317167511|gb|ADV11049.1| sigma-54 factor interaction domain-containing protein
           [Mesorhizobium ciceri biovar biserrulae WSM1271]
          Length = 511

 Score =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 173/502 (34%), Positives = 265/502 (52%), Gaps = 36/502 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI+D D  Q ++++  V  +GY   +V+        L      +V+V+ L L+    D 
Sbjct: 5   ILIVDDDPVQRRLLEAAVTRFGYSAIVVDGGAAALDILDGPGAREVSVVILDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-- 125
             +LK + ++   VP IVQT Q  I+ +   + +    F +   S  +L  SI  AL+  
Sbjct: 65  IGVLKAMRERDINVPAIVQTAQGGIETVVSAMRHGAFDFVVKPASPDRLQASIGNALKVE 124

Query: 126 --EGVVPSQENEHCAL---DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
             EG V         L     +I  SPAM +V+ L +KA    IPI+I+GE GVGK+ ++
Sbjct: 125 AVEGEVKRTSRRRGGLLTFKDMITHSPAMDRVIRLGQKAAASNIPILIEGESGVGKELVA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R I  SG R   PF  VNCG I  + +E  LFG      T  + +  GKF+EA+ GT+ L
Sbjct: 185 RAIQGSGDRRTKPFVTVNCGAIPDNLVESILFGHEKGSFTGATDKHTGKFVEAHSGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL VQ ++   ++ G+++    R  +R+D+RLI  T +NLL QVK   FR+DL+
Sbjct: 245 DEIGDLPLDVQVKLLRAVQDGEVDPVGGRSTVRVDIRLISATHRNLLQQVKDGKFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI-SISDKALSLLTKYPWIDNV 358
           YR++V+ I +  LR R +DIP+LV  F++     +  +++  IS  AL++L  Y W  N+
Sbjct: 305 YRLNVYPIFVPPLRDRRDDIPYLVTHFMEKVAPADPHRRLQGISAAALAVLQAYDWPGNI 364

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKEREFHTETACTCYTEGKSSDTILDN 417
           ++L+N + RA +  +   LT + F  + ++ EG    +   +            D   + 
Sbjct: 365 RQLENAVFRASVLCEGDMLTAEDFPQIRAQVEGTVNLDMDGDAPSPSLPLQARDD---EA 421

Query: 418 LSQESIPAIGQD------------------GEVRRLSDIEKEIIGLAMKLYRAQMSEVAR 459
           L  E  PAI  D                  G VR L+D+E E+I LA+  Y  QMSEVAR
Sbjct: 422 LPGEGGPAIAFDPPARLQPRFGTLRALDERGNVRALADVELEMIKLAIDHYNGQMSEVAR 481

Query: 460 RLGIGRSTLYRKIREYNIEVDS 481
           RLGIGRSTLYRK++E+ I+ ++
Sbjct: 482 RLGIGRSTLYRKLKEHGIDPET 503


>gi|260460648|ref|ZP_05808899.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Mesorhizobium opportunistum WSM2075]
 gi|259033753|gb|EEW35013.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Mesorhizobium opportunistum WSM2075]
          Length = 528

 Score =  261 bits (666), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 170/502 (33%), Positives = 267/502 (53%), Gaps = 33/502 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI+D D  Q ++++  V  +G+   + +        L       V+V+ L L+    D 
Sbjct: 19  ILIVDDDPVQRRLLEAAVTRFGHTAIVADGGAAGLEVLDGPGTRDVSVVILDLVMPGLDG 78

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-- 125
             +LK + ++   VP+IVQT Q  I+ +   + +    F +   S  +L  +I  AL+  
Sbjct: 79  IGVLKAMRERDISVPVIVQTAQGGIETVVSAMRHGAFDFVVKPASPDRLQAAIANALKVE 138

Query: 126 --EGVVPSQENEHCAL---DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
             EG V     +   L     +I  SPAM +V+ L +KA    IPI+I+GE GVGK+ ++
Sbjct: 139 AVEGEVKRTSRKRGGLLTFKDMITHSPAMDRVIRLGQKAAASNIPILIEGESGVGKELVA 198

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R I  SG R   PF  VNCG I  + +E  LFG      T  + +  GKF+EA+ GT+ L
Sbjct: 199 RAIQGSGDRRSKPFVTVNCGAIPDNLVESILFGHEKGSFTGATDKHTGKFVEAHSGTLFL 258

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL VQ ++   ++ G+++    R  +R+D+RLI  T +NLL QVK   FR+DL+
Sbjct: 259 DEIGDLPLDVQVKLLRAVQDGEVDPVGGRATVRVDIRLISATHRNLLQQVKDGKFREDLF 318

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWIDNV 358
           YR++V+ I +  LR R +DIP LV  F++     +   +++ IS  AL++L  Y W  N+
Sbjct: 319 YRLNVYPIFVPPLRDRRDDIPHLVRHFMEKVAPADPRHRLTGISAAALAVLQAYDWPGNI 378

Query: 359 QELKNILLRAVIGLKDSHLTEDRF---------VLLLSREGKKEREFHTETACTCYTEG- 408
           ++L+N + RA +  +   LT D F          + L  +G +E +           E  
Sbjct: 379 RQLENAVFRASVLCEGDVLTVDDFPQIRAQVEGTVNLGTDGDQEADGLAPPPLEPRDEDV 438

Query: 409 KSSDTILDNLSQESI---PAIG------QDGEVRRLSDIEKEIIGLAMKLYRAQMSEVAR 459
              D +  ++  +++   P  G      + G VR L+D+E E+I LA+  Y  QMSEVAR
Sbjct: 439 VPGDAVAASVHDQAVRTQPRFGTVRALDERGNVRALADVELEMIKLAIDHYNGQMSEVAR 498

Query: 460 RLGIGRSTLYRKIREYNIEVDS 481
           RLGIGRSTLYRK++EY I+ ++
Sbjct: 499 RLGIGRSTLYRKLKEYGIDPET 520


>gi|154252497|ref|YP_001413321.1| two component sigma-54 specific Fis family transcriptional
           regulator [Parvibaculum lavamentivorans DS-1]
 gi|154156447|gb|ABS63664.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Parvibaculum lavamentivorans DS-1]
          Length = 511

 Score =  259 bits (663), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 167/505 (33%), Positives = 265/505 (52%), Gaps = 39/505 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI+D D  Q +I+++ V   GY    V+  +     L      +++++ L L+    D 
Sbjct: 5   ILIVDDDPAQRRILEEVVNRDGYRAIPVDGGEAALAYLEGPGGAEISLVILDLVMPGIDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +LK +    P +P+IV T    I+ +   +    S F +  VS ++L  S+  AL+  
Sbjct: 65  MEVLKRVHPNKPNLPVIVLTAHGGIETVVNVMREGASDFVVKPVSPERLHVSMRNALKVN 124

Query: 128 VVPSQ-------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +  +       ++       +IA S AM  V+ L ++A    IPI+I+GE GVGK+ ++
Sbjct: 125 ALTGEISRLQKRKSGQLTFADIIAPSAAMAPVIRLGKRAAQSNIPILIEGESGVGKELIA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
             I   G RA  PF  VNCG I ++ +E  LFG +    T  S +  GKF EA+GGT+ L
Sbjct: 185 AAIQGEGDRAGKPFVTVNCGAIPENLVESILFGHEKGAFTGASDKHAGKFQEASGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++ G+++   S+  +++D+RLI  T + +L  VK   FR+DLY
Sbjct: 245 DEIGELPLDIQVKLLRALQQGEVDPVGSKKPVKVDIRLISATNREMLQMVKEGRFREDLY 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I++  LR R +DIP LV  F++    +     + IS  ALS+L  Y W  NV+
Sbjct: 305 YRLNVFPIHVPPLRERKDDIPELVAHFIRRLAAEEGKPVVGISRDALSMLCAYEWPGNVR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKE-------------------REFHTE 399
           +++N + RA++      L    F  + S  +G +E                       T+
Sbjct: 365 QIENTIFRAIVLCDGEMLEVSDFPQIASMVDGYQEAAMPRAAATTATHAPHAIGEAAATD 424

Query: 400 TACTCY-TEGKSSDTILD----NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQM 454
           T    Y  + + ++T+ D    N S + I    + G VR+L DIE E+I LA+  Y+  M
Sbjct: 425 TGAPLYAAQPQQTNTLADFARSNFS-DGISITDEAGNVRKLEDIEAEMIRLAIDKYKGHM 483

Query: 455 SEVARRLGIGRSTLYRKIREYNIEV 479
           +EVARRLGIGRSTLYRK+RE  +EV
Sbjct: 484 TEVARRLGIGRSTLYRKVREMGLEV 508


>gi|222149715|ref|YP_002550672.1| sigma 54 dependent transcriptional activator [Agrobacterium vitis
           S4]
 gi|221736697|gb|ACM37660.1| sigma 54 dependent transcriptional activator [Agrobacterium vitis
           S4]
          Length = 439

 Score =  259 bits (663), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 155/433 (35%), Positives = 250/433 (57%), Gaps = 32/433 (7%)

Query: 81  VPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-----EGVVPSQENE 135
           +P+IVQT Q  I  +   +      F +  VS +++  +I  ALR         P++ + 
Sbjct: 1   MPVIVQTGQGGIDTVVQAMRAGAFDFVVKPVSPERIASAIGNALRVDQRDAKSRPARRSR 60

Query: 136 HCAL--DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
             A+    +I+ SPAM +V+DL+R+A    IP++++GE GVGK+ ++R I     RA  P
Sbjct: 61  TGAVHFSDIISASPAMTRVIDLSRRAAQSNIPVVLEGESGVGKEMVARAIQSGSDRASRP 120

Query: 194 FFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ-FLGKFIEANGGTIVLEEPDALPLAVQGR 252
           F  VNC  I  + +E  LFG        + +  +GKF EA+GGT+ L+E   LPL  Q +
Sbjct: 121 FVTVNCAAIPANMVESILFGHEKGSFPGATERHIGKFAEADGGTLFLDEIGELPLDTQVK 180

Query: 253 IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTL 312
           +   ++ G+IE   +R   +++VRLI  T K+L+ +VK+  FR+DLYYR++VF I I  L
Sbjct: 181 LLRAVQEGEIEVIGARQTQKVNVRLISATNKDLIEEVKAGRFREDLYYRLNVFPITIPAL 240

Query: 313 RSRSEDIPWLVHFFLQSFCTKNAI-KQISISDKALSLLTKYPWIDNVQELKNILLRAVIG 371
           R R EDIP+L   F + F  +  + + +S+   AL+LLT + W  N+++L+N + RAVI 
Sbjct: 241 RRRKEDIPFLARAFTERFSAEQRLTRTLSLGAGALALLTAFDWPGNIRQLENAIYRAVIL 300

Query: 372 LKDSHLTEDRFVLLLSR--EGKKEREFHTETACTCYTE-----GKSSD----TILDNL-- 418
            + + LTE  F  +L++   G  + +F +    T  ++      + +D      +D L  
Sbjct: 301 AEGTDLTESDFPQILAQIPGGLAQDKFWSGLPGTAESQPEQVAPRGADRPELAFIDRLPA 360

Query: 419 --SQESIP--------AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
             +++  P        +I + G VR+L++IE+E+I  A+K YR QMS+VAR+LGIGRSTL
Sbjct: 361 PRAEDPRPVALDNVIVSIDESGNVRQLAEIEEELIRFALKFYRGQMSQVARKLGIGRSTL 420

Query: 469 YRKIREYNIEVDS 481
           YRK+++Y I+ D+
Sbjct: 421 YRKLKDYGIDPDN 433


>gi|114571083|ref|YP_757763.1| two component sigma54 specific Fis family transcriptional regulator
           [Maricaulis maris MCS10]
 gi|114341545|gb|ABI66825.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Maricaulis maris MCS10]
          Length = 487

 Score =  259 bits (662), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 167/488 (34%), Positives = 266/488 (54%), Gaps = 23/488 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
           K VLI+D D  Q ++++  +E  GY        +  L  +++  ++V+ L LI    D  
Sbjct: 3   KSVLIVDDDPTQRRLLQAVIEKQGYRAETAESGEAALDRVAEPGIDVMLLDLIMPGMDGM 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR--- 125
             L+ +  K P +P+IV T    I+ +   +      FF+   S +++  SI  AL+   
Sbjct: 63  ETLEALKRKQPDLPVIVLTASGGIETVVAAMRAGAVDFFVKPASPERITVSIRNALKVQN 122

Query: 126 -EGVVP--SQENEHC-ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
             G V   S++ E       +IA +P M QVV L  +A    IPI+I GE GVGK+ ++ 
Sbjct: 123 LSGEVKRLSRKAEGTLGFADMIAGAPTMRQVVRLGERAAQSDIPILITGESGVGKELVAG 182

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            I  + KRA  PF  VNCG I ++ +E  LFG +    T    + +GKF EA+GGT+ L+
Sbjct: 183 SIMAASKRAGGPFVAVNCGAIPENLVESTLFGHEKGAFTGAVGKHMGKFQEADGGTLFLD 242

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL +Q ++   ++ G+++    +  ++++VR+I  T ++L  QV +  FR+DL+Y
Sbjct: 243 EIGELPLDMQVKLLRALQEGEVDPVGGKRPVKVNVRIISATNRDLAEQVAAGAFREDLFY 302

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKAL---SLLTKYPWIDN 357
           R++VF I + +LRSR +DIP LV  F+  F   NA +  SI D A    +LL+ Y W  N
Sbjct: 303 RLNVFPIEVPSLRSRKDDIPALVRHFIGRF---NAQENKSIQDAAPETHALLSTYDWPGN 359

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           V++L+N + RAV+   D HL  + F  +         +           E  +S    D+
Sbjct: 360 VRQLENAVFRAVVLSDDDHLKPEDFPQISG----LTPQIGEMPDTGALAEIANSVAARDS 415

Query: 418 LSQESIPAI---GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
            + E +  +    + G +R L +IE+++I  A++ Y  +MSEVARRLG+GRSTLYRK+RE
Sbjct: 416 SAAEDLGPVDIMDEGGHLRSLEEIERDLIEFAIETYAGRMSEVARRLGVGRSTLYRKVRE 475

Query: 475 YNIEVDSL 482
           Y ++VD +
Sbjct: 476 YELDVDGV 483


>gi|13472640|ref|NP_104207.1| response regulatory protein [Mesorhizobium loti MAFF303099]
 gi|14023386|dbj|BAB49993.1| response regulatory protein [Mesorhizobium loti MAFF303099]
          Length = 511

 Score =  258 bits (659), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 172/503 (34%), Positives = 269/503 (53%), Gaps = 38/503 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI+D D  Q ++++  V  +G+   +V+  +     L       + V+ L L+    D 
Sbjct: 5   ILIVDDDPVQRRLLEAAVTRFGHTAIVVDGGEAGLDALDGPGARDICVVILDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-- 125
             +LK + ++   VP+IVQT Q  I+ +   + +    F +   S  +L  SI  AL+  
Sbjct: 65  IGVLKAMRERDITVPVIVQTAQGGIETVVLAMRHGAFDFVVKPASPDRLQASIANALKVE 124

Query: 126 --EGVVPSQENEHCAL---DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
             EG V     +   L     +I  SPAM +V+ L +KA   +IPI+I+GE GVGK+ ++
Sbjct: 125 AVEGEVKRTSRKRGGLLTFRDMITHSPAMDRVIRLGQKAAGSSIPILIEGESGVGKELVA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R I  SG R   PF  VNCG I  + +E  LFG      T  + +  GKF+EA+ GT+ L
Sbjct: 185 RAIQGSGDRRSKPFVTVNCGAIPDNLVESILFGHEKGSFTGATDKHTGKFVEAHSGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL VQ ++   ++ G+++    R  +++D+RLI  T +NLL QVK   FR+DL+
Sbjct: 245 DEIGDLPLDVQVKLLRAVQEGEVDPVGGRSTVKVDIRLISATHRNLLQQVKDGKFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI-SISDKALSLLTKYPWIDNV 358
           YR++V+ I +  LR R +DIP LV  F++     +  +++  IS  AL++L  Y W  N+
Sbjct: 305 YRLNVYPIFVPPLRDRRDDIPHLVTHFMEKVAPADPRRRLQGISPAALAVLEAYDWPGNI 364

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKEREFHTETACTCYTE--------GK 409
           ++L+N + RA +  +   L  D F  + ++ EG    E  T+ A    +         G 
Sbjct: 365 RQLENAVFRASVLCEGDVLDVDDFPQIRAQVEGTVNLE--TDDAAPRLSSPPELRDEGGP 422

Query: 410 SSDTILDNLSQESIPAIGQD-----------GEVRRLSDIEKEIIGLAMKLYRAQMSEVA 458
           + D      ++   PA+ Q            G VR L+D+E E+I LA+  Y  QMSEVA
Sbjct: 423 AGDDA--PAAEPDRPAVLQPRFGTLRALDERGNVRALADVELEMIKLAIDHYNGQMSEVA 480

Query: 459 RRLGIGRSTLYRKIREYNIEVDS 481
           RRLGIGRSTLYRK++EY I+ ++
Sbjct: 481 RRLGIGRSTLYRKLKEYGIDPET 503


>gi|27382241|ref|NP_773770.1| two-component response regulator [Bradyrhizobium japonicum USDA
           110]
 gi|27355412|dbj|BAC52395.1| two-component response regulator [Bradyrhizobium japonicum USDA
           110]
          Length = 499

 Score =  257 bits (657), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 165/484 (34%), Positives = 250/484 (51%), Gaps = 20/484 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI D D    ++I++ V+  GY+  +V+  D     L+      ++ + L L+    D 
Sbjct: 5   ILIADDDAVARRLIENMVQKCGYETVVVDSGDAAIAALTAPDAPAIDGVILDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L  I +    VP+IVQT    I  +   +    + F +  V  ++L  S+  AL   
Sbjct: 65  MGVLAKIREAGLSVPVIVQTAHGGIDNVISAMRAGAADFVVKPVGMERLQVSLRNALNAS 124

Query: 128 VVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +    Q   H          +I  + AM  V+  A+KA + +IP++I+GE GVGK+  +
Sbjct: 125 ALKGELQRIRHSREGRLTFSDIITRAEAMAGVMRTAQKAANSSIPVLIEGESGVGKEMFA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R IH SG+R   PF  VNCG I  + +E  LFG +    T  + +  GKF+EA+GGT+ L
Sbjct: 185 RAIHGSGERKAKPFVAVNCGAIPDNLVESILFGHEKGAFTGATERHTGKFVEAHGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPLA Q ++   ++ G +E    R  +++DVR+I  T + LL +VK   FR+DL+
Sbjct: 245 DEVSELPLAAQVKLLRALQEGAVEAVGGRKPVKVDVRIISATNRRLLERVKQGHFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + I +LR+R EDIP L+  FL  F  +       IS +A++ L +  W  N++
Sbjct: 305 YRLHVLPLTIPSLRTRREDIPHLLRHFLARFAAEENRTITGISGEAVAHLAQLDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTET------ACTCYTEGKSSDT 413
           +L+N + RAV+  +   L    F LL S+      E  T        A        S   
Sbjct: 365 QLENAVYRAVVMSEGDQLGLGDFPLLASQP-YPATEIPTAPLMLEPIAAPSVVSSGSEIP 423

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
           I    S  ++P +   G+VR L D+E EII  A+  YR QMSEVARRL IGRSTLYRK+ 
Sbjct: 424 IAPLPSVGTLPMLTATGDVRPLEDMENEIIRFAISHYRGQMSEVARRLKIGRSTLYRKLD 483

Query: 474 EYNI 477
           E  +
Sbjct: 484 EAGV 487


>gi|254295294|ref|YP_003061317.1| Fis family trnascriptional regulator [Hirschia baltica ATCC 49814]
 gi|254043825|gb|ACT60620.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Hirschia baltica ATCC 49814]
          Length = 498

 Score =  257 bits (657), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 161/481 (33%), Positives = 263/481 (54%), Gaps = 13/481 (2%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLS----TISKIQVNVIFLSLINCEDD 66
           K VLI+D D  Q ++++  VE  G+   +V   DL+    + +K  ++V+ L LI     
Sbjct: 8   KTVLIVDDDPTQRRLMQAAVERQGFRARLVESGDLALEEASDAKNGISVVLLDLIMPGLS 67

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR- 125
               L+ ++++ P +P+IV T    I  +   +      FF+   S +++  S+  AL+ 
Sbjct: 68  GMETLERLLERRPDLPVIVLTASGGIDTVVQAMRAGAVDFFVKPASPERIVVSLRNALKV 127

Query: 126 ---EGVVP--SQENEHC-ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
               G V   S+++E     D +IA +P M QVV L ++A    IPI+I GE GVGK+  
Sbjct: 128 SDLRGEVKRLSKKSEGTLGFDDMIAGAPLMRQVVRLGQRAAKSNIPILITGESGVGKEVA 187

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           S+ I  + +RA  PF  VNCG I ++ +E  LFG +    T    + LGKF EA+GGT+ 
Sbjct: 188 SQCIQSASERAGKPFITVNCGAIPENLVESILFGHEKGAFTGAHEKKLGKFAEADGGTLF 247

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   LPL +Q ++   ++ G+++   SR   ++DVR+I  T ++L   V    FR+DL
Sbjct: 248 LDEVGELPLDMQVKLLRVLQEGEVDAVGSRKPTKVDVRIISATNRDLAQAVSEGRFREDL 307

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           YYR++VF I + +LR R ED+P LV  F++ F  +  +     S + + ++  + W  NV
Sbjct: 308 YYRLNVFPIEMPSLRDRKEDLPALVDHFIRRFNAQEGMSITGASLETMGMIAAHDWPGNV 367

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNL 418
           ++L+N + RA+I  +   L    F  +       E    T       ++  ++ T L++ 
Sbjct: 368 RQLENSIFRAMILSEGDELQPVDFPHISGLTPNYEI-LKTPNNGASISDAATTATQLNSP 426

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
               +  +  +GE+R L  +E+++I  A+ LY   MS+VARRLGIGRSTLYRK+REY++ 
Sbjct: 427 LGGPVSIVDDNGELRPLESVERDLIQYAIDLYSGHMSQVARRLGIGRSTLYRKVREYDLR 486

Query: 479 V 479
           V
Sbjct: 487 V 487


>gi|90425451|ref|YP_533821.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Rhodopseudomonas palustris BisB18]
 gi|90107465|gb|ABD89502.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhodopseudomonas palustris BisB18]
          Length = 500

 Score =  256 bits (653), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 160/481 (33%), Positives = 250/481 (51%), Gaps = 19/481 (3%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI D D  Q +++++ V+  GY   +V+  D     L+      ++ + L L+    D 
Sbjct: 5   ILIADDDAVQRRLVENMVQKCGYRTVVVDSGDAAIETLTADDAPTIDAVVLDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L+ + D    +P+IVQT    I  +   +    + F +  V  ++L  S+  AL   
Sbjct: 65  MGVLERMRDAGLSIPVIVQTAHGGIDNVVSAMRAGATDFVVKPVGIERLQISLRNALNAS 124

Query: 128 VVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +    Q  +H          L+  S  M  V+ +A++    AIP++I+GE GVGK+ ++
Sbjct: 125 ALKGELQRLKHSRDGKLTFADLVTRSEPMGHVLRMAKRGATSAIPVLIEGESGVGKELIA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R IH S +R+  PF  VNCG I  + +E  LFG +    T  + +  GKF+EA+GGT+ L
Sbjct: 185 RAIHGSSERSAKPFVAVNCGAIPDNLVESILFGHEKGAFTGATERHTGKFVEASGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPLA Q ++   ++ G +E    R  +++DVR+I  T + LL +VK+  FR+DL+
Sbjct: 245 DEVSELPLAAQVKLLRALQEGAVEAVGGRRPLKVDVRIISATNRKLLDRVKAGQFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + I  LR+R EDIP L+  FL  FC +       +S +A++ L +  W  NV+
Sbjct: 305 YRLHVLPLTIPPLRNRREDIPHLLRHFLARFCAEENRTITGVSGEAMARLAQLDWPGNVR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N + RAV+  + +HL    F L  +     E           +           ++ 
Sbjct: 365 QLENAVYRAVVMSEGTHLDLADFPLTAAAPSVAELAGEPLLIEPAFHSTAPQLVAGHDIP 424

Query: 420 QESIPAIGQ------DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
              +PA G       DGEVR L ++E EII  A+  YR QMSEVARRL IGRSTLYRK+ 
Sbjct: 425 IAPMPAAGSLSMLTPDGEVRPLDELESEIIRFAISHYRGQMSEVARRLKIGRSTLYRKLD 484

Query: 474 E 474
           E
Sbjct: 485 E 485


>gi|83859913|ref|ZP_00953433.1| sigma-54 dependent DNA-binding response regulator [Oceanicaulis
           alexandrii HTCC2633]
 gi|83852272|gb|EAP90126.1| sigma-54 dependent DNA-binding response regulator [Oceanicaulis
           alexandrii HTCC2633]
          Length = 498

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 162/497 (32%), Positives = 266/497 (53%), Gaps = 30/497 (6%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGY--DVFIVNVSDLSTISKIQVNVIFLSLINCEDDKE 68
           K VLI+D D  Q ++++  +E  G+  +      + L  + +  V+V+ L ++    D  
Sbjct: 3   KTVLIVDDDPTQRRLMQAVLEKQGHLAETAEDGEAGLERVKRGGVDVVMLDMVMPGMDGI 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR--- 125
             L+ I  + P +P+IV T    I+ +   +      FF+   S +++  SI  AL+   
Sbjct: 63  ETLEAIKARNPDLPVIVLTAHGGIETVVKAMRAGAVDFFVKPASPERIAVSIRNALKVKD 122

Query: 126 -EGVVP---SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
             G V     +         +IA +PAM QVV L  +A    IPI+I GE GVGK+ ++R
Sbjct: 123 LSGEVTRLKKRTTGALGFSDMIAGAPAMRQVVRLGERAAKSNIPILITGESGVGKELVAR 182

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLE 240
            I     RA  PF  VNCG I ++ +E  LFG      T   A+ LGKF EA+GGT+ L+
Sbjct: 183 AIAAGSDRAGRPFVAVNCGAIPENLVESTLFGHEKGSFTGAVAKHLGKFQEADGGTLFLD 242

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL +Q ++   ++ G+++   S+  +++DVR++  T ++L  QVK+  FR+DL+Y
Sbjct: 243 EIGELPLDMQVKLLRALQEGEVDPVGSKRPVKVDVRIVSATNRDLAEQVKTGAFREDLFY 302

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++VF I + +LR R+EDIP LV  F+  F  +     +  + + + +L  + W  NV++
Sbjct: 303 RLNVFPIEVPSLRERTEDIPALVRHFIARFNAQEGKSVLDATAETMHMLANHDWKGNVRQ 362

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYT-------------E 407
           L+N + RAV+     +LTE+ F   +S      R+   ++A                  E
Sbjct: 363 LENAVFRAVVLSDSDYLTEEDFP-QISGLAPTLRDAPIQSAAPAQPAANAVPALPAEQFE 421

Query: 408 GKSSDTILDNLSQESIPA--IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGR 465
           G +     +   +E  P   + + G +R L  IE+++I  A++ Y  +M+EVARRLG+GR
Sbjct: 422 GAAP----NGAEEEHFPVDILDEGGHLRSLESIERDLIAFAIETYSGRMAEVARRLGVGR 477

Query: 466 STLYRKIREYNIEVDSL 482
           STLYRK+REY+++VD+ 
Sbjct: 478 STLYRKVREYDLDVDNF 494


>gi|148258071|ref|YP_001242656.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Bradyrhizobium sp. BTAi1]
 gi|146410244|gb|ABQ38750.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Bradyrhizobium sp. BTAi1]
          Length = 497

 Score =  255 bits (651), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 163/490 (33%), Positives = 252/490 (51%), Gaps = 25/490 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI D D  Q +++++ V+  GY+  +V+  D     L+      ++ I L L+    D 
Sbjct: 5   ILIADDDPVQRRLVENMVQKCGYEAIVVDTGDAVIEKLTHTDAGPIDAIVLDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L  + +    +P+IVQT    I  +   +      F +  V  ++L  S+  AL   
Sbjct: 65  MGVLSKMREAGISIPVIVQTAHGGIDNVVSAMRAGAQDFVVKPVGIERLQVSLRNALNTS 124

Query: 128 VVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +    Q   H        D +I  + AM  ++ +A KA   +IP++I+GE GVGK+  +
Sbjct: 125 ALKGELQRIRHSREGRLTFDDIITRAEAMAPILRIAEKAAASSIPVLIEGESGVGKELFA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R IH + +R   PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT+ L
Sbjct: 185 RAIHGTSERKTKPFVAVNCGAIPDNLVESILFGHEKGAFTGATERHMGKFVEAHGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPLA Q ++   ++ G +E    R  +++DVR+I  T + LL +VK   FR+DL+
Sbjct: 245 DEVSELPLAAQVKLLRALQEGAVEAVGGRKPVKVDVRIISATNRRLLERVKEGHFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + I  LR+R EDIP L+  FL  F  +       I+  A++ LTK  W  N++
Sbjct: 305 YRLHVLPLTIPPLRARREDIPHLLRHFLARFAAEENRAVTGIAGDAVAYLTKLDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGK--------KEREFHTETACTCYTEGKSS 411
           +L+N + RAV+  +   L    F L+ +             ER   +  A    +E    
Sbjct: 365 QLENAVYRAVVMSESDLLGVADFPLIPTHAPPVEPAPALTVERPIPSLPAVVPGSE---- 420

Query: 412 DTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
             I    S  ++P +   GEVR L ++E EII  A+  YR QMSEVARRL IGRSTLYRK
Sbjct: 421 VPIAPLPSHGALPLLTASGEVRPLEELEHEIIRFAIAHYRGQMSEVARRLKIGRSTLYRK 480

Query: 472 IREYNIEVDS 481
           + E N E  +
Sbjct: 481 LDEANGETPA 490


>gi|296447487|ref|ZP_06889411.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylosinus trichosporium OB3b]
 gi|296255025|gb|EFH02128.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylosinus trichosporium OB3b]
          Length = 494

 Score =  254 bits (649), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 158/481 (32%), Positives = 253/481 (52%), Gaps = 18/481 (3%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLINCEDDK 67
           +LI D D  Q ++++  V  +GYD          ++ L+      V+++ L L+  + D 
Sbjct: 5   ILIADDDPVQRRLLEAAVRRFGYDAETAEGGEQALARLTRTGAPPVDLLILDLVMPDLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKIL--------NCFLYNRISKFFLNLVSRKQLC-D 118
             +L  + D    +P+IVQT   +I+ +        N F+   +    L +  +  LC D
Sbjct: 65  MGVLTRMRDLKIAIPVIVQTANGSIETVISAMRAGANDFVVKPVGAERLQISIKNALCAD 124

Query: 119 SIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
           ++   LR   +  +         L++ S  M +V+ L  +A    IP++I+GE GVGK+ 
Sbjct: 125 ALAGELRR--INRRTQGSLTFKDLVSRSEEMTRVIRLGDRAARSGIPVLIEGESGVGKEI 182

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R I     R   PF  VNCG +  + +E  LFG +    T  + +  GKF+EANGGT+
Sbjct: 183 VARAIQGGSDRRGKPFVTVNCGALPANLVESILFGHEKGAFTGATEKHAGKFLEANGGTL 242

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL  Q ++   ++ G+I+   ++  +R+D+RLI  T +NL+  VK   FR+D
Sbjct: 243 FLDEIGELPLETQVKLLRALQEGEIDPVGAKRPVRVDIRLISATNQNLIELVKRGQFRED 302

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR++VF I I  LR+R +DI  L   F   F  +   K   ++ + +SLL+ Y W  N
Sbjct: 303 LFYRLNVFPITIPPLRARRDDIGDLARRFATRFAAEEGKKLRGVTHETISLLSSYDWPGN 362

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKEREFHTETACTCYTEGKSSDTILD 416
           V++L+N + RAV+      LT + F  + +  EG   R           +  +     ++
Sbjct: 363 VRQLENAVFRAVVLADGDELTVNEFPQIAAHVEGFSVRLPPLPAPAPAASAPEREIVRVE 422

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
                 +  +GQ GE+RRL DIE E+I  A+  YR QMSE+ARRLGIGRSTLYRK++EY 
Sbjct: 423 IRDPNVMSLLGQHGEMRRLEDIEAEVIKFALVHYRGQMSEIARRLGIGRSTLYRKMKEYG 482

Query: 477 I 477
           +
Sbjct: 483 L 483


>gi|170749211|ref|YP_001755471.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Methylobacterium radiotolerans JCM 2831]
 gi|170655733|gb|ACB24788.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylobacterium radiotolerans JCM 2831]
          Length = 494

 Score =  253 bits (647), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 161/484 (33%), Positives = 261/484 (53%), Gaps = 15/484 (3%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           VLI+D D  Q ++ +  V  +G++  I       LS +     +V+ L L+    D   +
Sbjct: 5   VLIVDDDPVQRRLAEAAVRRFGFEARIAETGADALSLLRSEGADVVLLDLVMPGLDGLGV 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           L  +       P+IVQT+  +I  +   +      F +     ++L  SI  ALR   + 
Sbjct: 65  LAEMRKSGLATPVIVQTSNGSIDTVVSAMRAGAVDFVVKPAGAERLQVSIKNALRVDTLE 124

Query: 131 SQENEHCALDS-------LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
            +        S       L + SP M +V+ LA +A    IP++I+GE GVGK+ L+R I
Sbjct: 125 EEVRRMRRRASGALTFKDLTSKSPDMERVIRLAERAAKSNIPVLIEGESGVGKEVLARAI 184

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEP 242
             SG R   PF  VNCG I ++ +E  LFG +    T  + +  GKF+EA+GGT+ L+E 
Sbjct: 185 QGSGDRRGKPFVTVNCGAIPENLVESTLFGHEKGAFTGATEKHAGKFVEASGGTLFLDEI 244

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             LPL  Q ++   ++ G+++    + ++R+D+RL+  T ++LL  VK   FR+DLYYR+
Sbjct: 245 GELPLDAQVKLLRALQEGEVDPVGGKRSVRVDIRLVSATNRSLLDLVKQGKFREDLYYRL 304

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           +VF + +  LR+R EDIP LV  F   F  +   +  +IS +A++LLT+YPW  NV++L+
Sbjct: 305 NVFPMTLPPLRARREDIPDLVRSFCARFSAEEGKRVRAISPEAMALLTRYPWPGNVRQLE 364

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSR-EGKKER--EFHTETACTCYTEGKSSDTI-LDNL 418
           N L RAV+      LT   F  + ++ EG   R      +     Y      + + ++  
Sbjct: 365 NALFRAVVLADGDELTVSEFPQIAAQVEGFDVRIPAAPVQPQMPAYAPEPVREIVRVEVR 424

Query: 419 SQESIPAIGQD-GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
              ++  + ++ GE++ +  +E EII  A++ YR +MSEV+RRLGIGRSTLYRK+++  +
Sbjct: 425 DPHAMSLVAEETGEMKPMDVLEAEIIRFALQFYRQRMSEVSRRLGIGRSTLYRKLKDLGL 484

Query: 478 EVDS 481
           E D+
Sbjct: 485 EDDA 488


>gi|146338287|ref|YP_001203335.1| putative response regulator in two-component regulatory system,
           sigma 54-dependent [Bradyrhizobium sp. ORS278]
 gi|146191093|emb|CAL75098.1| putative response regulator in two-component regulatory system,
           sigma 54-dependent [Bradyrhizobium sp. ORS278]
          Length = 498

 Score =  253 bits (646), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 162/488 (33%), Positives = 248/488 (50%), Gaps = 20/488 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI D D  Q +++++ V+  GY+  +V   D     L+      ++ I L L+    D 
Sbjct: 5   ILIADDDPVQRRLVENMVQKCGYEAVVVETGDAVIEKLTNPDAGPIDAIVLDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L  + +    +P+IVQT    I  +   +      F +  V  ++L  S+  AL   
Sbjct: 65  MGVLSKMREAGISIPVIVQTAHGGIDNVVSAMRAGAQDFVVKPVGIERLQVSLRNALNTS 124

Query: 128 VVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +    Q   H          ++  + AM  ++ +A KA   +IP++I+GE GVGK+  +
Sbjct: 125 ALKGELQRIRHSREGRLTFSDIVTRAEAMAPILRIAEKAAASSIPVLIEGESGVGKELFA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R IH + +R   PF  VNCG I  + +E  LFG +    T  + +  GKF+EA+GGT+ L
Sbjct: 185 RAIHGTSERKTKPFVAVNCGAIPDNLVESILFGHEKGAFTGATDRHTGKFVEAHGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL  Q ++   ++ G +E    R  +++DVR+I  T + LL +VK   FR+DL+
Sbjct: 245 DEVSELPLTAQVKLLRALQEGAVEAVGGRKPVKVDVRIISATNRRLLDRVKEGHFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + I  LR+R EDIP L+  FL  F  +       IS  A++ LTK  W  N++
Sbjct: 305 YRLHVLPLTIPPLRARREDIPHLLRHFLARFSAEENRPVSGISGDAVAYLTKLDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKER------EFHTETACTCYTEGKSSDT 413
           +L+N + RAV+  +   L  + F L+ +     E       E   +        G S   
Sbjct: 365 QLENAVYRAVVMSETDQLGVNDFPLIPTHAPPVEPAPPLVVERPAQATLPAMVPG-SEVP 423

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
           I    S  S+P +   G+VR L ++E EII  A+  YR QMSEVARRL IGRSTLYRK+ 
Sbjct: 424 IAPLPSHGSLPMLNAGGDVRPLEEMEHEIIRFAIAHYRGQMSEVARRLKIGRSTLYRKLD 483

Query: 474 EYNIEVDS 481
           E N E  S
Sbjct: 484 EANGETPS 491


>gi|307944487|ref|ZP_07659827.1| acetoacetate metabolism regulatory protein AtoC [Roseibium sp.
           TrichSKD4]
 gi|307772236|gb|EFO31457.1| acetoacetate metabolism regulatory protein AtoC [Roseibium sp.
           TrichSKD4]
          Length = 558

 Score =  252 bits (643), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 166/517 (32%), Positives = 266/517 (51%), Gaps = 47/517 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGY-----DVFIVNVSDLSTISKIQVNVIFLSLINCEDD 66
           R+LI+D D  Q +++++ V+  GY     +  +  +  +       +++I L ++  E D
Sbjct: 37  RILIVDDDPIQRRLLEEAVKKAGYKSRTAENGVQAIEIMMGPDGNDIDLIVLDMVMPELD 96

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
              +L  +  +    P+IVQT Q  I ++   +      F +  VS ++L  SI   L+ 
Sbjct: 97  GLGVLTKLRSEKIATPVIVQTAQGGIDVVVNAMNAGAQDFAVKPVSLERLNVSIRNLLKT 156

Query: 127 GVVP-------SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
             +         Q +     D +I  SPAM +V++L R+A    IPI+I+GE GVGK+ +
Sbjct: 157 SALEDEITRFRKQASGTLTFDDIITHSPAMERVINLGRRAASSQIPILIEGESGVGKELI 216

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +  I  SG R   P   VNCG I ++ +E  LFG +    T  + + +GKF EANGGT+ 
Sbjct: 217 ASAIQGSGDRKSKPMITVNCGAIPENLVESILFGHEKGAFTGANEKHVGKFQEANGGTLF 276

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   LP  VQ ++   ++  +I+   ++  ++++ RLI  T + L+ +VK  VFR+DL
Sbjct: 277 LDEVGELPQDVQVKLLRALQENEIDPIGAKRPVKVNFRLISATNRRLIEEVKDGVFREDL 336

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI-SISDKALSLLTKYPWIDN 357
           YYR++VF I I  LR R EDIP L H FL  F  +    Q+ S++   L LL  Y W  N
Sbjct: 337 YYRLNVFPIWIPPLRDRREDIPALTHHFLARFSAEEGKPQVASVATDTLDLLQSYHWPGN 396

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLL-------------------LSR---------- 388
           +++L+N + RAV+    + LT D F  +                   +SR          
Sbjct: 397 IRQLENAVFRAVVLCDGAQLTVDDFPQIAAAVDRPHPVRTRQAPSAAVSRPPTPPVDKHA 456

Query: 389 EGKKEREFHTETACTCYTEGKSSDTILDNLSQES----IPAIGQDGEVRRLSDIEKEIIG 444
           +   E+  + +TA   +  G++        S  +    +P +   G +R LS IE+E+I 
Sbjct: 457 QAPLEQSSNAQTAPQSHVIGENEIAPPAGFSSGAPFGFMPNLDDQGHIRSLSAIEEELIR 516

Query: 445 LAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVDS 481
            A+  Y  +M+EVA+RLGIGRSTLYRK++EY +E  S
Sbjct: 517 AAIDHYSGRMTEVAKRLGIGRSTLYRKLKEYGLEESS 553


>gi|75675185|ref|YP_317606.1| helix-turn-helix, Fis-type [Nitrobacter winogradskyi Nb-255]
 gi|74420055|gb|ABA04254.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Nitrobacter winogradskyi Nb-255]
          Length = 498

 Score =  251 bits (642), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 161/496 (32%), Positives = 252/496 (50%), Gaps = 47/496 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ-----VNVIFLSLINCEDDK 67
           +LI D D  Q +++++ V   GY+  +V   D +  +        ++ + L L+    D 
Sbjct: 5   ILIADDDAVQRRLVENMVRRCGYETIVVESGDAAVAAMTAGDGPVIDAVVLDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L  I +    +P+IVQT    I  +   +      F +  V  ++L  S+  AL   
Sbjct: 65  MGVLAEIREAGLSIPVIVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALNAS 124

Query: 128 VVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            + +  Q   H          +I  S AM  V+  A+KA   +IP++I+GE GVGK+  +
Sbjct: 125 ALKNELQRVRHSREGRLTFGDIITRSEAMADVMKAAKKAAGSSIPVLIEGESGVGKELFA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R IH +  R+  PF  VNCG I  + +E  LFG      T  + +  GKF++A+GGT+ L
Sbjct: 185 RAIHGTSDRSAKPFVTVNCGAIPDNLVESILFGHEKGSFTGATDRHAGKFVDASGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPLA Q ++   ++ G +E       +++DVR+I  T + LL +VK+ +FR+DL+
Sbjct: 245 DEVSELPLATQVKLLRALQEGAVEAVGGHKPVKVDVRIISATNRRLLDRVKAGLFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + I  LR R EDIP L+  FL  FC +       IS +A++ L++  W  N++
Sbjct: 305 YRLHVLPLTIPPLRKRREDIPNLLRHFLARFCAEENRLIKGISGEAMTALSQLDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTE---GKSSDTILD 416
           +L+N + RAV+  +D  L    F                +TA T + E     S   I++
Sbjct: 365 QLENAVYRAVVMSEDPQLGLPDFP-----------SIAQQTAATTHAETHAPASEPLIME 413

Query: 417 NLSQE--------------------SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSE 456
           +++Q+                    S+P   QDGEVR L ++E +II  A+  YR QMSE
Sbjct: 414 SIAQQTASQAIPGNEIPLAPAPDAGSLPLFAQDGEVRPLDELEADIIRFAVSHYRGQMSE 473

Query: 457 VARRLGIGRSTLYRKI 472
           VARRL IGRSTLYRK+
Sbjct: 474 VARRLKIGRSTLYRKL 489


>gi|91975887|ref|YP_568546.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhodopseudomonas palustris BisB5]
 gi|91682343|gb|ABE38645.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhodopseudomonas palustris BisB5]
          Length = 500

 Score =  250 bits (638), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 160/482 (33%), Positives = 249/482 (51%), Gaps = 18/482 (3%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           +R+LI D D  Q +++++ V+  GY+  + +  D     L+      ++ + L L+    
Sbjct: 3   ERILIADDDPVQRRLVENMVQKCGYEAVLADSGDAAIALLTAPDAAAIDAVVLDLVMPGL 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D   +L  I +    VP+IVQT    I  +   +      F +  V  ++L  S+  AL 
Sbjct: 63  DGLGVLGKIRESGLNVPVIVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALN 122

Query: 126 EGVVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
              +    Q   H          +I  S +M  V+  + KA   +IP++I+GE GVGK+ 
Sbjct: 123 ASALKGELQRIRHSREGRLTFADIITRSESMAAVLRASEKAAASSIPVLIEGESGVGKEM 182

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
            +R IH S +R   PF  VNCG I  + +E  LFG +    T  + + +GKF+EA GGT+
Sbjct: 183 FARAIHGSSERRSKPFVAVNCGAIPDNLVESILFGHEKGAFTGATDRHMGKFVEATGGTL 242

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPLA Q ++   ++ G +E    R  +++DVR+I  T + LL +VK+  FR+D
Sbjct: 243 FLDEVSELPLAAQVKLLRALQEGAVEAVGGRKPLKVDVRIISATNRRLLDRVKAGQFRED 302

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR+ V  + +  LRSR EDIP L+  FL  FC +       I+ +A++ L +  W  N
Sbjct: 303 LFYRLHVLPLTVPPLRSRREDIPPLLRHFLVRFCAEENRTIGGITGEAMARLAQLDWPGN 362

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSRE----GKKERE-FHTETACTCYTEGKSSD 412
           +++L+N + RAV+      L  D F L  +      G+ + E    E   +      +  
Sbjct: 363 IRQLENAVYRAVVMSDSDQLGVDDFPLASAPSTVPTGEADGEPLILEPPTSAQFVAANEA 422

Query: 413 TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            I    +  S+P +  D +VR L ++E EII  A+  YR QMSEVARRL IGRSTLYRK+
Sbjct: 423 PIAPLPTHGSLPMLNSDNDVRALDELESEIIRFAISHYRGQMSEVARRLKIGRSTLYRKL 482

Query: 473 RE 474
            E
Sbjct: 483 DE 484


>gi|328542490|ref|YP_004302599.1| Sigma-54 factor interaction domain-containing protein [polymorphum
           gilvum SL003B-26A1]
 gi|326412237|gb|ADZ69300.1| Sigma-54 factor interaction domain-containing protein [Polymorphum
           gilvum SL003B-26A1]
          Length = 500

 Score =  250 bits (638), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 161/486 (33%), Positives = 258/486 (53%), Gaps = 20/486 (4%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGY-----DVFIVNVSDLSTISKIQVNVIFLSLINCEDD 66
           R+LI+D D  Q +++++ V+ +GY     D     V  ++     +++++ L ++  E D
Sbjct: 7   RILIVDDDPIQRRLLQEAVQRFGYRFKTADNGAEAVRIMTGPEGAEIDLVILDMVMPELD 66

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSI-----I 121
              +L+ +  +    P+IVQT    I  +   +      F +  V+ ++L  SI     +
Sbjct: 67  GIGVLRRLRAERIATPVIVQTAHGGIDTVVNAMTAGAQDFVVKPVAPERLDVSIRNLLKV 126

Query: 122 CALREGVVP---SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
            AL EG +     Q         ++  SPAM +V+ L ++A    IPI+I+GE GVGK+ 
Sbjct: 127 SAL-EGEITRIRKQAAGTLTFADIVTKSPAMERVLRLGQRAASSTIPILIEGESGVGKEL 185

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R I  SG+R   PF  VNCG I  + +E  LFG +    T    + +GKF EA+GGT+
Sbjct: 186 IARAIQGSGERKSKPFVTVNCGAIPDNLVESILFGHEKGAFTGAVDRHVGKFQEAHGGTL 245

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LP+ VQ ++   ++ G+I+   +R   ++D RLI  T + L+  VK   FR+D
Sbjct: 246 FLDEVGELPMEVQVKLLRALQEGEIDPIGARRPAKVDFRLISATNRRLIDLVKEGRFRED 305

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI-SISDKALSLLTKYPWID 356
           LYYR++VF I I  LR R+EDIP LV  FL  F  +    Q+ S++ +AL++L  Y W  
Sbjct: 306 LYYRLNVFPIWIPPLRDRTEDIPALVRHFLARFAAEEGKPQVSSVAPEALAMLQAYAWPG 365

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRF---VLLLSREGKKEREFHTETACTCYTEGKSSDT 413
           N+++L+N + RAV+     HLT   F      L            E         + +  
Sbjct: 366 NIRQLENAVFRAVVLCDGDHLTVADFPQVAAALDHPLPAAEMPAVEAPAGARPAAEPAFA 425

Query: 414 ILDNLSQES-IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
             D  +    + ++  DG VR L  +E+E+I  A+  Y  +M+EVARRLGIGRSTLYRK+
Sbjct: 426 APDGSAPFGFMRSLADDGHVRTLEAVEEEMIRTAIHHYAGRMTEVARRLGIGRSTLYRKL 485

Query: 473 REYNIE 478
           ++Y ++
Sbjct: 486 KDYGLD 491


>gi|86748554|ref|YP_485050.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Rhodopseudomonas palustris HaA2]
 gi|86571582|gb|ABD06139.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhodopseudomonas palustris HaA2]
          Length = 500

 Score =  249 bits (636), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 161/483 (33%), Positives = 249/483 (51%), Gaps = 20/483 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           +R+LI D D  Q +++++ V+  GY+  + +  D     L+       + + L L+    
Sbjct: 3   ERILIADDDPVQRRLVENMVQKCGYEAVLADSGDAAMALLTAPDTAAFDAVVLDLVMPGL 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D   +L  I +    VP+IVQT    I  +   +      F +  V  ++L  S+  AL 
Sbjct: 63  DGLGVLGKIREAGLNVPVIVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALN 122

Query: 126 EGVVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
              +    Q   H          +I  S AM  V+  A+KA   +IP++I+GE GVGK+ 
Sbjct: 123 ASALKGELQRIRHSREGRLTFSDIITRSDAMAAVLRAAQKAAGSSIPVLIEGESGVGKEM 182

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
            +R IH S +R   PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT+
Sbjct: 183 FARAIHGSSERQSKPFVAVNCGAIPDNLVESILFGHEKGAFTGATDRHMGKFVEASGGTL 242

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPLA Q ++   ++ G +E    R  +++DVR+I  T + LL +VK+  FR+D
Sbjct: 243 FLDEVSELPLAAQVKLLRALQEGAVEAVGGRKPLKVDVRIISATNRRLLDRVKAGQFRED 302

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR+ V  + +  LR+R EDIP L+  FL  FC +   K   IS +A++ L +  W  N
Sbjct: 303 LFYRLHVLPLTVPPLRTRREDIPPLLRHFLVRFCAEENRKIGGISGEAMARLAQLDWPGN 362

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           +++L+N + RAV+  +   L  D F L  +       E   E        G +   + + 
Sbjct: 363 IRQLENAVYRAVVMSEGDQLGIDDFPLASAPSTVPTGEADGEP-LILEPPGSAQFVVANE 421

Query: 418 L------SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
                  +  S+  +   G+VR L ++E EII  A+  YR QMSEVARRL IGRSTLYRK
Sbjct: 422 APIAPLSTHGSLQMLNASGDVRALDELENEIIRFAISHYRGQMSEVARRLKIGRSTLYRK 481

Query: 472 IRE 474
           + E
Sbjct: 482 LDE 484


>gi|197106576|ref|YP_002131953.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Phenylobacterium zucineum HLK1]
 gi|196479996|gb|ACG79524.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Phenylobacterium zucineum HLK1]
          Length = 495

 Score =  249 bits (636), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 161/483 (33%), Positives = 255/483 (52%), Gaps = 16/483 (3%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST---ISKIQVNVIFLSLINCEDDK 67
           K VL++D D  Q ++I+  +E  G+ V      D +     S    +V+ L L+      
Sbjct: 3   KTVLVVDDDPTQRRLIQAVLEREGFAVAHAESGDQAISRLASGAAADVVLLDLVMPGISG 62

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
           ++ L  +  +    P+IV T    I  +   +      FF+   + +++  SI  AL  G
Sbjct: 63  QDTLVEMRARGFSQPVIVVTATGGIDTVVQAMQAGAVDFFVKPAAPERIIVSIRNALSMG 122

Query: 128 VVPSQEN---EHCA----LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +  + +   +H +     D LI  SPAM+ V  L  +A   +IPI+I GE GVGK+ ++
Sbjct: 123 ALKGEVDRLKKHASGRTTFDDLIGASPAMVMVKRLGERAARSSIPILITGESGVGKEVIA 182

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R +H S  RA  PF  VNCG I ++ +E  LFG      T  + + LGKF EANGGT+ L
Sbjct: 183 RAVHGSSDRAGKPFVAVNCGAIPENLVESILFGHEKGSFTGATDKHLGKFQEANGGTLFL 242

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++  +I+   S+ ++++DVR++  T ++L   V    FR+DLY
Sbjct: 243 DEVGELPLDMQVKLLRALQESEIDPIGSKRSVKVDVRIVSATNRDLSQAVAEGRFREDLY 302

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I   +LR R EDIP LV  F++ F  +     +  + + L+ LT + W  NV+
Sbjct: 303 YRLNVFPIEAPSLRERKEDIPALVDAFIRRFNVEEGKAVVGAAPETLACLTGFDWPGNVR 362

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEG--KSSDTILDN 417
           +L+N + RA++ L D+   +      +S       E     A T    G   S+  +   
Sbjct: 363 QLENAVYRAIV-LADAPYLQPHDFPAISGIAAPPPEALAPKAVTASAPGPVPSAGELAAE 421

Query: 418 LSQE--SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
           L Q    +P +   G +R L +IE+++I  A+++Y   MSEVARRLGIGRSTLYRK+RE 
Sbjct: 422 LPQPQAPVPILDARGHIRPLDEIERDLIQHAIEVYSGHMSEVARRLGIGRSTLYRKVREN 481

Query: 476 NIE 478
            +E
Sbjct: 482 GLE 484


>gi|85716086|ref|ZP_01047062.1| helix-turn-helix, Fis-type protein [Nitrobacter sp. Nb-311A]
 gi|85697085|gb|EAQ34967.1| helix-turn-helix, Fis-type protein [Nitrobacter sp. Nb-311A]
          Length = 498

 Score =  249 bits (635), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 158/485 (32%), Positives = 247/485 (50%), Gaps = 25/485 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTIS-----KIQVNVIFLSLINCEDDK 67
           +LI+D D  Q +++++ V   GY+  +V   D +  +        ++ + L L+    D 
Sbjct: 5   ILIVDDDAVQRRLVENMVRRCGYETMVVESGDAAVAAVTASDGPAIDALVLDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L  I +    +P+IVQT    I  +   +      F +  V  ++L  S+  AL   
Sbjct: 65  MGVLAGIREAGLNIPVIVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALNAS 124

Query: 128 VVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            + +  Q   H          +I  S  M  V+ +A+KA + +IP++I+GE GVGK+  +
Sbjct: 125 ALKNELQRVRHSREGRLTFADIITRSETMADVMRVAKKAANSSIPVLIEGESGVGKELFA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R IH +  R+  PF  VNCG I    +E  LFG      T  + +  GKF++A+GGT+ L
Sbjct: 185 RAIHGTSDRSTKPFVAVNCGAIPDSLVESILFGHEKGSFTGATERHTGKFVDASGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPLA Q ++   ++ G +E       +++DVR+I  T + LL +VK+  FR+DL+
Sbjct: 245 DEVSELPLAAQVKLLRALQEGAVEAVGGHKQVKVDVRIISATNRRLLDRVKAGHFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + I  LR R  DIP L+  FL  FC +       IS +A++ L++  W  N++
Sbjct: 305 YRLHVLPLTIPPLRMRRGDIPNLLRHFLARFCAEENRLIKGISGEAMAALSQLDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTILDNL 418
           +L+N + RAV+  +D+HL    F  +  +    + R    E       E     T  D +
Sbjct: 365 QLENAVYRAVVLSEDTHLGPSDFPSIGQQPATGDHRATDAEAGEPLIMEPMPQRTAPDRV 424

Query: 419 SQE-----------SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRST 467
                         S+P   QDGEVR L ++E +II  A+  YR QMSEVARRL IGRST
Sbjct: 425 PGNEIPLAPAPDAGSLPLFAQDGEVRPLEELEADIIRFAISHYRGQMSEVARRLKIGRST 484

Query: 468 LYRKI 472
           LYRK+
Sbjct: 485 LYRKL 489


>gi|115526099|ref|YP_783010.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Rhodopseudomonas palustris BisA53]
 gi|115520046|gb|ABJ08030.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhodopseudomonas palustris BisA53]
          Length = 495

 Score =  248 bits (633), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 157/480 (32%), Positives = 250/480 (52%), Gaps = 19/480 (3%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           +RVLI+D D  Q +++++ V+  GY+  +V+  D     L+      ++ + L L+    
Sbjct: 3   ERVLIVDDDPVQRRLVENMVQRCGYEAIVVDNGDAAIARLTAEDAPAIDALVLDLVMPGL 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D   +L  + +    VP+IVQT    I  +   +      F +  V  ++L  S+   L 
Sbjct: 63  DGMGVLSKMREAGLAVPVIVQTAHGGIDNVVSAMRAGAQDFVVKPVGIERLQVSLRNVLN 122

Query: 126 EGVVPSQ-------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
             V+  +        +   +    +  S  M   +  A++A   +IP+ I+G+ GVGK+ 
Sbjct: 123 VSVLRGELQRIRHSRDGKLSFADFVTRSEVMGNALRTAKRAAASSIPVQIEGDSGVGKEL 182

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R IH S  R+  PF  VNCG I  + +E  LFG +    T  + +  GKFIEA+GGT+
Sbjct: 183 IARAIHGSSDRSTKPFVAVNCGAIPDNLVESILFGHEKGAFTGATERHTGKFIEASGGTL 242

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL  Q ++   ++ G +E    R  +++DVR+I  T + LL +VK+  FR+D
Sbjct: 243 FLDEISELPLNAQVKLLRALQEGTVEAVGGRKPVKVDVRIISATNRKLLDRVKAGQFRED 302

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LYYR+ V  + I  LRSR EDIP LV  FL  FC +       +S +A++ L ++ W  N
Sbjct: 303 LYYRLHVLPLTIPPLRSRREDIPHLVRHFLARFCAEENRAITGVSGEAMARLVQFDWPGN 362

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSR-----EGKKEREFHTETACTCYTEGKSSD 412
           V++L+N + RAV+  +   L    F L  ++     E   E         T  + G  ++
Sbjct: 363 VRQLENAVYRAVVMSEGHTLDLADFPLAAAQPVAVTESIGEPLLLAPEVSTVPSMGSGAE 422

Query: 413 TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
             +   +  S+P +   GE+R L ++E +II  A+  YR QMSEVARRL IGRSTLYRK+
Sbjct: 423 MSIAP-AAGSLPLLTPAGEIRPLDELESDIIRFAISHYRGQMSEVARRLKIGRSTLYRKL 481


>gi|118588385|ref|ZP_01545794.1| response regulatory protein [Stappia aggregata IAM 12614]
 gi|118439091|gb|EAV45723.1| response regulatory protein [Stappia aggregata IAM 12614]
          Length = 524

 Score =  248 bits (632), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 162/510 (31%), Positives = 260/510 (50%), Gaps = 43/510 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLINCEDD 66
           ++LI+D D  Q +++++ V+ +GY           V  +S+    ++++I L ++  E D
Sbjct: 7   KILIVDDDPIQRRLLQEAVKKFGYRSKTAENGAEAVRIMSSAEASEIDLIILDMVMPELD 66

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR- 125
              +L+ +       P+IVQT    I  +   +      F +  V+ ++L  SI   L+ 
Sbjct: 67  GLGVLERLRSDKNATPVIVQTAHGGIDTVVTVMNAGAQDFVVKPVAPERLNVSIRNLLKT 126

Query: 126 ---EGVVP---SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
              EG +     Q +       +I  SPAM +V++L ++A    IPI+I+GE GVGK+ +
Sbjct: 127 SALEGEITRIRKQASGTLTFADIITHSPAMERVINLGKRAAASNIPILIEGESGVGKEMI 186

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +  I  S  R   P   VNCG I  + +E  LFG +    T    + +GKF EA+GGT+ 
Sbjct: 187 ASAIQGSSDRKSKPLVTVNCGAIPDNLVESILFGHEKGAFTGAVDKHIGKFQEAHGGTLF 246

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   LP  VQ ++   ++  +I+   +R  +++D RLI  T + L+ QVK  VFR+DL
Sbjct: 247 LDEVGELPQDVQVKLLRALQENEIDPIGARRPVKVDFRLISATNRRLIDQVKEGVFREDL 306

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWIDN 357
           YYR++VF I I  LR R EDIP L   FL  F  +    Q++ ++   L++L  Y W  N
Sbjct: 307 YYRLNVFPIWIPPLRDRREDIPALTRHFLARFAAEEGKPQVAGVTADTLAMLQDYHWPGN 366

Query: 358 VQELKNILLRAVIGLKDSHLTEDRF--VLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
           +++L+N + RAV+      LT + F  V   + +       H   A + Y +  S   + 
Sbjct: 367 IRQLENAVFRAVVLCDGPQLTINDFPQVAAATEQTAAPGVSHHLQAPSAYADRSSGGDLA 426

Query: 416 DNLSQESIPA---------------------------IGQDGEVRRLSDIEKEIIGLAMK 448
               + S P                            + QDG VR+L+DIE+E+I  A+ 
Sbjct: 427 AAPVRPSEPTATPHHAPSAPPPQAGFEQSAPFGFMRNLDQDGHVRKLTDIEEELIRAAIN 486

Query: 449 LYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            Y  +M+EVA+RLGIGRSTLYRK++EY ++
Sbjct: 487 HYSGRMTEVAKRLGIGRSTLYRKLKEYGLD 516


>gi|92116783|ref|YP_576512.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Nitrobacter hamburgensis X14]
 gi|91799677|gb|ABE62052.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Nitrobacter hamburgensis X14]
          Length = 492

 Score =  247 bits (631), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 156/480 (32%), Positives = 248/480 (51%), Gaps = 21/480 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +LI D D  Q +++++ V   GYD  +V   D     L+      ++ + L L+    D 
Sbjct: 5   ILIADDDAVQRRLVENMVRRCGYDAIVVEGGDAAIAALTASDGPVIDALILDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L  I +    VP++VQT    I  +   +      F +  V  ++L  S+  AL   
Sbjct: 65  MGVLAKIREAGISVPVVVQTAHGGIDNVVSAMRAGAHDFVIKPVGIERLQVSLRNALNAS 124

Query: 128 VVPSQ-------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +  +            +   +I  S  M  V+ +ARKA   +IP++I+GE GVGK+  +
Sbjct: 125 ALKGELRRVRHSREGRLSFADIITRSETMANVMRVARKAASSSIPVLIEGESGVGKELFA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R IH +G+R+  PF  VNCG I  + +E  LFG      T  + +  GKF+EA+GGT+ L
Sbjct: 185 RAIHGTGERSAKPFVAVNCGAIPDNLVESILFGHEKGSFTGATERHTGKFVEASGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL  Q ++   ++ G +E    R  +++DVR+I  T + LL +VK+  FR+DL+
Sbjct: 245 DEVSELPLTAQVKLLRALQEGAVEAVGGRKPVKVDVRVISATNRRLLDRVKAGQFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + I  LR+R +DIP L+  FL  FC +       IS +A++ L++  W  N++
Sbjct: 305 YRLHVLPLTIPPLRTRRDDIPNLLRHFLARFCAEENRTINGISGEAMAGLSQLNWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN-L 418
           +L+N + RAV+  +   L    F L+ ++    + E +            S D +  N +
Sbjct: 365 QLENAVYRAVVMSEGEQLGLPDFPLIGAQP-ATDAEANEPLIMEPMLRRPSPDVVSGNEI 423

Query: 419 SQESIPAIGQ------DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
               +P  G       DGE+R L ++E +I+  A+  YR QMSEVARRL IGRSTLYRK+
Sbjct: 424 PIAPLPDAGSLAMLTYDGEIRPLEELEADIVRFAISHYRGQMSEVARRLKIGRSTLYRKL 483


>gi|254503649|ref|ZP_05115800.1| Sigma-54 interaction domain family [Labrenzia alexandrii DFL-11]
 gi|222439720|gb|EEE46399.1| Sigma-54 interaction domain family [Labrenzia alexandrii DFL-11]
          Length = 520

 Score =  247 bits (630), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 166/507 (32%), Positives = 262/507 (51%), Gaps = 41/507 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLINCEDD 66
           ++LI+D D  Q +++++ V  +GY           V  ++     ++++I L ++  E D
Sbjct: 7   KILIVDDDPIQRRLLQEAVHKFGYRSKTAENGAEAVRIMTGPEASEIDLIILDMVMPELD 66

Query: 67  KENILKNI-VDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSI----- 120
              +L+ +  DKI   P+IVQT    I  +   +      F +  V+ ++L  SI     
Sbjct: 67  GLGVLERLRADKIS-TPVIVQTAHGGIDTVVSVMNAGAQDFAVKPVAPERLNVSIRNLLK 125

Query: 121 ICALREGVVPSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
             AL   +   Q+     L    +I  SPAM +V++L ++A    IPI+I+GE GVGK+ 
Sbjct: 126 TSALEGEITRIQKKASGTLTFADIITHSPAMERVINLGKRAAASNIPILIEGESGVGKEM 185

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++  I  S  R   P   VNCG I  + +E  LFG +    T    + +GKF EA+GGT+
Sbjct: 186 IASAIQGSSDRKSKPLITVNCGAIPDNLVESILFGHEKGAFTGAVDKHVGKFQEAHGGTL 245

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LP  VQ ++   I+  +I+   SR  +++D RLI  T + L+ QVK   FR+D
Sbjct: 246 FLDEVGELPQDVQVKLLRAIQENEIDPIGSRRPVKVDFRLISATNRRLIDQVKDSAFRED 305

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWID 356
           LYYR++VF I I  LR R EDIP LV  FL  F  +    Q+S ++  AL++L +Y W  
Sbjct: 306 LYYRLNVFPIWIPPLRDRREDIPALVRHFLARFAAEEGKPQVSGVAQDALAMLQEYAWPG 365

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLL---LSREGKKEREFHTETACTCYTEGK---- 409
           N+++L+N + RAV+    + LT D F  +   +   G +        A       +    
Sbjct: 366 NIRQLQNTVFRAVVLCDGAQLTIDDFPQVSAAIEHPGSQSGVLPPSVAAPFAAAPQDPAA 425

Query: 410 -----SSDTILDNLSQESIPA-------------IGQDGEVRRLSDIEKEIIGLAMKLYR 451
                 +      ++  + PA             +  +G VR+L+DIE+EII  A+K Y 
Sbjct: 426 VTPPPPAQPGAPTVANTTTPAGFEGSAPFGFMRNLDPEGHVRKLTDIEEEIIRAAIKHYS 485

Query: 452 AQMSEVARRLGIGRSTLYRKIREYNIE 478
            +M+EVA+RLGIGRSTLYRK++EY ++
Sbjct: 486 GRMTEVAKRLGIGRSTLYRKLKEYGLD 512


>gi|316935701|ref|YP_004110683.1| Fis family two component sigma54 specific transcriptional regulator
           [Rhodopseudomonas palustris DX-1]
 gi|315603415|gb|ADU45950.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhodopseudomonas palustris DX-1]
          Length = 495

 Score =  246 bits (629), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 163/487 (33%), Positives = 246/487 (50%), Gaps = 21/487 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           +R+LI D D  Q +++++ V+  GY+   V+  D     L+      ++ + L L+    
Sbjct: 3   ERILIADDDAVQRRLVENMVQKCGYETITVDSGDAAVDALTAPDSPAIDAVVLDLVMPGL 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D   +L  I      VP+IVQT    I  +   +      F +  V  ++L  S+  AL 
Sbjct: 63  DGLGVLSKIRASGIDVPVIVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALN 122

Query: 126 EGVVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
              +    Q   H          +I  S AM+ V+  A KA   AIP++I+GE GVGK+ 
Sbjct: 123 ASAMKGELQRIRHAREGRLTFSDIITRSEAMVPVLRAAEKAAGSAIPVLIEGESGVGKEL 182

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
            +R IH S  R   PF  VNCG I  + +E  LFG +    T  + +  GKF+EA+GGT+
Sbjct: 183 FARAIHGSSDRRAKPFVAVNCGAIPDNLVESILFGHEKGAFTGATERHDGKFVEASGGTL 242

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL+ Q ++   ++ G +E    R  +++DVR+I  T + LL +VK+  FR+D
Sbjct: 243 FLDEVSELPLSAQVKLLRALQEGAVEAVGGRRPVKVDVRIISATNRRLLDRVKAGRFRED 302

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR+ V  + I  LR+R EDIP L+  FL  FC +       I+ +A++ L +  W  N
Sbjct: 303 LFYRLHVLPLTIPPLRTRREDIPPLLRHFLMRFCAEEKRSIGGITGEAMARLAQLDWPGN 362

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           +++L+N + RAV+      L  D F L  +           E      +E +      + 
Sbjct: 363 IRQLENAVYRAVVMSDGDQLGLDDFPLASAPSVVPADGIDGEPLVIERSEPQF--VAANE 420

Query: 418 LSQESIPAIGQ------DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
           +    +P  G       D EVR L ++E+EII  A+  YR QMSEVARRL IGRSTLYRK
Sbjct: 421 VPIAPLPTAGNLSMLTADDEVRTLDEMEREIIRFAISHYRGQMSEVARRLKIGRSTLYRK 480

Query: 472 IREYNIE 478
           + E   E
Sbjct: 481 LDEIEAE 487


>gi|192293028|ref|YP_001993633.1| Fis family transcriptional regulator [Rhodopseudomonas palustris
           TIE-1]
 gi|192286777|gb|ACF03158.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Rhodopseudomonas palustris TIE-1]
          Length = 495

 Score =  246 bits (629), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 165/489 (33%), Positives = 249/489 (50%), Gaps = 23/489 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           +R+LI D D  Q +++++ V+  GY+   V+  D     L+      ++ + L L+    
Sbjct: 3   ERILIADDDAVQRRLVENMVQKCGYEAVSVDSGDAAVEALTAPDAPAIDAVVLDLVMPGL 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D   +L  I      VP+IVQT    I  +   +      F +  V  ++L  S+  AL 
Sbjct: 63  DGLGVLSKIRASGLDVPVIVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALN 122

Query: 126 EGVVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
              +    Q   H          +I  S AM  V+  A KA   AIP++I+GE GVGK+ 
Sbjct: 123 ASAMKGELQRIRHAREGRLTFSDIITRSEAMAPVLRAAEKAAGSAIPVLIEGESGVGKEL 182

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
            +R IH S  R   PF  VNCG I  + +E  LFG +    T  + +  GKF+EA+GGT+
Sbjct: 183 FARAIHGSSDRRSKPFVAVNCGAIPDNLVESILFGHEKGAFTGATERHDGKFVEASGGTL 242

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPLA Q ++   ++ G +E    R  +++DVR+I  T + LL +VK+  FR+D
Sbjct: 243 FLDEVSELPLAAQVKLLRALQEGAVEAVGGRRPVKVDVRIISATNRRLLDRVKAGQFRED 302

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR+ V  + I  LR+R EDIP L+  FL  FC +       I+ +A++ L +  W  N
Sbjct: 303 LFYRLHVLPLTIPPLRTRREDIPPLLRHFLMRFCAEEKRSIGGITGEAMARLAQLDWPGN 362

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           +++L+N + RAV+      L    F L ++       +   E      +E +        
Sbjct: 363 IRQLENAVYRAVVMSDGDQLGLADFPLAIAPSVVPAEDTTGEPLVIERSEPQF--VAASE 420

Query: 418 LSQESIPAIGQ------DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
           +    +P++G       D EVR L ++E+EII  A+  YR QMSEVARRL IGRSTLYRK
Sbjct: 421 VPIAPLPSVGNLSMLTADDEVRPLDEMEREIIRFAISHYRGQMSEVARRLKIGRSTLYRK 480

Query: 472 IREYNIEVD 480
           + E  IE D
Sbjct: 481 LDE--IEAD 487


>gi|39937247|ref|NP_949523.1| two component sigma-54-dependent Fis family transcriptional
           regulator [Rhodopseudomonas palustris CGA009]
 gi|39651105|emb|CAE29628.1| two component sigma-54-dependent transcriptional regulator, Fis
           family [Rhodopseudomonas palustris CGA009]
          Length = 495

 Score =  244 bits (624), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 165/489 (33%), Positives = 248/489 (50%), Gaps = 23/489 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           +R+LI D D  Q +++++ V+  GY+   V+  D     L+      ++ + L L+    
Sbjct: 3   ERILIADDDAVQRRLVENMVQKCGYEAVSVDSGDAAVEALTAPDAPAIDAVVLDLVMPGL 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D   +L  I      VP+IVQT    I  +   +      F +  V  ++L  S+  AL 
Sbjct: 63  DGLGVLSKIRASGLDVPVIVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALN 122

Query: 126 EGVVPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
              +    Q   H          +I  S AM  V+  A KA   AIP++I+GE GVGK+ 
Sbjct: 123 ASAMKGELQRIRHAREGRLTFSDIITRSEAMAPVLRAAEKAAGSAIPVLIEGESGVGKEL 182

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
            +R IH S  R   PF  VNCG I  + +E  LFG +    T  + +  GKF+EA+GGT+
Sbjct: 183 FARAIHGSSDRRSKPFVAVNCGAIPDNLVESILFGHEKGAFTGATERHDGKFVEASGGTL 242

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPLA Q ++   ++ G +E    R  +++DVR+I  T + LL +VK+  FR+D
Sbjct: 243 FLDEVSELPLAAQVKLLRALQEGAVEAVGGRRPVKVDVRIISATNRRLLDRVKAGQFRED 302

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR+ V  + I  LR+R EDIP L+  FL  FC +       I+ +A+  L +  W  N
Sbjct: 303 LFYRLHVLPLTIPPLRTRREDIPPLLRHFLMRFCAEEKRSIGGITGEAMVRLAQLDWPGN 362

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           +++L+N + RAV+      L    F L ++       +   E      +E +        
Sbjct: 363 IRQLENAVYRAVVMSDGDQLGLADFPLAIAPSVVPAEDTTGEPLVIERSEPQF--VAASE 420

Query: 418 LSQESIPAIGQ------DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
           +    +P++G       D EVR L ++E+EII  A+  YR QMSEVARRL IGRSTLYRK
Sbjct: 421 VPIAPLPSVGNLSMLTADDEVRPLDEMEREIIRFAISHYRGQMSEVARRLKIGRSTLYRK 480

Query: 472 IREYNIEVD 480
           + E  IE D
Sbjct: 481 LDE--IEAD 487


>gi|304321711|ref|YP_003855354.1| sigma-54 dependent DNA-binding response regulator [Parvularcula
           bermudensis HTCC2503]
 gi|303300613|gb|ADM10212.1| sigma-54 dependent DNA-binding response regulator [Parvularcula
           bermudensis HTCC2503]
          Length = 497

 Score =  244 bits (624), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 158/491 (32%), Positives = 256/491 (52%), Gaps = 26/491 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLS-----TISKIQVNVIFLSLINCEDDK 67
           VLI+D D  Q ++++   E  GY V  +    L+     +    +V V+ L L+      
Sbjct: 5   VLIVDDDPVQCRLMQGVCERAGYCVVTMQDGQLAIDLLRSSDGDRVGVVMLDLLMPNLSG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-- 125
             +L+ +    P +P+IV T Q  +  +   +    + FF+   S +++  S+   L   
Sbjct: 65  MELLEELKRFRPELPVIVLTGQGGVDTVVKAMQAGAADFFVKPASPERVVVSLRHVLDVK 124

Query: 126 --EGVVPSQENEH---CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
              G V   +  H    A + L+  SP++     +  KA    IPI+I GE GVGK+  +
Sbjct: 125 HLRGEVKRLQRRHDGGLAFNDLLESSPSLAACAKMGEKAASSTIPILITGESGVGKEMFA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R I     R+  PF  VNCG + ++ +E  LFG +    T  +++  GKF EA+GGTI L
Sbjct: 185 RAIQGCSARSGGPFVTVNCGALPENLVESILFGHEKGAFTGATSKHAGKFQEAHGGTIFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL  Q ++   ++ G+++   ++  +++DVR+I  T +NL  +V S  FR+DL+
Sbjct: 245 DEVGELPLEAQVKLLRVLQEGEVDPVGAKRPVKVDVRVISATNRNLETEVASGSFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I++  LR R  DIP L+  F+  +  +   +   +  + L +L    W  NV+
Sbjct: 305 YRLNVFPIHLPPLRERKADIPELIKHFISKYNAEENREVRGVRHEVLEVLVDQDWPGNVR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLS-------REGKKEREFHTETACTCYTEGKSSD 412
           +L+N + RAV+      L  D F LL           G      H   A T   +G+++ 
Sbjct: 365 QLENTIFRAVVLSAGKWLCADDFPLLADAFEEAGIASGPPPAMDHDGPANT--VDGETAA 422

Query: 413 TILDNLSQES----IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
               +   ++    +P +  DG +R L+DIE+++I +A+ LY+ QMSEVARRLGIGRSTL
Sbjct: 423 LAYYDHDHDAAPVPLPFLDGDGHIRPLADIERDLIEMAIDLYKGQMSEVARRLGIGRSTL 482

Query: 469 YRKIREYNIEV 479
           YRK++E NIEV
Sbjct: 483 YRKVQEQNIEV 493


>gi|315498562|ref|YP_004087366.1| two component, sigma54 specific, transcriptional regulator, fis
           family [Asticcacaulis excentricus CB 48]
 gi|315416574|gb|ADU13215.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Asticcacaulis excentricus CB 48]
          Length = 487

 Score =  243 bits (621), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 159/483 (32%), Positives = 253/483 (52%), Gaps = 20/483 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           K +LI D D  Q ++I+  +E  G+ V            L+T S I  + + L L+    
Sbjct: 3   KTILICDDDPTQRRLIQAVLEREGFAVVHAENGPQAYDRLTTTSGI--DAVILDLVMPGQ 60

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
              + LK+I       P++V T    I  +   +      FF+   S +++  S+  AL+
Sbjct: 61  SGIDTLKDIRAAGIRTPVVVLTASGGIDTVVKAMQAGAQDFFIKPASPERILVSVRNALQ 120

Query: 126 EGVVPS-------QENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
            G + +       Q     + + L+  S AM  V  L  +A    IP++I GE GVGK+ 
Sbjct: 121 MGDMAAEVTRLKKQVTNRTSFEDLVGTSGAMQMVRRLGERAARSGIPVLILGESGVGKEL 180

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTI 237
           ++R I  S  RA  PF  VNCG +  + +E  LFG      T  S + LGKF EA+GGT+
Sbjct: 181 IARAIQGSSDRAGKPFVAVNCGALPANLVESILFGHEKGSFTGASDKHLGKFQEASGGTL 240

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL +Q ++   ++ G+I+   ++  +++DVR+I  T +NL  QVK+  FR+D
Sbjct: 241 FLDEVGELPLDMQVKLLRALQEGEIDPIGAKRPVKVDVRIISATNRNLQDQVKAGHFRED 300

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR++VF I   +LR R EDIP L+  F++ F  +   +   ++  A+ LL  Y W  N
Sbjct: 301 LFYRLNVFPIEAPSLRERREDIPALIEHFIRRFNVEEGKRVAGVASDAIQLLCAYDWPGN 360

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETAC-TCYTEGKSSDTILD 416
           V++L+N + RA++     HL    F  +    G+   +    T       E +++ T LD
Sbjct: 361 VRQLENTIYRAIVLADTPHLQAYDFPAI---SGQHLPQAAVSTPVPPIIAEHQAAMTQLD 417

Query: 417 -NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
             L  + +  +   G +R+L +IE+++I  A+ +Y   MSEVARRLGIGRSTLYRK+R+ 
Sbjct: 418 AGLPDQPVKILDGAGHLRKLEEIERDLIEHAISVYAGHMSEVARRLGIGRSTLYRKVRDC 477

Query: 476 NIE 478
            +E
Sbjct: 478 GLE 480


>gi|16127545|ref|NP_422109.1| sigma-54 dependent DNA-binding response regulator [Caulobacter
           crescentus CB15]
 gi|221236360|ref|YP_002518797.1| AAA-family response regulator tacA [Caulobacter crescentus NA1000]
 gi|13425011|gb|AAK25277.1| sigma-54 dependent DNA-binding response regulator [Caulobacter
           crescentus CB15]
 gi|220965533|gb|ACL96889.1| AAA-family response regulator tacA [Caulobacter crescentus NA1000]
          Length = 488

 Score =  243 bits (620), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 155/481 (32%), Positives = 248/481 (51%), Gaps = 11/481 (2%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST---ISKIQVNVIFLSLINCEDDK 67
           K VL++D D  Q ++I+  +E  G+ V      D +     S    +VI L L+    + 
Sbjct: 3   KTVLVVDDDPTQRRLIQAVLERDGFAVSHAEGGDAAIAHLTSGAPADVILLDLVMPGLNG 62

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
           ++ LK +  +    P+IV T    +  +   +      FF+   S +++  SI  AL  G
Sbjct: 63  QDALKEMRARGFNQPVIVLTASGGVDTVVKAMQAGACDFFIKPASPERITVSIRNALSMG 122

Query: 128 VVPSQ-------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +  +                LI  SP M  V  +  +A    IP++I GE GVGK+ ++
Sbjct: 123 DLKGEVERLTKRAGGKTTFADLIGASPVMTMVKRMGERAAKSGIPVLITGESGVGKELIA 182

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R +H S  RA  PF  VNCG I ++ +E  LFG      T  + + LGKF EA+GGT+ L
Sbjct: 183 RAVHGSSDRAGKPFVAVNCGAIPENLVESILFGHEKGSFTGATDKHLGKFKEADGGTLFL 242

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++ G+I+   S+ +I++DVR++  T ++L   V    FR+DL+
Sbjct: 243 DEVGELPLDMQVKLLRALQEGEIDPIGSKRSIKVDVRIVSATNRDLQQAVSGGRFREDLF 302

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I   +LR R EDIP LV  F++ F  +   + I  S + + LLT + W  NV+
Sbjct: 303 YRLNVFPIEAPSLRERREDIPALVEAFIRRFNVEEGKRVIGASPETMQLLTSFDWPGNVR 362

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N + RA++     +L    F  +       E    + +         +   +   ++
Sbjct: 363 QLENTVYRAIVLADAPYLQPFDFPAISGLAAPIEAVSISPSPPPAALLQATHAAMAAAVA 422

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           +  +  +   G +R L +IE+++I  A+ +Y   MSEVARRLGIGRSTLYRK+RE  IEV
Sbjct: 423 EAPVRILDDRGHLRTLEEIERDLIQHAIDVYAGHMSEVARRLGIGRSTLYRKVREQGIEV 482

Query: 480 D 480
           D
Sbjct: 483 D 483


>gi|254473219|ref|ZP_05086617.1| response regulatory protein [Pseudovibrio sp. JE062]
 gi|211957940|gb|EEA93142.1| response regulatory protein [Pseudovibrio sp. JE062]
          Length = 518

 Score =  243 bits (620), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 166/510 (32%), Positives = 268/510 (52%), Gaps = 45/510 (8%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGY-DVFIVNVSD----LSTISKIQVNVIFLSLINCED 65
           +R+LI+D D  Q +++++ V+ +GY     V+  +    L+  ++ +++++ L L+  E 
Sbjct: 3   QRILIVDDDPVQRRLLEEAVKRFGYRSKSCVDGREALEILTGSAQSEIDLVILDLMMPEV 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D   +LK   +    VP+IVQT   +I+ +   +      F +     ++L  SI   L+
Sbjct: 63  DGFQVLKETREAKNAVPVIVQTANGSIETVIEAMRAGAQDFVVKPSRPERLQVSITNLLK 122

Query: 126 EGVVPSQENE------HC----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
              V + E E      H       D+++  S  M +V+ L  +A    IPI+I+GE GVG
Sbjct: 123 ---VATLEGELTRIRKHSEGTLTFDNIVTRSEPMDRVLRLGERAASSNIPILIEGESGVG 179

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANG 234
           K+ ++R I  S +R   PF  VNCG I    +E  LFG +    T    + +GKF EANG
Sbjct: 180 KELIARAIQGSSERRSKPFVTVNCGAIPDHLVESILFGHEKGAFTGAVDRHIGKFQEANG 239

Query: 235 GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF 294
           GT+ L+E   LPL VQ ++   ++ G+++   +R  +++D RLI  T + L+ QVK   F
Sbjct: 240 GTLFLDEVGELPLEVQVKLLRALQEGEVDPVGARKPVKVDFRLISATNRRLIDQVKEGKF 299

Query: 295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYP 353
           R+DLYYR++VF I I  LR RSEDIP L   FL  F  + +  Q++ I+   +++L  Y 
Sbjct: 300 REDLYYRLNVFPIWIPPLRDRSEDIPELTRHFLARFAAEESKPQVTGITSDTVNMLKSYD 359

Query: 354 WIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSRE------------GKKERE---FHT 398
           W  N+++L+N + RAV+      LT D F  +                GKKE +   + +
Sbjct: 360 WPGNIRQLENAVFRAVVLCDGPSLTCDDFPQIAQATDTPMSYAAAPSVGKKEPQADVYSS 419

Query: 399 ETACTCYTEGKSSDTIL-----DNLSQESIP-----AIGQDGEVRRLSDIEKEIIGLAMK 448
             +     E +  +  L          E  P     ++  +G VR L+ +E+E+I  A+ 
Sbjct: 420 SLSVASKWEEQQDEQFLHVEAVSAFDAEQPPFGYMRSLDGEGHVRTLTGVEEEMIRTAIS 479

Query: 449 LYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            Y  +M+EVA+RLGIGRSTLYRK++EY +E
Sbjct: 480 HYGGRMTEVAKRLGIGRSTLYRKLKEYGLE 509


>gi|329850361|ref|ZP_08265206.1| response regulator [Asticcacaulis biprosthecum C19]
 gi|328840676|gb|EGF90247.1| response regulator [Asticcacaulis biprosthecum C19]
          Length = 483

 Score =  243 bits (619), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 157/481 (32%), Positives = 251/481 (52%), Gaps = 20/481 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLINCED 65
           K +LI D D  Q ++I+  +E  G+ V            L+T+  I  + + L L+    
Sbjct: 3   KTILICDDDPTQRRLIQAVLEREGFMVMHAENGAQAYDRLTTLPGI--DAVILDLVMPGQ 60

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
              + LK +       P++V T    I  +   +      FF+   S +++  S+  AL+
Sbjct: 61  SGIDTLKEVRAAGIRTPVVVLTASGGIDTVVKAMQAGAQDFFIKPASPERILVSVRNALQ 120

Query: 126 EGVVPSQE-------NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
            G + ++            + D LI  S  M  V  L  +A   +IP++I GE GVGK+ 
Sbjct: 121 MGDMAAEVTRLKKHVGNRISFDDLIGTSGTMQMVRRLGERAAKSSIPVLILGESGVGKEL 180

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTI 237
           ++R I  S +RA  PF  VNCG + ++ +E  LFG      T  S + LGKF EANGGT+
Sbjct: 181 IARAIQGSSERAGKPFVAVNCGALPENLVESILFGHEKGSFTGASDKHLGKFQEANGGTL 240

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL +Q ++   ++ G+I+   S+  +++DVR+I  T +NL  QVK+  FR+D
Sbjct: 241 FLDEVGELPLDMQVKLLRALQEGEIDPVGSKRPVKVDVRIISATNRNLSDQVKTGQFRED 300

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR++VF +   +LR R EDIP L+  F++ F  +   +   +S +AL LL  Y W  N
Sbjct: 301 LFYRLNVFPVEAPSLRERREDIPALIEHFIRRFNVEEGKRVTGVSSEALQLLCAYDWPGN 360

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           V++L+N + RA++   + +L    F  +    G+       E       E  +    ++ 
Sbjct: 361 VRQLENTVYRAIVLADNPYLQAFDFPAI---SGQAMPMPAAEAPRLGMVE--AHHEAINA 415

Query: 418 LSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           L    +  +   G +R+L DIE+++I  A+ +Y   MSEVARRLGIGRSTLYRK+R+  +
Sbjct: 416 LPDAPVRILDAAGHLRKLEDIERDLIEHAIGVYAGHMSEVARRLGIGRSTLYRKVRDCGL 475

Query: 478 E 478
           E
Sbjct: 476 E 476


>gi|114797505|ref|YP_761716.1| sigma-54 dependent DNA-binding response regulator [Hyphomonas
           neptunium ATCC 15444]
 gi|114737679|gb|ABI75804.1| sigma-54 dependent DNA-binding response regulator [Hyphomonas
           neptunium ATCC 15444]
          Length = 491

 Score =  243 bits (619), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 150/486 (30%), Positives = 255/486 (52%), Gaps = 21/486 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD----LSTISKIQVNVIFLSLINCEDD 66
           K +L++D D  Q ++++  VE  G+        +    +++ ++  V+V+ L L      
Sbjct: 3   KTILVVDDDPTQRRLLQAAVEKAGFACRTAPDGETGLQMASDAREGVDVVLLDLTMPGLS 62

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
             + L+ +  K P +P+I+ T    I  +   +      F +   + +++  SI  AL+ 
Sbjct: 63  GMDTLERLNGKRPDLPVIMLTATSGIDTIVQTMRRGAVDFIVKPANPERVVVSIRNALKM 122

Query: 127 GVVPSQENE-------HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
             +  +              + +IA +PAM  V+ +A +     IP++I GE GVGK+ +
Sbjct: 123 QSLTGEVKRLSRKVEGGMKFEDMIASAPAMRSVIRMAERGAASDIPVLILGESGVGKEVV 182

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R I  + +RA  PF  VNCG I ++ +E  LFG +    T   ++  GKF+EA+GGT+ 
Sbjct: 183 ARCIQGASQRAGKPFVTVNCGAIPENLVESILFGHEKGAFTGAVSKAPGKFVEADGGTLF 242

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   LPL  Q ++   ++ G+++   SR   ++DVR+I  T ++L  QVK+  FR+DL
Sbjct: 243 LDEVGELPLDAQVKLLRALQEGEVDAVGSRRPTKVDVRIISATNRDLAGQVKAGTFREDL 302

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +YR++VF I++ +L  R EDIP LV  F+  F      K    S+  L +L  Y W  NV
Sbjct: 303 FYRLNVFPIDMPSLNERREDIPALVDHFIARFNASEGTKVAGASEDTLKMLYSYDWPGNV 362

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNL 418
           ++L+N + RAV+      L    F  +  +      +     A       ++     +++
Sbjct: 363 RQLENAVFRAVVLCDGDELRPQDFPQISGQMA----DVMMMPAIPAQRPPEAPPVPANDV 418

Query: 419 SQ---ESIPAI--GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
            +     +P     +DGE+R L DIE++++  A++ Y   MSEV+RRLGIGRSTLYRK+R
Sbjct: 419 KRGFVGDVPVAIKDEDGEIRSLQDIERDLLQYAIEFYDGHMSEVSRRLGIGRSTLYRKVR 478

Query: 474 EYNIEV 479
           EY++EV
Sbjct: 479 EYDLEV 484


>gi|295688045|ref|YP_003591738.1| Fis family two component sigma54 specific transcriptional regulator
           [Caulobacter segnis ATCC 21756]
 gi|295429948|gb|ADG09120.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Caulobacter segnis ATCC 21756]
          Length = 486

 Score =  242 bits (618), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 159/481 (33%), Positives = 251/481 (52%), Gaps = 13/481 (2%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST---ISKIQVNVIFLSLINCEDDK 67
           K VL++D D  Q ++I+  +E  G+ V   +  D +     S    +V+ L L+      
Sbjct: 3   KTVLVVDDDPTQRRLIQAVLERDGFAVSHADSGDAAIAHLTSGAPADVVLLDLVMPGLSG 62

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
           ++ LK +  +    P+IV T    +  +   +    S FF+   S +++  SI   L  G
Sbjct: 63  QDALKEMRARGFSQPVIVLTASGGVDTVVKAMQAGASDFFIKPASPERITVSIRNVLSMG 122

Query: 128 VVPSQENE-------HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +  +                LI  SPAM  V  +  +A   AIP++I GE GVGK+ ++
Sbjct: 123 DLKGEVERLTKRAVGKTTFSDLIGASPAMSLVKRMGERAAKSAIPVLITGESGVGKELIA 182

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R +H S  RA  PF  VNCG I ++ +E  LFG      T  + + LGKF EA+GGT+ L
Sbjct: 183 RAVHGSSDRAGKPFVAVNCGAIPENLVESILFGHEKGSFTGATDKHLGKFKEADGGTLFL 242

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL VQ ++   ++ G+I+   S+ ++++DVR++  T ++L   V +  FR+DLY
Sbjct: 243 DEVGELPLDVQVKLLRALQEGEIDPIGSKRSLKVDVRIVSATNRDLAQAVSAGRFREDLY 302

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I   +LR R EDIP LV  F++ F  +   + I  + + + LL  + W  NV+
Sbjct: 303 YRLNVFPIEAPSLRERREDIPALVEAFIRRFNVEEGKRVIGAAPETMRLLAAFDWPGNVR 362

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N + RA++     +L    F  +  +    E    T TA        ++       +
Sbjct: 363 QLENAVYRAIVLSDAPYLQPYDFPAISGQAAPAEPAAPTPTAAAMLQAAHAAMAAPAADA 422

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
              I  + + G +R L +IE+++I  A+ +Y   MSEVARRLGIGRSTLYRK+RE  IEV
Sbjct: 423 PVRI--LDERGHLRTLEEIERDLIQHAIDVYAGHMSEVARRLGIGRSTLYRKVREQGIEV 480

Query: 480 D 480
           D
Sbjct: 481 D 481


>gi|167644845|ref|YP_001682508.1| two component sigma54 specific Fis family transcriptional regulator
           [Caulobacter sp. K31]
 gi|167347275|gb|ABZ70010.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Caulobacter sp. K31]
          Length = 489

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 155/483 (32%), Positives = 252/483 (52%), Gaps = 14/483 (2%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTI---SKIQVNVIFLSLINCEDDK 67
           K VL++D D  Q ++I+  +E  G+ V      D +     S   V+V+ L L+      
Sbjct: 3   KTVLVVDDDPTQRRLIQAVLERDGFAVSHAENGDAAMAHLASGAPVDVVLLDLVMPGLSG 62

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
           ++ LK +  +    P+IV T    +  +   +    + FF+   S +++  SI  AL  G
Sbjct: 63  QDTLKEMRARGFAQPVIVLTASGGVDTVVRAMQAGATDFFIKPASPERITVSIRNALSMG 122

Query: 128 VVPSQ-------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +  +        N       LI  SPAM  V  +  +A   +IPI+I GE GVGK+ ++
Sbjct: 123 DLKGEVERLTKRTNNRTTFADLIGASPAMTLVKRMGERAAKSSIPILITGESGVGKELIA 182

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R +H    RA  PF  VNCG I ++ +E  LFG      T  + + LGKF EA+GGT+ L
Sbjct: 183 RAVHGGSDRAGKPFVAVNCGAIPENLVESILFGHEKGSFTGATDKHLGKFKEADGGTLFL 242

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++ G+I+   S+ + ++DVR++  T +++   V+   FR+DLY
Sbjct: 243 DEVGELPLDMQVKLLRALQEGEIDPVGSKRSQKVDVRIVSATNRDVAHAVEQGRFREDLY 302

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I   +LR R EDIP LV  F++ F  +   + +  + + L +L+ + W  NV+
Sbjct: 303 YRLNVFPIEAPSLRERREDIPALVEAFIRRFNVEEGKRVVGATPETLKILSVFDWPGNVR 362

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N + RA+I L D+   +      +S       E             +++  ++    
Sbjct: 363 QLENAVYRAII-LADAPYLQPYDFPAVSGIMAPPPEALAAVQPDLPAVLQAAHAVMARSP 421

Query: 420 QESIPA--IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
               P   +   G +R L +IE+++I  A+++Y   MSEVARRLGIGRSTLYRK+RE  I
Sbjct: 422 NMDSPVRILDDRGHLRTLEEIERDLIQHAIEVYAGHMSEVARRLGIGRSTLYRKVREQGI 481

Query: 478 EVD 480
           E+D
Sbjct: 482 EID 484


>gi|209884232|ref|YP_002288089.1| transcriptional regulatory protein ZraR [Oligotropha
           carboxidovorans OM5]
 gi|209872428|gb|ACI92224.1| transcriptional regulatory protein ZraR [Oligotropha
           carboxidovorans OM5]
          Length = 499

 Score =  242 bits (617), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 157/484 (32%), Positives = 240/484 (49%), Gaps = 22/484 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTI----SKIQVNVIFLSLINCEDDKE 68
           +LI D D  Q +++ + V+  GY   +V   D +          ++ + L L+    D  
Sbjct: 5   ILIADDDAVQRRLLDNMVQRCGYRTIVVESGDAAMTVLADETQPIDAVVLDLVMPGLDGL 64

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
            +L  + D    VP++VQT    I  +   +      F +  V  ++L  S+  AL    
Sbjct: 65  GVLARMRDASLHVPVVVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALDASA 124

Query: 129 VPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           +    Q   H          ++  S AM  V+ + +KA   AIP++I+GE GVGK+  +R
Sbjct: 125 LKGELQRIRHSREGRLTFKDIVTRSEAMAHVLAIGQKAAASAIPVLIEGESGVGKELFAR 184

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            IH S +RA  PF  VNCG I  + +E  LFG +    T  + +  GKF+EA+GGT+ L+
Sbjct: 185 AIHGSSERASKPFVTVNCGAIPDNLVESILFGHEKGAFTGATERHAGKFVEASGGTLFLD 244

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL  Q ++   ++ G++E    R  +++DVR+I  T +NLL  VK+  FR DL+Y
Sbjct: 245 EVSELPLTAQVKLLRALQQGEVEAVGGRKPVKVDVRIISATNRNLLNHVKAGHFRDDLFY 304

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R+ V  + I  LR+R EDIP L+  FL  F  +       +S  A+  L    W  NV++
Sbjct: 305 RLHVLPLTIPPLRARREDIPHLLRHFLARFGAEENRAIARVSAGAMERLVTADWPGNVRQ 364

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREG-KKEREFHTETACTCYTEGKSSDTILDNLS 419
           L+N + RAV+      L  + F  ++  +   +E       A T     +     +    
Sbjct: 365 LENAVYRAVVLSDGDELRAEDFPAIVGTDAIGEESPIPAAEALTLPQPSRVPGQDIPIAP 424

Query: 420 QESIPA---------IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
            + +PA         + + GE R L ++E EII  A+  YR QMSEVARRL IGRSTLYR
Sbjct: 425 AQPVPAMLPHGNLSMLDEQGETRPLEEMEAEIIRFAVSHYRGQMSEVARRLKIGRSTLYR 484

Query: 471 KIRE 474
           K+ E
Sbjct: 485 KMDE 488


>gi|323137998|ref|ZP_08073072.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylocystis sp. ATCC 49242]
 gi|322396717|gb|EFX99244.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylocystis sp. ATCC 49242]
          Length = 500

 Score =  241 bits (616), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 156/481 (32%), Positives = 253/481 (52%), Gaps = 15/481 (3%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLINCEDDK 67
           +LI D D  Q ++++  V  +GY+   V      ++ L+      + ++ L L+  + D 
Sbjct: 5   ILIADDDPVQRRLLEAMVRRFGYEAETVEGGEQALARLTQPGAPPIALLILDLVMPDLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L  + D     P+IVQT   +I+ +   +      F +  V  ++L  SI  AL   
Sbjct: 65  MGVLTRMRDTKIATPVIVQTAHGSIEAVISAMRAGAHDFVVKPVGAERLQISIKNALSAD 124

Query: 128 VVPSQ-------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +  +        +       L++ S  M +V+ L  +A   +IP++I+GE GVGK+ ++
Sbjct: 125 ALAGEIRRISRRASGALTFRDLVSRSDDMARVIRLGERAAHSSIPVLIEGESGVGKELVA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R I     R   PF  VNCG +  + +E  LFG +    T  + +  GKF+EANGGT+ L
Sbjct: 185 RAIQGGSDRRGKPFVTVNCGALPANLVESILFGHEKGAFTGATEKHSGKFLEANGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++ G+I+   +R  +R+D+RLI  T +NL+  VK   FR+DL+
Sbjct: 245 DEIGELPLDIQVKLLRALQEGEIDPVGARRPVRVDIRLISATNQNLIELVKRGQFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I+I  LR+R +DI  L   F   F  +       ++ +ALSLLT Y W  NV+
Sbjct: 305 YRLNVFPISIPPLRARRQDIADLARRFAARFAAEEGRNIRGVTAEALSLLTTYDWPGNVR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKEREFHTETACTCYTEGKSSDTILDNL 418
           +L+N + RAV+      LT   F  + +  +G   R              +  + +   +
Sbjct: 365 QLENAVFRAVVLADGDELTVAEFPQIAAHVDGYDVRVPPAPALAPAADAPRQREIVHVEI 424

Query: 419 SQES-IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
              + I  +G +GE+R+L D+E E I  A+  YR QMSE+ARRLGIGRSTLYRK++EY +
Sbjct: 425 RDPNVISMLGANGEMRKLQDLEAETIRFALTHYRGQMSEIARRLGIGRSTLYRKMKEYGL 484

Query: 478 E 478
           +
Sbjct: 485 D 485


>gi|2317696|gb|AAC45640.1| putative sigma 54 activator [Caulobacter crescentus CB15]
          Length = 488

 Score =  241 bits (616), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 154/481 (32%), Positives = 247/481 (51%), Gaps = 11/481 (2%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST---ISKIQVNVIFLSLINCEDDK 67
           K VL++D D  Q ++I+  +E  G+ V      D +     S    +VI L L+    + 
Sbjct: 3   KTVLVVDDDPTQRRLIQAVLERDGFAVSHAEGGDAAIAHLTSGAPADVILLDLVMPGLNG 62

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
           ++ LK +  +    P+IV T    +  +   +      FF+   S +++  SI  AL  G
Sbjct: 63  QDALKEMRARGFNQPVIVLTASGGVDTVVKAMQAGACDFFIKPASPERITVSIRNALSMG 122

Query: 128 VVPSQ-------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +  +                LI  SP M  V  +  +A    IP++I GE GVGK+ ++
Sbjct: 123 DLKGEVERLTKRAGGKTTFADLIGASPVMTMVKRMGERAAKSGIPVLITGESGVGKELIA 182

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R +H S  RA  PF  VNCG I ++ +E  LFG      T  + + LGKF EA+ GT+ L
Sbjct: 183 RAVHGSSDRAGKPFVAVNCGAIPENLVESILFGHEKGSFTGATDKHLGKFKEADAGTLFL 242

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++ G+I+   S+ +I++DVR++  T ++L   V    FR+DL+
Sbjct: 243 DEVGELPLDMQVKLLRALQEGEIDPIGSKRSIKVDVRIVSATNRDLQQAVSGGPFREDLF 302

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I   +LR R EDIP LV  F++ F  +   + I  S + + LLT + W  NV+
Sbjct: 303 YRLNVFPIEAPSLRERREDIPALVEAFIRRFNVEEGKRVIGASPETMQLLTSFDWPGNVR 362

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N + RA++     +L    F  +       E    + +         +   +   ++
Sbjct: 363 QLENTVYRAIVLADAPYLQPFDFPAISGLAAPIEAVSISPSPPPAALLQATHAAMAAAVA 422

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           +  +  +   G +R L +IE+++I  A+ +Y   MSEVARRLGIGRSTLYRK+RE  IEV
Sbjct: 423 EAPVRILDDRGHLRTLEEIERDLIQHAIDVYAGHMSEVARRLGIGRSTLYRKVREQGIEV 482

Query: 480 D 480
           D
Sbjct: 483 D 483


>gi|188582121|ref|YP_001925566.1| Fis family transcriptional regulator [Methylobacterium populi
           BJ001]
 gi|179345619|gb|ACB81031.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylobacterium populi BJ001]
          Length = 496

 Score =  240 bits (612), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 161/485 (33%), Positives = 256/485 (52%), Gaps = 17/485 (3%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDLSTI--SKIQVNVIFLSLINCED-DKE 68
           VLIID D  Q ++ +  V   G++  I  N  D   +      V+V+ L L+     D  
Sbjct: 5   VLIIDDDPVQRRLAEAMVRRLGFEPRIAENGHDGLNLLRGGGNVDVVLLDLVMPGGMDGL 64

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR--- 125
           ++L  +       P+IVQT+  +I  +   +      F +     ++L  SI  ALR   
Sbjct: 65  SVLSEMRKSGIDTPVIVQTSNGSIDAVVNAMRAGAVDFVVKPAGAERLQVSIKNALRVDQ 124

Query: 126 ----EGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
                  +  + +       L + SP M +V+ LA +A    IP++I+GE GVGK+ L+R
Sbjct: 125 LEEEVRRMRRRASGALGFKDLASKSPDMERVIRLAERAAKSNIPVLIEGESGVGKEVLAR 184

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            I  SG R   PF  VNCG I ++ +E  LFG +    T  + + +GKF+EA+GGT+ L+
Sbjct: 185 AIQGSGDRRGKPFVTVNCGAIPENLVESTLFGHEKGAFTGATEKHVGKFVEASGGTLFLD 244

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL  Q ++   ++ G+++    + A+R+D+RLI  T ++LL  VK   FR+DLYY
Sbjct: 245 EIGELPLDAQVKLLRALQEGEVDPVGGKRAVRVDIRLISATNRSLLDLVKQGKFREDLYY 304

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++VF + +  LR+R EDIP LV  F   F  +   +   I+ +A++LL++YPW  NV++
Sbjct: 305 RLNVFPMTLPPLRARREDIPDLVRSFCARFAAEEGKRLRGITAEAMALLSRYPWPGNVRQ 364

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           L+N L RAV+      LT   F  + ++ EG   R             G      +  + 
Sbjct: 365 LENALFRAVVLADGDELTVAEFPQIAAQVEGFDVRIPPLPVQAAMPAGGLEPVREIVRVE 424

Query: 420 QESIPAIG----QDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
                A+     + G+++ +  +E E+I  A++ YR +MSEV+RRLGIGRSTLYRK++E 
Sbjct: 425 VRDPHAMSLVVEETGDMKTMEAVEAEVIRFALQFYRGRMSEVSRRLGIGRSTLYRKLKEL 484

Query: 476 NIEVD 480
            ++ D
Sbjct: 485 GLDED 489


>gi|170741334|ref|YP_001769989.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Methylobacterium sp. 4-46]
 gi|168195608|gb|ACA17555.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylobacterium sp. 4-46]
          Length = 495

 Score =  239 bits (611), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 161/491 (32%), Positives = 260/491 (52%), Gaps = 29/491 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLS----TISKIQVNVIFLSLINCED-DK 67
           VLI+D D  Q ++ +  V   G++  +    + +         +V+V+ L L+     D 
Sbjct: 5   VLIVDDDPVQRRLAEAMVRRLGFEAAVAEGGEAALAVLRAPDTRVDVVLLDLVMPGGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +L  +      VP+IVQT   +I  +   +    + F +     ++L  SI  AL+  
Sbjct: 65  LGVLAEMRKAGLDVPVIVQTANGSIDAVVTAMRAGATDFVVKPAGAERLQVSIKNALQ-- 122

Query: 128 VVPSQENE----------HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
            V   ++E            +   L + SP M +V+ LA +A    IP++I+GE GVGK+
Sbjct: 123 -VDQLQDEIRRMRRRASGALSFKDLTSKSPDMGRVIRLAERAAKSNIPVLIEGESGVGKE 181

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            L+R I  SG+R   PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT
Sbjct: 182 VLARAIQGSGERRGKPFVTVNCGAIPDNLVESTLFGHEKGAFTGATERHVGKFVEASGGT 241

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   LPL  Q ++   ++ G+++    R ++R+D+RLI  T ++LL  VK   FR+
Sbjct: 242 LFLDEIGELPLDAQVKLLRALQEGEVDPVGGRKSVRVDIRLISATNRSLLDLVKQGRFRE 301

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DLYYR++VF + +  LR+R EDIP L   F   F  +   +   I+ +A++LLT+Y W  
Sbjct: 302 DLYYRLNVFPMTLPPLRARREDIPDLARSFCARFAAEEGKRVRGITAEAMALLTRYEWPG 361

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           NV++L+N L RAV+      LT   F  + ++    E       A     E  +S   L 
Sbjct: 362 NVRQLENALFRAVVLADGDELTVAEFPQIAAQVDGFEVRI---PAAPSLPEAVASAAPLR 418

Query: 417 NLSQ------ESIPAIGQD-GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
            + +       +I  + ++ GE++ +  +E EII  A++ YR +MSEV+RRLGIGRSTLY
Sbjct: 419 EIVRVEVRDPHAISLVAEETGEMKTMEGLEGEIIRYALQFYRGRMSEVSRRLGIGRSTLY 478

Query: 470 RKIREYNIEVD 480
           RK+++  I+ D
Sbjct: 479 RKLKDLGIDED 489


>gi|220920261|ref|YP_002495562.1| Fis family two component sigma54 specific transcriptional regulator
           [Methylobacterium nodulans ORS 2060]
 gi|219944867|gb|ACL55259.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylobacterium nodulans ORS 2060]
          Length = 495

 Score =  239 bits (609), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 158/490 (32%), Positives = 260/490 (53%), Gaps = 27/490 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLS----TISKIQVNVIFLSLINCED-DK 67
           VLI+D D  Q ++ +  V   G++  +    + +          ++V+ L L+     D 
Sbjct: 5   VLIVDDDPVQRRLAEAMVRRLGFEAIVAEGGEAALACLRAPDAGIDVVLLDLVMPGGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-- 125
             +L  +       P+IVQT   +I  +   +      F +     ++L  SI  AL+  
Sbjct: 65  LGVLAEMRRSAIDTPVIVQTANGSIDAVVTAMRAGAIDFVVKPAGAERLQVSIKNALQVD 124

Query: 126 ---EGVVPSQENEHCAL--DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
              + +   +     AL    L + SP M +++ LA +A    IP++I+GE GVGK+ L+
Sbjct: 125 QLQDEIRRMRRRASGALTFKDLTSKSPDMGRIIRLAERAAKSNIPVLIEGESGVGKEVLA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R I  SG+R   PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGT+ L
Sbjct: 185 RAIQGSGERRGKPFVTVNCGAIPDNLVESTLFGHEKGAFTGATERHVGKFVEASGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL  Q ++   ++ G+++    R ++R+D+RLI  T ++LL  VK   FR+DLY
Sbjct: 245 DEIGELPLDAQVKLLRALQEGEVDPVGGRKSVRVDIRLISATNRSLLDLVKQGRFREDLY 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF + +  LR+R EDIP L   F   F  +   +  +I+ +A++L+T+Y W  NV+
Sbjct: 305 YRLNVFPMTLPPLRARREDIPDLARSFCARFAAEEGKRVRAITPEAMALITRYDWPGNVR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKEREFHTE-TACTCYTEGKSSDTILDN 417
           +L+N L RAV+      LT   F  + ++ EG     F     A     E  ++   L  
Sbjct: 365 QLENALFRAVVLADGDELTVAEFPQIAAQVEG-----FDVRIPAAPSLPEAVAASAPLRE 419

Query: 418 LSQ------ESIPAIGQD-GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
           + +       +I  + ++ GE++ +  +E EII  A++ YR +MSEV+RRLGIGRSTLYR
Sbjct: 420 IVRVEVRDPHAISLVSEESGEMKTMEGLEGEIIRYALQFYRGRMSEVSRRLGIGRSTLYR 479

Query: 471 KIREYNIEVD 480
           K+++  I+ D
Sbjct: 480 KLKDLGIDED 489


>gi|299132061|ref|ZP_07025256.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Afipia sp. 1NLS2]
 gi|298592198|gb|EFI52398.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Afipia sp. 1NLS2]
          Length = 498

 Score =  239 bits (609), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 159/482 (32%), Positives = 241/482 (50%), Gaps = 24/482 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTI----SKIQVNVIFLSLINCEDDKE 68
           +LI D D  Q +++++ V+  GY   +V   D +          V+ I L L+    D  
Sbjct: 5   ILIADDDAVQRRLLENMVQRCGYQTIVVESGDAAMTVIADEMRTVDAIVLDLVMPGLDGL 64

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
            +L  + +    +P++VQT    I  +   +      F +  V  ++L  S+  AL    
Sbjct: 65  GVLSKMREMGLHIPVVVQTAHGGIDNVVSAMRAGAHDFVVKPVGIERLQVSLRNALDASA 124

Query: 129 VPS--QENEHC-----ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           +    Q   H          ++  S AM  V+ + +KA   AIP++I+GE GVGK+ ++R
Sbjct: 125 LKGELQRIRHSREGRLTFKDIVTRSEAMGHVLAMGKKAAASAIPVLIEGESGVGKELVAR 184

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            IH S +RA  PF  VNCG I  + +E  LFG +    T  + +  GKF+EA+GGT+ L+
Sbjct: 185 AIHGSSERASKPFVTVNCGAIPDNLVESILFGHEKGAFTGATERHAGKFVEASGGTLFLD 244

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL  Q ++   ++ G++E    R  +++DVR+I  T +NLL  VK+  FR DL+Y
Sbjct: 245 EVGELPLTAQVKLLRALQQGEVEAVGGRKPVKVDVRIISATNRNLLNHVKAGHFRDDLFY 304

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R+ V  + I  LRSR EDIP L+  FL  F  +       +   A++ L    W  NV++
Sbjct: 305 RLHVLPLTIPPLRSRREDIPHLLRHFLARFSAEENRAIARVGADAMARLVNADWPGNVRQ 364

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETA-CTCYTEGKSSDTILDNLS 419
           L+N + RAV+      L  D F  +    G    +   E    T     + +   +    
Sbjct: 365 LENAVYRAVVLSDGEELRADDFPAI--NGGPLGPDAGPEIGPLTLAQPARVAAHEIPIAP 422

Query: 420 QESIPA---------IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
            +S PA         + +DGE R L ++E EII  A+  YR QMSEVARRL IGRSTLYR
Sbjct: 423 AQSAPALLPHGALTMLDEDGECRALDEMEAEIIRFAISHYRGQMSEVARRLKIGRSTLYR 482

Query: 471 KI 472
           K+
Sbjct: 483 KM 484


>gi|182677143|ref|YP_001831289.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Beijerinckia indica subsp. indica ATCC 9039]
 gi|182633026|gb|ACB93800.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Beijerinckia indica subsp. indica ATCC 9039]
          Length = 517

 Score =  238 bits (606), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 155/499 (31%), Positives = 254/499 (50%), Gaps = 42/499 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ--------------VNVIF 57
           R+LI D D  Q ++++  V+ +GY    V+ +  + +++++              ++++ 
Sbjct: 4   RILIADDDPVQRRLLEAQVQRFGYVTETVD-NGAAALARVKAQGQAQGQGHGHAPLDLLI 62

Query: 58  LSLINCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLC 117
           L L   + D   +LK +  +   VP IVQT   +I+ +   +    + F +  V  ++L 
Sbjct: 63  LDLAMPDIDGLGVLKTLRKEGYRVPAIVQTANGSIETVIAAMRAGAADFVVKPVGTERLQ 122

Query: 118 DSIICALREGVVPSQ---ENEHCA----LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQG 170
            SI  ALR   +  +    N H A       LIA S AM +V+ L  +A    IPI+++G
Sbjct: 123 VSIKNALRADALEDEIRRMNRHAAGALSFKDLIAGSEAMERVIRLGERAAKSTIPILLEG 182

Query: 171 EFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKF 229
           E GVGK+ ++R I     R   PF  VNCG + +  +E  LFG +    T  + + +GKF
Sbjct: 183 ESGVGKEVIARAIQGLSDRRGKPFITVNCGALPEPLVESILFGHEKGAFTGANERHVGKF 242

Query: 230 IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQV 289
           +EANGGT+ L+E   LPL  Q ++   ++ G+++   ++  +++D+RLI  T +NL+ QV
Sbjct: 243 VEANGGTLFLDEIGELPLETQVKLLRALQEGEVDPIGAKRPVKVDIRLISATNRNLIEQV 302

Query: 290 KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLL 349
           K   FR+DLYYR++VF I++  LR+R EDI  L   F   F  +       ++ +  +LL
Sbjct: 303 KRGRFREDLYYRLNVFPIHVPALRARREDITELARTFATRFAAEEGKPLRGLTPETEALL 362

Query: 350 TKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGK 409
             Y W  NV++L+N + RAV+      LT   F  + +         H      C     
Sbjct: 363 CAYDWPGNVRQLENAVFRAVVLADGDELTVTEFPQIAA---------HVHGFDICVPPAP 413

Query: 410 SSDTILDNLSQESIPA----------IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVAR 459
               +      E +P           +  +GE+  L  +E EII  ++  YR QMS +AR
Sbjct: 414 LPVALQPARETEFVPVELRDPHVLRLLDDEGEILPLERLEAEIIRFSLIHYRGQMSAMAR 473

Query: 460 RLGIGRSTLYRKIREYNIE 478
           +LGIGRSTLYRK++EY ++
Sbjct: 474 KLGIGRSTLYRKLKEYGLQ 492


>gi|163852172|ref|YP_001640215.1| sigma-54 factor interaction domain-containing protein
           [Methylobacterium extorquens PA1]
 gi|218530930|ref|YP_002421746.1| Fis family transcriptional regulator [Methylobacterium
           chloromethanicum CM4]
 gi|240139504|ref|YP_002963979.1| two-component sigma-54 specific transcriptional regulator, Fis
           subfamily; with N-terminal response receiver, GAF and
           putative ATPase domains [Methylobacterium extorquens
           AM1]
 gi|254561918|ref|YP_003069013.1| two-component sigma-54 specific nitrogen transcriptional regulator
           [Methylobacterium extorquens DM4]
 gi|163663777|gb|ABY31144.1| sigma-54 factor interaction domain-containing protein
           [Methylobacterium extorquens PA1]
 gi|218523233|gb|ACK83818.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylobacterium chloromethanicum CM4]
 gi|240009476|gb|ACS40702.1| two-component sigma-54 specific transcriptional regulator, Fis
           subfamily; with N-terminal response receiver, GAF and
           putative ATPase domains [Methylobacterium extorquens
           AM1]
 gi|254269196|emb|CAX25162.1| two-component sigma-54 specific transcriptional regulator, Fis
           subfamily; with N-terminal response receiver, GAF and
           putative ATPase domains [Methylobacterium extorquens
           DM4]
          Length = 496

 Score =  237 bits (604), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 160/483 (33%), Positives = 260/483 (53%), Gaps = 17/483 (3%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDLSTI--SKIQVNVIFLSLINCED-DKE 68
           VLIID D  Q ++ +  V   G+   I  N  D   +  S   V+V+ L L+     D  
Sbjct: 5   VLIIDDDPVQRRLAEAMVRRLGFQAQIAENGHDGLNLLRSGESVDVVLLDLVMPGGMDGL 64

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR--- 125
           ++L  +       P+IVQT+  +I  +   +      F +     ++L  SI  ALR   
Sbjct: 65  SVLAEMRKSGIDTPVIVQTSNGSIDAVVNAMRAGAVDFVVKPAGAERLQVSIKNALRVDQ 124

Query: 126 ----EGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
                  +  + +       L + SP M +V+ LA ++    IP++I+GE GVGK+ L+R
Sbjct: 125 LEEEVRRMRRRASGALGFKDLASKSPDMERVIRLAERSAKSNIPVLIEGESGVGKEVLAR 184

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            I  SG R    F  VNCG I ++ +E  LFG +    T  + + +GKF+EA+GGT+ L+
Sbjct: 185 AIQGSGDRRGKAFVTVNCGAIPENLVESTLFGHEKGAFTGATEKHVGKFVEASGGTLFLD 244

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL  Q ++   ++ G+++    + A+R+D+RLI  T ++LL  VK   FR+DLYY
Sbjct: 245 EIGELPLDAQVKLLRALQEGEVDPVGGKRAVRVDIRLISATNRSLLDLVKQGKFREDLYY 304

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++VF + +  LR+R EDIP LV  F   F  +   +   I+ +A++LL++YPW  NV++
Sbjct: 305 RLNVFPMTLPPLRARREDIPDLVRSFCARFAAEEGKRLRGITAEAMALLSRYPWPGNVRQ 364

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKER--EFHTETACTCYTEGKSSDTI-LD 416
           L+N L RAV+      LT   F  + ++ EG   R     T+ A          + + ++
Sbjct: 365 LENALFRAVVLADGDELTVAEFPQIAAQVEGFDVRIPPLPTQAALPAGGLEPVREIVRVE 424

Query: 417 NLSQESIPAIGQD-GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
                ++  + +D G+++ +  +E E+I  A++ YR +MSEV+RRLGIGRSTLYRK++E 
Sbjct: 425 VRDPHAMSLVVEDTGDMKTMEAVEAEVIRFALQFYRGRMSEVSRRLGIGRSTLYRKLKEL 484

Query: 476 NIE 478
            ++
Sbjct: 485 GLD 487


>gi|300024142|ref|YP_003756753.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Hyphomicrobium denitrificans ATCC 51888]
 gi|299525963|gb|ADJ24432.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Hyphomicrobium denitrificans ATCC 51888]
          Length = 502

 Score =  236 bits (603), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 155/496 (31%), Positives = 256/496 (51%), Gaps = 28/496 (5%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           KRVLI+D D  Q +I+++ V+ +G++       +     L +  +  + ++ L L+    
Sbjct: 3   KRVLIVDDDPAQRRILEETVKRFGFETKTCGSGEQALQILESQERDPIALVILDLVMPGV 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D   +L+ +     + PIIVQT   +I+     +      F +   S ++L  SI  AL+
Sbjct: 63  DGMAVLERVGHAQGMPPIIVQTAHGSIETAINAMRRGAVDFVVKPASPERLEVSIKSALK 122

Query: 126 EGVVPSQENE-------HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
              +  + N              L+    AM +V+ L ++A    IP++I+GE GVGK+ 
Sbjct: 123 IEALAGEINRIKKKVEGTLTFGDLVMRGDAMKRVISLGKRAAASTIPVLIEGESGVGKEL 182

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R I    +R   PF  VNCG I ++ +E  LFG +    T    + +GKF EA+GGT+
Sbjct: 183 IARAIQGESERVGRPFITVNCGAIPENLVESILFGHEKGAFTGAVDKRIGKFQEADGGTL 242

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL  Q ++   ++ G+I+   S+  ++++ RLI  T ++++  VK   FR+D
Sbjct: 243 FLDEVGELPLDAQVKLLRALQEGEIDPVGSKKPVKVNFRLISATNRDMIQLVKDGKFRED 302

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LYYR++VF I +  LR R +D+P L   F   F  +   +  +IS++A++LL  Y W  N
Sbjct: 303 LYYRLNVFPIFVPPLRERIDDVPELARHFAARFAAEEGKRVAAISERAMALLQAYSWPGN 362

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSR-------EGKKEREFHTETACTCYTEGKS 410
           V++L+N + RAV+      LT   F  + +                  + A T      +
Sbjct: 363 VRQLENTIFRAVVLADGPELTVAEFPQIAAHVDGFEAEIPAAPAAVQKQPAYTGPALIGA 422

Query: 411 SDTILDNL--------SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLG 462
            +T+   +        S   I A+ +DGE+R L  IE ++I LA+  YR  M+EVA+RL 
Sbjct: 423 ENTVPHTVEIKSTASGSSLGIQAVAEDGEIRSLEAIEADMIRLALGRYRGHMTEVAKRLN 482

Query: 463 IGRSTLYRKIREYNIE 478
           IGRSTLYRK++EY +E
Sbjct: 483 IGRSTLYRKMQEYGLE 498


>gi|302384082|ref|YP_003819905.1| Fis family transcriptional regulator [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302194710|gb|ADL02282.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Brevundimonas subvibrioides ATCC 15264]
          Length = 481

 Score =  234 bits (597), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 152/480 (31%), Positives = 245/480 (51%), Gaps = 20/480 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ----VNVIFLSLINCEDD 66
           K VL++D D  Q ++++  ++  GY V +   S    I ++      +V+ L L+     
Sbjct: 3   KTVLVVDDDPTQRRLVQAVLDREGY-VVVHAESGGEAIDRLTKGGGADVVLLDLVMPGMS 61

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
               L  I       P+IV T    I+ +   +      FF+   S +++   I  AL+ 
Sbjct: 62  GMEALAEIRTAGVTTPVIVLTANGGIETVVKAMQAGAQDFFIKPASPERILVGIRNALQL 121

Query: 127 GVVPSQEN---EHCA----LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
             + ++     +H A       L+  S  M  V  L  +A    IP++I GE GVGK+ +
Sbjct: 122 TQLTAEVGRLKKHVAGRVTFADLVGDSRPMQMVKQLGTRAARSTIPVLITGESGVGKEVI 181

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIV 238
           +R +H +  RA  PF  VNCG +  + +E  LFG      T  S + LGKF+EANGGT+ 
Sbjct: 182 ARALHGASDRAGKPFVAVNCGALPANLVESILFGHEKGSFTGASDKHLGKFMEANGGTLF 241

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   LPL +Q ++   ++ G+I+   ++ A+++DVR++  T ++L   V    FR+DL
Sbjct: 242 LDEIGELPLDMQVKLLRALQEGEIDPVGAKRAVKVDVRIVSATNRDLSSAVAEGRFREDL 301

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +YR++VF I   +LR R EDIP L+  F+  F  +   +    +   L+LLT + W  NV
Sbjct: 302 FYRLNVFPIEAPSLRERREDIPALIDHFIGRFNVEEGKRIAGAAPDTLALLTAFDWPGNV 361

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNL 418
           ++L+N + RA++      L    F  +       E       A   Y +       L  L
Sbjct: 362 RQLENTIYRAIVLADAPFLQSHDFPAISGIAMPLEPHDRPSAAIVSYAD-------LPPL 414

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            ++ I  + + G +R L DIE+++I  A+++Y   MSE+ARRLGIGRSTLYRK+RE  +E
Sbjct: 415 PEQPIRILDERGHLRTLEDIERDLIQHAIEVYAGHMSEIARRLGIGRSTLYRKVREQGLE 474


>gi|329890416|ref|ZP_08268759.1| mutant NtrC-like activator [Brevundimonas diminuta ATCC 11568]
 gi|328845717|gb|EGF95281.1| mutant NtrC-like activator [Brevundimonas diminuta ATCC 11568]
          Length = 489

 Score =  233 bits (594), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 155/485 (31%), Positives = 246/485 (50%), Gaps = 22/485 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ----VNVIFLSLINCEDD 66
           K VL++D D  Q ++I+  ++  GY V     S    I ++      +V+ L L+     
Sbjct: 3   KTVLVVDDDPTQRRLIQAVLDREGYAVVHAE-SGGEAIDRLTKGGGADVVLLDLVMPGLS 61

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
               L  +       P+IV T    I+ +   +      FF+  V   +L   +  AL+ 
Sbjct: 62  GMEALAEMRTAGVATPVIVLTANGGIETVVKAMQAGAQDFFVKPVGPDRLLVGVRNALQM 121

Query: 127 -------GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
                  G +  +     + D ++  S  M  V  L ++A   +IP++I GE GVGK+ +
Sbjct: 122 TQLTAEIGRLKKRATGRSSFDDMVGDSEPMRMVKALGQRAAKSSIPVLITGESGVGKEVI 181

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R +H +  RA  PF  VNCG +  + +E  LFG +    T    +  GKF+EANGGT+ 
Sbjct: 182 ARALHGASDRAGKPFVAVNCGALPANLVESILFGHEKGAFTGAHEKHAGKFVEANGGTLF 241

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   LPL +Q ++   ++ G+++    +  +++DVR++  T ++   QVK   FR+DL
Sbjct: 242 LDEIGELPLDMQVKLLRALQEGEVDPVGGKRPVKVDVRIVSATNRDPAQQVKEGAFREDL 301

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +YR++VF I    LR R EDIP LV  F+  F  +   +    S + L+LL  + W  NV
Sbjct: 302 FYRLNVFPIEAPALRERREDIPALVEHFIARFNVEEGKRVAGCSPETLALLQGHDWPGNV 361

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKK----EREFHTETACTCYTEGKSSDTI 414
           ++L+N + RA++ L DS L +      +S               E A    +E  SSD  
Sbjct: 362 RQLENAVYRALV-LADSPLLQPHDFPAISGVAVPLDAVAAPPSGEHAPASASESVSSD-- 418

Query: 415 LDNLSQESIPAIGQD-GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
            ++   +S   I  D G VR L  IE+++I  A+++Y   MSE+ARRLGIGRSTLYRK+R
Sbjct: 419 -EDAQHDSPVRITDDRGHVRTLEQIERDLIQHAIEVYSGHMSEIARRLGIGRSTLYRKVR 477

Query: 474 EYNIE 478
           E  +E
Sbjct: 478 EQGLE 482


>gi|254418366|ref|ZP_05032090.1| Sigma-54 interaction domain family [Brevundimonas sp. BAL3]
 gi|196184543|gb|EDX79519.1| Sigma-54 interaction domain family [Brevundimonas sp. BAL3]
          Length = 482

 Score =  226 bits (576), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 149/480 (31%), Positives = 244/480 (50%), Gaps = 19/480 (3%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKI----QVNVIFLSLINCEDD 66
           K VL++D D  Q ++++  +E  GY V +        I ++      +++ L ++  E  
Sbjct: 3   KTVLVVDDDPTQRRLLQAVLERDGYAV-VHAAGGGEAIDRMLRGGGADMLLLDMVMPEMS 61

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
               L  +       P+IV T    I  +   +      FF+  V  ++L   +  AL+ 
Sbjct: 62  GLECLAELRSAGVTTPVIVLTANGGIDTVVKAMQAGAQDFFVKPVGPERLLVGVRNALKM 121

Query: 127 -------GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
                  G +  +     + D +I  S  M  V  L  +A   +IP++I GE GVGK+ +
Sbjct: 122 TQLTAEVGRLTKRAQGRASFDDIIGDSAPMRMVKALGTRAAKSSIPVLITGESGVGKEVI 181

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R +H +  RA  PF  VNCG +  +  E  LFG +    T    + LGKF EA+GGT+ 
Sbjct: 182 ARALHGASDRAGKPFVAVNCGALPANLAESILFGHEKGAFTGAVDKTLGKFREADGGTLF 241

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   LPL +Q ++   ++  +I+    +  +++DVR++  T ++   QVK   FR+DL
Sbjct: 242 LDEIGELPLDLQVKLLRALQESEIDPVGGKRPVKIDVRIVSATNRDPAQQVKDGAFREDL 301

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +YR++VF I   +LR R EDIP LV  F+  F  +   + ++ + +  ++L  + W  NV
Sbjct: 302 FYRLNVFPIEAPSLRDRREDIPALVDHFIARFNAEEGKRIVACAPETQAMLQAFDWPGNV 361

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNL 418
           ++L+N + RA++ L DS   +      +S       E  T  A T       S   L  L
Sbjct: 362 RQLENAVFRAIV-LADSPFLQPYDFPSISGVVAPMPEATTTPAQTA-----PSYADLPPL 415

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            ++ I  +   G +R L DIE+++I  A+++Y   MSE+ARRLGIGRSTLYRK+RE  +E
Sbjct: 416 PEQPIRILDDRGHLRTLEDIERDLIQHAIEVYAGHMSEIARRLGIGRSTLYRKVREQGLE 475


>gi|90418904|ref|ZP_01226815.1| putative sigma-54 depenedent response regulator [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90336984|gb|EAS50689.1| putative sigma-54 depenedent response regulator [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 491

 Score =  226 bits (576), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 156/488 (31%), Positives = 243/488 (49%), Gaps = 21/488 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGY-----DVFIVNVSDLSTISKIQVNVIFLSLINCEDDK 67
           VLI+D D  Q ++++  ++  G      D  +  +  L      +++ I L L+  +   
Sbjct: 5   VLIVDDDPIQRRLVEAQIDRMGLRPLTCDGGLAALRALDAHQPGEISAIVLDLMMPDKGG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             ++  +  +   +P+IVQT + +I  +   +      F +  VS  +L   I  AL+  
Sbjct: 65  SEVMAEMRRRHLDIPVIVQTGKGSIDTVVEAMRAGAFDFIVKPVSPDKLKSVIDSALKMR 124

Query: 128 VVPSQENEHCA----LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
              ++     A    LD   A SPA+  V+  A KA    IP++I GE GVGK+ L+  I
Sbjct: 125 GAATRRTTSKARAVRLDQGDA-SPALRPVLAAAAKAARSGIPVLISGETGVGKEWLASAI 183

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ-FLGKFIEANGGTIVLEEP 242
              G RA  PF  VNCG +  D +E  LFG       ++ Q   GKF EANGGT++L+E 
Sbjct: 184 QAGGDRAKAPFVKVNCGALPGDLVESILFGHAKGAFTDAGQPHEGKFAEANGGTLLLDEV 243

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             L  + Q ++   ++ G I+    R A++ DVR+I  T ++L   V +  FR+DLYYR+
Sbjct: 244 GELSASAQVKLLRVLQDGVIDPVGGRQAVKTDVRIISATNRDLAAGVTAGRFREDLYYRL 303

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI-SISDKALSLLTKYPWIDNVQEL 361
           + F + +  LR R  +I  L   F+  +        +  ++  A++LL +Y W  N+++L
Sbjct: 304 NAFELTVPPLRERRSEIAKLARRFVDRYVAMEPQSPVRHLAADAIALLQRYDWPGNIRQL 363

Query: 362 KNILLRAVIGLKDSHLTEDRF--VLLLSREGKKEREF---HTETACTCYTEGKSSDTILD 416
           +N + RAV+  +   LT   F  +  L   G  E E    H  +     T          
Sbjct: 364 ENAIHRAVVLGESESLTAADFPQIAALIAAGPAEAEVADAHAASHAGHGTRAPGDTAPAA 423

Query: 417 NLSQESIPA----IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
           N      PA      Q+GEVRR+ ++E ++I LA   Y  +MSE+ARRLGIGRSTLYRK+
Sbjct: 424 NGHGRGEPADFAVRDQNGEVRRVEEVEADLIRLAHAQYHGRMSEIARRLGIGRSTLYRKM 483

Query: 473 REYNIEVD 480
           REY I+ D
Sbjct: 484 REYKIDAD 491


>gi|304393277|ref|ZP_07375205.1| acetoacetate metabolism regulatory protein AtoC [Ahrensia sp.
           R2A130]
 gi|303294284|gb|EFL88656.1| acetoacetate metabolism regulatory protein AtoC [Ahrensia sp.
           R2A130]
          Length = 508

 Score =  224 bits (570), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 160/492 (32%), Positives = 254/492 (51%), Gaps = 28/492 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLINCEDDK 67
           +LI D +  Q +I+++ +   GY    V      ++ L++     V  + L L+    D 
Sbjct: 5   ILIADDEPVQRRILENTILKLGYRCQQVEDGEAALAHLASPQGANVAAVILDLVMPGLDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-- 125
             +L  + ++    P+IVQT+Q +I  +   +      F +  VS ++L  SI  AL+  
Sbjct: 65  MGVLARMREQGLSQPVIVQTSQGSIDAVVSAMRAGACDFCVKPVSFERLKVSIANALKFD 124

Query: 126 --EGVVPSQENEHCA---LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
             E  V   E           +IA SPAM + +DL R+A    IP++I+GE GVGK+ ++
Sbjct: 125 AMESAVRRVERAGTGTFTFADMIASSPAMDRAMDLGRRAAASTIPVLIEGESGVGKEVIA 184

Query: 181 RFIH-ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           R I  ES KR   PF  VNCG + ++  E  LFG +    T      +GKF +A+GGT+ 
Sbjct: 185 RAIQGESAKRGK-PFITVNCGALPENLAESILFGHEKGAFTGADRAHVGKFKQADGGTLF 243

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   L L +Q ++   I+ G+I+   SR  ++ DVRLI  T ++++ QVK+  FR+DL
Sbjct: 244 LDEVGELSLELQVKLLRAIQEGEIDPVGSRKPVKTDVRLISATNRDMIAQVKAGEFREDL 303

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI-SISDKALSLLTKYPWIDN 357
           YYR++VF + +  LR R EDI  L   F      +   + I  +S +A++LL +Y W  N
Sbjct: 304 YYRLNVFPLTVPPLRKRVEDIAPLAQHFAARIALEEGRRGIQGLSREAIALLGEYDWPGN 363

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKK-EREFHTETACTCYTEGKSSDTILD 416
           V++L+N + RAV+    + LT   F  +L+  GK       +  A    T   +  +I  
Sbjct: 364 VRQLENAIFRAVVLCDGAELTPTEFPQILAALGKDVPLPLPSSMASKPRTVVDAVVSIAP 423

Query: 417 NL-----SQESIPAIGQ------DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGR 465
            L     S E +   G       +G VR L ++E + I  A+  +R +M+ VAR L IGR
Sbjct: 424 ELPVMQASSEPVQHYGSARLLNDEGAVRALEEVEADAIRFAIDHHRGRMTRVARSLRIGR 483

Query: 466 STLYRKIREYNI 477
           STLYR+++E  +
Sbjct: 484 STLYRRLKELGL 495


>gi|307293944|ref|ZP_07573788.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sphingobium chlorophenolicum L-1]
 gi|306880095|gb|EFN11312.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sphingobium chlorophenolicum L-1]
          Length = 482

 Score =  214 bits (544), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 140/484 (28%), Positives = 243/484 (50%), Gaps = 31/484 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +++ID +  Q +++       G+     N  D     L T   ++++ + L   +   + 
Sbjct: 9   LMLIDDEPAQRRLVSALAARAGWRTIFANDGDTAIATLGTQDGMRLDAVLLDQWSPSYEP 68

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL--- 124
             +++ +  + P +PI++ T  +N+ +    +    + +    ++ ++L  ++   L   
Sbjct: 69  TGLIRELRARRPALPIMILTAHNNVAVAVEAMRAGATDYLAKPIAPERLLAALNATLNGE 128

Query: 125 --REGVVPSQENEHCAL--DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
             +  + P  E    AL  + ++  +P     + +A KA    +P++I+GE GVGK  L+
Sbjct: 129 HGKGELRPLTEKIPAALSFEDVVGAAPQFRAALAIAAKAARARVPVLIEGESGVGKDVLA 188

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R IH +  R       VNCG I  + +E  LFG +    T    + +GKF+ A+ GTI L
Sbjct: 189 RAIHAASPRHKQAMITVNCGAIPANLVESDLFGHERGAFTGAFDRQVGKFVAADMGTIFL 248

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +PL  Q ++   ++ G+++   +R  I +DVR+I  T K L  ++++  FR+DLY
Sbjct: 249 DEVSEMPLDAQVKLLRVLQDGEVQPIGARRPIHVDVRVIAATNKRLHDEIEAGRFREDLY 308

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + I  LR R  D+P L    L     +  ++ + ++D AL+LL ++ W  NV+
Sbjct: 309 YRLNVVQLTIPPLRDRLGDVPALCRHLLTRIAGQPGMRGLGLTDDALALLMQHDWPGNVR 368

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N L RA +  +   LT   F          E   H     T    G +    L  + 
Sbjct: 369 QLQNALFRAAVLCEGDALTAQDF---------PEIAAHIRGRAT----GDTPQARLRAVP 415

Query: 420 QESIPAIG-----QDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
           Q    A G      DG VR+L++IE ++I LA+  YR +M+EVARRLGIGRSTLYRK+ E
Sbjct: 416 QPHREAAGITLFESDGHVRQLAEIEADVIRLAIGHYRGRMTEVARRLGIGRSTLYRKLAE 475

Query: 475 YNIE 478
             I+
Sbjct: 476 LGID 479


>gi|294012551|ref|YP_003546011.1| two-component system response regulator HydG [Sphingobium japonicum
           UT26S]
 gi|292675881|dbj|BAI97399.1| two-component system response regulator HydG [Sphingobium japonicum
           UT26S]
          Length = 481

 Score =  213 bits (543), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 136/480 (28%), Positives = 245/480 (51%), Gaps = 24/480 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK 67
           +++ID +  Q +++       G+     N  D     L T   ++++ + L   +   + 
Sbjct: 9   LMLIDDEPAQRRLVSALAARAGWRTIFANDGDTAIAMLGTQDGMRLDAVLLDQWSPSYEP 68

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL--- 124
             +++ +  + P +PI++ T  +N+ +    +    + +    ++ ++L  ++   L   
Sbjct: 69  TGLVRELRARRPALPILILTAHNNVAVAVEAMRAGATDYLAKPIAPERLLAALNATLNGE 128

Query: 125 --REGVVPSQENEHCAL--DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
             +  + P  E    AL  + ++  +P     + +A KA    +P++I+GE GVGK  ++
Sbjct: 129 HGKGELRPLTEKIPAALSFEDVVGAAPQFRAALAIAAKAARARVPVLIEGESGVGKDVIA 188

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R IH +  R       VNCG I  + +E  LFG +    T    + +GKF+ A+ GTI L
Sbjct: 189 RAIHAASPRHKQAMITVNCGAIPANLVESDLFGHERGAFTGAFDRQVGKFVAADMGTIFL 248

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +PL  Q ++   ++ G+++   +R  I +DVR+I  T K L  ++++  FR+DLY
Sbjct: 249 DEVSEMPLDAQVKLLRVLQDGEVQPIGARRPIHVDVRVIAATNKRLHDEIEAGRFREDLY 308

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + I  LR R  D+P L    L    T+  ++ + ++D AL+LL ++ W  NV+
Sbjct: 309 YRLNVVQLTIPPLRERLGDVPALCRHLLARIATQPGLRGLGLTDDALALLMQHDWPGNVR 368

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSR-EGKKEREFHTETACTCYTEGKSSDTILDNL 418
           +L+N L RA +  +   LT   F  + ++  G+   E          + G+       + 
Sbjct: 369 QLQNALFRAAVLCEGDALTPQDFPQIAAQIRGRAHGE----------SRGRLHAVPQPHR 418

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
               I     DG VR+L++IE ++I LA+  YR +M+EVARRLGIGRSTLYRK+ E  I+
Sbjct: 419 EAAGITLFEGDGHVRQLAEIEADVIRLAIGHYRGRMTEVARRLGIGRSTLYRKLAELGID 478


>gi|114706841|ref|ZP_01439741.1| response regulatory protein [Fulvimarina pelagi HTCC2506]
 gi|114537789|gb|EAU40913.1| response regulatory protein [Fulvimarina pelagi HTCC2506]
          Length = 476

 Score =  213 bits (543), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 151/484 (31%), Positives = 254/484 (52%), Gaps = 30/484 (6%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS----DLSTISKIQ-VNVIFLSLINCED 65
           ++VL++D D  Q +++   +   G      +      D+ T  K + V V+ L L+  + 
Sbjct: 3   RQVLVVDDDPIQRRLLDAQISRIGLQPIHCDGGRAALDVLTGPKARDVAVVVLDLLMPDK 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
               ++  +  +   +P++VQT +D+++ +   + +    F +  VS  +L   +  A+R
Sbjct: 63  SGTEVMAEMRRRSIEIPVVVQTAKDSVETVVAAMRSGAFDFIVKPVSPDRLRTVLTNAIR 122

Query: 126 EGVVPSQENEHCALDSL--IAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
             ++ ++ N     D+L    +   M  V+  A KA   AIP++I GE GVGK+ ++R I
Sbjct: 123 --MLETRPNPMRVPDNLRQTNLPEPMASVIASAAKAAKSAIPVLISGETGVGKECIARAI 180

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSA-QFLGKFIEANGGTIVLEEP 242
              G RA  PF  +NCG +  D +E  LFG V     ++A + +GKF EA+ GT+ L+E 
Sbjct: 181 QTWGPRAGKPFVTINCGALPSDLVESILFGHVKGAFTDAAKEHVGKFREADTGTLFLDEV 240

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             L  + Q ++   I+ G ++   +   +++DVR++  T ++LL  V    FRKDLYYR+
Sbjct: 241 GELSPSAQVKLLRVIQEGLVDPVGADSPVKVDVRILSATNQSLLAAVSQGRFRKDLYYRL 300

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFC-TKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           + F +++  LR R  +I  L   FLQ F  +++       S   + LL ++ W  N+++L
Sbjct: 301 NAFELSVPPLRQRRAEIASLAKEFLQRFTESESQSPARRFSSATVDLLERFDWPGNIRQL 360

Query: 362 KNILLRAVIGLKDSHLTEDRF-VLLLSREGKKEREFHT-------ETACTCYTEGKSSDT 413
           +N++ RAV+  +   L    F  L+L+ E ++  E  +       E +     +G +SD 
Sbjct: 361 ENVVHRAVVLAETETLQPSDFGALVLANEARQVAELRSPADQQLAEPSRQFSGQGSTSDL 420

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
           I D             GE+R+L +IE +II +A+  Y   MSEVARRLGIGRSTLYRK+R
Sbjct: 421 IRDG-----------RGELRKLDEIEADIIRIALDQYNGHMSEVARRLGIGRSTLYRKLR 469

Query: 474 EYNI 477
           EY I
Sbjct: 470 EYEI 473


>gi|218507839|ref|ZP_03505717.1| sigma-54-dependent transcriptional regulator (activator) protein
           [Rhizobium etli Brasil 5]
          Length = 350

 Score =  213 bits (542), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 123/310 (39%), Positives = 182/310 (58%), Gaps = 21/310 (6%)

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R I   G+R+  PF  VNCG I  + +E  LFG +    T  + + +GKF+EA+GGTI
Sbjct: 1   MARAIQSGGERSNKPFVTVNCGAIPHNLVESILFGHEKGAFTGATERHIGKFMEADGGTI 60

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL VQ ++   ++ G+IE   +R A +++VRLI  T K+L+ +VK+  FR+D
Sbjct: 61  FLDEIGDLPLEVQVKLLRAVQQGEIETVGARTAHKVNVRLISATNKDLIEEVKNGHFRED 120

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFC--TKNAIKQISISDKALSLLTKYPWI 355
           LYYR++VF I I  LR R EDIP LV  F   F    KN  ++++++  AL+LLT Y W 
Sbjct: 121 LYYRLNVFPITIPALRKRKEDIPHLVRVFADRFSGEQKNG-RRMTVNSGALALLTAYDWP 179

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI- 414
            N+++L+N + RAV+  +   LTE  F  + ++    E E     A      G   D   
Sbjct: 180 GNIRQLENAIFRAVVLAEGPELTEADFPQIAAQ--LPEYEVVDHLALVADNTGLDPDEAY 237

Query: 415 --------------LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARR 460
                         L   S+ +I ++   G+VR+L+D+E+E+I  A+K YR QMS+VAR+
Sbjct: 238 SEEYRAPPEVHHHRLSEASENAIASVNPSGDVRKLADVEEELIRFALKFYRGQMSQVARK 297

Query: 461 LGIGRSTLYR 470
           LGIGRSTLYR
Sbjct: 298 LGIGRSTLYR 307


>gi|94497182|ref|ZP_01303754.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [Sphingomonas sp. SKA58]
 gi|94423287|gb|EAT08316.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [Sphingomonas sp. SKA58]
          Length = 474

 Score =  207 bits (527), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 136/481 (28%), Positives = 244/481 (50%), Gaps = 25/481 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGY-DVFIVN----VSDLSTISKIQVNVIFLSLINCEDDK 67
           +++ID +  Q +++       G+  +F  +    ++ L T   + ++ + L   + + + 
Sbjct: 1   MMLIDDEPAQRRLVSALASRAGWRTIFAADAETALAMLGTQDGMLLDAVILDQWSPDYEP 60

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +++++  + P +PI+V T  +N+ +    +    S +    ++ ++L  ++   L +G
Sbjct: 61  SGLIRDLRAERPALPILVLTAHNNVAVAVEAMRAGASDYLSKPIAPERLLAALNATLADG 120

Query: 128 VV-----PSQENEHCAL--DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
                  P  E     L  + ++  +P     + +A KA    +P++I+GE GVGK  ++
Sbjct: 121 AAAGELRPLTEKITAPLSFEDVVGSAPQFRAALAIAAKAARARVPVLIEGESGVGKDVIA 180

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R +H +  R       VNCG I  + +E  LFG +    T    + +GKF+ A+ GTI L
Sbjct: 181 RAVHAASPRHKQAMVTVNCGAIPANLVESELFGHERGAFTGAFDRHVGKFVAADMGTIFL 240

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +PL  Q ++   ++ G+++   +R  + +DVR+I  T K L  ++++  FR+DLY
Sbjct: 241 DEVSEMPLDAQVKLLRVLQDGEVQPIGARRPVHVDVRVIAATNKRLSEEIEAGRFREDLY 300

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R  DIP L    L     +  ++ + ++D ALSLL ++PW  NV+
Sbjct: 301 YRLNVVQLTVPPLRERMGDIPALCRHLLARIAGQPGLRSLGLTDDALSLLMQHPWPGNVR 360

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLS--REGKKEREFHTETACTCYTEGKSSDTILDN 417
           +L+N L RA +      LT   F  + +  R G        +           +   L  
Sbjct: 361 QLQNALFRAAVLCDGDALTPQDFPQIAAQIRAGGMVDRMTPQVRSISQPHRDGAGITLFE 420

Query: 418 LSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           L          DG VR+L++IE ++I LA+  YR +M+EVARRLGIGRSTLYRK+ E  I
Sbjct: 421 L----------DGHVRQLAEIEADVIRLAIGHYRGRMTEVARRLGIGRSTLYRKLAELGI 470

Query: 478 E 478
           +
Sbjct: 471 D 471


>gi|326387699|ref|ZP_08209305.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Novosphingobium nitrogenifigens DSM 19370]
 gi|326207745|gb|EGD58556.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Novosphingobium nitrogenifigens DSM 19370]
          Length = 463

 Score =  207 bits (527), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 147/482 (30%), Positives = 234/482 (48%), Gaps = 39/482 (8%)

Query: 14  LIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLINCEDDKE 68
           ++ID +  QI+++       G+   +       ++ L T   +Q+  I L      D   
Sbjct: 1   MLIDDEPAQIRLVTALAAREGWRTIVARDAETAIATLGTRQGMQLGAIILDQWVPGDAAC 60

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
           +++  +  + P +PI++ TT ++  +    +    + + +  VS     D ++ ALR   
Sbjct: 61  HLISELKARRPALPILMLTTSNSPLLAVEAMRAGATDYLIKPVS----PDRMMQALRAAT 116

Query: 129 VP-SQENEHCAL----------DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
            P +Q +E   L          DS+I  + +    + +A KA      ++I+GE G GK+
Sbjct: 117 TPEAQRSELHPLTEKLEAALDFDSMIGAASSFRAALAIAAKAARTHAHVLIEGESGTGKE 176

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNS-AQFLGKFIEANGGT 236
            L R +H +  RA  P  IVN   I  ++IE  LFG        +  + +G    A+GGT
Sbjct: 177 MLVRAMHAASPRAKMPLRIVNAAGIPPNQIESVLFGHEKGAFAGAFERHVGALQHADGGT 236

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           +V++E D L L VQ R+  F+  G ++   +R + RLDVRLI  +   L   V S +   
Sbjct: 237 LVIDEIDRLALPVQRRLAQFLVRGDVQPIGARHSFRLDVRLIACSNAPLRDLVDSGLADA 296

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           +LY R+S  L+ + +LR R+ DIP L   FL     +  ++ + I+D AL+LL  Y W  
Sbjct: 297 ELYERLSGTLVRLPSLRERAGDIPALARHFLARIGEQPGLRPLGITDSALALLGAYDWPG 356

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           NV++L+  L RA +      LT   F  L +  G+  R                +  I D
Sbjct: 357 NVRQLQATLFRAAVFCDGEALTAQDFPNLSTMVGEAPRH---------------NAPISD 401

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
                 +   G DG +R L DIE ++I LA+  YR +M+EVARRLGIGRSTLYRK+ E  
Sbjct: 402 G---AGVMLFGPDGNLRPLEDIEADVIRLAIGHYRGRMTEVARRLGIGRSTLYRKLSELG 458

Query: 477 IE 478
           I+
Sbjct: 459 ID 460


>gi|87199859|ref|YP_497116.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Novosphingobium aromaticivorans DSM 12444]
 gi|87135540|gb|ABD26282.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Novosphingobium aromaticivorans DSM 12444]
          Length = 472

 Score =  204 bits (518), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 147/479 (30%), Positives = 228/479 (47%), Gaps = 31/479 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLINCEDDK 67
           +++ID +  Q ++I       G+   I       ++ L T   +Q+  I L      DD 
Sbjct: 9   LMLIDDEPAQCRLISALASREGWRTIIARDSESAIATLGTRQGMQLGAIILDQWVPGDDA 68

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL-RE 126
             ++  +  + P +PI++ TT  +  +    +    + + +  V+ ++L  ++  A  RE
Sbjct: 69  CTLIAELKARRPALPILMLTTSSSPLLAVEAMRAGATDYLIKPVAPERLLQALRSATSRE 128

Query: 127 GVV----PSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
                  P  E     LD  S+I  SPA    + +A KA      ++I+GE G GK+ L 
Sbjct: 129 TSASELQPLTEKIGATLDFDSMIGASPAFRAALAVAAKAARTHGTVLIEGESGTGKEMLV 188

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNS-AQFLGKFIEANGGTIVL 239
           R +H +  RA  P  IVN G     ++E  LFG        +  + +G F  A+GGT+V+
Sbjct: 189 RAMHAASPRAKAPLRIVNAGGTSASQLESALFGHEKGAFPGAFERNIGMFQHADGGTLVI 248

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E D LP +VQ R+  F+  G I+   +R + R+DVRLI      L   V    F  DL+
Sbjct: 249 DEVDRLPASVQERLVRFLTRGDIQPVGARHSFRVDVRLIVCANAGLRDLVHIGDFDADLH 308

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
             ++   + + +LR R  DIP L   FL     +  ++ + I+D AL+LL  Y W  NV+
Sbjct: 309 ALLTQTQVQLPSLRERPADIPALARHFLARIGEQPGLRPLGITDGALALLAAYDWPGNVR 368

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+  L RA +      LT   F  L +  G+  R           T+G           
Sbjct: 369 QLQATLFRAAVFCDGEALTAQDFPSLSNMIGEGSRR------APSVTDGA---------- 412

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
              I     DG +R L DIE ++I LA+  YR +M+EVARRLGIGRSTLYRK+ E  I+
Sbjct: 413 --GITLFAADGNLRPLEDIEADVIRLAIGHYRGRMTEVARRLGIGRSTLYRKLSELGID 469


>gi|85707879|ref|ZP_01038945.1| sigma-54 dependent DNA-binding response regulator [Erythrobacter
           sp. NAP1]
 gi|85689413|gb|EAQ29416.1| sigma-54 dependent DNA-binding response regulator [Erythrobacter
           sp. NAP1]
          Length = 490

 Score =  196 bits (498), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 142/488 (29%), Positives = 234/488 (47%), Gaps = 38/488 (7%)

Query: 8   DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLIN 62
           D  + V++ID +  Q ++I       G+   +       ++ L T   +Q++ I L    
Sbjct: 21  DDARIVMLIDDEPAQSRLITAIAAREGWRTVVAGDAETAIAMLGTREGMQLSAILLDQWV 80

Query: 63  CEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIIC 122
             DD  +++  + ++ P +PI++ TT  +  +    +    S + +  VS  +L +++  
Sbjct: 81  PGDDACSLIAELKERRPALPILMLTTSASPLLAVEAMRAGASDYLVKPVSPDRLMEALRA 140

Query: 123 -----ALREGVVPSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
                A R+ + P  E    +LD  ++I  +P     +  A KA       +I+GE G G
Sbjct: 141 VTTREAPRDELAPLTEKMSASLDFDAMIGTAPTFRTALAQAAKAARGHGHALIEGENGTG 200

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANG 234
           K+ L R +H +  RA     I+N   +  + IE  LFG + +       + +G     +G
Sbjct: 201 KEMLMRAMHAASPRAKENLRIINVASVPPNSIESVLFGHEPNAFPGAFDRQIGALQHCDG 260

Query: 235 GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF 294
           GT+VL+E D L +AVQ R+ + +ETG +    +    R+DVR++     NL   V+  +F
Sbjct: 261 GTLVLDEVDRLSMAVQTRLRDALETGIVRPVGAAHGFRVDVRILSAANSNLAQIVEGGLF 320

Query: 295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW 354
            + L  ++    I +  LR R+ DIP L   FLQ    +  +  +S+SD AL LL  + W
Sbjct: 321 DEILAEQLCATRIKLPPLRERTGDIPALTRHFLQRIGEQPGLTHLSVSDSALGLLGAFDW 380

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE----REFHTETACTCYTEGKS 410
             NV++L+++L RA +  +   LT D F  L    G+ E       H       YTE   
Sbjct: 381 PGNVRQLQSVLFRAAVYCEGDTLTADSFPQLSELIGELEAGCSSHLHEGVGVMLYTE--- 437

Query: 411 SDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
                             DG +R L +IE ++I LA+  YR +M+EVARRLGIGRSTLYR
Sbjct: 438 ------------------DGNLRPLEEIEADVIRLAIGHYRGRMTEVARRLGIGRSTLYR 479

Query: 471 KIREYNIE 478
           K+ +  I+
Sbjct: 480 KLSDLGID 487


>gi|332188928|ref|ZP_08390629.1| response regulator [Sphingomonas sp. S17]
 gi|332011039|gb|EGI53143.1| response regulator [Sphingomonas sp. S17]
          Length = 473

 Score =  195 bits (496), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 138/483 (28%), Positives = 230/483 (47%), Gaps = 38/483 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLS-----TISKIQVNVIFLSLINCEDDK 67
           +L+ID +  Q ++I    +  G+       +D++     +    +++ + +       D 
Sbjct: 9   LLLIDDEPAQRRLIAALAQRGGWRTLFATDADMAASIMGSAQGRELDAVLIDHWAPGADA 68

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             ++       P +PI++ T  D++      +    + F +     K L    + A  E 
Sbjct: 69  TALIAECHALRPELPILMLTANDSVAQAVAAMRAGATDFLV-----KPLAPERLLAALEA 123

Query: 128 VVPSQENEHC-----------ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
            V +Q +              A D ++  +P     + +A KA    + ++I+GE GVGK
Sbjct: 124 CVAAQTSGELRPLTEKIPALLAFDEIVGDAPEFRAALGVAAKAARARVAVLIEGEGGVGK 183

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNS-AQFLGKFIEANGG 235
           + L+  IH +  RA      VNC     + ++  +FG  +     +  + +GK +EA+G 
Sbjct: 184 ESLAEAIHVASPRAQREMVRVNCAATPANMLDSIIFGHEEGAFAGAFERRIGKIVEADGS 243

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T+ L+E   +PL  QGR+ + ++TG I    +R A  +DVR+I   +  LL  V++  FR
Sbjct: 244 TLFLDEIAGMPLDTQGRLLDMLQTGAIVPLGARHAREVDVRVIAAADGRLLEAVEAGRFR 303

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DLYY+++V  + I  LR R++DIP L    L     +  +  + I+D+AL LL +Y W 
Sbjct: 304 EDLYYKLNVVHVAIPPLRDRADDIPALTRHLLDRIAQQPGLFALDITDEALDLLRRYDWP 363

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV++L+N L RA +  +   LT   F  + S   +                G  S    
Sbjct: 364 GNVRQLQNALFRAAVLCEGDALTAADFPQIASLGDRP-----------STASGPQS---- 408

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
             L    I     DG +R L DIE ++I LA+  YR +M+EVARRLGIGRSTLYRK+ E 
Sbjct: 409 -TLHNGGINLFRPDGNLRPLEDIEADVIRLAIGHYRGRMTEVARRLGIGRSTLYRKLGEL 467

Query: 476 NIE 478
            I+
Sbjct: 468 GID 470


>gi|148554107|ref|YP_001261689.1| two component sigma-54 specific Fis family transcriptional
           regulator [Sphingomonas wittichii RW1]
 gi|148499297|gb|ABQ67551.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sphingomonas wittichii RW1]
          Length = 480

 Score =  192 bits (487), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 137/487 (28%), Positives = 227/487 (46%), Gaps = 29/487 (5%)

Query: 8   DRHKRVLIIDKDDEQIKIIKDHVESYGYDVF----IVNVSDLSTISKIQVNVIFLSLINC 63
           D    +L+ID +  Q  ++    +  G+ V     +    + S  + I+++   + L + 
Sbjct: 4   DTPPGLLLIDAEPAQAGLMSALAQRAGWRVLRAADVAEAVERSGNADIRLDAALIDLWSP 63

Query: 64  EDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLC------ 117
           ++     +  + + +P +PIIV T QD++ +    +        +  ++R +L       
Sbjct: 64  DEASVRSVARLRESLPALPIIVVTAQDSVDLAVRAVRAGAHDVLVKPIARHRLLAALDHV 123

Query: 118 ---DSIICALREGVVPSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEF 172
              D     LR    P  E    ALD   ++  +P+  + +D+A +A      I+I+GE 
Sbjct: 124 VADDPPAGELR----PLVEKWSEALDFAEIVGSAPSFRRALDVAMRAAATPATILIEGES 179

Query: 173 GVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIE 231
           GVGK+ L++ IH +  R   P   VNC  I  + +E  LFG +    T    +  G F +
Sbjct: 180 GVGKELLAQAIHRASARQAGPLITVNCAAIPANLVESELFGHERGAFTGAFERRPGLFAD 239

Query: 232 ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKS 291
           A+GGTI L+E   LP   Q ++   +++G+I    +    ++ VR+I  T + L   V  
Sbjct: 240 ADGGTIFLDEIGDLPGDAQAKLLRVLQSGEIRPIGATRPRQVSVRVIAATNRRLSDDVAR 299

Query: 292 HVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTK 351
             FR+DL+YR++V  + +  LR R  D+  L    L     +  +  +++   A++LL  
Sbjct: 300 GRFREDLFYRLAVVPLTLPALRDRIGDVAPLAAHLLDRIARQLGLPGLAVDASAIALLET 359

Query: 352 YPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSS 411
           + W  NV++L N+L RA I      LT   F  L        R  H         +    
Sbjct: 360 HDWPGNVRQLHNVLFRAAIFRDGGTLTASDFPQL--------RAAHAGPQPAANDD-APV 410

Query: 412 DTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
                     S+   G DG VR + +IE ++I LA+  YR +M+EVARRL IGRSTLYRK
Sbjct: 411 PADAAAPPAGSLALFGADGHVRPIDEIEADLIRLAIGHYRGRMTEVARRLRIGRSTLYRK 470

Query: 472 IREYNIE 478
           + E  IE
Sbjct: 471 LGELGIE 477


>gi|239834490|ref|ZP_04682818.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Ochrobactrum intermedium LMG 3301]
 gi|239822553|gb|EEQ94122.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Ochrobactrum intermedium LMG 3301]
          Length = 501

 Score =  191 bits (484), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 153/487 (31%), Positives = 243/487 (49%), Gaps = 26/487 (5%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCED-DKE 68
           R+LI D D  Q + ++  V   GY   + +   S LS +S+ +  V+ L  ++  D D  
Sbjct: 4   RILIADDDPIQRRNLEAVVMRMGYRTILADGGASALSFVSQRKDIVLMLLDLSMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSI-----ICA 123
            +L+ + +    VP+IV    D+++ +   +      F    V+ +++  S+     I A
Sbjct: 64  TVLRRMREAGNSVPVIVLVQNDDLQPVLQAMKMGAVDFVTKPVAFERVQVSVSNVLKIDA 123

Query: 124 LREGV--VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           L + +    S    H  L  +   SP M +V  LAR+A     P++I+GE G GK+ L+R
Sbjct: 124 LTQEIRRARSSLKAHLTLSDMAIKSPEMERVGILARRASALDAPLLIEGEPGSGKETLAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG----DVDLQTKNSAQFLGKFIEANGGTI 237
            I     R   PF  V+C  +  D  ++  FG      D +  ++ + LGK  EA+GGT+
Sbjct: 184 AICSGSVRWRGPFVTVDCRTLTVDNADEVFFGVSTARRDRRDGDALRSLGKLAEADGGTL 243

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRL-DVRLIFLTEKNLLPQVKSHVFRK 296
            L+E  ALP   Q +++  +++G+   F+S G   L + R++    + L   V    F  
Sbjct: 244 FLDEVGALPRHTQIKLFAAMQSGQ---FESGGERTLSNARIMASNSRPLADLVDMGRFHA 300

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWI 355
            LY+ +  F + +  LR+R EDIP L+H F+  F ++  +  I+ I+  AL  L  Y W 
Sbjct: 301 GLYHLLGSFAVAMPPLRNRPEDIPILLHQFMMRFVSEERMGHITGITTHALEKLKAYHWP 360

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+ELKN + RAVI      LT   F  + +  G +      ++A     +     T  
Sbjct: 361 GNVRELKNAVYRAVILCDTGELTAGDFAQIGA--GSESMRPAQQSARFNLVDQDPGVT-- 416

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
              S      I   GEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++EY
Sbjct: 417 ---SAGLFSGIDGAGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLKEY 473

Query: 476 NIEVDSL 482
            I+V S+
Sbjct: 474 GIDVASI 480


>gi|217978716|ref|YP_002362863.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylocella silvestris BL2]
 gi|217504092|gb|ACK51501.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylocella silvestris BL2]
          Length = 508

 Score =  189 bits (480), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 134/482 (27%), Positives = 234/482 (48%), Gaps = 22/482 (4%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGY-----DVFIVNVSDLSTISKIQVNVIFLSLINCEDD 66
           R+LI+D D  + ++  + +  +G+     D     ++ L +     V+++ L L+  + D
Sbjct: 4   RILIVDDDPLERQLAAEIIRKFGFATETADSGEAALARLKSAGAAPVDLLLLDLVMPDLD 63

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
              ++  +  +    PI+VQTT   +      L      F +   S ++L  +I   LR 
Sbjct: 64  GLGVIARLRAQAFTPPIVVQTTASAVDAAGAALGAGALDFVVKPASPERLKAAIGNGLRL 123

Query: 127 GVVPS-------QENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
             + +       Q + H +          + + V LA +A   A+P++I+GE G GK+ +
Sbjct: 124 AALEAELRRAARQASGHFSFADYFGAGEEIERAVRLAERAAKTAMPVLIEGEEGAGKETM 183

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVL 239
           +R IH +  R   PF  + C  +    +E  LFG+     ++  +  GK  EA GG++ +
Sbjct: 184 ARAIHAASDRRGRPFVTLRCAGLAAADMETLLFGESGAGPES--RRPGKIAEAQGGSLYI 241

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
            +   L   +Q R+   +  G+I+F      +R D+RLI  T +NL+ +VK+H FR+DLY
Sbjct: 242 ADICELSQNLQARLLRLVRDGEIDFLRGPRPVRADIRLIASTRRNLIERVKAHRFREDLY 301

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V+ I    LR R ++I  L   F   F  +        S +A+SLL+ Y W  N++
Sbjct: 302 YRLNVYPIFAPPLRRRRDEIEGLARGFCARFAAEAGKILRGPSAEAVSLLSAYDWPKNIR 361

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGK-----KEREFHTETACTCYTEGKSSDTI 414
           +L+  + RAV   + + LT   F  + ++ G                       + +  I
Sbjct: 362 QLETAMFRAVAFAEGADLTVMDFPQIAAQVGGFDVRIPPLPLAAPEPAAALAPERPAAEI 421

Query: 415 LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
            D     ++  I   G++RRL ++E E I  A+  YR +MS++A++LGIGRSTLYRK++E
Sbjct: 422 RD---PNALALIDPSGDMRRLVELEAEAIRFALGHYRGRMSKMAKKLGIGRSTLYRKMKE 478

Query: 475 YN 476
           Y 
Sbjct: 479 YG 480


>gi|62317041|ref|YP_222894.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 1 str. 9-941]
 gi|83269035|ref|YP_418326.1| response regulator receiver [Brucella melitensis biovar Abortus
           2308]
 gi|189022308|ref|YP_001932049.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           S19]
 gi|237816604|ref|ZP_04595596.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           str. 2308 A]
 gi|254695229|ref|ZP_05157057.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 3 str. Tulya]
 gi|254698328|ref|ZP_05160156.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 2 str. 86/8/59]
 gi|254731771|ref|ZP_05190349.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 4 str. 292]
 gi|260544277|ref|ZP_05820098.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           NCTC 8038]
 gi|260759535|ref|ZP_05871883.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella abortus bv. 4 str. 292]
 gi|260762779|ref|ZP_05875111.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella abortus bv. 2 str. 86/8/59]
 gi|261215591|ref|ZP_05929872.1| transcriptional regulatory protein [Brucella abortus bv. 3 str.
           Tulya]
 gi|62197234|gb|AAX75533.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 1 str. 9-941]
 gi|82939309|emb|CAJ12247.1| Response regulator receiver:Sigma-54 factor interaction
           domain:Helix-turn-helix, Fis-type:AAA ATPase [Brucella
           melitensis biovar Abortus 2308]
 gi|189020882|gb|ACD73603.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           S19]
 gi|237787417|gb|EEP61633.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           str. 2308 A]
 gi|260097548|gb|EEW81422.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           NCTC 8038]
 gi|260669853|gb|EEX56793.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella abortus bv. 4 str. 292]
 gi|260673200|gb|EEX60021.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella abortus bv. 2 str. 86/8/59]
 gi|260917198|gb|EEX84059.1| transcriptional regulatory protein [Brucella abortus bv. 3 str.
           Tulya]
          Length = 496

 Score =  189 bits (479), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 150/489 (30%), Positives = 236/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPLIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHAQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPPLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGRSTLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRSTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|254691475|ref|ZP_05154729.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 6 str. 870]
 gi|256256660|ref|ZP_05462196.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 9 str. C68]
 gi|260757095|ref|ZP_05869443.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella abortus bv. 6 str. 870]
 gi|260882904|ref|ZP_05894518.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 9 str. C68]
 gi|260677203|gb|EEX64024.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella abortus bv. 6 str. 870]
 gi|260872432|gb|EEX79501.1| sigma-54 dependent DNA-binding response regulator [Brucella abortus
           bv. 9 str. C68]
          Length = 496

 Score =  188 bits (477), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 149/489 (30%), Positives = 236/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPLIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + ++E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFMDEVGALPHHAQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPPLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGRSTLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRSTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|212704721|ref|ZP_03312849.1| hypothetical protein DESPIG_02784 [Desulfovibrio piger ATCC 29098]
 gi|212671848|gb|EEB32331.1| hypothetical protein DESPIG_02784 [Desulfovibrio piger ATCC 29098]
          Length = 454

 Score =  188 bits (477), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 129/476 (27%), Positives = 233/476 (48%), Gaps = 36/476 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLS--TISKIQVNVIFLSLINCEDDKENI 70
           +L++D DD    +++  ++++GY V      DL+   +     +V+   +     D  + 
Sbjct: 5   ILVVDDDDAHRGMLRMMLQAWGYSVDEAADGDLAVEAVRAKPYDVVLTDVRMGRMDGIHA 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQL---CDSIICA 123
           L+ I+D  P +P+++ T   +++     L    Y+ ++K       R+ L    D    +
Sbjct: 65  LRGILDYNPALPVVLMTAYSSVETAVDALRLGAYDYLTKPLDFDALRETLQRAVDHSRMS 124

Query: 124 LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
           +    +  Q +E  A   ++  SPA+  + ++          ++I GE G GK+ ++R +
Sbjct: 125 VENRELRRQLSEAAAGPEILGRSPAVSAMREIIATVAPTEATVLITGESGTGKELVARAV 184

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEP 242
           H +  RA  P   VNC  + ++ +E  LFG +    T    +  G+F++A+GGT+ L+E 
Sbjct: 185 HGASARANKPLVTVNCAALAENLLESELFGHERGAFTGADRRREGRFLQADGGTLFLDEI 244

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             +PL++Q ++   ++ G+++   S   I +DVR+I  T +NL  +V+   FR+DL++R+
Sbjct: 245 GEMPLSLQAKLLRALQQGEVQRVGSDSPITVDVRVIAATNRNLREEVEQKRFREDLFFRL 304

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           +V  I +  LR RSEDIP L   FL+ F  +N       + +AL +L +Y W  NV+EL+
Sbjct: 305 NVISIEVPALRERSEDIPLLAAHFLEKFAARNRKNVKGFAPQALDMLRRYSWPGNVRELQ 364

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           N + RAVI      +T           G +     T  A       ++++  L  LS E+
Sbjct: 365 NAVERAVILCTGDLIT-----------GPELPASITGAAEQAAPVPETAEASLAGLSLEA 413

Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
                          +E+  I   ++      SE ARRLGI R+TL+ K+R+Y +E
Sbjct: 414 ---------------LERRAIEDTLRQTEDNKSEAARRLGITRATLHNKLRKYGLE 454


>gi|225685948|ref|YP_002733920.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [Brucella melitensis ATCC 23457]
 gi|256043007|ref|ZP_05445953.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [Brucella melitensis bv. 1 str. Rev.1]
 gi|256112009|ref|ZP_05452954.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [Brucella melitensis bv. 3 str. Ether]
 gi|256261839|ref|ZP_05464371.1| sigma-54 dependent DNA-binding response regulator [Brucella
           melitensis bv. 2 str. 63/9]
 gi|260564240|ref|ZP_05834725.1| sigma-54 dependent DNA-binding response regulator [Brucella
           melitensis bv. 1 str. 16M]
 gi|265989444|ref|ZP_06102001.1| sigma-54 dependent DNA-binding response regulator [Brucella
           melitensis bv. 1 str. Rev.1]
 gi|265993455|ref|ZP_06106012.1| sigma-54 dependent DNA-binding response regulator [Brucella
           melitensis bv. 3 str. Ether]
 gi|225642053|gb|ACO01966.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [Brucella melitensis ATCC 23457]
 gi|260151883|gb|EEW86976.1| sigma-54 dependent DNA-binding response regulator [Brucella
           melitensis bv. 1 str. 16M]
 gi|262764325|gb|EEZ10357.1| sigma-54 dependent DNA-binding response regulator [Brucella
           melitensis bv. 3 str. Ether]
 gi|263000113|gb|EEZ12803.1| sigma-54 dependent DNA-binding response regulator [Brucella
           melitensis bv. 1 str. Rev.1]
 gi|263091314|gb|EEZ15850.1| sigma-54 dependent DNA-binding response regulator [Brucella
           melitensis bv. 2 str. 63/9]
 gi|326410270|gb|ADZ67334.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [Brucella melitensis M28]
 gi|326553563|gb|ADZ88202.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [Brucella melitensis M5-90]
          Length = 496

 Score =  187 bits (476), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 149/489 (30%), Positives = 236/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPLIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHAQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPPLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|23499849|ref|NP_699289.1| sigma-54 dependent DNA-binding response regulator [Brucella suis
           1330]
 gi|163844281|ref|YP_001621936.1| hypothetical protein BSUIS_B0087 [Brucella suis ATCC 23445]
 gi|254702516|ref|ZP_05164344.1| hypothetical protein Bsuib36_00867 [Brucella suis bv. 3 str. 686]
 gi|256014878|ref|YP_003104887.1| sigma-54 dependent DNA-binding response regulator [Brucella microti
           CCM 4915]
 gi|256059671|ref|ZP_05449866.1| hypothetical protein Bneo5_04895 [Brucella neotomae 5K33]
 gi|260568578|ref|ZP_05839047.1| sigma-54 dependent DNA-binding response regulator [Brucella suis
           bv. 4 str. 40]
 gi|261323642|ref|ZP_05962839.1| sigma-54 dependent DNA-binding response regulator [Brucella
           neotomae 5K33]
 gi|261753089|ref|ZP_05996798.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella suis bv. 3 str. 686]
 gi|23463420|gb|AAN33294.1| sigma-54 dependent DNA-binding response regulator [Brucella suis
           1330]
 gi|163675004|gb|ABY39114.1| Hypothetical protein, conserved [Brucella suis ATCC 23445]
 gi|255997538|gb|ACU49225.1| sigma-54 dependent DNA-binding response regulator [Brucella microti
           CCM 4915]
 gi|260155243|gb|EEW90324.1| sigma-54 dependent DNA-binding response regulator [Brucella suis
           bv. 4 str. 40]
 gi|261299622|gb|EEY03119.1| sigma-54 dependent DNA-binding response regulator [Brucella
           neotomae 5K33]
 gi|261742842|gb|EEY30768.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella suis bv. 3 str. 686]
          Length = 496

 Score =  187 bits (475), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 149/489 (30%), Positives = 236/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPVIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHTQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPPLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|306841139|ref|ZP_07473855.1| sigma-54 dependent DNA-binding response regulator [Brucella sp.
           BO2]
 gi|306288765|gb|EFM60083.1| sigma-54 dependent DNA-binding response regulator [Brucella sp.
           BO2]
          Length = 496

 Score =  187 bits (474), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 149/489 (30%), Positives = 236/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLAMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPVIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHTQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPPLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|256158191|ref|ZP_05456100.1| hypothetical protein BcetM4_05025 [Brucella ceti M490/95/1]
 gi|265996703|ref|ZP_06109260.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           M490/95/1]
 gi|262551000|gb|EEZ07161.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           M490/95/1]
          Length = 496

 Score =  187 bits (474), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 149/489 (30%), Positives = 236/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPVIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHTQLRLFTAMQSGQYESNGSR--VTSNTRIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPLLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|254706357|ref|ZP_05168185.1| hypothetical protein BpinM_05040 [Brucella pinnipedialis
           M163/99/10]
 gi|254711352|ref|ZP_05173163.1| hypothetical protein BpinB_14065 [Brucella pinnipedialis B2/94]
 gi|254711951|ref|ZP_05173762.1| hypothetical protein BcetM6_00857 [Brucella ceti M644/93/1]
 gi|254715021|ref|ZP_05176832.1| hypothetical protein BcetM_00867 [Brucella ceti M13/05/1]
 gi|256030019|ref|ZP_05443633.1| hypothetical protein BpinM2_05095 [Brucella pinnipedialis
           M292/94/1]
 gi|261216724|ref|ZP_05931005.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           M13/05/1]
 gi|261313804|ref|ZP_05953001.1| sigma-54 dependent DNA-binding response regulator [Brucella
           pinnipedialis M163/99/10]
 gi|261318955|ref|ZP_05958152.1| sigma-54 dependent DNA-binding response regulator [Brucella
           pinnipedialis B2/94]
 gi|261319591|ref|ZP_05958788.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           M644/93/1]
 gi|265987041|ref|ZP_06099598.1| hypothetical protein BALG_02852 [Brucella pinnipedialis M292/94/1]
 gi|260921813|gb|EEX88381.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           M13/05/1]
 gi|261292281|gb|EEX95777.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           M644/93/1]
 gi|261298178|gb|EEY01675.1| sigma-54 dependent DNA-binding response regulator [Brucella
           pinnipedialis B2/94]
 gi|261302830|gb|EEY06327.1| sigma-54 dependent DNA-binding response regulator [Brucella
           pinnipedialis M163/99/10]
 gi|264659238|gb|EEZ29499.1| hypothetical protein BALG_02852 [Brucella pinnipedialis M292/94/1]
          Length = 496

 Score =  186 bits (473), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 149/489 (30%), Positives = 236/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPVIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHTQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPLLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|158520444|ref|YP_001528314.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Desulfococcus oleovorans Hxd3]
 gi|158509270|gb|ABW66237.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfococcus oleovorans Hxd3]
          Length = 458

 Score =  186 bits (473), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 132/476 (27%), Positives = 229/476 (48%), Gaps = 36/476 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKENI 70
           +LI+D D   +K ++  V S+GY V   +  V  + T+ +    +I + +   +      
Sbjct: 9   ILIVDDDLNHLKTLQTIVRSWGYQVSTADDGVKAVDTVKERPFALILMDVRMAQMSGIEA 68

Query: 71  LKNIVDKIPIVPIIVQTTQDNI----KILNCFLYNRISK---FFLNLVSRKQLCDSIICA 123
           LK I    P +PI++ T   ++    + L    Y+ ++K   F +  +S  +  +     
Sbjct: 69  LKQIKQYNPAIPILIMTAYSSVDSAVEALKSGAYDYLTKPLDFEVLKISLARALEHSGLK 128

Query: 124 LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
                + S+ +    L+++I  S  M ++VD+          ++I GE G GK+ +++ I
Sbjct: 129 AENATLKSKMSADYELENIIGRSRPMKELVDMMSMVAPSEATVLITGESGTGKELIAKSI 188

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEP 242
           H + +R      +VNC  + +  +E  LFG +    T    +  G+F +A+ GTI L+E 
Sbjct: 189 HHNSQRKDRALVVVNCAALTETLLESELFGHEKGAFTGADKRREGRFKQADKGTIFLDEI 248

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
                A+Q ++   I+  +I+       + +DVR++  T +NL   VK+  FR+DL+YR+
Sbjct: 249 GETSAAMQAKLLRVIQEREIQRVGGEETLSVDVRILAATNRNLEEDVKNGKFREDLFYRL 308

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           +V  + I  LR R +D P L   FL+ +  KN  +    S  A+ +L KY W  NV+EL+
Sbjct: 309 NVVTLRIPPLRERQDDTPLLAQHFLEKYAKKNHKQVKGFSPLAMDMLLKYAWPGNVRELE 368

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           N++ RAVI L D H+TE    +               T  + Y E   S+ +        
Sbjct: 369 NVIERAVILLPDEHITEKELPV---------------TITSSYAE--KSEWVA------P 405

Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            P +  +   R L ++EKE I   +       SE ARRLGI R TL++K+++Y I+
Sbjct: 406 PPPVAAN---RPLEEVEKEAILATLDDSGGNKSETARRLGINRKTLHKKLKDYGID 458


>gi|225628562|ref|ZP_03786596.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           str. Cudo]
 gi|260166930|ref|ZP_05753741.1| sigma-54 dependent DNA-binding response regulator [Brucella sp.
           F5/99]
 gi|261756315|ref|ZP_06000024.1| sigma-54 dependent DNA-binding response regulator [Brucella sp.
           F5/99]
 gi|225616408|gb|EEH13456.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           str. Cudo]
 gi|261736299|gb|EEY24295.1| sigma-54 dependent DNA-binding response regulator [Brucella sp.
           F5/99]
          Length = 496

 Score =  186 bits (472), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 149/489 (30%), Positives = 236/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPVIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTARFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHTQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPLLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|306845297|ref|ZP_07477872.1| sigma-54 dependent DNA-binding response regulator [Brucella sp.
           BO1]
 gi|306274213|gb|EFM56025.1| sigma-54 dependent DNA-binding response regulator [Brucella sp.
           BO1]
          Length = 496

 Score =  186 bits (472), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 149/489 (30%), Positives = 235/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLAMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPVIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++    + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHTQLRLFTAMQSGQYESNGSR--VTSNARIMTSNSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPPLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|296121892|ref|YP_003629670.1| sigma-54 factor interaction domain-containing protein [Planctomyces
           limnophilus DSM 3776]
 gi|296014232|gb|ADG67471.1| sigma-54 factor interaction domain-containing protein [Planctomyces
           limnophilus DSM 3776]
          Length = 473

 Score =  186 bits (472), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 141/481 (29%), Positives = 234/481 (48%), Gaps = 38/481 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNV---SDLSTISKIQV---NVIFLSLINCED 65
           RVLI+D D+   + + D +   GYD  + +    S    +  I+V   +VI   L+  E 
Sbjct: 16  RVLIVDNDEAHAQAVADSLTRVGYDCTVASAGAESGKKALDLIEVENFDVIITELMMDEV 75

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFF---LNLVSRKQLCD---S 119
           D   IL+    ++P   +I+ T   +IK       +    +    L++   +Q  D   S
Sbjct: 76  DGLEILRRSKAELPDAEVILLTGHASIKSALTAGQHGAHTYLTKPLDISELRQAVDRASS 135

Query: 120 IICALREGVVPSQE-NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
            I  LR+    S+  +E    + +I  SP+M ++++  R        ++IQGE G GK+ 
Sbjct: 136 RIRLLRKTFELSRRLDEKFGFEGVIGNSPSMHRLIEKLRSVAPTDSTVLIQGESGTGKEL 195

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R IH++ +R   PF  +N   + +  +E  LFG +    T  + + +GKF  ANGGT+
Sbjct: 196 VARAIHQNSERKNKPFVPLNISALPESILESELFGHEAGAFTGAATKRIGKFEYANGGTL 255

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   +P+A Q ++   +E  +I    +   I ++VRL+  T  +L   +K   FRKD
Sbjct: 256 FLDEVGEMPMATQIKLLRVLEERRITRLGANDEIPINVRLVAATNADLQDMIKKGTFRKD 315

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LY+R+SV  I +  L  R  DIP+L+  FL+ F  +      +++ +    L  Y W  N
Sbjct: 316 LYFRLSVVTIVLPPLSDRRADIPFLIDHFLKQFAERQKRPIPTVTRQVQQALMAYAWPGN 375

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           ++EL+N++                 +++L  +GK + +   E     + E    D I + 
Sbjct: 376 IRELRNVV---------------EGMMVLDIDGKLDVDDLPEGIGAGHHEHSEVDLIQN- 419

Query: 418 LSQESIPAIGQDGEV-RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
                 PA G DG + R L+D+EK  I  A++L   +  E A  LGIG  TLYRKIREY 
Sbjct: 420 ------PA-GNDGLIGRSLNDVEKYYIARALELTGGKRDEAANLLGIGERTLYRKIREYE 472

Query: 477 I 477
           +
Sbjct: 473 L 473


>gi|153011574|ref|YP_001372788.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Ochrobactrum anthropi ATCC 49188]
 gi|151563462|gb|ABS16959.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Ochrobactrum anthropi ATCC 49188]
          Length = 504

 Score =  186 bits (472), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 146/487 (29%), Positives = 237/487 (48%), Gaps = 23/487 (4%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCED-DKE 68
           R+LI D D    + ++  V   GY   + +   S L  +S+ +  V+ L  ++  D D  
Sbjct: 4   RILIADDDPIHRRNLEAIVMRMGYRTILADGGASALGFVSQRKDIVLMLLDLSMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSI-----ICA 123
            +L+ + +    VP+IV    D+++ +   +      F    V+ +++  S+     I A
Sbjct: 64  TVLRRMREAGNNVPVIVLVQNDDLQPVLQAMKMGAVDFVTKPVAFERVQVSVSNVLKIDA 123

Query: 124 LREGV--VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           L + +    S    H  L  +   SP M +V  LAR+A     P++I+GE G GK+ L+R
Sbjct: 124 LTQEIRRARSSLKAHLTLSDMAIKSPEMERVSILARRASALDAPLLIEGEPGSGKETLAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG----DVDLQTKNSAQFLGKFIEANGGTI 237
            I   G R   PF  V+C  +  D  ++  FG      D +  +  + LGK +EA+GGT+
Sbjct: 184 AICSGGARWRGPFVTVDCRTLTVDNADEVFFGVSTARRDRREDDVIRSLGKLVEADGGTL 243

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E  ALP   Q +++  +++G+ E          + R++    + L   V    F   
Sbjct: 244 FLDEVGALPRHTQIKLFAAMQSGQFEAGGGGERTLSNARIMASNSRPLADLVDMGRFHAG 303

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWID 356
           LY+ +  F + +  LR+R EDIP L+H F+  + ++  +  I+ I+  AL  L  Y W  
Sbjct: 304 LYHLLGSFAVAMPPLRNRLEDIPILLHQFMMRYVSEERMGHITGITTHALEKLKTYHWPG 363

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDTIL 415
           NV+ELKN + RAV+  +   LT   F  +    E  +  +         +    S  + L
Sbjct: 364 NVRELKNAVYRAVLLCETGELTAADFAQIGAGAEAARAVQQSVRFNLVDHDPTVSGQSGL 423

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
                     I   GEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++EY
Sbjct: 424 -------FSGIDGAGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLKEY 476

Query: 476 NIEVDSL 482
            I+V S+
Sbjct: 477 GIDVTSI 483


>gi|17988355|ref|NP_540988.1| transcriptional regulatory protein hydG [Brucella melitensis bv. 1
           str. 16M]
 gi|17984131|gb|AAL53252.1| transcriptional regulatory protein hydg [Brucella melitensis bv. 1
           str. 16M]
          Length = 496

 Score =  185 bits (470), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 148/489 (30%), Positives = 235/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPLIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  E +GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAERDGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHAQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPPLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|256252867|ref|ZP_05458403.1| hypothetical protein BcetB_00840 [Brucella ceti B1/94]
 gi|261219954|ref|ZP_05934235.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           B1/94]
 gi|260918538|gb|EEX85191.1| sigma-54 dependent DNA-binding response regulator [Brucella ceti
           B1/94]
          Length = 496

 Score =  184 bits (468), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 148/489 (30%), Positives = 235/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPVIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHTQLRLFTAMQSGQYESNGSR--VTSNTRIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPLLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + R V+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRVVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIGR+TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGRTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|254699398|ref|ZP_05161226.1| hypothetical protein Bsuib55_00844 [Brucella suis bv. 5 str. 513]
 gi|261749847|ref|ZP_05993556.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella suis bv. 5 str. 513]
 gi|261739600|gb|EEY27526.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Brucella suis bv. 5 str. 513]
          Length = 496

 Score =  184 bits (467), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 148/489 (30%), Positives = 235/489 (48%), Gaps = 35/489 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQ-VNVIFLSLINCEDDKE 68
           R+LI D D  Q + ++  V   GY   + +  VS L  IS+ + + ++ L L   + D  
Sbjct: 4   RILIADDDPIQRRNLEAIVMRMGYRTILADGGVSALGFISQRKDIVLVLLDLTMPDMDGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIK-------------ILNCFLYNRISKFFLNLVSRKQ 115
            +L  +      VP+IV    D++              ++   ++ R+     N++    
Sbjct: 64  TVLSRMRAAGVAVPVIVLVHSDDMHRVAQAIRLGAADFMIKPVIFERVQVSVANVLKLDA 123

Query: 116 LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L   I  A       S    H +L  ++A SP M +V+ LAR+A     P++++GE G G
Sbjct: 124 LTHEIQRAR------SSPRVHLSLSEMVAKSPEMERVMVLARRAAALDAPLLVEGETGSG 177

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG 235
           ++ L+R I   G R   PF  ++C  +  +  +  LFG       +     GK  EA+GG
Sbjct: 178 RQTLARAICGGGSRWRGPFVSLDCRGLTMENADDILFGTAKFCPDDPIVSAGKLAEADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E  ALP   Q R++  +++G+ E   SR  +  + R++  + + L+  V    F 
Sbjct: 238 VLFLDEVGALPHHTQLRLFTAMQSGQYESNGSR--VTSNARIMTSSSQPLVDFVHMGRFH 295

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPW 354
             LY+ +  F I +  LR R EDI  LVH F   F ++  +  I+ I+   L  L  Y W
Sbjct: 296 AGLYHLLGSFSIAMPPLRERVEDISILVHQFAVRFASEERLSHITGIAPHLLERLKAYQW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLL-LSREGKKEREFHTETACTCYTEGKSSDT 413
             NV+ELKN + RAV+    S LT + F  L L   G    +   +      + G++   
Sbjct: 356 PGNVRELKNAVYRAVLLCDKSELTVEDFAQLNLGAAGFAGAQAMWQKPAAPLSVGRAG-- 413

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                   +   I  DGEVR L+  E+E+I  A+  Y  Q+SEVARRLGIG +TLYRK++
Sbjct: 414 -------TAFSGIDADGEVRTLAAAEEEMIRFAIAHYDGQISEVARRLGIGGTTLYRKLK 466

Query: 474 EYNIEVDSL 482
           EY I+V S+
Sbjct: 467 EYGIDVASI 475


>gi|320104997|ref|YP_004180588.1| Fis family two component sigma54 specific transcriptional regulator
           [Isosphaera pallida ATCC 43644]
 gi|319752279|gb|ADV64039.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Isosphaera pallida ATCC 43644]
          Length = 465

 Score =  184 bits (467), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 134/480 (27%), Positives = 224/480 (46%), Gaps = 35/480 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           RVL++D D+   + + + +E  GY+  +     S L  I +   +++   L+  E     
Sbjct: 6   RVLVVDDDEAHAQAVAESLERVGYECVVATDGRSALRLIEEQTFDIVLTDLMMGEIGGLE 65

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFF---LNLVSRKQLCDSIICALRE 126
           +L     ++P V +I+ T    I+     +    + +    L++   + + D    + R 
Sbjct: 66  VLAKAKRELPDVEVIILTGHGTIRTAVTAMQAGAATYLTKPLDIDELRMVVDKASQSQR- 124

Query: 127 GVVPS------QENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            +V S      Q +E    + ++  SP M Q+V+  R+       ++I GE G GK+ ++
Sbjct: 125 -LVRSNIELRKQLHERFGFEGVVGNSPLMHQLVERLRQIAPTTATVLITGESGTGKELVA 183

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV-DLQTKNSAQFLGKFIEANGGTIVL 239
           R +H +  RA  PF  +NC  ++++ ++  LFG V    T       G F  ANGGT+ L
Sbjct: 184 RALHVNSPRANKPFVPLNCAALNENLLDSELFGHVKGAYTGAERDRKGLFEHANGGTLFL 243

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LP++ Q R+   +E G+I    +   I+++VRLI  T ++    +    FR+DLY
Sbjct: 244 DEVGDLPMSTQVRLLRVLENGEIVRVGTNEPIKVNVRLISATNRDFAEAIAQGKFRQDLY 303

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           +R+ V  I I  LR+R EDIP L   FL+ FC  +  K   +S     +LT Y W  NV+
Sbjct: 304 HRLKVVSIKIPPLRARREDIPLLTDSFLKQFCKTHDKKIQGVSPAVRKVLTAYDWPGNVR 363

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           EL+N +              +  V++ +       +   E   T    G+S+        
Sbjct: 364 ELRNTI--------------ESMVVMDTDGLLDLDDLVEELQPTAQAVGESAGKARAGAG 409

Query: 420 --QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
             Q +   +G+      + +IE+  I   +KL R    E AR LGIG  TLYRKI+EY I
Sbjct: 410 TCQAANALVGKT-----MDEIEQYYIAETLKLTRGNREEAARILGIGERTLYRKIKEYGI 464


>gi|85373292|ref|YP_457354.1| sigma-54 dependent DNA-binding response regulator [Erythrobacter
           litoralis HTCC2594]
 gi|84786375|gb|ABC62557.1| sigma-54 dependent DNA-binding response regulator [Erythrobacter
           litoralis HTCC2594]
          Length = 472

 Score =  184 bits (466), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 135/486 (27%), Positives = 232/486 (47%), Gaps = 35/486 (7%)

Query: 8   DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLIN 62
           D  + +++ID +  Q ++I       G+   +V      ++ L T   +Q++ I L    
Sbjct: 4   DETRLLMLIDDEPAQSRLIGALAAREGWRTLVVADAETAIATLGTRQGMQLSAIILDQWV 63

Query: 63  CEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIIC 122
             DD   ++  +  + P +PI++ T   +  +    +    + + +  V+ ++L  ++  
Sbjct: 64  PGDDACQLIGELKSRRPALPILMLTQSASPLLAVEAMRAGATDYLIKPVAPERLMRALRS 123

Query: 123 ALR-----EGVVPSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           A +     + + P  E     LD  ++I   PA    +  A K       ++I+GE G G
Sbjct: 124 ATKREAPKDELQPLTEKMPAVLDFDAMIGTEPAFRTALARAAKIARGHGHVLIEGESGTG 183

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF---LGKFIEA 232
           K+ L R +H +  RA  PF ++N G I  + IE  LFG    Q      F   +G     
Sbjct: 184 KEMLLRAMHAASPRAKAPFRMINIGGIPANSIESALFGHE--QNAFPGAFDRQVGALQFC 241

Query: 233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH 292
           +GGT++++E D L   +Q R+   +  G +    ++   ++D+RL+  +   L   V++ 
Sbjct: 242 DGGTLIIDEIDRLSGELQQRLSATLAEGIVRPIGAKHGFKIDIRLLTASNLPLEDLVEAG 301

Query: 293 VFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY 352
            F  DL  +I+   I +  LR R  DIP L   FL     +  +K +S++D AL LL  Y
Sbjct: 302 HFEADLLEQIAATKICLPPLRERPGDIPALARHFLGRIGEQPGLKHLSLADSALGLLGAY 361

Query: 353 PWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD 412
            W  NV++L+ +L RA +  +   LT        SR+  +  E   E A T  +  ++  
Sbjct: 362 DWPGNVRQLQAVLFRAAVFCEGEALT--------SRDFPQLSEIVGELAETGASLPEAVG 413

Query: 413 TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +L            +DG +R L +IE ++I LA+  YR +M+EVARRLGIGRSTLYRK+
Sbjct: 414 VMLYT----------EDGNLRPLDEIEADVIRLAIGHYRGRMTEVARRLGIGRSTLYRKL 463

Query: 473 REYNIE 478
            +  I+
Sbjct: 464 SDLGID 469


>gi|295695766|ref|YP_003589004.1| GAF modulated sigma54 specific transcriptional regulator, Fis
           family [Bacillus tusciae DSM 2912]
 gi|295411368|gb|ADG05860.1| GAF modulated sigma54 specific transcriptional regulator, Fis
           family [Bacillus tusciae DSM 2912]
          Length = 631

 Score =  184 bits (466), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 114/351 (32%), Positives = 177/351 (50%), Gaps = 39/351 (11%)

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
           P     H  +DS+I  +P +++   LA KA + + P+ + GE G GK+  +  IH SG R
Sbjct: 316 PVDWTTHYTMDSIIGRTPVILEAKRLAHKAANLSAPVFLAGESGTGKELFAHAIHASGPR 375

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVD---LQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
              PF  VNCG + ++     LFG  +      K   Q  GKF+ A+ GTI L+E   LP
Sbjct: 376 RSGPFVAVNCGTLQRELAASELFGYEEGAFTGAKKHGQ-RGKFLLADKGTIFLDEIAELP 434

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
           +  Q  +   +E G++        I +DVR+I  T KNL  +V+S  FRKDL+YR+S   
Sbjct: 435 IDCQSLLLRVLEEGRVVPVGGTRPIHVDVRVITATHKNLDQEVQSGRFRKDLFYRLSALW 494

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR RSEDIP LV  FL+ F  +     + +S +A+  LT++ W  N++ELKN+L 
Sbjct: 495 IRLPSLRERSEDIPLLVDTFLRQFAKEMGRTSVRLSPEAMQRLTEHSWPGNIRELKNVLQ 554

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV  L D ++ E R + L                   +    S DT             
Sbjct: 555 RAVF-LCDGNVIEPRHICL----------------AGPFENAPSVDT------------- 584

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
                 ++   I + ++  A++     ++E A+ LGI R+T+YRK++ +N+
Sbjct: 585 -----AKKRRSIHRSLVEQALRESGGNVTEAAQTLGISRATMYRKMKLFNL 630


>gi|242281135|ref|YP_002993264.1| Fis family transcriptional regulator [Desulfovibrio salexigens DSM
           2638]
 gi|242124029|gb|ACS81725.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio salexigens DSM 2638]
          Length = 463

 Score =  184 bits (466), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 137/486 (28%), Positives = 241/486 (49%), Gaps = 41/486 (8%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
           K +LI+D +D     ++  +E  G+DV      +  L  +++ Q +++FL +     D  
Sbjct: 3   KNILIVDDEDGIRYSLRGILEDEGFDVSEAESGEKALEHLNEDQPDLVFLDIWLPGMDGL 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
            +L  I  +   +P+++ +   NI+       + I K   + + +    + ++    + V
Sbjct: 63  EVLDRIKKEWDWLPVVMISGHGNIETA----VSAIKKGAFDFIEKPLSLEKVVITAEKAV 118

Query: 129 VPSQ-ENEHCALDSLIAVS-PAMI----QVVDLARKAGDCAIP----IMIQGEFGVGKKR 178
             S+ ++E+ AL + IA   PA +    + +D  R+      P    ++I GE G GK+ 
Sbjct: 119 EFSRLQSENKALRTRIAAEQPARLTGQSESIDSMREVIGQVAPTDAWVLITGENGTGKEI 178

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R IH   +RA  P   VNC  I ++ IE  LFG +    T       GKF  A+ GT+
Sbjct: 179 VARSIHSQSQRADKPLVAVNCAAIPEELIESELFGHEKGAFTGAEKAQEGKFELADNGTL 238

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   + L  Q +I   ++  + E    R  I +DVR+I  T K+L  ++K+  FR+D
Sbjct: 239 FLDEIGDMSLKTQAKILRILQEQRFERVGGRKTINVDVRVIAATNKDLFQEIKNGNFRED 298

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LYYR+ VF + +  LR R++DIP L+  F+ S   ++  K ++ ++ AL++LT+Y W  N
Sbjct: 299 LYYRLKVFPLEVPPLRDRNKDIPLLIDEFITSLNRQHGFKPLTFTEPALNILTEYSWPGN 358

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           V+ELKN + R +I      +  D+                 E A     E   +D     
Sbjct: 359 VRELKNFVERMLIMFGGKEVGPDK--------------LPPEIANGPRIEKPETD----- 399

Query: 418 LSQESIPAIGQDGEV---RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
             QE +P    +GEV   +  +D E + +   ++ Y+  +S++A  +G+ RS+LYRK++ 
Sbjct: 400 --QEQLPLPLPEGEVDFKKARADFEAQFLEAKLREYKGNVSKLAEAVGLERSSLYRKLKA 457

Query: 475 YNIEVD 480
           Y I+VD
Sbjct: 458 YEIQVD 463


>gi|158522817|ref|YP_001530687.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Desulfococcus oleovorans Hxd3]
 gi|158511643|gb|ABW68610.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfococcus oleovorans Hxd3]
          Length = 466

 Score =  183 bits (465), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 131/491 (26%), Positives = 235/491 (47%), Gaps = 46/491 (9%)

Query: 3   RKKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ---VNVIFLS 59
           +K+++ +H  +LI+D D     +++  +E +G+     +   L+ +  +Q    +++ + 
Sbjct: 5   QKENMKKHATILIVDDDAGHRSMLRTLLEGWGHQTAEAD-DGLAAVEYVQTRPADIVLMD 63

Query: 60  LINCEDDKENILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFFLNLVSRKQ 115
           L          L+ I    P VP+I+ T        ++ L    Y+ ++K  L+    + 
Sbjct: 64  LKMVHMSGMEALEQIRSFNPGVPVIIMTAFSSVDTAVEALKKGAYDYLTKP-LDFEKLRL 122

Query: 116 LCDSIICALREGVVPSQENEHC--------ALDSLIAVSPAMIQVVDLARKAGDCAIPIM 167
             + I+ A R      +EN H         + D +I  SPAM ++++   +A      I+
Sbjct: 123 TLERILEAARL----RKENRHLKERLGSRFSRDQIIGNSPAMTRLLETVEQAAPSDASIL 178

Query: 168 IQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFL 226
           I GE G GK+ ++  +H +  R   PF  +NC  I +  +E  LFG      T       
Sbjct: 179 ITGESGTGKELIAGALHFNSARREGPFVKINCAAITETLLESELFGHEKGSFTGADKAKK 238

Query: 227 GKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLL 286
           G+F++A+ GTI+L+E   +PL++Q ++   ++  ++        I +DVR+I  T K+L 
Sbjct: 239 GRFVQADTGTILLDEIGEMPLSMQAKLLRVLQEKEVTPVGGERTIHVDVRVIASTNKDLH 298

Query: 287 PQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKAL 346
             V++  FR+DL++R++V  + +  LR+R EDIP L H FL  F  KN  +    +  A+
Sbjct: 299 ALVEAGTFREDLFFRLNVVNLEVPPLRNRKEDIPELAHHFLTLFSAKNKKQVQGFTPDAM 358

Query: 347 SLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYT 406
             L  Y W  NV+EL N + RAV+  +  +L+ +  +L+  R+   +      T      
Sbjct: 359 EALLAYSWPGNVRELMNAVERAVVLARSEYLSREDVLLMAERQAPAQ-----ATPPLAAG 413

Query: 407 EGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
            G +S           +P          LS++EK+ I   ++      SE ARRLGI R 
Sbjct: 414 AGPAS---------HGLP----------LSEVEKDAILRTLEATDNNKSEAARRLGITRK 454

Query: 467 TLYRKIREYNI 477
           TL +K+++Y +
Sbjct: 455 TLQKKLKQYGV 465


>gi|218778199|ref|YP_002429517.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfatibacillum alkenivorans AK-01]
 gi|218759583|gb|ACL02049.1| Two-component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfatibacillum alkenivorans AK-01]
          Length = 458

 Score =  183 bits (465), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 132/490 (26%), Positives = 232/490 (47%), Gaps = 55/490 (11%)

Query: 6   SLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST--ISKIQVNVIFLSLINC 63
           +L+ +  +L++D D+   K +   ++S+GY+V       ++   + +   +VI + +   
Sbjct: 2   NLENNADILVVDDDEGHRKTLYTVIKSWGYNVKTAEDGSIAVDMVREGPYDVILMDVRMA 61

Query: 64  EDDKENILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQ 115
           E D    LK I +  P +P+++ T     +  I+ +    Y+ ++K      L L     
Sbjct: 62  EMDGIQALKLIKEYNPSIPVLIMTAYSSVESAIEAMKTGAYDYLTKPLDFEDLRLT---- 117

Query: 116 LCDSIICALREGVVPSQENEH--------CALDSLIAVSPAMIQVVDLARKAGDCAIPIM 167
                I   RE     +EN+           L  +I  S  M ++ D+          ++
Sbjct: 118 -----IERAREYAGLREENKELKQALGFRAGLRDIIGKSSVMKELTDMVSMIAPTEATVL 172

Query: 168 IQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFL 226
           I GE G GK+ ++R IHE  +R   P  ++NC  + +  +E  LFG +    T    +  
Sbjct: 173 ITGESGTGKELVARSIHEGSQRKDGPLVVLNCAALTETLLESELFGHEKGAFTGADKKRD 232

Query: 227 GKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLL 286
           G+F++A+ GT+ L+E   +PL +Q ++   I+  +++   S   + +DVR+I  T ++L 
Sbjct: 233 GRFVQADQGTLFLDEIGEMPLTMQAKLLRAIQEKEVQRVGSDATVTVDVRIIAATNRDLE 292

Query: 287 PQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKAL 346
            +V    FR+DL+YR++V  + I  LR R  DI  L  +FL+ F  +N      I+ +A+
Sbjct: 293 QEVAEGKFREDLFYRLNVVTLRIPPLRERDGDIHLLAQYFLEKFAERNRKHVKGITPQAM 352

Query: 347 SLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYT 406
            +L K+PW  NV+EL+N + RAVI L    +TE    L +                 C  
Sbjct: 353 DMLLKHPWPGNVRELENAMERAVILLTGDFITEKELPLSIC-------------GPVC-- 397

Query: 407 EGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
                D  ++ + QE I        ++ L ++EK+ I   +K      SE ARRLGI R 
Sbjct: 398 ----DDEPMEQIEQEPI--------LQSLEEVEKKAILATLKAVDGNKSEAARRLGITRK 445

Query: 467 TLYRKIREYN 476
           TL+ K+ +Y+
Sbjct: 446 TLHSKLAKYD 455


>gi|158320115|ref|YP_001512622.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Alkaliphilus oremlandii OhILAs]
 gi|158140314|gb|ABW18626.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Alkaliphilus oremlandii OhILAs]
          Length = 451

 Score =  182 bits (463), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 148/484 (30%), Positives = 240/484 (49%), Gaps = 51/484 (10%)

Query: 10  HKRVLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSD-LSTISKIQVNVIFLSL-INCEDD 66
           +KR+LIID +      IK  +E  GY+++   N  D L  + +I  ++I L L +   D 
Sbjct: 2   NKRILIIDDEKNMRWAIKKALEKEGYNIYEAENGQDGLEKLEEIYPDLILLDLRMPVMDG 61

Query: 67  KENI--LKNIVDKIPIVPIIVQTTQDN-IKILNCFLYNRISKFF----LNLVSRKQL--- 116
            E +  +K I   IP++ +    T ++ ++ +     + ISK F    L ++ +K L   
Sbjct: 62  MEALQRIKEINQDIPVIMLTAHGTMESAVEAMKLGALDYISKPFDIEELKVLIKKALNVG 121

Query: 117 -CDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
              S +  LRE      E E     ++I  SP M +V+++  +       I+I GE G G
Sbjct: 122 ELKSEVNYLRE------ELEKNTGKTVIGESPKMKKVLEIVERVASTNATILILGESGTG 175

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANG 234
           K+ ++  IH +  R   P+  VNCG I ++ IE  LFG +    T   A+ +GKF  A G
Sbjct: 176 KEVIANTIHYNSDRKDKPYVKVNCGAIPENLIESELFGYEKGAFTGAIARKIGKFERARG 235

Query: 235 GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF 294
           GTI L+E   L L +Q ++   ++  + E       I++D+R+I  T K+L   ++   F
Sbjct: 236 GTIFLDEIGELDLGMQVKLLRVLQEREFERVGGNETIKIDIRVIAATNKDLFKMMQEGNF 295

Query: 295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW 354
           R+DLYYR++V  I +  LR R EDIP L+  FL  +  +   K +SIS KA+  L +Y W
Sbjct: 296 REDLYYRLNVIPIELPALRDRKEDIPLLIEHFLNYYGKEIGRKNMSISKKAMEKLIQYKW 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
             N++EL+N++ R VI L D  + E+R               H  +     TE       
Sbjct: 356 SGNIRELENMIERLVI-LVDGDIIEER---------------HLPSEVFTRTE------- 392

Query: 415 LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
           +DN  +  +P  G +     L  +EK +I  A+++     +  A+ LGI R TL  +I +
Sbjct: 393 MDNAFK--LPENGVN-----LEQVEKSLISQALEISNGNQTHAAKLLGITRHTLIYRIEK 445

Query: 475 YNIE 478
           YN++
Sbjct: 446 YNLQ 449


>gi|317487013|ref|ZP_07945821.1| sigma-54 interaction domain-containing protein [Bilophila
           wadsworthia 3_1_6]
 gi|316921695|gb|EFV42973.1| sigma-54 interaction domain-containing protein [Bilophila
           wadsworthia 3_1_6]
          Length = 455

 Score =  182 bits (463), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 125/474 (26%), Positives = 234/474 (49%), Gaps = 33/474 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD----LSTISKIQVNVIFLSLINCEDDKE 68
           VL++D D     +++  +  +G  + + +  D    ++ + +   +V+ + +   + D  
Sbjct: 9   VLVVDDDPGHRGMLEALLGRWG--LAVTSAGDGKEAVARVCERPFDVVLMDIRMPDMDGI 66

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG- 127
             LK I    P VP+++ T    ++     + +    + +  +   QL  ++   L    
Sbjct: 67  TALKEIRKYNPAVPVVLMTAYSAVESAVEAMKSGAVDYLIKPLDFDQLKSTLFKTLEHSE 126

Query: 128 VVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
            V S E     ++ ++  SPA+ +++++          ++I G+ G GK+ ++R IH   
Sbjct: 127 AVRSGERFPVPVEGIVGNSPAVRRMLEMIHTVAPSEATVLINGKSGTGKELVARAIHNQS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
           +R   P+  VNC  + +  +E  LFG +    T    +  G+F++A+GGT+ L+E   + 
Sbjct: 187 QRKDGPWVAVNCAALTESLLESELFGHEKGAFTGADKRRDGRFLQADGGTLFLDEIGEIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
           L +Q ++   I+  +I+       +++DVR++  T +NLL +V +  FR+DLYYR++V  
Sbjct: 247 LLMQVKLLRAIQQREIQRVGGDATLKVDVRIVAATNRNLLDEVAAGRFREDLYYRLNVVS 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +L+ RSEDIP L   FL+ F  +N       + KA+ +L KYPW  NV+EL+N + 
Sbjct: 307 IQVPSLQERSEDIPLLAEHFLKVFGERNRKDVKGFTPKAMDMLIKYPWPGNVRELENAVE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+ L  S+++E    L +++  ++E +    +A +   EG +                
Sbjct: 367 RAVVLLFGSYVSERELPLAVTQAYEQEDDAEP-SALSVPLEGAT---------------- 409

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
                   L D+E+E I   +       SE A+RLGI R TL+ K++ Y  E D
Sbjct: 410 --------LEDVEREAILRMLDSVGDNKSEAAKRLGISRKTLHTKLKRYGQEQD 455


>gi|323963777|gb|EGB59276.1| sigma-54 interaction domain-containing protein [Escherichia coli
           M863]
 gi|327250477|gb|EGE62187.1| transcriptional regulatory protein zraR [Escherichia coli STEC_7v]
          Length = 441

 Score =  182 bits (463), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 134/468 (28%), Positives = 226/468 (48%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVVLAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           + L +Q R+   I+  +++   S   I +DVRLI  T ++L  +VK+  FR+DLYYR++V
Sbjct: 245 ISLMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVKAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLANHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|189499900|ref|YP_001959370.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Chlorobium phaeobacteroides BS1]
 gi|189495341|gb|ACE03889.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Chlorobium phaeobacteroides BS1]
          Length = 480

 Score =  182 bits (462), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 135/487 (27%), Positives = 238/487 (48%), Gaps = 42/487 (8%)

Query: 8   DRHKRVLIIDKDDEQIKIIKDH-VESYGY-DVFIVNVSD-LSTISKIQVNVIFLSLINCE 64
           ++H RVL+ D D +  +I+ +H ++  GY  +  V+ ++ +S + K +++++ L +    
Sbjct: 18  NKHYRVLVAD-DHKSTRIVLNHFLKKMGYLPIEAVDGNECVSILEKEKIDILLLDINMPN 76

Query: 65  DDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFL-------------YNRISKFFLNLV 111
            D   ++  +  +   +P+I+ T  D+I     F+             ++R+     N +
Sbjct: 77  KDGSEVMNYLQKQGITIPVIMITALDDIPNTVKFIKMGAYEYLTKPLDFDRLQIVMRNAI 136

Query: 112 SRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGE 171
           S   L D +    +E  + S+E       ++I  S  + Q ++ A    +  + ++I GE
Sbjct: 137 SESALHDKVSQLKKE--LKSKE----IFRNIIGKSAQIKQTMEQALHVMETDLNVLIIGE 190

Query: 172 FGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFI 230
            G GK+  ++ IHE  KR   PF  VNC  I  +  E  LFG      T  +    G F 
Sbjct: 191 SGTGKELFAQAIHEGSKRKNGPFISVNCAAISHELAESLLFGHTKGSFTGANNDHQGFFE 250

Query: 231 EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK 290
           +A+GGT+ L+E   +   +Q ++   I+  KI     +    +D R+I  T  +    + 
Sbjct: 251 QADGGTLFLDEIGDMNADIQAKVLRAIQEKKIRRVGEKSERSIDFRVISATHWDFAQALD 310

Query: 291 SHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLT 350
           S+ FR DLYYR+  F + +  LR R ED+P+L   FL+ FC+ N +KQ+S S +AL  + 
Sbjct: 311 SNSFRDDLYYRLEEFPLYLPPLRERKEDVPFLAKHFLEEFCSANNLKQLSFSHEALEEIE 370

Query: 351 KYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKS 410
           +Y W  N++ELKN + R  I  K+S    D    +LS +G + R+  T  A         
Sbjct: 371 EYHWPGNIRELKNAIQRTAISCKNS----DEIASILSHKGGRLRKNATPLAAE------- 419

Query: 411 SDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
                +N  Q  I    +  +++ L +IE+  I    K      ++ A+ LGIGR+TLYR
Sbjct: 420 -----ENGIQ--IETADRKTKIQSLEEIERHAIEETFKACEGNPTKTAQVLGIGRATLYR 472

Query: 471 KIREYNI 477
           K++++ +
Sbjct: 473 KLKKFGL 479


>gi|39996106|ref|NP_952057.1| nitrogen regulation protein NR(I) [Geobacter sulfurreducens PCA]
 gi|39982871|gb|AAR34330.1| nitrogen regulation protein NR(I) [Geobacter sulfurreducens PCA]
 gi|298505122|gb|ADI83845.1| nitrogen fixation master sigma-54-dependent transcriptional
           response regulator [Geobacter sulfurreducens KN400]
          Length = 481

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 118/342 (34%), Positives = 182/342 (53%), Gaps = 10/342 (2%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
           ++I  SPAM +V     K     + +++QGE G GK+ ++R IH + KR   PF  +NC 
Sbjct: 144 NIIGNSPAMREVYKTIGKVAPSDVTVLVQGESGTGKELIARAIHFNSKRIGKPFIALNCA 203

Query: 201 MIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            I +D +E  LFG +    T    + LGKF +ANGGTI L+E   +PL +Q +I   ++ 
Sbjct: 204 AIPKDLLESELFGFEKGAFTGAVERKLGKFEQANGGTIFLDEIGDMPLDLQAKILRVLQE 263

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
            ++        I +DVR++  T +NL   V+   FR+DL+YR++V  I +  LR R ED+
Sbjct: 264 KEVTRTGGSQNIAVDVRIVAATNQNLEELVRKKQFREDLFYRLNVVPIQLVPLRERKEDV 323

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
           P LV +FLQ+ C +  +     S +A++LLT + W  NV+EL+N + RAVI   D  LT 
Sbjct: 324 PLLVDYFLQNACAELEVSPKKCSPEAMALLTTHSWPGNVRELENTIKRAVILSSDPLLTP 383

Query: 380 DRFVLLLSREGKKEREFHTETACTCYTEGK--SSDTILDNLSQESIPAIGQDGEVRRLSD 437
             F  L +R+   E     + +     + K  +S T LD +    I  +        L  
Sbjct: 384 SDFPGLRARQTGSEATAADDLSLEALVDMKLRASLTNLDKMESGDIYNL-------VLKQ 436

Query: 438 IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           IE+ +I   ++  R    + A  LGI R+TL +KI+E  IE+
Sbjct: 437 IERPLIRFVLEKTRGNQVKGAEILGINRNTLRKKIQELGIEL 478


>gi|284924096|emb|CBG37195.1| two-component system response regulator [Escherichia coli 042]
          Length = 441

 Score =  181 bits (460), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 134/468 (28%), Positives = 225/468 (48%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +VK+  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVKAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I +  LR R EDIP L  +FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPALRQRREDIPLLADYFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                  SIP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------SIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|262043755|ref|ZP_06016858.1| transcriptional regulatory protein ZraR [Klebsiella pneumoniae
           subsp. rhinoscleromatis ATCC 13884]
 gi|259038879|gb|EEW40047.1| transcriptional regulatory protein ZraR [Klebsiella pneumoniae
           subsp. rhinoscleromatis ATCC 13884]
          Length = 449

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 131/469 (27%), Positives = 228/469 (48%), Gaps = 42/469 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKE 68
           ++L++D D     I++  +  +GY V + + + L  + +I   V  L L +    E D  
Sbjct: 13  QILVVDDDVSHCTILQALLRGWGYQVGLAH-NGLQALEQIHQQVFDLVLCDIRMAEMDGI 71

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             LK I    P +P+++ T   ++      + +    + +  +    L  +++ AL    
Sbjct: 72  ATLKEIKAYNPAIPVLIMTAFSSVGTAVEAIKSGALDYLVKPLDFDTLQQTLVQALAH-T 130

Query: 129 VPSQENEHCALDS---LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
             S+ +   A DS   +I  SPAM  +++           ++I GE G GK+ ++R IH 
Sbjct: 131 RQSESDPSVATDSRWGMIGDSPAMQALLNDITLVAPSDATVLIYGESGTGKELVARAIHA 190

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
             +R   P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 191 CSERRDKPLVTLNCAALNESLLESELFGHEKGAFTGADRRREGRFVEADGGTLFLDEIGD 250

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   + +DVRLI  T +NL  +V +  FR+DLYYR++V
Sbjct: 251 ISPVMQVRLLRAIQEREVQRVGSNQTLAVDVRLIAATHRNLAEEVSAGRFRQDLYYRLNV 310

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I I  LR R EDIP L   FL+ +  +N       + +A+ LL  YPW  N++EL+N 
Sbjct: 311 VTIEIPPLRRRREDIPQLAQHFLKRYTERNRKTVKGFTPQAMDLLIHYPWPGNIRELENA 370

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+ L  ++++E              RE     A T                   +P
Sbjct: 371 VERAVVLLTGNYISE--------------RELPLAIAGT------------------PLP 398

Query: 425 AIG-QDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
           ++G ++G ++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 399 SVGSEEGGIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 447


>gi|153003885|ref|YP_001378210.1| two component sigma54 specific Fis family transcriptional regulator
           [Anaeromyxobacter sp. Fw109-5]
 gi|152027458|gb|ABS25226.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter sp. Fw109-5]
          Length = 460

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 129/485 (26%), Positives = 222/485 (45%), Gaps = 50/485 (10%)

Query: 12  RVLIIDKDDEQIKI-IKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKE 68
           RVL++D D+  +++ +K+ VE+ G++  +       L  + +    V   S+   E D  
Sbjct: 3   RVLLVD-DEPSVRVALKELVEARGWEPLLARSGAEALDLVDRADAVVTDFSM--PEMDGM 59

Query: 69  NILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
            +L+ + ++   +P+I+ T   +    ++ +    Y  ++K F          D ++ AL
Sbjct: 60  TLLRAVRERDASLPVILLTAHGSERLAVRAIKAGAYEYVTKPFD--------VDEMLVAL 111

Query: 125 R---EGVVPSQEN-----EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
               E     Q N     EH     ++  S  M Q++D   +     I ++++GE G GK
Sbjct: 112 ERALEARALRQRNRQLTAEHAIGRRVVCESTVMRQLLDATSRVAGKEITVLVRGETGTGK 171

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF-LGKFIEANGG 235
           + +   +H   +RA  P    NCG I  +  E  LFG        ++Q   G F EAN G
Sbjct: 172 ELIGSLLHAQSRRAEGPLVRFNCGAIPAELAEAELFGHTRGAFTGASQARAGFFAEANHG 231

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T+VL+E   LPLA+Q ++   ++ G+I+   S    ++DVR++  T ++L  +V++  FR
Sbjct: 232 TLVLDEVGELPLAIQAKLLRALQDGEIQPVGSGRVEKVDVRIVACTNRDLAAEVRAGRFR 291

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DLYYR++V  + +  LR R EDIP L H F   +  +   +++ ++   +  LT   W 
Sbjct: 292 EDLYYRLAVVELVVPPLRDRREDIPALAHEFALRYAERFGAEEVRLAPALVERLTAEEWP 351

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV++L+N++ R V       L    F       G    E           +G    T+ 
Sbjct: 352 GNVRQLENVIARMVALSGGGELGPTAFA------GSAAVEESPRPPAVDAADGSGVHTLR 405

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
           + L                   +E+ +I   M   R   SE ARRLGI R+TL  ++R Y
Sbjct: 406 EQLDT-----------------LERSVIARTMTAVRGNQSEAARRLGISRNTLTERLRRY 448

Query: 476 NIEVD 480
           +I  D
Sbjct: 449 DIAAD 453


>gi|197118787|ref|YP_002139214.1| sigma-54-dependent transcriptional response regulator [Geobacter
           bemidjiensis Bem]
 gi|197088147|gb|ACH39418.1| sigma-54-dependent transcriptional response regulator [Geobacter
           bemidjiensis Bem]
          Length = 482

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 140/481 (29%), Positives = 238/481 (49%), Gaps = 21/481 (4%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           ++LI+D D + + ++K       Y++ + + S+  L  +   + NV  + +   +     
Sbjct: 4   KLLILDDDHDILLMLKSVFAGEDYELLLESDSEGALKRVISDRPNVAIMDISLPQKSGIE 63

Query: 70  ILKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFF----LNLVSRKQL-CDSI 120
           +LK      P + +I+    +TTQ+ I+ +    ++ ++K F    L    +K L C+ +
Sbjct: 64  VLKEAKKIDPGLAVIMATGYKTTQNAIEAMKHGAFDYVTKPFDMTKLKGAVKKALECNLL 123

Query: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
              +R      Q  E    D +I  SP MI++  +     D    ++IQGE G GK+ L+
Sbjct: 124 SRKVRYTRERPQVEEDLTEDLMIGSSPEMIEIWKMVGTVADSDATVLIQGESGTGKELLA 183

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R ++ + KR   PF  VNC  + +  +E  LFG +    T   ++ +GKF + NGGTI L
Sbjct: 184 RAVYNNSKRKNRPFLAVNCAALPEALLESELFGHEKGAFTDAHSRRIGKFEQCNGGTIFL 243

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +  A QG+    +E  + E       I++DVR+I  T K+L+  VK   FR DLY
Sbjct: 244 DEIGEMSQANQGKFLRVLENQEFERVGGNETIKVDVRVIAATNKSLITNVKEKTFRMDLY 303

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V    +  LR R+EDIP LV  F++ F  K      +++ + L++LT +PW  N++
Sbjct: 304 YRLRVVNFFLPPLRDRAEDIPLLVELFVKKFSKKYGKNIKAVAPETLAMLTSHPWEGNIR 363

Query: 360 ELKNILLRAVIGLKDSHLTEDRF-VLLLSREGKKEREFHTETACTCYTEGKSS--DTILD 416
           ELKN++  A +  +   L    F   L ++ G KE +   E A   Y E   S  + + D
Sbjct: 364 ELKNVINSATVFCRGDILVPGDFESFLTAKAGFKEVDL--EAAGDDYYEVFWSMLEPVFD 421

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
            + Q++  AI +   +     +EK +I +AM+         A+ LGI R+TL  ++  Y 
Sbjct: 422 GICQKNKGAIYESVNM----GLEKALIHMAMEKSNNNQVFAAKLLGISRNTLRDRLERYR 477

Query: 477 I 477
           I
Sbjct: 478 I 478


>gi|152972866|ref|YP_001338012.1| transcriptional regulatory protein ZraR [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|150957715|gb|ABR79745.1| response regulator in two-component reguatory system with ZraS,
           regulates zraP expression (EBP family) [Klebsiella
           pneumoniae subsp. pneumoniae MGH 78578]
          Length = 443

 Score =  181 bits (459), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 131/469 (27%), Positives = 228/469 (48%), Gaps = 42/469 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKE 68
           ++L++D D     I++  +  +GY V + + + L  + +I   V  L L +    E D  
Sbjct: 7   QILVVDDDVSHCTILQALLRGWGYQVGLAH-NGLQALEQIHQQVFDLVLCDIRMAEMDGI 65

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             LK I    P +P+++ T   ++      + +    + +  +    L  +++ AL    
Sbjct: 66  ATLKEIKAYNPAIPVLIMTAFSSVGTAVEAIKSGALDYLVKPLDFDTLQQTLVQALAH-T 124

Query: 129 VPSQENEHCALDS---LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
             S+ +   A DS   +I  SPAM  +++           ++I GE G GK+ ++R IH 
Sbjct: 125 RQSESDPSVATDSRWGMIGDSPAMQALLNDITLVAPSDATVLIYGESGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
             +R   P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 CSERRDKPLVTLNCAALNESLLESELFGHEKGAFTGADRRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   + +DVRLI  T +NL  +V +  FR+DLYYR++V
Sbjct: 245 ISPVMQVRLLRAIQEREVQRVGSNQTLAVDVRLIAATHRNLAEEVSAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I I  LR R EDIP L   FL+ +  +N       + +A+ LL  YPW  N++EL+N 
Sbjct: 305 VTIEIPPLRRRREDIPQLAQHFLKRYTERNRKTVKGFTPQAMDLLIHYPWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+ L  ++++E              RE     A T                   +P
Sbjct: 365 VERAVVLLTGNYISE--------------RELPLAIAGT------------------PLP 392

Query: 425 AIG-QDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
           ++G ++G ++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 SVGSEEGGIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 441


>gi|157157738|ref|YP_001465500.1| transcriptional regulatory protein ZraR [Escherichia coli E24377A]
 gi|300925874|ref|ZP_07141717.1| response regulator receiver domain protein [Escherichia coli MS
           182-1]
 gi|301325713|ref|ZP_07219172.1| response regulator receiver domain protein [Escherichia coli MS
           78-1]
 gi|157079768|gb|ABV19476.1| response regulator ZraR [Escherichia coli E24377A]
 gi|300418064|gb|EFK01375.1| response regulator receiver domain protein [Escherichia coli MS
           182-1]
 gi|300847502|gb|EFK75262.1| response regulator receiver domain protein [Escherichia coli MS
           78-1]
          Length = 441

 Score =  181 bits (458), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 134/468 (28%), Positives = 225/468 (48%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP LV  FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLVGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|253700432|ref|YP_003021621.1| Fis family transcriptional regulator [Geobacter sp. M21]
 gi|251775282|gb|ACT17863.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. M21]
          Length = 482

 Score =  181 bits (458), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 140/481 (29%), Positives = 238/481 (49%), Gaps = 21/481 (4%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           ++LI+D D + + ++K       Y++ + + S+  L  +   + NV  + +   +     
Sbjct: 4   KLLILDDDHDILLMLKSVFAGEDYELLLESDSEGALKRVISDRPNVAIMDISLPQKSGIE 63

Query: 70  ILKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFF----LNLVSRKQL-CDSI 120
           +LK      P + +I+    +TTQ+ I+ +    ++ ++K F    L    +K L C+ +
Sbjct: 64  VLKEAKKIDPGLAVIMATGYKTTQNAIEAMKHGAFDYVTKPFDMTKLKGAVKKALECNLL 123

Query: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
              +R      Q  E    D +I  SP MI++  +     D    ++IQGE G GK+ L+
Sbjct: 124 SRKVRYTRERPQVEEDLTEDLMIGSSPEMIEIWKMVGTVADSDATVLIQGESGTGKELLA 183

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R ++ + KR   PF  VNC  + +  +E  LFG +    T   ++ +GKF + NGGTI L
Sbjct: 184 RAVYNNSKRKNRPFLAVNCAALPEALLESELFGHEKGAFTDAHSRRIGKFEQCNGGTIFL 243

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +  A QG+    +E  + E       I++DVR+I  T K+L+  VK   FR DLY
Sbjct: 244 DEIGEMSQANQGKFLRVLENQEFERVGGNETIKVDVRVIAATNKSLIANVKDKTFRMDLY 303

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V    +  LR R+EDIP LV  F++ F  K      +++ + L++L  +PW  N++
Sbjct: 304 YRLRVVNFFLPPLRDRTEDIPLLVDLFVKKFSKKYGKNIKAVAPETLAMLMSHPWEGNIR 363

Query: 360 ELKNILLRAVIGLKDSHLTEDRF-VLLLSREGKKEREFHTETACTCYTEGKSS--DTILD 416
           ELKN++  A +  +   L    F   L ++ G KE +   ETA   Y E   S  + + D
Sbjct: 364 ELKNVINSATVFCRGDILVPGDFESFLTAKAGFKEVDL--ETAGDDYYEVFWSMLEPVFD 421

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
            + Q++  AI +   +     +EK +I +AM+         A+ LGI R+TL  ++  Y 
Sbjct: 422 GICQKNKGAIYESVNM----GLEKALIHMAMEKSNNNQVFAAKLLGISRNTLRDRLERYR 477

Query: 477 I 477
           I
Sbjct: 478 I 478


>gi|24115288|ref|NP_709798.1| transcriptional regulatory protein ZraR [Shigella flexneri 2a str.
           301]
 gi|30064714|ref|NP_838885.1| transcriptional regulatory protein ZraR [Shigella flexneri 2a str.
           2457T]
 gi|24054583|gb|AAN45505.1| response regulator of hydrogenase 3 activity (sensor HydH)
           [Shigella flexneri 2a str. 301]
 gi|30042974|gb|AAP18696.1| response regulator of hydrogenase 3 activity (sensor HydH)
           [Shigella flexneri 2a str. 2457T]
 gi|281603388|gb|ADA76372.1| Two component, sigma54 specific, transcriptional regulator, Fis
           family [Shigella flexneri 2002017]
 gi|313648655|gb|EFS13095.1| transcriptional regulatory protein zraR [Shigella flexneri 2a str.
           2457T]
 gi|332749202|gb|EGJ79624.1| transcriptional regulatory protein zraR [Shigella flexneri 2747-71]
 gi|332751441|gb|EGJ81843.1| transcriptional regulatory protein zraR [Shigella flexneri 4343-70]
 gi|332762843|gb|EGJ93102.1| response regulator [Shigella flexneri 2930-71]
 gi|332765543|gb|EGJ95757.1| transcriptional regulatory protein zraR [Shigella flexneri K-671]
 gi|332998986|gb|EGK18576.1| transcriptional regulatory protein zraR [Shigella flexneri K-218]
 gi|333014344|gb|EGK33697.1| transcriptional regulatory protein zraR [Shigella flexneri K-304]
          Length = 441

 Score =  180 bits (457), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGAQDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|194434761|ref|ZP_03067012.1| response regulator ZraR [Shigella dysenteriae 1012]
 gi|194416985|gb|EDX33103.1| response regulator ZraR [Shigella dysenteriae 1012]
 gi|320179532|gb|EFW54483.1| Response regulator of zinc sigma-54-dependent two-component system
           [Shigella boydii ATCC 9905]
 gi|332085401|gb|EGI90571.1| transcriptional regulatory protein zraR [Shigella dysenteriae
           155-74]
          Length = 441

 Score =  180 bits (457), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 134/468 (28%), Positives = 225/468 (48%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +VK+  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVKAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAGT------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|327399108|ref|YP_004339977.1| putative two component sigma54 specific transcriptional regulator
           [Hippea maritima DSM 10411]
 gi|327181737|gb|AEA33918.1| putative two component, sigma54 specific, transcriptional regulator
           [Hippea maritima DSM 10411]
          Length = 386

 Score =  179 bits (455), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 121/384 (31%), Positives = 204/384 (53%), Gaps = 15/384 (3%)

Query: 12  RVLIIDKDDEQIKI-IKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
           ++L++D DDEQ+++ +K  ++  GY+  +   +   L  + K + + I   L   + D  
Sbjct: 3   KILVVD-DDEQMRVALKATLDHLGYNPTLAKDAKEALKLLKKNEFDFILSDLKMPKMDGV 61

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             LK + +  P +P ++ T   +IK     +      F L   S+  L   I  A+    
Sbjct: 62  EFLKEVKNIKPHIPFVMITAFGDIKTAVEAMKLGAFDFILKPFSQDALKKIIEMAISHTS 121

Query: 129 V-------PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           +       P+Q+     LD  +  S +M  ++ LA+K       +++ GE G GK+ L+R
Sbjct: 122 IKQSIQKNPTQQK---GLDHFVFKSKSMENIITLAQKVAQTDATVLLIGESGTGKEVLAR 178

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ-FLGKFIEANGGTIVLE 240
           +IH    RA   F  VNC  I Q+ +E  +FG        +A+   GKF +AN GTI+L+
Sbjct: 179 YIHSISSRAKGNFIAVNCAAIPQNLLESEMFGYEKGAFSGAAKSHPGKFEQANRGTILLD 238

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL +Q ++   I+   I+   S   I++DVR+I  T +++  +VK+  FR+DLYY
Sbjct: 239 EISEMPLELQAKLLRVIQEKTIDRIGSTTPIKVDVRIICTTNRDIEEEVKNGNFREDLYY 298

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           RISVF I I  LR R E+IP L++FF++ F  +     I I + A+ +L  YPW  N++E
Sbjct: 299 RISVFPIKIPPLRQRKEEIPELINFFIRKFSNQFNKNVIGIKEDAIEILINYPWPGNIRE 358

Query: 361 LKNILLRAVIGLKDSHLTEDRFVL 384
           L+N++ RAV+  + +++T+D   L
Sbjct: 359 LQNVIERAVVLTEKNYITKDEIFL 382


>gi|332998847|gb|EGK18442.1| transcriptional regulatory protein zraR [Shigella flexneri K-272]
 gi|333014307|gb|EGK33661.1| transcriptional regulatory protein zraR [Shigella flexneri K-227]
          Length = 441

 Score =  179 bits (455), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVASSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|206576089|ref|YP_002241055.1| transcriptional regulatory protein ZraR [Klebsiella pneumoniae 342]
 gi|206565147|gb|ACI06923.1| transcriptional regulatory protein ZraR [Klebsiella pneumoniae 342]
          Length = 443

 Score =  179 bits (455), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 130/468 (27%), Positives = 226/468 (48%), Gaps = 40/468 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKE 68
           ++L++D D     I++  +  +GY V + + + L  + +IQ  V  L L +    E D  
Sbjct: 7   QILVVDDDVSHCTILQALLRGWGYQVALAH-NGLQALEQIQNQVFDLVLCDIRMAEMDGI 65

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             LK I    P +P+++ T   ++      + +    + +  +    L  +++ AL    
Sbjct: 66  ATLKEIKAYNPAIPVLIMTAFSSVGTAVEAIKSGALDYLVKPLDFDTLQQTLVQALAH-T 124

Query: 129 VPSQENEHCALDS---LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
             S+ +   A DS   +I  SPAM  +++           ++I GE G GK+ ++R IH 
Sbjct: 125 QQSKIDPSVATDSRWGMIGESPAMQALINNITLVAPSDATVLICGESGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
             +R   P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 CSERREKPLVTLNCAALNESLLESELFGHEKGAFTGADRRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   + +DVRLI  T +NL  +V +  FR+DLYYR++V
Sbjct: 245 ISPLMQVRLLRAIQEREVQRVGSNQTLAVDVRLIAATHRNLAEEVSAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I++  LR R EDIP L   FL+ +  +N       + +A+ LL  YPW  N++EL+N 
Sbjct: 305 VTIDMPPLRQRREDIPLLAQHFLKRYAERNRKTVQGFTPQAMDLLIHYPWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+ L  ++++              ERE     A T    G S + +          
Sbjct: 365 VERAVVLLTGNYIS--------------ERELPLAIAGTPLPSGGSENAL---------- 400

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
                  ++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 401 -------IQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 441


>gi|288937700|ref|YP_003441759.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Klebsiella variicola At-22]
 gi|288892409|gb|ADC60727.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Klebsiella variicola At-22]
          Length = 443

 Score =  179 bits (455), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 130/468 (27%), Positives = 226/468 (48%), Gaps = 40/468 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKE 68
           ++L++D D     I++  +  +GY V + + + L  + +IQ  V  L L +    E D  
Sbjct: 7   QILVVDDDVSHCTILQALLRGWGYQVALAH-NGLQALEQIQHQVFDLVLCDIRMAEMDGI 65

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             LK I    P +P+++ T   ++      + +    + +  +    L  +++ AL    
Sbjct: 66  ATLKEIKAYNPAIPVLIMTAFSSVGTAVEAIKSGALDYLVKPLDFDTLQQTLVQALAH-T 124

Query: 129 VPSQENEHCALDS---LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
             S+ +   A DS   +I  SPAM  +++           ++I GE G GK+ ++R IH 
Sbjct: 125 QQSKIDPSVATDSRWGMIGESPAMQALINNITLVAPSDATVLICGESGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
             +R   P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 CSERREKPLVTLNCAALNESLLESELFGHEKGAFTGADRRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   + +DVRLI  T +NL  +V +  FR+DLYYR++V
Sbjct: 245 ISPLMQVRLLRAIQEREVQRVGSNQTLAVDVRLIAATHRNLAEEVSAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I++  LR R EDIP L   FL+ +  +N       + +A+ LL  YPW  N++EL+N 
Sbjct: 305 VTIDMPPLRQRREDIPLLAQHFLKRYAERNRKTVQGFTPQAMDLLIHYPWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+ L  ++++              ERE     A T    G S + +          
Sbjct: 365 VERAVVLLTGNYIS--------------ERELPLAIAGTPLPSGGSENAL---------- 400

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
                  ++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 401 -------IQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 441


>gi|187730825|ref|YP_001882690.1| transcriptional regulator ZraR [Shigella boydii CDC 3083-94]
 gi|191168666|ref|ZP_03030447.1| response regulator ZraR [Escherichia coli B7A]
 gi|300824615|ref|ZP_07104723.1| response regulator receiver domain protein [Escherichia coli MS
           119-7]
 gi|300907558|ref|ZP_07125196.1| response regulator receiver domain protein [Escherichia coli MS
           84-1]
 gi|301302183|ref|ZP_07208315.1| response regulator receiver domain protein [Escherichia coli MS
           124-1]
 gi|307315022|ref|ZP_07594608.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli W]
 gi|309797709|ref|ZP_07692095.1| response regulator receiver domain protein [Escherichia coli MS
           145-7]
 gi|331680128|ref|ZP_08380789.1| transcriptional regulatory protein ZraR [Escherichia coli H591]
 gi|187427817|gb|ACD07091.1| response regulator ZraR [Shigella boydii CDC 3083-94]
 gi|190901306|gb|EDV61074.1| response regulator ZraR [Escherichia coli B7A]
 gi|300400725|gb|EFJ84263.1| response regulator receiver domain protein [Escherichia coli MS
           84-1]
 gi|300522864|gb|EFK43933.1| response regulator receiver domain protein [Escherichia coli MS
           119-7]
 gi|300842346|gb|EFK70106.1| response regulator receiver domain protein [Escherichia coli MS
           124-1]
 gi|306905527|gb|EFN36060.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli W]
 gi|308118721|gb|EFO55983.1| response regulator receiver domain protein [Escherichia coli MS
           145-7]
 gi|315063330|gb|ADT77657.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator/sigma54 interaction
           protein [Escherichia coli W]
 gi|315252727|gb|EFU32695.1| response regulator receiver domain protein [Escherichia coli MS
           85-1]
 gi|323174483|gb|EFZ60108.1| transcriptional regulatory protein zraR [Escherichia coli LT-68]
 gi|323380606|gb|ADX52874.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli KO11]
 gi|331072283|gb|EGI43617.1| transcriptional regulatory protein ZraR [Escherichia coli H591]
 gi|333010738|gb|EGK30166.1| transcriptional regulatory protein zraR [Shigella flexneri VA-6]
          Length = 441

 Score =  179 bits (454), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|170021993|ref|YP_001726947.1| transcriptional regulatory protein ZraR [Escherichia coli ATCC
           8739]
 gi|194439783|ref|ZP_03071850.1| response regulator ZraR [Escherichia coli 101-1]
 gi|253775366|ref|YP_003038197.1| transcriptional regulatory protein ZraR [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254163946|ref|YP_003047054.1| transcriptional regulatory protein ZraR [Escherichia coli B str.
           REL606]
 gi|300928824|ref|ZP_07144332.1| response regulator receiver domain protein [Escherichia coli MS
           187-1]
 gi|169756921|gb|ACA79620.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli ATCC 8739]
 gi|194421280|gb|EDX37300.1| response regulator ZraR [Escherichia coli 101-1]
 gi|242379535|emb|CAQ34351.1| ZraR transcriptional activator [Escherichia coli BL21(DE3)]
 gi|253326410|gb|ACT31012.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253975847|gb|ACT41518.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator/sigma54 interaction
           protein [Escherichia coli B str. REL606]
 gi|253980003|gb|ACT45673.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator/sigma54 interaction
           protein [Escherichia coli BL21(DE3)]
 gi|300463205|gb|EFK26698.1| response regulator receiver domain protein [Escherichia coli MS
           187-1]
 gi|309704420|emb|CBJ03769.1| two-component system response regulator [Escherichia coli ETEC
           H10407]
 gi|323958931|gb|EGB54606.1| sigma-54 interaction domain-containing protein [Escherichia coli
           H489]
 gi|323969078|gb|EGB64386.1| sigma-54 interaction domain-containing protein [Escherichia coli
           TA007]
 gi|332345995|gb|AEE59329.1| transcriptional regulatory protein ZraR [Escherichia coli UMNK88]
          Length = 441

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|290513208|ref|ZP_06552569.1| two-component system, NtrC family, response regulator HydG
           [Klebsiella sp. 1_1_55]
 gi|289774305|gb|EFD82312.1| two-component system, NtrC family, response regulator HydG
           [Klebsiella sp. 1_1_55]
          Length = 443

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 129/468 (27%), Positives = 225/468 (48%), Gaps = 40/468 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKE 68
           ++L++D D     I++  +  +GY V + + + L  + +I   V  L L +    E D  
Sbjct: 7   QILVVDDDISHCTILQALLRGWGYQVALAH-NGLQALEQIHQQVFDLVLCDIRMAEMDGI 65

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             LK I    P +P+++ T   ++      + +    + +  +    L  +++ AL    
Sbjct: 66  ATLKEIKAYNPAIPVLIMTAFSSVGTAVEAIKSGALDYLVKPLDFDTLQQTLVQALAH-T 124

Query: 129 VPSQENEHCALDS---LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
             S+ +   A DS   +I  SPAM  +++           ++I GE G GK+ ++R IH 
Sbjct: 125 QQSESDPSVATDSRWGMIGDSPAMRALINNIMLVAPSDATVLICGESGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
             +R   P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 CSERREKPLVTLNCAALNESLLESELFGHEKGAFTGADRRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   + +DVRLI  T +NL  +V +  FR+DLYYR++V
Sbjct: 245 ISPLMQVRLLRAIQEREVQRVGSNQTLAVDVRLIAATHRNLAEEVSAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I++  LR R EDIP L   FL+ +  +N       + +A+ LL  YPW  N++EL+N 
Sbjct: 305 VTIDMPPLRQRREDIPLLAQHFLKRYAERNRKTVQGFTPQAMDLLIHYPWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+ L  ++++              ERE     A T    G S + +          
Sbjct: 365 VERAVVLLTGNYIS--------------ERELPLAIAGTPLPSGGSENAL---------- 400

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
                  ++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 401 -------IQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 441


>gi|293417506|ref|ZP_06660129.1| two-component system [Escherichia coli B185]
 gi|291430833|gb|EFF03830.1| two-component system [Escherichia coli B185]
          Length = 441

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAGT------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|330005100|ref|ZP_08305110.1| fused DNA-binding response regulator [Klebsiella sp. MS 92-3]
 gi|328536433|gb|EGF62786.1| fused DNA-binding response regulator [Klebsiella sp. MS 92-3]
          Length = 449

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 130/468 (27%), Positives = 224/468 (47%), Gaps = 40/468 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKE 68
           ++L++D D     I++  +  +GY V + + + L  + +I   V  L L +    E D  
Sbjct: 13  QILVVDDDISHCTILQALLRGWGYQVGLAH-NGLQALEQIHQQVFDLVLCDIRMAEMDGI 71

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             LK I    P +P+++ T   ++      + +    + +  +    L  +++ AL    
Sbjct: 72  ATLKEIKAYNPAIPVLIMTAFSSVGTAVEAIKSGALDYLVKPLDFDTLQQTLVQALAH-T 130

Query: 129 VPSQENEHCALDS---LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
             S+ +   A DS   +I  SPAM  +++           ++I GE G GK+ ++  IH 
Sbjct: 131 RQSESDPSVATDSRWGMIGDSPAMQALLNDITLVAPSDATVLIYGESGTGKELVAHAIHA 190

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
             +R   P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 191 CSERRDKPLVTLNCAALNESLLESELFGHEKGAFTGADRRREGRFVEADGGTLFLDEIGD 250

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   + +DVRLI  T +NL  +V +  FR+DLYYR++V
Sbjct: 251 ISPVMQVRLLRAIQEREVQRVGSNQTLAVDVRLIAATHRNLAEEVSAGRFRQDLYYRLNV 310

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I I  LR R EDIP L   FL+ +  +N       + +A+ LL  YPW  N++EL+N 
Sbjct: 311 VTIEIPPLRRRREDIPQLAQHFLKRYTERNRKTVKGFTPQAMDLLIHYPWPGNIRELENA 370

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+ L  ++++E              RE     A T    G S              
Sbjct: 371 VERAVVLLTGNYISE--------------RELPLAIAGTPLPSGGS-------------- 402

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              ++G ++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 403 ---EEGGIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 447


>gi|323974204|gb|EGB69336.1| sigma-54 interaction domain-containing protein [Escherichia coli
           TW10509]
          Length = 441

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 132/470 (28%), Positives = 228/470 (48%), Gaps = 48/470 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +      D++   L + +V
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLD----FDNLQATLEKALV 122

Query: 130 PSQ--ENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
            +   + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R I
Sbjct: 123 HTHSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAI 182

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEP 242
           H S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E 
Sbjct: 183 HASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEI 242

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             +   +Q R+   I+  +++   S  +I +DVRLI  T ++L  +VK+  FR+DLYYR+
Sbjct: 243 GDISPMMQVRLLRAIQEREVQRVGSNQSISVDVRLIAATHRDLAAEVKAGRFRQDLYYRL 302

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           +V  I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+
Sbjct: 303 NVVAIEVPSLRQRREDIPLLANHFLQRFAERNRKAVKWFTPQAMDLLIHYDWPGNIRELE 362

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           N + RAV+              LL+ E   ERE     A T                   
Sbjct: 363 NAVERAVV--------------LLTGEYISERELPLAIAST------------------P 390

Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
           IP + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 391 IPLV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|215489336|ref|YP_002331767.1| transcriptional regulatory protein ZraR [Escherichia coli O127:H6
           str. E2348/69]
 gi|312965342|ref|ZP_07779575.1| transcriptional regulatory protein zraR [Escherichia coli 2362-75]
 gi|215267408|emb|CAS11859.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator/sigma 54
           interaction protein [Escherichia coli O127:H6 str.
           E2348/69]
 gi|312290016|gb|EFR17903.1| transcriptional regulatory protein zraR [Escherichia coli 2362-75]
 gi|323190138|gb|EFZ75416.1| transcriptional regulatory protein zraR [Escherichia coli RN587/1]
          Length = 441

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 131/466 (28%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHS 126

Query: 130 PSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E    +    S++  SPAM  ++            ++I G+ G GK+ ++R IH S 
Sbjct: 127 VDAETPAVSASQFSMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T                   IP +
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAST------------------PIPPV 394

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 395 -QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|326796472|ref|YP_004314292.1| Fis family transcriptional regulator [Marinomonas mediterranea
           MMB-1]
 gi|326547236|gb|ADZ92456.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Marinomonas mediterranea MMB-1]
          Length = 450

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 141/480 (29%), Positives = 232/480 (48%), Gaps = 45/480 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTIS-KIQVNVIFLSLINCED-DKEN 69
           ++L+++ D    + ++D +   GYD  +V  S+ + +S K Q   + +S IN    D   
Sbjct: 5   KLLVVEDDRGLAEALEDTLLLAGYDCSMVGSSEEAILSLKKQSYDMVVSDINLPGMDGYG 64

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +LK++ D  P +PI++ T   +I      +      + L      +L + I         
Sbjct: 65  LLKHVTDHYPELPIMLMTAYGDIAHAVEAMREGAVDYLLKPFEEAELLEVI--------- 115

Query: 130 PSQENEHCALD----SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
             Q++   ALD    +LIAV P+   +VDLA++       ++I GE G GK+ L+ +IH 
Sbjct: 116 --QKHTAGALDNKSSTLIAVDPSSKAMVDLAKRVAVTDSTVLICGESGTGKEVLANYIHT 173

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R   PF  +NC  I ++ +E  LFG +    T   +   GKF +ANGG+I+L+E   
Sbjct: 174 SSDRVNQPFVAINCAAIPENMLEAILFGYEKGAYTGAVSSQAGKFEQANGGSILLDEITE 233

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           + + +Q ++   ++  ++E    +  I+LDVR+I  T ++L   VK   FR+DLYYR++V
Sbjct: 234 MDVGLQAKLLRVLQEQEVERLGGKKPIKLDVRIIATTNRDLASYVKEGGFREDLYYRLNV 293

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
           F +  S +R R  DI  +    L+    K  + ++ +   A S L  + W  NV+EL N+
Sbjct: 294 FPLKWSPIRERKGDIIPIAESLLKKHAVKMRLGEVVLMPSAQSKLESHRWPGNVRELDNV 353

Query: 365 LLRAVIGLKDSHLTEDRFVL-LLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESI 423
           + RA+I    S + E   V  +LS E   E E   E       E + + +IL    Q+  
Sbjct: 354 IQRALILCSGSSVEEQHVVFDMLSSEQVVEPESQLE-------ENEDAASILGKGVQQH- 405

Query: 424 PAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVD 480
                          E  II  A+   + +  +VA +LGI   TL  KI   RE+ +EVD
Sbjct: 406 ---------------EFRIIAQALIEAKGKRKDVAEKLGISPRTLRYKIAKMREFGLEVD 450


>gi|331655705|ref|ZP_08356695.1| transcriptional regulatory protein ZraR [Escherichia coli M718]
 gi|331046630|gb|EGI18717.1| transcriptional regulatory protein ZraR [Escherichia coli M718]
          Length = 441

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLEATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISIDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAGT------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|78222273|ref|YP_384020.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Geobacter metallireducens GS-15]
 gi|78193528|gb|ABB31295.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter metallireducens GS-15]
          Length = 508

 Score =  179 bits (453), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 153/507 (30%), Positives = 242/507 (47%), Gaps = 47/507 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           +VLIID + +     +  +   GYDV   +     +  I + +  V  + L   + D   
Sbjct: 5   KVLIIDDEADVCTFFRRLLTRKGYDVVTASKEPEAMRAIEEHRFTVAMVDLKLPDTDGLT 64

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQLCDSIICA-- 123
           +L+ I  + P   +I+ T    IK     +    Y  + K F ++   + L +       
Sbjct: 65  LLQAIKARQPACEVIIMTGYSTIKTAVAAMQLGAYEYLEKPFDDIDEIEALIEKAASHGF 124

Query: 124 -LREG--VVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            L++G            A+   +  S  M ++V +A K     + ++IQG  G GK+ L+
Sbjct: 125 NLQQGSAAAEEWAEVARAVGFQVGASLGMRRLVSVAHKIAGKNVTVLIQGSTGTGKEVLA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ-FLGKFIEANGGTIVL 239
           RFIH +  RA   F  VNCG + ++ +E  LFG        +AQ   G F  AN GT+ L
Sbjct: 185 RFIHSASGRADQAFIPVNCGALPENLLESELFGHEKGAFTGAAQPRRGIFELANRGTLFL 244

Query: 240 EE-PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           +E  DA P  +Q ++   +ETG+         I+ DVR+I  T  +L   ++   FR+DL
Sbjct: 245 DEIGDASP-QIQVKLLRVLETGEFMRVGGEKPIKTDVRVIAATNVDLEQAIREKTFREDL 303

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           YYR++V  + I  LRSRSEDIP L   F++     NA   + IS  AL LL  Y W  N+
Sbjct: 304 YYRLNVVRLEIPPLRSRSEDIPQLAEHFVRQL---NA--ALRISPPALRLLQGYGWPGNI 358

Query: 359 QELKNILLRAVIG---------------LKDSHLTEDRFVLLLSREGK------KEREFH 397
           ++L N++ RAV+                L  + L  D F  + S+ G+       ER + 
Sbjct: 359 RQLANVIRRAVVMCSGDTILPEHLESTLLNSAALAGDTFSPVSSQAGEGAVSLSPERLWR 418

Query: 398 TETACTCYTEGKSSD--TILDN---LSQESIPAIGQDGEVRR--LSDIEKEIIGLAMKLY 450
           T+ +     +  + +   +LD+   L    I A+G+ G   R  L D E+E I  A++ Y
Sbjct: 419 TDVSVEELRKLGADELKRMLDSLRALEGRLITAMGEGGGAARRCLKDTEEETIRQALEQY 478

Query: 451 RAQMSEVARRLGIGRSTLYRKIREYNI 477
           R  ++E A+ LGIGR+TLYRKI++Y +
Sbjct: 479 RWNITETAKVLGIGRNTLYRKIKQYGL 505


>gi|149178748|ref|ZP_01857331.1| acetoacetate metabolism regulatory protein atoC [Planctomyces maris
           DSM 8797]
 gi|148842446|gb|EDL56826.1| acetoacetate metabolism regulatory protein atoC [Planctomyces maris
           DSM 8797]
          Length = 346

 Score =  178 bits (452), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 112/355 (31%), Positives = 194/355 (54%), Gaps = 17/355 (4%)

Query: 133 ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF 192
           E++   L+ ++ +SPAM  +  L R+A   +  +++ GE G GK+ ++R IHE   RA  
Sbjct: 2   EDDRPILEDMVGLSPAMRNIYRLTRRAAATSSTVLLTGETGTGKELIARAIHELSPRATG 61

Query: 193 PFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQG 251
           PF  VNCG + +  +E  LFG +    T       G+F  A+GGTI L+E +++   +Q 
Sbjct: 62  PFIRVNCGALSESLLESELFGHIKGAFTSAVENRTGRFEAAHGGTIFLDEINSVSFTLQV 121

Query: 252 RIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIST 311
           ++   ++  + E      +I++D R++  T ++LL ++++  FR+DLYYR++V  IN+  
Sbjct: 122 KLLRVLQEHEFERVGDTRSIQVDCRIVAATNRDLLDEIEAERFREDLYYRLNVIPINLPP 181

Query: 312 LRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI- 370
           LR R+EDIP LVHFF + F  +  I     S++ LS    Y W  NV+EL+N + R ++ 
Sbjct: 182 LRERAEDIPELVHFFAKQFSAEEKIPLPEFSEEVLSTFKNYSWPGNVRELQNYVERLIVL 241

Query: 371 -GLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ- 428
            GL    L     +L     GK         A +  ++ +  +T+  +L    +  +G+ 
Sbjct: 242 SGLDGPSLD----LLPGHVTGKS-------LARSLPSKAQDPETMCRDLVNMELQRVGES 290

Query: 429 --DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVDS 481
             D   + +S +EKE+I   ++  +   ++ A RLGI R+TL++KI EY +E ++
Sbjct: 291 STDVHTQIVSLVEKEVILQVLRSCQGVQTKTATRLGINRNTLHKKISEYELESEA 345


>gi|260892434|ref|YP_003238531.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Ammonifex degensii KC4]
 gi|260864575|gb|ACX51681.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Ammonifex degensii KC4]
          Length = 470

 Score =  178 bits (452), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 138/477 (28%), Positives = 238/477 (49%), Gaps = 37/477 (7%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKE 68
           K VL++D +    + +KD +E  GY V         L  ++ I+ + + L +   E D  
Sbjct: 3   KLVLVVDDEKSVCEALKDVLEESGYSVVTATSGREALEKVNLIRPHAVLLDIRMPEMDGI 62

Query: 69  NILKNIVDKIPIVPIIVQTT-QDNIKILNCFLYNRISKFFLNLVSRKQLCDSI--ICALR 125
            +L+ + +K P VP+I+ T   D    +N   Y    ++ +  ++  +L  ++     + 
Sbjct: 63  KVLQALREKHPGVPVILMTAYSDTQTTINAMRYGAF-EYIVKPINLDELLSTLEKATTVT 121

Query: 126 EGVVPSQENEHCA-LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
           E +V   + E      +LI  SPAM +V     +  D  + ++IQGE G GK+ ++  IH
Sbjct: 122 EPLVTVGKGEIAPRPGTLIGCSPAMQEVYKTIGRIADSDVTVLIQGESGTGKELVAEAIH 181

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPD 243
            +  R   PF  ++C  I ++ +E  LFG +    T    + LGKF  A+GGT+ L+E  
Sbjct: 182 YNSPRQGKPFVKIDCTAIPENLLESELFGHEKGAFTGAHTRKLGKFELADGGTVFLDEIG 241

Query: 244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS 303
            +  A+Q ++  F++    E        R+DVR+I  T K+L  +VKS +FR+DLYYR++
Sbjct: 242 DISPALQAKLLRFLQEKAFERVGGTETRRVDVRIIAATNKDLEERVKSGLFREDLYYRLN 301

Query: 304 VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWIDNVQELK 362
           V  I +  LR R EDI  LV +F+ S   +   KQ++ ++     +L +Y W  NV+EL+
Sbjct: 302 VVEIKLPPLRERKEDIMLLVDYFV-SLSNRKFGKQVTGLTRSVADILLQYNWPGNVRELR 360

Query: 363 NILLRAVIGLKDSHLTEDRF--VLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           N+  RAV+  + + +T +     LL +  G+ E  +H            + D  +  L +
Sbjct: 361 NVCERAVLMARGNVITPESLPEYLLRAVRGRTE-AWH-----------PAEDRGVLPLKE 408

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
                         ++++E+  I  A++ YR   + VAR LG+ R+TLY K++E  I
Sbjct: 409 -------------MVAEMERSAILRALEEYRGNKTAVARALGMSRTTLYAKMKELGI 452


>gi|238892480|ref|YP_002917214.1| transcriptional regulatory protein ZraR [Klebsiella pneumoniae
           NTUH-K2044]
 gi|238544796|dbj|BAH61147.1| DNA-binding response regulator in two-component regulatory system
           with ZraS [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
          Length = 443

 Score =  178 bits (452), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 130/468 (27%), Positives = 224/468 (47%), Gaps = 40/468 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKE 68
           ++L++D D     I++  +  +GY V + + + L  + +I   V  L L +    E D  
Sbjct: 7   QILVVDDDISHCTILQALLRGWGYQVGVAH-NGLQALEQIHQQVFDLVLCDIRMAEMDGI 65

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             LK I    P +P+++ T   ++      + +    + +  +    L  +++ AL    
Sbjct: 66  ATLKEIKAYNPAIPVLIMTAFSSVGTAVEAIKSGALDYLVKPLDFDTLQQTLVQALAH-T 124

Query: 129 VPSQENEHCALDS---LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
             S+ +   A DS   +I  SPAM  +++           ++I GE G GK+ ++  IH 
Sbjct: 125 RQSESDPSVATDSRWGMIGDSPAMQALLNDITLVAPSDATVLIYGESGTGKELVAHAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
             +R   P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 CSERRDKPLVTLNCAALNESLLESELFGHEKGAFTGADRRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   + +DVRLI  T +NL  +V +  FR+DLYYR++V
Sbjct: 245 ISPLMQVRLLRAIQEREVQRVGSNQTLAVDVRLIAATHRNLAEEVSAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I I  LR R EDIP L   FL+ +  +N       + +A+ LL  YPW  N++EL+N 
Sbjct: 305 VTIEIPPLRRRREDIPQLAQHFLKRYTERNRKTVKGFTPQAMDLLIHYPWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+ L  ++++E              RE     A T    G S              
Sbjct: 365 VERAVVLLTGNYISE--------------RELPLAIAGTPLPSGGS-------------- 396

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              ++G ++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ---EEGGIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 441


>gi|110807854|ref|YP_691374.1| transcriptional regulatory protein ZraR [Shigella flexneri 5 str.
           8401]
 gi|110617402|gb|ABF06069.1| Transcriptional Regulatory protein [Shigella flexneri 5 str. 8401]
          Length = 441

 Score =  178 bits (452), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSVRSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|331649858|ref|ZP_08350936.1| transcriptional regulatory protein ZraR [Escherichia coli M605]
 gi|330908320|gb|EGH36839.1| response regulator of zinc sigma-54-dependent two-component system
           [Escherichia coli AA86]
 gi|331041324|gb|EGI13476.1| transcriptional regulatory protein ZraR [Escherichia coli M605]
          Length = 441

 Score =  178 bits (452), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 225/468 (48%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP LV+ FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLVNHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|197119178|ref|YP_002139605.1| nitrogen fixation master sigma-54-dependent transcriptional
           response regulator [Geobacter bemidjiensis Bem]
 gi|197088538|gb|ACH39809.1| nitrogen fixation master sigma-54-dependent transcriptional
           response regulator [Geobacter bemidjiensis Bem]
          Length = 478

 Score =  178 bits (452), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 123/372 (33%), Positives = 192/372 (51%), Gaps = 17/372 (4%)

Query: 111 VSRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQG 170
           VSR +   S +  L+E +    ++ +    ++I  SPAM +V     K     + +++QG
Sbjct: 118 VSRAREMTSQVSLLKEEL----KDRYQLEKTIIGNSPAMREVYKTIGKVAPSDVTVLVQG 173

Query: 171 EFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKF 229
           E G GK+ ++R IH + KR   PF  +NC  I ++ +E  LFG +    T  + + LGKF
Sbjct: 174 ESGTGKELIARAIHYNSKRLGKPFIPLNCAAIPKELLESELFGFEKGAFTGATERKLGKF 233

Query: 230 IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQV 289
            +ANGGTI L+E   +PL +Q +I   ++  +I       +I +DVR++  T ++L   V
Sbjct: 234 EQANGGTIFLDEIGDMPLDLQAKILRVLQEREITRTGGNQSIPVDVRVVAATNQDLEESV 293

Query: 290 KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLL 349
            +  FR+DLYYR++V  I++  LR R ED+P LV +FL   C +  + Q   S  A+ LL
Sbjct: 294 HNKQFREDLYYRLNVIPIHLVPLRDRKEDVPLLVQYFLTKICAELEVPQKRCSADAIKLL 353

Query: 350 TKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSR--EGKKEREFHTETACTCYTE 407
           T Y W  N++EL+N + R VI   D  L    F  L +R  EGK E E   E        
Sbjct: 354 TNYSWPGNIRELENTIKRGVILSPDPLLVASDFPGLRNRQSEGKGE-ELSLEGIVDLKLR 412

Query: 408 GKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRST 467
           G  S+  ++ +    + A+        L  +E+ +I   ++  R      A  LGI R+T
Sbjct: 413 GCFSN--MEKMESGDVHAM-------VLEQVERPLIRFVLEKTRGNQVRAADILGINRNT 463

Query: 468 LYRKIREYNIEV 479
           L +KI E  IE+
Sbjct: 464 LRKKITELGIEL 475


>gi|193067813|ref|ZP_03048779.1| response regulator ZraR [Escherichia coli E110019]
 gi|192958788|gb|EDV89225.1| response regulator ZraR [Escherichia coli E110019]
          Length = 441

 Score =  178 bits (452), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLASHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           +              +R V+LL+ E   ERE     A T                   IP
Sbjct: 365 V--------------ERSVVLLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|16131834|ref|NP_418432.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator/sigma54 interaction
           protein [Escherichia coli str. K-12 substr. MG1655]
 gi|89110034|ref|AP_003814.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS [Escherichia coli str. K-12 substr.
           W3110]
 gi|170083465|ref|YP_001732785.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator; sigma54
           interaction protein [Escherichia coli str. K-12 substr.
           DH10B]
 gi|238903061|ref|YP_002928857.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator/sigma54 interaction
           protein [Escherichia coli BW2952]
 gi|254039261|ref|ZP_04873310.1| transcriptional regulatory protein zraR [Escherichia sp. 1_1_43]
 gi|256026320|ref|ZP_05440185.1| transcriptional regulatory protein ZraR [Escherichia sp. 4_1_40B]
 gi|300947388|ref|ZP_07161581.1| response regulator receiver domain protein [Escherichia coli MS
           116-1]
 gi|300954764|ref|ZP_07167194.1| response regulator receiver domain protein [Escherichia coli MS
           175-1]
 gi|301023375|ref|ZP_07187165.1| response regulator receiver domain protein [Escherichia coli MS
           196-1]
 gi|301645739|ref|ZP_07245660.1| response regulator receiver domain protein [Escherichia coli MS
           146-1]
 gi|307140696|ref|ZP_07500052.1| transcriptional regulatory protein ZraR [Escherichia coli H736]
 gi|312974209|ref|ZP_07788379.1| transcriptional regulatory protein zraR [Escherichia coli 1827-70]
 gi|331644741|ref|ZP_08345859.1| transcriptional regulatory protein ZraR [Escherichia coli H736]
 gi|417166|sp|P14375|ZRAR_ECOLI RecName: Full=Transcriptional regulatory protein zraR
 gi|396343|gb|AAC43102.1| ORF_o441 [Escherichia coli str. K-12 substr. MG1655]
 gi|1790437|gb|AAC76978.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator/sigma54 interaction
           protein [Escherichia coli str. K-12 substr. MG1655]
 gi|85676065|dbj|BAE77315.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS [Escherichia coli str. K12 substr.
           W3110]
 gi|169891300|gb|ACB05007.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator; sigma54
           interaction protein [Escherichia coli str. K-12 substr.
           DH10B]
 gi|226838496|gb|EEH70526.1| transcriptional regulatory protein zraR [Escherichia sp. 1_1_43]
 gi|238861185|gb|ACR63183.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator/sigma54 interaction
           protein [Escherichia coli BW2952]
 gi|260451167|gb|ACX41589.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli DH1]
 gi|299880895|gb|EFI89106.1| response regulator receiver domain protein [Escherichia coli MS
           196-1]
 gi|300318263|gb|EFJ68047.1| response regulator receiver domain protein [Escherichia coli MS
           175-1]
 gi|300452992|gb|EFK16612.1| response regulator receiver domain protein [Escherichia coli MS
           116-1]
 gi|301075988|gb|EFK90794.1| response regulator receiver domain protein [Escherichia coli MS
           146-1]
 gi|310331376|gb|EFP98641.1| transcriptional regulatory protein zraR [Escherichia coli 1827-70]
 gi|315138561|dbj|BAJ45720.1| transcriptional regulatory protein ZraR [Escherichia coli DH1]
 gi|315617369|gb|EFU97975.1| transcriptional regulatory protein zraR [Escherichia coli 3431]
 gi|323933954|gb|EGB30428.1| sigma-54 interaction domain-containing protein [Escherichia coli
           E1520]
 gi|323938879|gb|EGB35099.1| sigma-54 interaction domain-containing protein [Escherichia coli
           E482]
 gi|331036041|gb|EGI08278.1| transcriptional regulatory protein ZraR [Escherichia coli H736]
          Length = 441

 Score =  178 bits (452), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQIISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|74314498|ref|YP_312917.1| transcriptional regulatory protein ZraR [Shigella sonnei Ss046]
 gi|73857975|gb|AAZ90682.1| response regulator of hydrogenase 3 activity (sensor HydH)
           [Shigella sonnei Ss046]
 gi|323167475|gb|EFZ53183.1| transcriptional regulatory protein zraR [Shigella sonnei 53G]
          Length = 441

 Score =  178 bits (451), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADRRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAVHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAGT------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|188492788|ref|ZP_03000058.1| response regulator ZraR [Escherichia coli 53638]
 gi|188487987|gb|EDU63090.1| response regulator ZraR [Escherichia coli 53638]
          Length = 441

 Score =  178 bits (451), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQIISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|117626266|ref|YP_859589.1| transcriptional regulatory protein ZraR [Escherichia coli APEC O1]
 gi|218561070|ref|YP_002393983.1| transcriptional regulatory protein ZraR [Escherichia coli S88]
 gi|237702771|ref|ZP_04533252.1| transcriptional regulatory protein ZraR [Escherichia sp. 3_2_53FAA]
 gi|115515390|gb|ABJ03465.1| ZraR, fused DNA-binding response regulator in two-component
           regulatory system with ZraS: response regulator/sigma54
           interaction protein [Escherichia coli APEC O1]
 gi|218367839|emb|CAR05634.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator ; sigma54
           interaction protein [Escherichia coli S88]
 gi|226903084|gb|EEH89343.1| transcriptional regulatory protein ZraR [Escherichia sp. 3_2_53FAA]
 gi|294492135|gb|ADE90891.1| response regulator ZraR [Escherichia coli IHE3034]
 gi|323948825|gb|EGB44722.1| sigma-54 interaction domain-containing protein [Escherichia coli
           H252]
 gi|323953784|gb|EGB49591.1| sigma-54 interaction domain-containing protein [Escherichia coli
           H263]
          Length = 441

 Score =  178 bits (451), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +I+     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSIETAVEALKTGALDYLIKPLDFDNLQSTLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|26250776|ref|NP_756816.1| transcriptional regulatory protein ZraR [Escherichia coli CFT073]
 gi|110644339|ref|YP_672069.1| transcriptional regulatory protein ZraR [Escherichia coli 536]
 gi|191174305|ref|ZP_03035813.1| response regulator ZraR [Escherichia coli F11]
 gi|300985437|ref|ZP_07177440.1| response regulator receiver domain protein [Escherichia coli MS
           200-1]
 gi|306812019|ref|ZP_07446227.1| transcriptional regulatory protein ZraR [Escherichia coli NC101]
 gi|26111207|gb|AAN83390.1|AE016770_190 Transcriptional Regulatory protein zraR [Escherichia coli CFT073]
 gi|110345931|gb|ABG72168.1| transcriptional regulatory protein ZraR [Escherichia coli 536]
 gi|190905437|gb|EDV65068.1| response regulator ZraR [Escherichia coli F11]
 gi|300306529|gb|EFJ61049.1| response regulator receiver domain protein [Escherichia coli MS
           200-1]
 gi|305854624|gb|EFM55060.1| transcriptional regulatory protein ZraR [Escherichia coli NC101]
 gi|324015258|gb|EGB84477.1| response regulator receiver domain protein [Escherichia coli MS
           60-1]
          Length = 441

 Score =  178 bits (451), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLANHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|320197100|gb|EFW71718.1| Response regulator of zinc sigma-54-dependent two-component system
           [Escherichia coli WV_060327]
          Length = 441

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 131/466 (28%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHS 126

Query: 130 PSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E    +    S++  SPAM  ++            ++I G+ G GK+ ++R IH S 
Sbjct: 127 VDAETPAVSASQFSMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T                   IP +
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAST------------------PIPLV 394

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 395 -QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|218697712|ref|YP_002405379.1| transcriptional regulatory protein ZraR [Escherichia coli 55989]
 gi|256021675|ref|ZP_05435540.1| transcriptional regulatory protein ZraR [Shigella sp. D9]
 gi|332282918|ref|ZP_08395331.1| transcriptional regulatory protein ZraR [Shigella sp. D9]
 gi|218354444|emb|CAV01260.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator ; sigma54
           interaction protein [Escherichia coli 55989]
 gi|332105270|gb|EGJ08616.1| transcriptional regulatory protein ZraR [Shigella sp. D9]
          Length = 441

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDTLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLASHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           +              +R V+LL+ E   ERE     A T                   IP
Sbjct: 365 V--------------ERSVVLLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|218692285|ref|YP_002400497.1| transcriptional regulatory protein ZraR [Escherichia coli ED1a]
 gi|218429849|emb|CAR10817.2| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator ; sigma54
           interaction protein [Escherichia coli ED1a]
          Length = 441

 Score =  177 bits (450), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG      T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKRAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLANHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|253700033|ref|YP_003021222.1| Fis family transcriptional regulator [Geobacter sp. M21]
 gi|251774883|gb|ACT17464.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. M21]
          Length = 478

 Score =  177 bits (450), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 123/372 (33%), Positives = 192/372 (51%), Gaps = 17/372 (4%)

Query: 111 VSRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQG 170
           VSR +   S +  L+E +    ++ +    ++I  SPAM  V     K     + +++QG
Sbjct: 118 VSRAREMTSQVSLLKEEL----KDRYQLEKTIIGNSPAMRDVYKTIGKVAPSDVTVLVQG 173

Query: 171 EFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKF 229
           E G GK+ ++R IH + KR   PF  +NC  I ++ +E  LFG +    T  + + LGKF
Sbjct: 174 ESGTGKELIARAIHYNSKRLGKPFIPLNCAAIPKELLESELFGFEKGAFTGATERKLGKF 233

Query: 230 IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQV 289
            +ANGGTI L+E   +PL +Q +I   ++  +I       +I++DVR++  T ++L   V
Sbjct: 234 EQANGGTIFLDEIGDMPLDLQAKILRVLQEREITRTGGNQSIQVDVRVVAATNQDLEESV 293

Query: 290 KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLL 349
           ++  FR+DLYYR++V  I++  LR R ED+P LV +FL   C +  +     S  A+ LL
Sbjct: 294 RNKQFREDLYYRLNVIPIHLVPLRDRKEDVPLLVQYFLTKICAELEVPLKRCSADAIKLL 353

Query: 350 TKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSR--EGKKEREFHTETACTCYTE 407
           T Y W  N++EL+N + R VI   D  L    F  L SR  EGK E E   E        
Sbjct: 354 TNYSWPGNIRELENTIKRGVILSPDPLLVASDFPGLRSRQSEGKGE-ELSLEGIVDLKLR 412

Query: 408 GKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRST 467
           G  S+  ++ +    + A+        L  +E+ +I   ++  R      A  LGI R+T
Sbjct: 413 GCFSN--MEKMESGDVHAM-------VLEQVERPLIRFVLEKTRGNQVRAADILGINRNT 463

Query: 468 LYRKIREYNIEV 479
           L +KI E  IE+
Sbjct: 464 LRKKITELGIEL 475


>gi|239906255|ref|YP_002952995.1| NtrC family two-component response regulator [Desulfovibrio
           magneticus RS-1]
 gi|239796120|dbj|BAH75109.1| NtrC family two-component response regulator [Desulfovibrio
           magneticus RS-1]
          Length = 473

 Score =  177 bits (450), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 122/411 (29%), Positives = 207/411 (50%), Gaps = 20/411 (4%)

Query: 79  PIVPIIVQT----TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE--GVVPSQ 132
           P +P+I+ T    T+  I+      Y+ I K F ++    +L D  + A R     V   
Sbjct: 72  PRLPVIIMTAYGTTEIAIEATKMGAYDYILKPF-DIPEILKLIDKAVAAGRSMRSRVAVG 130

Query: 133 ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF 192
            +   A +++I  SPAM ++     +A      ++++GE G GK+ ++R +++   RA  
Sbjct: 131 VDAEAATEAIIGQSPAMQELYKAIGRAAPTDATVLVRGESGAGKELVARAVYQHSLRADK 190

Query: 193 PFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQG 251
           PF ++NC  I +  +E  LFG +    T  + + +GK  +AN GT+ L+E   +P+A+Q 
Sbjct: 191 PFLVINCVAIPETLLESELFGYEKGAFTGAAGRKVGKIEQANHGTVFLDEIGDMPMAIQA 250

Query: 252 RIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIST 311
           ++   ++   +E    R  I +DVR+I  T ++L   V+   FR+DLYYR+ V  + +  
Sbjct: 251 KLLRLLQEKNVERLGGRQVIPVDVRIIAATNRDLEAAVRQGQFREDLYYRLKVVTLALPP 310

Query: 312 LRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIG 371
           LR R  DIP LV +FL     +       +S +A++ LT + W  NV+EL N+L +A+I 
Sbjct: 311 LRERPGDIPLLVRYFLSRHAREMGQSDPGVSPEAMAKLTAHDWPGNVRELGNVLKKALIF 370

Query: 372 LKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGE 431
            + + L+ D     L    ++  E  T         G+  D I + + +E   A G+DG 
Sbjct: 371 SRGAPLSPDEVRKALGAPLRQGAEAAT---------GEDGDPIAETIRREL--ASGRDGL 419

Query: 432 VRRLSD-IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVDS 481
              L D     +I LA++      S+ AR LG+ R TL  KI +Y + ++S
Sbjct: 420 FEELMDRFGHMVIRLALEATGGNRSQAARLLGLSRPTLIAKIEKYGLRIES 470


>gi|323182104|gb|EFZ67514.1| transcriptional regulatory protein zraR [Escherichia coli 1357]
          Length = 441

 Score =  177 bits (450), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDTLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGNSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLASHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           +              +R V+LL+ E   ERE     A T                   IP
Sbjct: 365 V--------------ERSVVLLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|315300747|gb|EFU59972.1| response regulator receiver domain protein [Escherichia coli MS
           16-3]
          Length = 441

 Score =  177 bits (449), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQSTLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|300919423|ref|ZP_07135927.1| response regulator receiver domain protein [Escherichia coli MS
           115-1]
 gi|300413516|gb|EFJ96826.1| response regulator receiver domain protein [Escherichia coli MS
           115-1]
          Length = 441

 Score =  177 bits (449), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 133/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLCGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|293413440|ref|ZP_06656100.1| transcriptional regulatory protein ZraR [Escherichia coli B354]
 gi|291468035|gb|EFF10534.1| transcriptional regulatory protein ZraR [Escherichia coli B354]
 gi|325499264|gb|EGC97123.1| transcriptional regulatory protein ZraR [Escherichia fergusonii
           ECD227]
          Length = 441

 Score =  177 bits (449), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLANHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|170680150|ref|YP_001746389.1| transcriptional regulatory protein ZraR [Escherichia coli SMS-3-5]
 gi|170517868|gb|ACB16046.1| response regulator ZraR [Escherichia coli SMS-3-5]
          Length = 441

 Score =  177 bits (449), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLTNHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|322420176|ref|YP_004199399.1| Fis family two component sigma54 specific transcriptional regulator
           [Geobacter sp. M18]
 gi|320126563|gb|ADW14123.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. M18]
          Length = 478

 Score =  177 bits (449), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 122/371 (32%), Positives = 189/371 (50%), Gaps = 15/371 (4%)

Query: 111 VSRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQG 170
           VSR +   S +  L+E +    + E     ++I  SPAM +V     K     + +++QG
Sbjct: 118 VSRAREMTSQVSLLKEELADRYQLEK----TIIGNSPAMREVYKTIGKVAPSDVTVLVQG 173

Query: 171 EFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKF 229
           E G GK+ ++R IH + KR   PF  +NC  I ++ +E  LFG +    T  + + LGKF
Sbjct: 174 ESGTGKELIARAIHYNSKRLGKPFIPLNCAAIPKELLESELFGFEKGAFTGATERKLGKF 233

Query: 230 IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQV 289
            +ANGGTI L+E   +P  +Q +I   ++  +I       +I +DVR++  T ++L   V
Sbjct: 234 EQANGGTIFLDEIGDMPFDLQAKILRVLQEREITRTGGNQSIPVDVRVVAATNQDLEESV 293

Query: 290 KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLL 349
           ++  FR+DLYYR++V  I +  LR R EDIP LV +FL   C +        S  A+ LL
Sbjct: 294 RNKQFREDLYYRLNVIPIQLVPLRERKEDIPLLVQYFLNKICAELEAPLKRCSADAVKLL 353

Query: 350 TKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGK-KEREFHTETACTCYTEG 408
           T Y W  N++EL+N + RAVI   D  L    F  L +R+G+ K  E   E        G
Sbjct: 354 TNYNWPGNIRELENTIKRAVILSPDPLLVASDFPGLRTRQGEGKGEELSLEGIVDLKLRG 413

Query: 409 KSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
             S+  ++ +    + A+        L  +E+ +I   ++  R      A  LGI R+TL
Sbjct: 414 CFSN--MEKMESGDVHAM-------VLEQVERPLIRFVLEKTRGNQVRAADILGINRNTL 464

Query: 469 YRKIREYNIEV 479
            +KI E  IE+
Sbjct: 465 RKKITELGIEL 475


>gi|78223760|ref|YP_385507.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Geobacter metallireducens GS-15]
 gi|78195015|gb|ABB32782.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter metallireducens GS-15]
          Length = 480

 Score =  177 bits (449), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 125/403 (31%), Positives = 205/403 (50%), Gaps = 21/403 (5%)

Query: 87  TTQDNIKILNCFLYNRISKFF--------LNLVSRKQLCDSIICALREGVVPSQENEHCA 138
           + ++ ++ +    Y+ I+K F        +  V+R +   S +  LRE +    ++ +  
Sbjct: 86  SMKNAVEAMKRGAYDYITKPFDLDVIDAIIEKVNRAREITSQMSILREEL----KDRYLL 141

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
             +++  SPAM +V     K     + +++QGE G GK+ ++R IH + KR   PF  +N
Sbjct: 142 EKNIVGNSPAMREVYKTIGKVAPSDVTVLVQGESGTGKELIARAIHFNSKRIGKPFIALN 201

Query: 199 CGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
           C  I ++ +E  LFG +    T  + + LGKF +ANGGTI L+E   +PL +Q +I   +
Sbjct: 202 CAAIPKELLESELFGFEKGAFTGAAERKLGKFEQANGGTIFLDEIGDMPLDLQAKILRVL 261

Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
           +  ++        I +DVR++  T +NL    ++  FR+DLYYR++V  I +  LR R E
Sbjct: 262 QEKEVTRTGGSQNIAVDVRIVAATNQNLEELARNKQFREDLYYRLNVVPIQLVPLRERKE 321

Query: 318 DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHL 377
           DIP LV +FL   C +  +   + S + ++LLT Y W  NV+EL+N + RAVI   D  L
Sbjct: 322 DIPALVEYFLHKTCAELEVPGRTCSPETMALLTAYSWPGNVRELENTIKRAVILSSDPLL 381

Query: 378 TEDRFV-LLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
           T   F  L + R G+               + ++S T LD +    I  +        L 
Sbjct: 382 TPADFPGLRIQRTGEAVATDELSLEALVDMKLRASLTNLDKMETGDIYNL-------VLK 434

Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
            IE+ +I   ++  R    + A  LGI R+TL +KI+E  IE+
Sbjct: 435 QIERPLIRFVLEKTRGNQVKGAEILGINRNTLRKKIQELGIEI 477


>gi|331660565|ref|ZP_08361498.1| transcriptional regulatory protein ZraR [Escherichia coli TA206]
 gi|222035715|emb|CAP78460.1| Transcriptional regulatory protein zraR [Escherichia coli LF82]
 gi|312948578|gb|ADR29405.1| transcriptional regulatory protein ZraR [Escherichia coli O83:H1
           str. NRG 857C]
 gi|331052348|gb|EGI24386.1| transcriptional regulatory protein ZraR [Escherichia coli TA206]
          Length = 441

 Score =  177 bits (448), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|301019445|ref|ZP_07183618.1| response regulator receiver domain protein [Escherichia coli MS
           69-1]
 gi|300399260|gb|EFJ82798.1| response regulator receiver domain protein [Escherichia coli MS
           69-1]
          Length = 441

 Score =  177 bits (448), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVVLAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLADHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIASTL------------------IP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|218702639|ref|YP_002410268.1| transcriptional regulatory protein ZraR [Escherichia coli IAI39]
 gi|218372625|emb|CAR20500.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator ; sigma54
           interaction protein [Escherichia coli IAI39]
          Length = 441

 Score =  177 bits (448), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLTNHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|218707623|ref|YP_002415142.1| transcriptional regulatory protein ZraR [Escherichia coli UMN026]
 gi|293407621|ref|ZP_06651539.1| transcriptional regulatory protein ZraR [Escherichia coli FVEC1412]
 gi|298383369|ref|ZP_06992961.1| two-component system [Escherichia coli FVEC1302]
 gi|300897581|ref|ZP_07115990.1| response regulator receiver domain protein [Escherichia coli MS
           198-1]
 gi|331665661|ref|ZP_08366557.1| transcriptional regulatory protein ZraR [Escherichia coli TA143]
 gi|218434720|emb|CAR15652.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator ; sigma54
           interaction protein [Escherichia coli UMN026]
 gi|291425389|gb|EFE98429.1| transcriptional regulatory protein ZraR [Escherichia coli FVEC1412]
 gi|298276248|gb|EFI17769.1| two-component system [Escherichia coli FVEC1302]
 gi|300358657|gb|EFJ74527.1| response regulator receiver domain protein [Escherichia coli MS
           198-1]
 gi|331057179|gb|EGI29171.1| transcriptional regulatory protein ZraR [Escherichia coli TA143]
          Length = 441

 Score =  177 bits (448), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLADHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|218551012|ref|YP_002384803.1| transcriptional regulatory protein ZraR [Escherichia fergusonii
           ATCC 35469]
 gi|218358553|emb|CAQ91201.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator ; sigma54
           interaction protein [Escherichia fergusonii ATCC 35469]
 gi|324110916|gb|EGC04908.1| sigma-54 interaction domain-containing protein [Escherichia
           fergusonii B253]
          Length = 441

 Score =  176 bits (447), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|291285419|ref|YP_003502237.1| transcriptional regulatory protein ZraR [Escherichia coli O55:H7
           str. CB9615]
 gi|209751638|gb|ACI74126.1| response regulator HydG [Escherichia coli]
 gi|209751644|gb|ACI74129.1| response regulator HydG [Escherichia coli]
 gi|290765292|gb|ADD59253.1| transcriptional regulatory protein ZraR [Escherichia coli O55:H7
           str. CB9615]
 gi|320639095|gb|EFX08735.1| transcriptional regulatory protein ZraR [Escherichia coli O157:H7
           str. G5101]
 gi|320644489|gb|EFX13552.1| transcriptional regulatory protein ZraR [Escherichia coli O157:H-
           str. 493-89]
 gi|320649808|gb|EFX18329.1| transcriptional regulatory protein ZraR [Escherichia coli O157:H-
           str. H 2687]
 gi|320655141|gb|EFX23097.1| transcriptional regulatory protein ZraR [Escherichia coli O55:H7
           str. 3256-97 TW 07815]
 gi|320660785|gb|EFX28239.1| transcriptional regulatory protein ZraR [Escherichia coli O55:H7
           str. USDA 5905]
 gi|320665903|gb|EFX32934.1| transcriptional regulatory protein ZraR [Escherichia coli O157:H7
           str. LSU-61]
          Length = 441

 Score =  176 bits (447), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 219/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL    +
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHI 126

Query: 130 PSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E          ++  SPAM  ++            ++I G+ G GK+ ++R IH S 
Sbjct: 127 IDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T                   IP +
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAST------------------PIP-L 393

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 394 AQSLDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|237727859|ref|ZP_04558340.1| transcriptional regulatory protein ZraR [Citrobacter sp. 30_2]
 gi|226910416|gb|EEH96334.1| transcriptional regulatory protein ZraR [Citrobacter sp. 30_2]
          Length = 441

 Score =  176 bits (447), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 132/466 (28%), Positives = 219/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S  + + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYEVALA-YSGRAALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAFSSVETAVGALKTGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM Q+++           ++I G+ G GK+ ++R +H S 
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQQLLNEIAMVAPSDATVLIHGDSGTGKELVARALHASS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R   P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARRDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T +NL  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTIAVDVRLIAATHRNLAEEVSAGRFRQDLYYRLNVVT 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I +  L  R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPALCQRREDIPLLAEHFLQRFAARNRKAVKGFTPQAMDLLIHYDWPGNIRELENAI- 365

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
                        +R V+LL+ E   ERE     A T      S                
Sbjct: 366 -------------ERSVVLLTGEYISERELPMAIAATPIKTEFS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKE+I  A++      +E AR+LGI R TL  KI
Sbjct: 397 ---GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKI 439


>gi|281181068|dbj|BAI57398.1| two-component regulator [Escherichia coli SE15]
          Length = 441

 Score =  176 bits (447), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|78187276|ref|YP_375319.1| two component Fis family transcriptional regulator [Chlorobium
           luteolum DSM 273]
 gi|78167178|gb|ABB24276.1| two component transcriptional regulator, Fis family [Chlorobium
           luteolum DSM 273]
          Length = 492

 Score =  176 bits (447), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 135/486 (27%), Positives = 227/486 (46%), Gaps = 28/486 (5%)

Query: 4   KKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSL- 60
           +K   R   VLI D D+   +I    V   GY   +V   +  + +I++   +VI L + 
Sbjct: 19  RKPAARKNTVLIADDDETSRRIFSHFVRKMGYTALVVQNGMECIESITEQSPDVILLDIN 78

Query: 61  INCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCF---LYNRISKFF----LNLVSR 113
           +  +D  E +L    + I    II+  + D  + + C     Y  ++K      L +V R
Sbjct: 79  MPGKDGFEVMLHMKTEHIKTPVIIITASHDIPQAVKCIKLGAYEYLTKPLNIDRLEIVMR 138

Query: 114 KQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFG 173
             L +S +  +    +  +         +I  S A+   ++ A +  +  + ++I GE G
Sbjct: 139 NSLAESAL-QIEVKNLKKELRTRDIFQHIIGRSRAIKASMEQAVQVMETDLNVLILGESG 197

Query: 174 VGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEA 232
            GK+  ++ IH+  +R   PF  VNC  I     +  LFG      T  +    G F +A
Sbjct: 198 TGKELFAQAIHQGSRRNCGPFVSVNCAAISSTLADSILFGHAKGSFTGAATDHTGFFEQA 257

Query: 233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH 292
           + GTI L+E   +   +Q ++   I+  KI     +    +D R+I  T +N    ++S+
Sbjct: 258 DKGTIFLDEIGDMEADIQAKVLRAIQERKIRRVGEKHERSVDFRVISATNRNFADAIRSN 317

Query: 293 VFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY 352
            FR+DLYYR+  F + +  LR R EDIP L   FL  F + N I+++S +D+AL+   +Y
Sbjct: 318 QFREDLYYRLEEFPLFLPPLRERPEDIPLLARHFLDEFASANNIEKLSFTDEALAGSKEY 377

Query: 353 PWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD 412
            W  N++ELKN + RA +  K   +   R +L   + G               T G  + 
Sbjct: 378 HWPGNIRELKNAVQRAAVTRKGDEVDSLRPIL---KHGNGS------------TAGHPAS 422

Query: 413 TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +  + +Q S    G D +   L + E+E I  A K     +++ AR LGIGR+TLYRK+
Sbjct: 423 ALAGSAAQRSA-GHGPDMQSYSLEEHEREAILKAYKASNGNLTKTARMLGIGRATLYRKL 481

Query: 473 REYNIE 478
            ++ +E
Sbjct: 482 DKFGLE 487


>gi|260870715|ref|YP_003237117.1| fused DNA-binding response regulator ZraR in two-component
           regulatory system with ZraS: response regulator/sigma 54
           interaction protein [Escherichia coli O111:H- str.
           11128]
 gi|257767071|dbj|BAI38566.1| fused DNA-binding response regulator ZraR in two-component
           regulatory system with ZraS: response regulator/sigma 54
           interaction protein [Escherichia coli O111:H- str.
           11128]
 gi|323177560|gb|EFZ63145.1| transcriptional regulatory protein zraR [Escherichia coli 1180]
          Length = 441

 Score =  176 bits (446), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDTLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCVALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLASHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           +              +R V+LL+ E   ERE     A T                   IP
Sbjct: 365 V--------------ERSVVLLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|20141026|sp|Q9APD9|ZRAR_KLEOX RecName: Full=Transcriptional regulatory protein zraR
 gi|12584125|gb|AAG59807.1|AF305914_2 HydG [Klebsiella oxytoca]
          Length = 443

 Score =  176 bits (445), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 128/470 (27%), Positives = 221/470 (47%), Gaps = 46/470 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY V + N + L  + K++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYRVALAN-NGLQALEKVREKVFDLVLCDIRMAEMDGIE 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   ++      L +    + +  +      D +   L E + 
Sbjct: 67  TLKEIKTFNPSIPVLIMTAYSSVDTAVEALKSGALDYLIKPLD----FDKLQLTLSEALA 122

Query: 130 PSQENEHCALDS------LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
            ++ +E    ++      ++  SPAM  +++           ++I GE G GK+ ++R +
Sbjct: 123 HTRLSESPVTETPAAQFGMVGDSPAMRALLNNITLVAPSDATVLIHGESGTGKELVARAL 182

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEP 242
           H S  R+  P  I+NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E 
Sbjct: 183 HASSARSRRPLVILNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEI 242

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             +   +Q R+   I+  +++   S   + +DVRLI  T ++L  +V +  FR+DLYYR+
Sbjct: 243 GDISPLMQVRLLRAIQEREVQRVGSNQTLSVDVRLIAATHRDLAEEVSAGRFRQDLYYRL 302

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           +V  I++  LR R EDIP L  +FLQ +  +N       + +A+ LL  Y W  N++EL+
Sbjct: 303 NVVTIDMPPLRHRREDIPPLARYFLQRYAERNRKAVQGFTPQAMDLLIHYAWPGNIRELE 362

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           N + RAV+              LL+ E   ERE       T   +    D          
Sbjct: 363 NAVERAVV--------------LLTGEYISERELPLAITGTPVADAPHGDD--------- 399

Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
                    ++ L ++EKE I  A++      +E ARRLGI R TL  K+
Sbjct: 400 --------SIQPLVEVEKEAILAALERTGGNKTEAARRLGITRKTLLAKL 441


>gi|320200155|gb|EFW74744.1| Response regulator of zinc sigma-54-dependent two-component system
           [Escherichia coli EC4100B]
          Length = 441

 Score =  176 bits (445), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  S AM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSSAMQHLLSEIALVAPSEATVLIHGDSGTGKELIARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|331685747|ref|ZP_08386329.1| transcriptional regulatory protein ZraR [Escherichia coli H299]
 gi|331077057|gb|EGI48273.1| transcriptional regulatory protein ZraR [Escherichia coli H299]
          Length = 441

 Score =  176 bits (445), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 219/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHS 126

Query: 130 PSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E          ++  SPAM  ++            ++I G+ G GK+ ++R IH S 
Sbjct: 127 IDAETPVVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEVPSLRQRREDIPLLANHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENTVE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T                   IP +
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAST------------------PIPLV 394

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 395 -QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|82778820|ref|YP_405169.1| transcriptional regulatory protein ZraR [Shigella dysenteriae
           Sd197]
 gi|309783961|ref|ZP_07678606.1| transcriptional regulatory protein zraR [Shigella dysenteriae 1617]
 gi|81242968|gb|ABB63678.1| sensor HydH response regulator of hydrogenase 3 activity [Shigella
           dysenteriae Sd197]
 gi|308928332|gb|EFP73794.1| transcriptional regulatory protein zraR [Shigella dysenteriae 1617]
          Length = 441

 Score =  176 bits (445), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 131/468 (27%), Positives = 222/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S+   + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SERQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALKPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGHFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +  +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEANAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   F Q F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFFQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAGT------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|118581482|ref|YP_902732.1| two component sigma54 specific Fis family transcriptional regulator
           [Pelobacter propionicus DSM 2379]
 gi|118504192|gb|ABL00675.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Pelobacter propionicus DSM 2379]
          Length = 480

 Score =  176 bits (445), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 118/349 (33%), Positives = 188/349 (53%), Gaps = 12/349 (3%)

Query: 135 EHCALD-SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
           EH  ++ ++I  S AM  +     K  D  I I+IQGE G GK+ ++R IH +  R   P
Sbjct: 137 EHYQVEKNIIGNSAAMQSIYKTIGKVADSDITILIQGESGTGKEMVARAIHFNSGRLGKP 196

Query: 194 FFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGR 252
           F  +NC  I +D +E  LFG +    T  S +  GKF +AN GTI L+E   +PL +Q +
Sbjct: 197 FVAINCAAIPRDLLESELFGSERGAFTGASERKQGKFEQANQGTIFLDEIGDMPLDLQAK 256

Query: 253 IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTL 312
           I   ++  ++       +I ++VR++  T + L  +V+   FR+DLYYR++V  I ++ L
Sbjct: 257 ILRVLQEHEVTRVGGTQSIAVNVRIVAATNQELQERVRQREFREDLYYRLNVVPITLAPL 316

Query: 313 RSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGL 372
           R R +DIP LV +FL   CT+ +I    ++ +A++LL+++ W  NV+EL+N + RAVI  
Sbjct: 317 RERRDDIPELVRYFLDRTCTELSIPPKQLTPEAMALLSRHSWPGNVRELENTIKRAVILS 376

Query: 373 KDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGK--SSDTILDNLSQESIPAIGQDG 430
            D  LTE  F   L  EG++      + +     E K  S  T ++ L +  I A     
Sbjct: 377 NDPMLTEADFD-GLQPEGEETAMTPQDASLEAIVEAKLRSCLTGIEKLDKSDIHA----- 430

Query: 431 EVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
             + L  +E+ +I   ++  R    + A  LGI R+TL +KI +  IE+
Sbjct: 431 --KVLQQVERPLIRFILEKTRWNQVKAADILGINRNTLRKKIHDLEIEL 477


>gi|193066408|ref|ZP_03047455.1| response regulator ZraR [Escherichia coli E22]
 gi|194429958|ref|ZP_03062467.1| response regulator ZraR [Escherichia coli B171]
 gi|218556559|ref|YP_002389473.1| transcriptional regulatory protein ZraR [Escherichia coli IAI1]
 gi|260846804|ref|YP_003224582.1| fused DNA-binding response regulator ZraR in two-component
           regulatory system with ZraS: response regulator/sigma 54
           interaction protein [Escherichia coli O103:H2 str.
           12009]
 gi|293474312|ref|ZP_06664721.1| two-component system [Escherichia coli B088]
 gi|300819816|ref|ZP_07100003.1| response regulator receiver domain protein [Escherichia coli MS
           107-1]
 gi|192925932|gb|EDV80579.1| response regulator ZraR [Escherichia coli E22]
 gi|194411987|gb|EDX28300.1| response regulator ZraR [Escherichia coli B171]
 gi|218363328|emb|CAR00978.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator ; sigma54
           interaction protein [Escherichia coli IAI1]
 gi|257761951|dbj|BAI33448.1| fused DNA-binding response regulator ZraR in two-component
           regulatory system with ZraS: response regulator/sigma 54
           interaction protein [Escherichia coli O103:H2 str.
           12009]
 gi|291321342|gb|EFE60783.1| two-component system [Escherichia coli B088]
 gi|300527637|gb|EFK48699.1| response regulator receiver domain protein [Escherichia coli MS
           107-1]
 gi|323161303|gb|EFZ47212.1| transcriptional regulatory protein zraR [Escherichia coli E128010]
 gi|323943607|gb|EGB39715.1| sigma-54 interaction domain-containing protein [Escherichia coli
           H120]
          Length = 441

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  S AM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSSAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|326625883|gb|EGE32228.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
          Length = 441

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 133/467 (28%), Positives = 223/467 (47%), Gaps = 42/467 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE-PDAL 245
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E  D  
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIT 246

Query: 246 PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF 305
           PL +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V 
Sbjct: 247 PL-MQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVV 305

Query: 306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNIL 365
            I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W+ N++EL+N +
Sbjct: 306 AIEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWLGNIRELENAI 365

Query: 366 LRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPA 425
            RAV+              LL+ E   ERE     A T      S               
Sbjct: 366 ERAVV--------------LLTGEYISERELPLAIAATPIKTEYS--------------- 396

Query: 426 IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
               GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ----GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|283836743|ref|ZP_06356484.1| transcriptional regulatory protein ZraR [Citrobacter youngae ATCC
           29220]
 gi|291067296|gb|EFE05405.1| transcriptional regulatory protein ZraR [Citrobacter youngae ATCC
           29220]
          Length = 441

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 132/466 (28%), Positives = 219/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S  + + ++   V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYEVALA-YSGRAALEQVHERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAFSSVETAVEALKTGALDYLIKPLDFDRLQETLEKALAHTRD 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM Q+++           ++I G+ G GK+ ++R +H S 
Sbjct: 127 TGAELPSASAAQFGMIGRSPAMQQLLNEIAMVAPSDATVLIHGDSGTGKELVARALHASS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEQEVQRVGSNQTIGVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVT 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I +  L  R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPALCQRREDIPLLAEHFLQRFAARNRKAVKGFTPQAMDLLIHYNWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPMAIAATPIKAEFS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKE+I  A++      +E AR+LGI R TL  KI
Sbjct: 397 ---GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKI 439


>gi|209921484|ref|YP_002295568.1| transcriptional regulatory protein ZraR [Escherichia coli SE11]
 gi|209914743|dbj|BAG79817.1| two-component regulator [Escherichia coli SE11]
 gi|324017342|gb|EGB86561.1| response regulator receiver domain protein [Escherichia coli MS
           117-3]
          Length = 441

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDTLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  S AM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSSAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGHFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|227885465|ref|ZP_04003270.1| transcriptional regulatory protein ZraR [Escherichia coli 83972]
 gi|227837539|gb|EEJ48005.1| transcriptional regulatory protein ZraR [Escherichia coli 83972]
 gi|307556147|gb|ADN48922.1| transcriptional regulatory protein [Escherichia coli ABU 83972]
          Length = 441

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 131/468 (27%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLANHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            + Q  +++ L ++EKE+I  A++      +E AR+LG  R TL  K+
Sbjct: 393 LV-QSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGSTRKTLLAKL 439


>gi|260858114|ref|YP_003232005.1| fused DNA-binding response regulator ZraR in two-component
           regulatory system with ZraS: response regulator/sigma 54
           interaction protein [Escherichia coli O26:H11 str.
           11368]
 gi|257756763|dbj|BAI28265.1| fused DNA-binding response regulator ZraR in two-component
           regulatory system with ZraS: response regulator/sigma 54
           interaction protein [Escherichia coli O26:H11 str.
           11368]
 gi|323155546|gb|EFZ41723.1| transcriptional regulatory protein zraR [Escherichia coli EPECa14]
          Length = 441

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 224/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDTLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCVALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLASHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           +              +R V+LL+ E   ERE     A T                   IP
Sbjct: 365 V--------------ERSVVLLTGEYISERELPLAIAST------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTCGNKTEAARQLGITRKTLLAKL 439


>gi|157163473|ref|YP_001460791.1| transcriptional regulatory protein ZraR [Escherichia coli HS]
 gi|157069153|gb|ABV08408.1| response regulator ZraR [Escherichia coli HS]
          Length = 441

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  S AM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSSAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGHFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAGT------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|103486459|ref|YP_616020.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Sphingopyxis alaskensis RB2256]
 gi|98976536|gb|ABF52687.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Sphingopyxis alaskensis RB2256]
          Length = 487

 Score =  175 bits (443), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 130/490 (26%), Positives = 232/490 (47%), Gaps = 44/490 (8%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD-----LSTISKIQVNVIFLSLINCED 65
           + V+I+D +  Q + +   V   G+   +   +D     L T   + ++ + +       
Sbjct: 19  RMVMIVDSEPAQQRFLSALVSRGGWRSVVAADTDTALAKLGTQEGMALDAVLIDQGAPGM 78

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           D    +  +    P +P++V T ++ +++    +    S F    ++  +L +++   + 
Sbjct: 79  DIAQFVIELRRWRPALPLVVITMRNGVEVAVAAMRAGASDFVQKPIAPDRLLEALDRVMA 138

Query: 126 EGVVPSQE--------NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
           +   P  E            A + +I  SP     + +A KA    +P+MI G+ G GK+
Sbjct: 139 DSG-PQGELRPLTEKLRAPLAFEEIIGSSPNFRTALAIAAKAARARVPVMINGKPGTGKE 197

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNS-AQFLGKFIEANGGT 236
             +R IH +  RA  P  +V+C  +    I   LFG        +  + +G+ ++A+GG+
Sbjct: 198 VFARAIHGASPRARGPLVMVDCSAVSPGLIGSGLFGHERGAFPGAFDRQIGRLVQADGGS 257

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIR--LDVRLIFLTEKNLLPQVKSHVF 294
           I+++  + +PL  Q ++  F+  G+++     G+IR  +DVR+I  +   L   +++  F
Sbjct: 258 IIIDHVECIPLDTQAKLVEFLNNGELQMIG--GSIRQTVDVRIIATSASPLDKLIEAGHF 315

Query: 295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW 354
           R+DL+Y +S   + + +L  R  D+  L    L        +  I I+D AL LL  Y W
Sbjct: 316 REDLFYALSSAQLTLPSLSERRGDVGPLARHLLARIGGLPGMGSIGITDDALRLLAAYAW 375

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
             NV++L+++L RA +G     LT   F           R      A    ++G+ +   
Sbjct: 376 PGNVRQLQDVLFRAAVGSTTDVLTAADF-----------RAIEATLAGGTASDGEVA--- 421

Query: 415 LDNLSQESIPAIG-----QDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
              ++ E   AIG      DG +R L +IE ++I LA+  YR +MSEVARRLGIGRSTLY
Sbjct: 422 ---INGE---AIGVTLYLPDGNLRPLEEIEADVIRLAIGHYRGRMSEVARRLGIGRSTLY 475

Query: 470 RKIREYNIEV 479
           RK+ +  I+ 
Sbjct: 476 RKLGDLGIDT 485


>gi|331670859|ref|ZP_08371694.1| transcriptional regulatory protein ZraR [Escherichia coli TA271]
 gi|331061947|gb|EGI33871.1| transcriptional regulatory protein ZraR [Escherichia coli TA271]
          Length = 441

 Score =  175 bits (443), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  S AM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSSAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAGT------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|324115436|gb|EGC09381.1| sigma-54 interaction domain-containing protein [Escherichia coli
           E1167]
          Length = 441

 Score =  175 bits (443), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 132/468 (28%), Positives = 223/468 (47%), Gaps = 44/468 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDTLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  S AM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSIDAETPAVTASQFGMVGKSSAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGHFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIP 424
           + RAV+              LL+ E   ERE     A T                   IP
Sbjct: 365 VERAVV--------------LLTGEYISERELPLAIAGT------------------PIP 392

Query: 425 AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +GQ  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 393 -LGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|189425842|ref|YP_001953019.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter lovleyi SZ]
 gi|189422101|gb|ACD96499.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter lovleyi SZ]
          Length = 480

 Score =  175 bits (443), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 115/344 (33%), Positives = 184/344 (53%), Gaps = 15/344 (4%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
           ++I  S AM +V     K     I ++IQGE G GK+ ++R IH +  R   PF  +NC 
Sbjct: 144 NIIGNSAAMREVYKTIGKVAGSDITVLIQGESGTGKELIARAIHFNSTRLGKPFVAINCA 203

Query: 201 MIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            I +D +E  LFG +    T  + +  GKF +AN GTI L+E   +PL +Q +I   ++ 
Sbjct: 204 AIPKDLLESELFGSERGAFTGATERKTGKFEQANHGTIFLDEIGDMPLDLQAKILRVLQE 263

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
            +I        + +DVR++  T + L  +V++  FR+DLYYR++V  IN++ LR RSEDI
Sbjct: 264 QEITRIGGSQNLSVDVRVVAATNQELQERVRNREFREDLYYRLNVVPINLAPLRERSEDI 323

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
           P LV +FL+  C +  I     + +A+ LL+ Y W  NV+EL+N + R VI   D +LT 
Sbjct: 324 PALVEYFLERACAELEIPTKQCAPEAMELLSNYSWPGNVRELENTIKRGVILSSDPYLTT 383

Query: 380 DRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ--DGEV--RRL 435
             F  L +R+         ET      E +S +++++   + S+  I +   G++  R L
Sbjct: 384 ADFASLTNRQ---------ETIHAIPQE-QSLESLVEMKLRNSMNGIEKLDKGDIYDRVL 433

Query: 436 SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
             +E+ +I   ++  R      A  LGI R+TL +KI E  + +
Sbjct: 434 EQVERPLIRYVLEKTRGNQVRAADILGINRNTLRKKISELGVSI 477


>gi|148262989|ref|YP_001229695.1| two component, sigma-54 specific, Fis family transcriptional
           regulator [Geobacter uraniireducens Rf4]
 gi|146396489|gb|ABQ25122.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter uraniireducens Rf4]
          Length = 480

 Score =  175 bits (443), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 115/343 (33%), Positives = 177/343 (51%), Gaps = 13/343 (3%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
           ++I  SPAM ++     K     + +++QGE G GK+ ++R IH + KR   PF  +NC 
Sbjct: 144 TIIGNSPAMREIYKTIGKVAPSDVTVLVQGESGTGKELIARAIHFNSKRLGKPFIALNCA 203

Query: 201 MIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            I ++ +E  LFG +    T  + + LGKF +ANGGTI L+E   +P+ +Q +I   ++ 
Sbjct: 204 AIPKELLESELFGFEKGAFTGATERKLGKFEQANGGTIFLDEIGDMPIDLQAKILRVLQE 263

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
            ++       +I +DVR++  T ++L   V+   FR+DLYYR++V  + +  LR R+EDI
Sbjct: 264 KEVTRTGGNQSINVDVRIVAATNQDLEESVRRKAFREDLYYRLNVIPLQLVPLRERNEDI 323

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
           P LV +FL   C +  +     S  AL LLT Y W  NV+EL+N L RAVI   D  LT 
Sbjct: 324 PLLVEYFLAKICAELEVPVKRCSSDALRLLTGYTWPGNVRELENTLKRAVILSSDPLLTI 383

Query: 380 DRFVLLLSREGK---KEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
             F  L  ++G    +  E   E        G  S T ++ +    +  +        L 
Sbjct: 384 ADFPGLRVQKGGELVQSEELSLEGIVDIKLRG--SFTNMEKMESGDVYTM-------VLE 434

Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
            +E+ +I   ++  R      A  LGI R+TL +KI E  IEV
Sbjct: 435 QVERPLIRFVLEKTRGNQVRAADILGINRNTLRKKITELGIEV 477


>gi|256828819|ref|YP_003157547.1| Fis family two component sigma5-4 specific transcriptional
           regulator [Desulfomicrobium baculatum DSM 4028]
 gi|256577995|gb|ACU89131.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfomicrobium baculatum DSM 4028]
          Length = 445

 Score =  174 bits (442), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 122/476 (25%), Positives = 222/476 (46%), Gaps = 44/476 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST--ISKIQVNVIFLSLINCEDDKEN 69
           R+L++D D   + ++   + S+GY+V   +   ++   + +   +V+   +   E D   
Sbjct: 4   RILVVDDDRAHMTMLVAMLGSWGYEVDTADDGAMAVARVRERAYDVVLTDVRMAEVDGIE 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            L+ I    P +P+++ T   ++ +    L      +    +  ++L   +  AL +G+ 
Sbjct: 64  ALRRIKSYNPYLPVLIMTAYSSVDVAVQALKAGALDYLHKPLDFEELRLGLARALEQGMA 123

Query: 130 ------PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
                 PS E +  +   +I  S  M ++  + R        ++I GE G GK+ +++ +
Sbjct: 124 HRSAQAPSGEADPVS--EMIGDSLPMRELAAMIRAVAPSEASVLILGESGTGKELVAKAL 181

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEP 242
           HE   R       VNC  + ++ +E  LFG +    T    Q  G+F++A+GGT+ L+E 
Sbjct: 182 HEGSPRKARQLVTVNCAALAENLLESELFGHEKGAYTGAQRQRDGRFVQADGGTLFLDEI 241

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             +  A+Q ++   ++ G+++   S  +IR+DVR++  T ++L  +V+   FR+DLYYR+
Sbjct: 242 GEMAPALQAKLLRALQQGEVQRLGSDRSIRVDVRVLAATNRDLEAEVRDGGFREDLYYRL 301

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           +V  + +  LR R EDIP L   FL  F  +N       + + + L+  Y W  NV+EL+
Sbjct: 302 NVIALRVPALRERPEDIPLLARHFLHRFAQRNRKTYRGFTPRVMDLMLHYDWPGNVRELE 361

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           N++ RAVI      L+   FV              TE        G             +
Sbjct: 362 NVVERAVI------LSPGEFV--------------TENDLPANMRGAEKPV--------N 393

Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            PA+G       L D E+E I   ++      SE AR LG+ R TL  K++++ ++
Sbjct: 394 GPAVGLS-----LEDAEREAIARTLEQVGNNKSEAARVLGVTRVTLRNKMKKFGLD 444


>gi|254693827|ref|ZP_05155655.1| nitrogen regulation protein NtrC [Brucella abortus bv. 3 str.
           Tulya]
 gi|261214111|ref|ZP_05928392.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           3 str. Tulya]
 gi|260915718|gb|EEX82579.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           3 str. Tulya]
          Length = 491

 Score =  174 bits (442), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 134/490 (27%), Positives = 238/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV++  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVWVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR+SV  + +  LR RSED+P LV HFF +    +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLSVVPLRLPPLRERSEDVPDLVRHFFKR--AAEEGLPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|209518153|ref|ZP_03266982.1| putative sigma54 specific transcriptional regulator [Burkholderia
           sp. H160]
 gi|209501457|gb|EEA01484.1| putative sigma54 specific transcriptional regulator [Burkholderia
           sp. H160]
          Length = 598

 Score =  174 bits (441), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 108/337 (32%), Positives = 174/337 (51%), Gaps = 7/337 (2%)

Query: 142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM 201
           ++ +SPA    V    +       +++ GE GVGK   +R +HE  +RA  PF  +NC  
Sbjct: 243 IVGLSPAYQAAVGKINRVAATGATVLLLGESGVGKSTFARLLHEQSRRAGGPFVAINCAT 302

Query: 202 IDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETG 260
           I +  +E  LFG +    T   A   G+F  A GGT+ L+E   LPL  QG++   +ETG
Sbjct: 303 IPETLMESELFGVERGAFTGADAARAGRFELAEGGTLFLDEVATLPLVAQGKLLRVLETG 362

Query: 261 KIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIP 320
           + E   S  A + DVR++  T ++L   V++  FR+DL++R+ VF I I  LR R ED+P
Sbjct: 363 QFERLGSGTARQADVRIVAATNEDLWQAVRAGRFREDLFFRLHVFPIEIPPLRQRKEDLP 422

Query: 321 WLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTED 380
            L+  F+Q F          ++ +A+S+L  Y W  N++EL N++ RAVI  +D    + 
Sbjct: 423 VLIEHFMQRFTHAYGRNAYGLTPEAMSMLLGYSWPGNIRELSNVVERAVILSEDGRAIDA 482

Query: 381 RFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS---QESIPAIGQDGEVRRLSD 437
             V+L+ ++  ++R    E A       K++    +  S   QE +  + +D  +  L D
Sbjct: 483 VHVVLM-KDLTRDRAVGAERAAPEPLHAKAASAAPEQPSRSLQEIVGGLMKDRGL-TLED 540

Query: 438 IEKEIIGLAMKLYRAQMSEVARRLGIGRST-LYRKIR 473
           +E  ++  A++     M+  A  LGI R   LYR+ R
Sbjct: 541 MENTMVDAAIQRSDGNMTRAAALLGISRGQLLYRRKR 577


>gi|260892098|ref|YP_003238195.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Ammonifex degensii KC4]
 gi|260864239|gb|ACX51345.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Ammonifex degensii KC4]
          Length = 463

 Score =  174 bits (441), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 139/482 (28%), Positives = 230/482 (47%), Gaps = 44/482 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           RVL++D ++   +++KD +E+ GY+V         L  + + +VN   + +   + D   
Sbjct: 3   RVLVVDDEESVCQMLKDLLETEGYEVVTALEAREALEKLDQEEVNAALVDIRMPDIDGLA 62

Query: 70  ILKNIVDKIPIVPIIVQT----TQDNIKILNCFLYNRISKFF----LNLVSRKQLCDSII 121
             K + +K    P+I+ T    T   I+ +    ++ + K F    L L  +K +    +
Sbjct: 63  FFKLLKEKGYTFPVILITAYGSTDTAIEAMKLGAFDYVLKPFNIEELLLTVKKAVEVEAL 122

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
               E +      E  A + +I  SPAMI+V     K  D    ++I GE G GK+ ++ 
Sbjct: 123 ARETEALRRELAGEAPA-EEIIGRSPAMIEVFKQIGKFADTDYTVLIVGETGTGKELVAG 181

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H + +R   PF  +NC  I ++ +E  LFG +    T   ++ +GKF  A GGT+ L+
Sbjct: 182 ALHRNSRRCNGPFVRINCAAIPENLLESELFGYEKGAFTGAISRKIGKFELAEGGTLFLD 241

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL++Q ++   ++  + E       I+L+ R+I  T ++L+  VK   FR+DLYY
Sbjct: 242 EIGELPLSMQAKLLRVLQEKEFERVGGTKTIKLNARIIAATNRDLVRMVKEGTFREDLYY 301

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++V  I++  LR R EDIP L   FL+    K        S +AL+LL  Y W  NV+E
Sbjct: 302 RLNVVTIHVPPLRERKEDIPLLAEHFLRQAVAKLGKTVKGFSPEALNLLKAYDWPGNVRE 361

Query: 361 LKNILLRAVIGLKDSH-LTEDRFVLLLSRE----GKKEREFHTETACTCYTEGKSSDTIL 415
           L+N+  RAV+  +    L ED  V L   E    G+ E E    +  T            
Sbjct: 362 LRNVCERAVVLAQGPLILPEDLPVTLRQPEELGLGEGEIELRLRSGQTL----------- 410

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
                          E+  L D+E+ +I  A++ +    +  A+ LGI R TL+ K++EY
Sbjct: 411 --------------AEI--LHDVERTVILKALREHNYNRTRTAQALGISRRTLHLKLKEY 454

Query: 476 NI 477
            +
Sbjct: 455 GL 456


>gi|323699827|ref|ZP_08111739.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio sp. ND132]
 gi|323459759|gb|EGB15624.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio desulfuricans ND132]
          Length = 467

 Score =  174 bits (441), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 135/484 (27%), Positives = 232/484 (47%), Gaps = 35/484 (7%)

Query: 12  RVLIIDKDDEQIKI-IKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
           ++LIID D+E I++ ++  +E  G  V      +  L  +     ++IFL +     D  
Sbjct: 4   KILIID-DEESIRLSLRGILEDEGLSVVEAESGEEGLELLGTDIPDLIFLDIWLPGMDGL 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
             L+ +      +P+I+ +    I+         + K   + + +    + ++ + R G+
Sbjct: 63  EALEILSRDYEGLPVIMISGHGTIETA----VKALKKGAFDFIEKPLSLEKVVVSARNGL 118

Query: 129 VPSQ-ENEHCALDS---------LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
             S+   E+ AL +         L  VS A+  + ++  +       ++I GE G GK+ 
Sbjct: 119 EFSRLRQENLALKTRISSEQPVTLTGVSKAIGDLREVIGRVAPTESWVLITGENGTGKEI 178

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R IH    RA  P   VNC  I ++ IE  LFG +    T       GKF  A+G T+
Sbjct: 179 VARSIHNQSTRADRPLVAVNCAAIPEELIESELFGHEKGAFTGAEKAQEGKFELADGSTL 238

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   + L  Q +I   ++    E    R  I++DVR+I  T K+L  ++++  FR+D
Sbjct: 239 FLDEIGDMSLKTQAKILRILQEQAFEHVGGRKTIKVDVRVIAATNKDLAREIEAGNFRED 298

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LYYR+ VF + +  LR R EDIP L++ F+ +   ++  K I  S +ALS+LT+YPW  N
Sbjct: 299 LYYRLKVFPLELPPLRDRVEDIPLLINDFMDTLVRQHGFKPIVFSPEALSVLTRYPWPGN 358

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI-LD 416
           V+ELKN + R  I      +T DR             EF           G +++   LD
Sbjct: 359 VRELKNFVERMFIMFAGDTVTADRL----------PPEFKPAPRAAEPGAGHAAEAAPLD 408

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
           +L  +    + Q       +D E   +   ++ +   +S++A+ +G+ RS+LYRK++ YN
Sbjct: 409 DLINQGPADLKQ-----ARADFEARFLEAKLREFDGNISQLAKAIGLERSSLYRKLKAYN 463

Query: 477 IEVD 480
           I+ D
Sbjct: 464 IQTD 467


>gi|320190898|gb|EFW65548.1| Response regulator of zinc sigma-54-dependent two-component system
           [Escherichia coli O157:H7 str. EC1212]
          Length = 441

 Score =  174 bits (440), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 129/466 (27%), Positives = 218/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL    +
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHI 126

Query: 130 PSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E          ++  SPAM  ++            ++I G+ G GK+ ++R IH S 
Sbjct: 127 IDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +  R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PMMLVRLLRAIQEREVQCVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T                   IP +
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAST------------------PIP-L 393

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 394 AQSLDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|200388170|ref|ZP_03214782.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|199605268|gb|EDZ03813.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
          Length = 441

 Score =  174 bits (440), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 127/466 (27%), Positives = 223/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P++PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPVIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+ L   +++E    L ++    K       T C+                       
Sbjct: 367 RAVVLLTGEYISERELPLAIAATPIK-------TECS----------------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L ++EKE+I  A++      +E AR+LGI R TL  KI
Sbjct: 397 ---GEIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKI 439


>gi|167553822|ref|ZP_02347566.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|168823112|ref|ZP_02835112.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|198244110|ref|YP_002218090.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|197938626|gb|ACH75959.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|205321823|gb|EDZ09662.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205340579|gb|EDZ27343.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|320088604|emb|CBY98363.1| Transcriptional regulatory protein zraR [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
          Length = 441

 Score =  174 bits (440), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 133/467 (28%), Positives = 222/467 (47%), Gaps = 42/467 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE-PDAL 245
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E  D  
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIT 246

Query: 246 PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF 305
           PL +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V 
Sbjct: 247 PL-MQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVV 305

Query: 306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNIL 365
            I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N +
Sbjct: 306 AIEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAI 365

Query: 366 LRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPA 425
            RAV+              LL+ E   ERE     A T      S               
Sbjct: 366 ERAVV--------------LLTGEYISERELPLAIAATPIKTEYS--------------- 396

Query: 426 IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
               GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ----GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|168239600|ref|ZP_02664658.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|194736973|ref|YP_002117075.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|194712475|gb|ACF91696.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197287727|gb|EDY27118.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|322616283|gb|EFY13193.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322617274|gb|EFY14176.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322625954|gb|EFY22769.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322626648|gb|EFY23450.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322631483|gb|EFY28240.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322635196|gb|EFY31914.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322642599|gb|EFY39195.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322646810|gb|EFY43314.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322650808|gb|EFY47201.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322655892|gb|EFY52193.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322657291|gb|EFY53570.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322665553|gb|EFY61738.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322669736|gb|EFY65881.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322670985|gb|EFY67117.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322679191|gb|EFY75244.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322679349|gb|EFY75396.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322688116|gb|EFY84080.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195791|gb|EFZ80966.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323200696|gb|EFZ85769.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202185|gb|EFZ87241.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323209296|gb|EFZ94231.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323211621|gb|EFZ96458.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323218041|gb|EGA02754.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323221330|gb|EGA05752.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323225743|gb|EGA09964.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230969|gb|EGA15086.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323235751|gb|EGA19833.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323240065|gb|EGA24111.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323242602|gb|EGA26624.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323249690|gb|EGA33597.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323252573|gb|EGA36414.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323256933|gb|EGA40645.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323262044|gb|EGA45608.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323263950|gb|EGA47464.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323268437|gb|EGA51907.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 441

 Score =  173 bits (439), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 131/466 (28%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKEII  A++      +E AR+LGI R TL  K+
Sbjct: 397 ---GEIQPLVDVEKEIILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|78355156|ref|YP_386605.1| two component Fis family transcriptional regulator [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|78217561|gb|ABB36910.1| two component transcriptional regulator, Fis family [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 466

 Score =  173 bits (439), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 128/483 (26%), Positives = 232/483 (48%), Gaps = 40/483 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ---VNVIFLSLINCEDDKEN 69
           +LI+D D     +++  +  + Y     +   ++ +SK+Q    + I + +         
Sbjct: 7   ILIVDDDQAHRTMLRTMLRGWQYSAEEADDGSVA-VSKVQERAYDAILMDIRMARMSGIE 65

Query: 70  ILKNIVDKIPIVPIIVQTTQDNI----KILNCFLYNRISKFF----LNLVSRKQLCDSII 121
            L++I+   P +P+++ T   ++    + L    Y+ ++K      L L   + L  + +
Sbjct: 66  ALRHIMAHNPAIPVLIMTAYSSVNTAVEALKIGAYDYLTKPLDFDELKLTLERALDHTRL 125

Query: 122 CA----LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
            +    LR  +   Q     A   +I  S A+ ++ +L          ++I GE G GK+
Sbjct: 126 ASENRELRSSLSAGQ-----AASRIIGRSEAVRRLTELVATVAPSDATVLITGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            ++R IHE   R   P   VNC  + +  +E  LFG +    T    +  G+F++A+GGT
Sbjct: 181 LVARAIHEGSSRRDRPLVTVNCAALTESLLESELFGHEKGAFTGADKKRDGRFVQADGGT 240

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   + LA+Q ++   ++ G+I+   S   +R+DVR+I  T +NL  +V +  FR+
Sbjct: 241 LFLDELGEMSLALQAKLLRALQQGEIQRVGSDNPLRVDVRVIAATNRNLTAEVTAGRFRE 300

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DL+YR++V  I +  LR R +DIP L   FL  +  +N       + +A++ L  Y W  
Sbjct: 301 DLFYRLNVIGIAVPALRERRDDIPLLAGHFLTRYAERNRKMLKGFTPQAMNCLVNYDWPG 360

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVL-LLSREGKKEREFHTETACTCYTEGKSSDTIL 415
           NV+EL+N + RAVI     ++T       + + +G+ +      TA    T+    DT+ 
Sbjct: 361 NVRELENAVERAVIMSMGEYVTGRELPPDIAAADGETD-----ITAAVPDTDTPLPDTVH 415

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
           D  +  S            L ++E+  I   ++      SE ARRLGI R+TL+ K+++Y
Sbjct: 416 DPYAGLS------------LENLERRAIEATLRECADNKSEAARRLGITRATLHNKLKKY 463

Query: 476 NIE 478
            +E
Sbjct: 464 GME 466


>gi|163793262|ref|ZP_02187238.1| Response regulator containing CheY-like receiver [alpha
           proteobacterium BAL199]
 gi|159181908|gb|EDP66420.1| Response regulator containing CheY-like receiver [alpha
           proteobacterium BAL199]
          Length = 490

 Score =  173 bits (439), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 139/498 (27%), Positives = 231/498 (46%), Gaps = 54/498 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           +LI D D     ++   +   GYDV     +      +   + +++   ++  +++  ++
Sbjct: 8   ILIADDDRAIRTVLNQALARLGYDVKSTGTAAGLWQWVEDGEGDLVITDVVMPDENGLDM 67

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF----LNLVSRKQLCDSIIC 122
           L  I    P + +IV + Q+     +K      ++ + K F    L    RK L      
Sbjct: 68  LPRIRKARPDLRVIVMSAQNTLLTAVKASERGAFDYLPKPFDLNELIATVRKALSAPTAA 127

Query: 123 AL-----REGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
            +     +E   P++E    AL  LI  SPAM  +  +  +     + +MI GE G GK+
Sbjct: 128 PVATLDQKEPAFPAEE----AL-PLIGRSPAMQDIYRVLARLMGTDLTVMITGESGTGKE 182

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            ++R +H+ GKR   PF  +N   I ++ IE  LFG +    T  + +  G+F +A GGT
Sbjct: 183 LVARALHDYGKRRDGPFVAINMAAIPRELIESELFGHEKGAFTGATVRATGRFEQAQGGT 242

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +PL  Q R+   ++ G+      R  IR DVR++  T ++L   ++  +FR+
Sbjct: 243 LFLDEIGDMPLEAQTRLLRVLQEGEYTTVGGRLPIRADVRIVAATHRDLRQLIRQGLFRE 302

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DL+YR++V  I +  LR R ED+P L  HFFLQ    +  +    +   AL+ L +Y W 
Sbjct: 303 DLFYRLNVVPIRLPALRERVEDVPDLARHFFLQ--LPQEGLPVKHLDQGALARLQRYAWP 360

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+EL+N+                R   L + E   E     E A T   E  S+D+  
Sbjct: 361 GNVRELENLC--------------RRLSALYAEETIGEEAIDAELAETVEREALSNDSSP 406

Query: 416 DNLS--------------QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRL 461
           DNLS              Q+ +PA G    +  L ++E+ ++ L +   R    + A  L
Sbjct: 407 DNLSSAVEHHLTLYFSAHQDGLPAPGLYDRI--LREVERPLVTLCLNATRGNQIKAAEVL 464

Query: 462 GIGRSTLYRKIREYNIEV 479
           G+ R+TL +KIRE +I V
Sbjct: 465 GLNRNTLRKKIRELDIPV 482


>gi|15804595|ref|NP_290636.1| transcriptional regulatory protein ZraR [Escherichia coli O157:H7
           EDL933]
 gi|15834181|ref|NP_312954.1| transcriptional regulatory protein ZraR [Escherichia coli O157:H7
           str. Sakai]
 gi|168752030|ref|ZP_02777052.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4113]
 gi|168758599|ref|ZP_02783606.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4401]
 gi|168764585|ref|ZP_02789592.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4501]
 gi|168771477|ref|ZP_02796484.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4486]
 gi|168777382|ref|ZP_02802389.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4196]
 gi|168780390|ref|ZP_02805397.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4076]
 gi|168790365|ref|ZP_02815372.1| response regulator ZraR [Escherichia coli O157:H7 str. EC869]
 gi|168798361|ref|ZP_02823368.1| response regulator ZraR [Escherichia coli O157:H7 str. EC508]
 gi|195939630|ref|ZP_03085012.1| transcriptional regulatory protein ZraR [Escherichia coli O157:H7
           str. EC4024]
 gi|208805812|ref|ZP_03248149.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4206]
 gi|208812972|ref|ZP_03254301.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4045]
 gi|208821649|ref|ZP_03261969.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4042]
 gi|209396243|ref|YP_002273521.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4115]
 gi|217326117|ref|ZP_03442201.1| response regulator ZraR [Escherichia coli O157:H7 str. TW14588]
 gi|254796002|ref|YP_003080839.1| transcriptional regulatory protein ZraR [Escherichia coli O157:H7
           str. TW14359]
 gi|261227284|ref|ZP_05941565.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator, sigma54
           [Escherichia coli O157:H7 str. FRIK2000]
 gi|261257031|ref|ZP_05949564.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator, sigma54
           [Escherichia coli O157:H7 str. FRIK966]
 gi|20140981|sp|Q8X613|ZRAR_ECO57 RecName: Full=Transcriptional regulatory protein zraR
 gi|12518936|gb|AAG59201.1|AE005632_2 response regulator of hydrogenase 3 activity (sensor HydH)
           [Escherichia coli O157:H7 str. EDL933]
 gi|13364403|dbj|BAB38350.1| response regulator HydG [Escherichia coli O157:H7 str. Sakai]
 gi|187767371|gb|EDU31215.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4196]
 gi|188014032|gb|EDU52154.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4113]
 gi|189001862|gb|EDU70848.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4076]
 gi|189354602|gb|EDU73021.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4401]
 gi|189359769|gb|EDU78188.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4486]
 gi|189365464|gb|EDU83880.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4501]
 gi|189370154|gb|EDU88570.1| response regulator ZraR [Escherichia coli O157:H7 str. EC869]
 gi|189379122|gb|EDU97538.1| response regulator ZraR [Escherichia coli O157:H7 str. EC508]
 gi|208725613|gb|EDZ75214.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4206]
 gi|208734249|gb|EDZ82936.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4045]
 gi|208741772|gb|EDZ89454.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4042]
 gi|209157643|gb|ACI35076.1| response regulator ZraR [Escherichia coli O157:H7 str. EC4115]
 gi|209751640|gb|ACI74127.1| response regulator HydG [Escherichia coli]
 gi|209751642|gb|ACI74128.1| response regulator HydG [Escherichia coli]
 gi|209751646|gb|ACI74130.1| response regulator HydG [Escherichia coli]
 gi|217322338|gb|EEC30762.1| response regulator ZraR [Escherichia coli O157:H7 str. TW14588]
 gi|254595402|gb|ACT74763.1| fused DNA-binding response regulator in two-component regulatory
           system with ZraS: response regulator, sigma54
           interaction protein [Escherichia coli O157:H7 str.
           TW14359]
 gi|326347144|gb|EGD70874.1| Response regulator of zinc sigma-54-dependent two-component system
           [Escherichia coli O157:H7 str. 1125]
 gi|326347605|gb|EGD71327.1| Response regulator of zinc sigma-54-dependent two-component system
           [Escherichia coli O157:H7 str. 1044]
          Length = 441

 Score =  173 bits (439), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 129/466 (27%), Positives = 218/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVRERVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL    +
Sbjct: 67  TLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHI 126

Query: 130 PSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E          ++  SPAM  ++            ++I G+ G GK+ ++R IH S 
Sbjct: 127 IDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +  R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PMMLVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T                   IP +
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAST------------------PIP-L 393

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            Q  +++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 394 AQSLDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|197262022|ref|ZP_03162096.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197240277|gb|EDY22897.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
          Length = 441

 Score =  173 bits (439), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ---GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|168234404|ref|ZP_02659462.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|194470992|ref|ZP_03076976.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|205354424|ref|YP_002228225.1| transcriptional regulator ZraR [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207859352|ref|YP_002246003.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|194457356|gb|EDX46195.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|205274205|emb|CAR39223.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205331650|gb|EDZ18414.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|206711155|emb|CAR35529.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|326629556|gb|EGE35899.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 441

 Score =  173 bits (438), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ---GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|238913752|ref|ZP_04657589.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
          Length = 441

 Score =  173 bits (438), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 127/466 (27%), Positives = 221/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   + +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTVSVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+ L   +++E    L +             TA    TE                   
Sbjct: 367 RAVVLLTGEYISERELPLAI-------------TATPIKTE------------------- 394

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 395 -YSGEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|39997087|ref|NP_953038.1| sigma-54 dependent DNA-binding response regulator [Geobacter
           sulfurreducens PCA]
 gi|39983977|gb|AAR35365.1| sigma-54 dependent DNA-binding response regulator [Geobacter
           sulfurreducens PCA]
 gi|298506101|gb|ADI84824.1| sigma-54-dependent transcriptional response regulator [Geobacter
           sulfurreducens KN400]
          Length = 444

 Score =  173 bits (438), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 124/479 (25%), Positives = 225/479 (46%), Gaps = 53/479 (11%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKI----QVNVIFLSLINCEDDKE 68
           VLI+D +    +++   +   G+ V     SD S    I     V+ I   L     D  
Sbjct: 5   VLIVDDEPNAARVLSAILAGEGHTVL--TASDASKAEHILKSRDVDAIITDLRMPGRDGM 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
            + +++ + +P +P+I  T    +      +      +F+      +L   +  A+ +  
Sbjct: 63  QLFEHVTEHLPDIPVIFLTAYGTVDSAVNAITRGAFYYFIKPPDYVKLKSMVARAVEQRA 122

Query: 129 VPSQENE-------HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           +  +  E           D +I VSP M+++ +      D    +++ GE G GK+ ++R
Sbjct: 123 LKREVAELRKRVAAGSGADRIIGVSPGMLKIFNTIEAVKDSMSSVLVSGETGTGKELIAR 182

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H    R   PF  VNC  I ++ +E  LFG +    +  SA+ +G+F  A  GTI L+
Sbjct: 183 SLHYGSVRRDRPFVAVNCAAIPRELMESELFGYEKGAFSGASARRIGRFEAAADGTIFLD 242

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   L L++Q ++   ++  ++E   S   I+++ R+I  T ++L+ ++ +  FR+DLYY
Sbjct: 243 EISELELSLQAKLLRVLQEKEVERLGSNRKIKVNFRVISSTNRDLMREIAAGTFREDLYY 302

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++V  +N+ +LR R EDIP LV  F++ F  +   K +++SD  L  L  Y W  N+++
Sbjct: 303 RLNVVQLNVPSLRERREDIPLLVSEFVKEFGLREG-KSLTLSDDVLRALVGYEWPGNIRQ 361

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L+N + RAV+  + + +T                                    L +L +
Sbjct: 362 LRNTIERAVVLARGAKIT------------------------------------LKHLPE 385

Query: 421 ESIPAIG-QD-GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           E     G +D  E R L ++E+E I  A++  R   S VA++LGI R TLY+++ +  +
Sbjct: 386 EVAAGAGCRDVAEPRTLRELEEEAIQSALRECRGNKSLVAKKLGISRKTLYKRLEQLGL 444


>gi|218887239|ref|YP_002436560.1| Fis family transcriptional regulator [Desulfovibrio vulgaris str.
           'Miyazaki F']
 gi|218758193|gb|ACL09092.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio vulgaris str. 'Miyazaki F']
          Length = 477

 Score =  173 bits (438), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 122/484 (25%), Positives = 228/484 (47%), Gaps = 30/484 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ---VNVIFLSLINCEDDKEN 69
           +LI+D D     +++  +  +GY     +  + S ++K++    + + + +     D   
Sbjct: 6   ILIVDDDAAHRSMLRTMLRGWGYATEEADDGE-SAVAKVRQRAWDAVLMDVRMARMDGIA 64

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            L++I+D  P  P+++ T   ++      L      + +  +    L  ++  AL    +
Sbjct: 65  ALRHILDWNPATPVLIMTAFSSVDTAVEALRTGAYDYLIKPLDFDVLRHTLERALDHTRL 124

Query: 130 PSQENE-------------HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
            S+  E               A   +I  S  M ++V++          ++I GE G GK
Sbjct: 125 ASENRELRERLSSQGGAGAPGASHGIIGRSAPMHELVEMIATVAPSEATVLITGESGTGK 184

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGG 235
           + ++R +H +  R+  P   VNC  + +  +E  LFG +    T    +  G+F++A+GG
Sbjct: 185 ELVARALHAASHRSAKPLVTVNCAALTETLLESELFGHERGAFTGADRRREGRFVQADGG 244

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T+ L+E   +PL +Q ++   ++ G+++   S   + +DVR+I  T ++L  +  +  FR
Sbjct: 245 TLFLDEIGEMPLTLQAKLLRALQQGEVQRVGSDTPLTVDVRVIAATNRDLREEAAAGRFR 304

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DLYYR++V  +++  LR R+ D+P L  FFL  +  KN       + +A+ +L ++ W 
Sbjct: 305 EDLYYRLNVIAVHVPALRERAGDVPLLAAFFLDRYTEKNRKHLKGFTPQAMDMLLRHDWP 364

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKS-SDTI 414
            NV+EL+N + RAVI     ++TE    L     G                 G + +D  
Sbjct: 365 GNVRELENAIERAVILATGDYVTERELPLHFGGGGSGIAGSGGSAGTGEAGAGNAPADG- 423

Query: 415 LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
            D L+    P  G       L D+E+  I   ++      SE ARRLGI R+TL+ K+++
Sbjct: 424 -DGLA----PYAGLS-----LEDLERRAIIATLRETADNKSEAARRLGITRATLHNKLKK 473

Query: 475 YNIE 478
           Y++E
Sbjct: 474 YDLE 477


>gi|168245130|ref|ZP_02670062.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|194448874|ref|YP_002048159.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194407178|gb|ACF67397.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|205336107|gb|EDZ22871.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
          Length = 441

 Score =  173 bits (438), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 221/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V ++  S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNV-VLAYSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L ++EKE+I  A++      +E AR+LGI R TL  KI
Sbjct: 397 ---GEIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKI 439


>gi|145219817|ref|YP_001130526.1| two component Fis family transcriptional regulator
           [Prosthecochloris vibrioformis DSM 265]
 gi|145205981|gb|ABP37024.1| two component transcriptional regulator, Fis family [Chlorobium
           phaeovibrioides DSM 265]
          Length = 481

 Score =  173 bits (438), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 135/483 (27%), Positives = 224/483 (46%), Gaps = 35/483 (7%)

Query: 10  HKRVLIIDKDDEQIKIIKDHV-ESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDD 66
            K VLI D D   I+ +  H+ ++ GY        +  + ++ +  V+++ L L     +
Sbjct: 7   QKTVLIAD-DSSVIRTLTVHLLKNLGYTALSAENGESCIKSLEQHPVDLLMLDLNMPVKN 65

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNI-KILNC-------FLYNRISKFFLNLVSRKQLCD 118
            + +L+ + ++   +P+I+ T  ++I + + C       +L   +    L  + R  L +
Sbjct: 66  GQEVLQWVKERGLDIPVIIVTALEDINQAVQCMKMGAYEYLTKPVENDRLETILRNALAE 125

Query: 119 SIICALREGVVPSQENEHCALDSLIAV---SPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           S    L+E VV + E E  A D    V   SPA+ Q V+ A +     + ++I GE G G
Sbjct: 126 S---GLKEKVV-ALEKELMAKDIFWEVRGRSPALRQAVEEAMQVMGTDMNVLINGESGTG 181

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANG 234
           K+  ++ IH   +R   PF I+NC  I  +  +  LFG      T  +    G F +A+G
Sbjct: 182 KELFAKAIHNGSRRKEGPFVIINCAAISNELADSLLFGHCKGSFTGAATDHAGYFEQADG 241

Query: 235 GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF 294
           GTI L+E   + + +Q +I   ++  K+     +    +D RLI  T ++    +    F
Sbjct: 242 GTIFLDEIGDMDIDIQAKILRALQEKKVRRVGEKKERSVDFRLISATHRDFSEAITGSTF 301

Query: 295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW 354
           R DLYYR+  + + +  LR RSEDI  L   FL+ FC  N I    I   A+SLL ++ W
Sbjct: 302 RADLYYRLEEYPLFVPPLRERSEDIAILAEHFLKEFCKANDIAIPGIDASAMSLLEQHSW 361

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
             N++EL+N++ RAVI L+   +        + +   +E E   + A     + +  D  
Sbjct: 362 PGNIRELQNVIRRAVITLEGDEIKS----FAIGKPASREEETRLKAAAVEAVQPEGEDV- 416

Query: 415 LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
                       G+  E   L DIE + I  A +      S  A  LGI RSTL RK++ 
Sbjct: 417 ----------GKGKSDERPMLRDIELQAIVEAYRKCSGNQSRTATLLGISRSTLIRKMKR 466

Query: 475 YNI 477
           Y +
Sbjct: 467 YGL 469


>gi|294011190|ref|YP_003544650.1| Nif-specific regulatory protein [Sphingobium japonicum UT26S]
 gi|292674520|dbj|BAI96038.1| Nif-specific regulatory protein [Sphingobium japonicum UT26S]
          Length = 555

 Score =  172 bits (437), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 101/336 (30%), Positives = 175/336 (52%), Gaps = 17/336 (5%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
           SLI  SPA ++ V+L R+A D  I +++ GE GVGK+  + ++H++G R   PF  +NCG
Sbjct: 232 SLIGQSPAFLKSVNLLRRAADSNITVLLTGETGVGKEVFAHWLHDNGPRRDRPFVAINCG 291

Query: 201 MIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            I  D IE  LFG +    T    Q LG+F  A+GGT+ L+E   LPL  Q ++   ++T
Sbjct: 292 AIPHDLIESELFGVEPGAYTGAQRQRLGRFERADGGTLFLDEVGDLPLPAQVKLLRVLQT 351

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
           G++E       + +DVR++  T  +L   V +  FR DL+YR++ F + I  LR R+ DI
Sbjct: 352 GEVERLGGDRPVHVDVRIVAATNVDLTSAVAARTFRADLFYRLNPFPVAIPPLRERAADI 411

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI-GLKDSHLT 378
           P  V   ++    ++      +SD+A+  L  Y W  NV+EL+N+L R V+       + 
Sbjct: 412 PLFVEALVERLARRHGKPVRGVSDQAMRALIAYRWPGNVRELENVLERGVLLAEPGGRID 471

Query: 379 EDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDI 438
            D   ++L  + +++     +          +   ++ ++  E  P +        L+D 
Sbjct: 472 VDTLSIMLEPDSREQAHVRPDGRLAV-----TGAPLIPDI--ERAPLL--------LADY 516

Query: 439 EKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
           E  ++G A++     +++ AR LG+ R  L  ++++
Sbjct: 517 EAALVGEALRRAGGNVADAARMLGMSRRQLDYRLKQ 552


>gi|330972433|gb|EGH72499.1| helix-turn-helix, Fis-type [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 470

 Score =  172 bits (437), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 135/479 (28%), Positives = 229/479 (47%), Gaps = 28/479 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNV-IFLSLINCED-DKENI 70
           VL+++ D    + + + +E  GYD   V  ++ + ++       + +S +N    D   +
Sbjct: 5   VLLVEDDRSLREALGETLELAGYDYQAVGSAEEALVAAEATPFSLVISDVNMPGMDGHQL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           L  +  + P +P+++ T    ++     +    + + +     K L   I    R  +  
Sbjct: 65  LSLLRSRHPQLPVLLMTAHGAVERAVDAMRQGAADYLVKPFEPKAL---IALVARHALGR 121

Query: 131 SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
            +  E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  RA
Sbjct: 122 LEPAER---DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPRA 178

Query: 191 FFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAV 249
             PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL +
Sbjct: 179 DKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLGL 238

Query: 250 QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINI 309
           Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF +  
Sbjct: 239 QAKLLRVLQEREVERVGARKPIVLDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLAW 298

Query: 310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
             LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA+
Sbjct: 299 QALRQRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVSYPWPGNVRELDNAVQRAL 358

Query: 370 IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN----LSQESIPA 425
           I  +   +    F L                A +    G  + T  +N    +S ES+ A
Sbjct: 359 ILQQGGVIQAQDFCL-------SGPVTSLPVAASVEAAGAVTGTTAENAGAGVSPESVGA 411

Query: 426 IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           +G D  +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 412 LGDD--LRRH---EFQMIIDTLRSERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 465


>gi|148264421|ref|YP_001231127.1| two component, sigma-54 specific, Fis family transcriptional
           regulator [Geobacter uraniireducens Rf4]
 gi|146397921|gb|ABQ26554.1| two component, sigma-54 specific, transcriptional regulator, Fis
           family [Geobacter uraniireducens Rf4]
          Length = 483

 Score =  172 bits (437), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 132/405 (32%), Positives = 203/405 (50%), Gaps = 22/405 (5%)

Query: 86  QTTQDNIKILNCFLYNRISKFF----LNLVSRKQL-CDSIICALREGVVPSQ--ENEHCA 138
           +TTQ+ I+ +    Y+ ++K F    L     K L C+ +   +R      Q  E+EH A
Sbjct: 84  KTTQNAIEAMKYGAYDYVTKPFDMNKLKSAVHKALECNLLSRKVRYTKDTKQLSEDEH-A 142

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            D +I  SP MI++  +  K  D    ++IQGE G GK+ L+R I+ + +R   PF  VN
Sbjct: 143 DDIMIGSSPEMIEIWKMVGKVADSDATVLIQGESGTGKELLARAIYNNSRRKNRPFLAVN 202

Query: 199 CGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
           C  + +  +E  LFG +    T   A+ +GKF + NGGTI L+E   + L+ QG++   +
Sbjct: 203 CAALPEALLESELFGHEKGAFTDAHARRIGKFEQCNGGTIFLDEIGEMSLSNQGKLLRVL 262

Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
           E  + E       IR+DVR+I  T K+L+  VK  VFR DL+YR+ V    +  LR R E
Sbjct: 263 ENQEFERVGGNETIRVDVRIIAATNKSLINSVKEKVFRMDLFYRLRVVNFFLPPLRERIE 322

Query: 318 DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHL 377
           DIP L+  F++ F  K       I+ + L LL  +PW  N++ELKN++  A +  K   L
Sbjct: 323 DIPLLIDLFIKKFSRKYGKSIKRIAKETLELLIAHPWEGNIRELKNVINSATVFCKSGIL 382

Query: 378 T-EDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPA--IGQDGEVRR 434
             ED    L ++ G KE +   + A   Y E      +  N+ +       I   G +  
Sbjct: 383 MPEDLESFLQAKAGFKEVDL--DIAGEDYYE------VFWNMLEPVFEGICIKNKGTIYE 434

Query: 435 LSD--IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
             +  +EK +I +AM+         A+ LGI R+TL  ++  Y I
Sbjct: 435 SVNMGLEKALIHMAMEKSNNNQVFAAKLLGISRNTLRDRLERYKI 479


>gi|204931260|ref|ZP_03222020.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|204319875|gb|EDZ05082.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
          Length = 441

 Score =  172 bits (437), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 131/466 (28%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVKLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKEII  A++      +E AR+LGI R TL  K+
Sbjct: 397 ---GEIQPLVDVEKEIILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|168467894|ref|ZP_02701731.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|195629026|gb|EDX48418.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
          Length = 441

 Score =  172 bits (437), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 219/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++     +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALFRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ---GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|62182625|ref|YP_219042.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|62130258|gb|AAX67961.1| response regulator in two-component reguatory system with HydH,
           regulates hydrogenase 3 activity (EBP family)
           [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|322717122|gb|EFZ08693.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 441

 Score =  172 bits (436), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 127/466 (27%), Positives = 222/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+ L   +++E    L ++    K       T C+                       
Sbjct: 367 RAVVLLTGEYISERELPLAIAATPIK-------TECS----------------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L ++EKE+I  A++      +E AR+LGI R TL  KI
Sbjct: 397 ---GEIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKI 439


>gi|158521375|ref|YP_001529245.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Desulfococcus oleovorans Hxd3]
 gi|158510201|gb|ABW67168.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfococcus oleovorans Hxd3]
          Length = 485

 Score =  172 bits (436), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 124/485 (25%), Positives = 237/485 (48%), Gaps = 31/485 (6%)

Query: 13  VLIIDKDDEQ----IKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKE 68
           +LI+D DD+      K++K+  E Y  D+     + L  +     +++ L +        
Sbjct: 4   ILIVDDDDQLRQSFAKLLKE--EGYSVDMAPSGEAGLEAVRDKAFDLVVLDVQMPGMSGL 61

Query: 69  NILKNIVDKIPIVPIIVQT----TQDNIKILNCFLYNRISKFF-----LNLVSRKQLCDS 119
                I +    +P++V T    T+  I+      ++ I K F     L+L+++      
Sbjct: 62  EAFARIREIDATLPVVVMTAYGTTETAIEATKLGAFDYILKPFDIAGVLDLITQALEAGH 121

Query: 120 IICALRE-GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
           ++ A  E  V P    +     ++I  SP M +V     +       ++I+GE G GK+ 
Sbjct: 122 MMRARVEMNVAP----DSARPGAIIGSSPPMQEVYKAIGRVAQTDATVLIRGESGTGKEL 177

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R I++  KRA  PF ++NC  + +  +E  LFG +    T  +++ +GK  +ANGGT+
Sbjct: 178 VARAIYQHSKRAGKPFLVINCVALPETLLESELFGYEKGAFTGAASRRIGKIEQANGGTV 237

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   +PL++Q +I   ++   +E      +I +DVR++  T +NL   +++ VFR+D
Sbjct: 238 FLDEIGDMPLSIQAKILRLLQERSLEPLGGNASIDVDVRILAATNRNLEKAIENEVFRED 297

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LYYR+ V  +N+  LR R  D+  L  +F+  F  +  +    ++D+A  ++  +PW  N
Sbjct: 298 LYYRLKVVTVNLPPLRDRVNDVNLLADYFMTLFSKEMKMDNPGLTDEARKMIRHHPWPGN 357

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           V+EL N L +++I  +   +  +    +++           + A    T+G   D ++  
Sbjct: 358 VRELANALKKSLIFSRGYPVRPEDISQVIA---------GPDQAGPSVTDGSDMDRVVGE 408

Query: 418 LSQESIPAIGQDGEVRRLSD-IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
            ++E + A G       L+D +   II  A+++ R   S+ A+ LG+ R TL  KI + N
Sbjct: 409 WAREMLTAGGDTARFDYLTDRLTAIIIREALQMTRGNRSQAAKLLGLARPTLLSKIDKLN 468

Query: 477 IEVDS 481
           + +++
Sbjct: 469 LSIET 473


>gi|328543925|ref|YP_004304034.1| Response regulator containing chemotaxis protein CheY, AAA-t ype
           ATPase, and DNA-binding domains [polymorphum gilvum
           SL003B-26A1]
 gi|326413669|gb|ADZ70732.1| Response regulator containing CheY-like receiver, AAA-t ype ATPase,
           and DNA-binding domains [Polymorphum gilvum SL003B-26A1]
          Length = 479

 Score =  172 bits (436), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 141/486 (29%), Positives = 234/486 (48%), Gaps = 36/486 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY V +  N + L   +S    +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYTVRLTSNAATLWRWVSSGDGDLVVTDVVMPDENIFDV 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P+IV + Q+     I+      Y  + K F      K+L   I  AL E
Sbjct: 66  LPRIKKLRPDLPVIVMSAQNTFMTAIRASEKGAYEYLPKPF----DLKELTGIISRALEE 121

Query: 127 GVV--PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
                P + ++      L+  SPAM ++  +  +     + +MI GE G GK+ ++R +H
Sbjct: 122 PKARRPIEMDDMGEAIPLVGRSPAMQEIYRVLARLMQTDLTVMINGESGTGKELVARALH 181

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPD 243
           + GKR   PF  +N   I +D IE  LFG +    T   A+  G+F +A+GGT+ L+E  
Sbjct: 182 DYGKRRNGPFVAINMAAIPRDLIEAELFGHEKGAFTGAQARSSGRFEQADGGTLFLDEIG 241

Query: 244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS 303
            +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   +   +FR+DL++R++
Sbjct: 242 DMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIVAATNKDLRQLINQGLFREDLFFRLN 301

Query: 304 VFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           V  I +  LR R EDIP LV HFF  +   K  +    I   AL+LL +Y W  NV+EL+
Sbjct: 302 VVPIRLPPLRERVEDIPDLVRHFF--ALAEKEGLPPKQIDQGALNLLRRYRWPGNVRELE 359

Query: 363 NILLRA-------VIG--LKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDT 413
           N++ R        VIG  L +  L++     L   EG   +E +   +   Y  G   DT
Sbjct: 360 NLVRRLAALYPQDVIGEALLEQELSQPTVSPL---EGDGAQEINLGASVERYL-GTYFDT 415

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
             D L    +         R L ++E  +I  A+   R    + A  LG+ R+TL +KIR
Sbjct: 416 FGDALPPPGL-------YHRILREVEYPLISAALAATRGNQIKAAELLGVNRNTLRKKIR 468

Query: 474 EYNIEV 479
           + +I+V
Sbjct: 469 DLDIQV 474


>gi|328952445|ref|YP_004369779.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfobacca acetoxidans DSM 11109]
 gi|328452769|gb|AEB08598.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfobacca acetoxidans DSM 11109]
          Length = 463

 Score =  172 bits (436), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 128/486 (26%), Positives = 227/486 (46%), Gaps = 55/486 (11%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
           + +L++D +   ++ +   ++  G++V      +  L  + +   +++FL +     D  
Sbjct: 3   RTILVVDDEPPILQTLSGILQDEGFEVLTAQDGETALKVVEEETPDLVFLDIALPGMDGL 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
            +L+++ ++ P+ P+++ +   +++  N     R   +  + + +    D II  +R  +
Sbjct: 63  EVLRHLKEQQPLTPVVMISAFGSVE--NAVKATRWGAY--DFIEKPPHADKIIVTVRNAL 118

Query: 129 VPSQENEH--------CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
             S+  E              +I  SPAM Q+ +  R        ++I GE G GK+ ++
Sbjct: 119 EMSRLTEENLQLRQRAVHPQEIIGQSPAMQQLREQVRIVAPTNAWVLITGENGTGKELVA 178

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
             IH   KRA  PF  VNC  I +D IE  LFG +    T  +A+  GKF +A+ GT+ L
Sbjct: 179 WAIHRFSKRAAKPFVEVNCAAIPEDLIESELFGHEKGAFTGATAKRRGKFDQAHEGTLFL 238

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   + L  Q ++   ++  + E       I++DVR++  T KNL   +    FR+DLY
Sbjct: 239 DEIADMSLKTQAKVLRILQEQRFERVGGNRPIQVDVRVVAATNKNLEELIGQGQFREDLY 298

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YRI+V  I +  L+ R+EDIP L+ +FL+ F   +A +   ++ +A+ +L + PW  NV+
Sbjct: 299 YRINVIPIAVPPLKERTEDIPLLIEYFLKEFARADASRPKIMTPEAVDILRRQPWPGNVR 358

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           ELKN + R  I      LT  R +                           +  + DNL 
Sbjct: 359 ELKNFVHRLAI------LTPGRVI--------------------------DAPHLPDNLR 386

Query: 420 QESIPAIGQDGEVRRL-------SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
           QE  P    +    ++       S  EKE I   +  ++  +   A  +G+ RS LY+KI
Sbjct: 387 QEK-PRTESESHFLQINSFKEARSRFEKEFIRRKLVEFQGNVGLTAEAIGLERSHLYKKI 445

Query: 473 REYNIE 478
           R Y +E
Sbjct: 446 RSYGLE 451


>gi|16767428|ref|NP_463043.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161617313|ref|YP_001591278.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167994976|ref|ZP_02576066.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|20141880|sp|P25852|ZRAR_SALTY RecName: Full=Transcriptional regulatory protein zraR
 gi|6960346|gb|AAF33506.1| Salmonella typhimurium transcriptional regulatory protein (HYDG)
           (SW:P25852); contains similarity to Pfam domain PF00158
           (sigma54), Score=609.2, E=2.4e-179, N=1 and PF00072
           (response_reg), Score=158, E=1.6e-43, N=1 [Salmonella
           enterica subsp. enterica serovar Typhimurium str. LT2]
 gi|16422733|gb|AAL23002.1| response regulator in two-component reguatory system with HydH
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. LT2]
 gi|161366677|gb|ABX70445.1| hypothetical protein SPAB_05164 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|205327257|gb|EDZ14021.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|261249278|emb|CBG27140.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267996475|gb|ACY91360.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301160670|emb|CBW20201.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312915280|dbj|BAJ39254.1| transcriptional regulator ZraR [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321223374|gb|EFX48441.1| Response regulator of zinc sigma-54-dependent two-component system
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. TN061786]
 gi|323132510|gb|ADX19940.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|332990993|gb|AEF09976.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 441

 Score =  172 bits (436), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ---GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|153006247|ref|YP_001380572.1| two component sigma54 specific Fis family transcriptional regulator
           [Anaeromyxobacter sp. Fw109-5]
 gi|152029820|gb|ABS27588.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter sp. Fw109-5]
          Length = 455

 Score =  172 bits (435), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 122/478 (25%), Positives = 229/478 (47%), Gaps = 47/478 (9%)

Query: 13  VLIIDKDDEQIKIIKDH---VESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           +L++D D++ I++       +E Y  +        L  I+ + V+ + + +   + D   
Sbjct: 5   ILVVD-DEKNIQLTLSRALSMEGYVVEAASGGREALDKIAALPVDAVVMDVRMPDLDGLE 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L+   +  P +P+++ +   +++ +          +    ++ K   D ++ A++  + 
Sbjct: 64  VLRRARETRPDLPVVIMSGHGSLETVRSAFKLGAFDYLEKPITEK---DKLLVAVKNALA 120

Query: 130 PS---QENEH----CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
                +EN           ++   PAM ++ +L R+A      +++ GE G GK+ ++R 
Sbjct: 121 LRTLREENAELRRAAGPAEMVGSGPAMQRLFELIRRAAPSEGRVLVTGENGTGKELVARA 180

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           IHES +R   PF  +NC  +  + IE  LFG +    T   A   GKF  A+GGT+ L+E
Sbjct: 181 IHESSRRKAGPFVKLNCAAVPAELIESELFGHERGAFTGAVAARRGKFELADGGTLFLDE 240

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +P A+Q ++   ++ G+ E       +++DVR++  T K+L  +V++  FR+DL+YR
Sbjct: 241 VGDMPAAMQAKVLRVLQEGEFERVGGAHTLKVDVRVVAATNKDLAAEVQAGRFREDLFYR 300

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           +SV  ++   LR R EDIP L   FL   C +N  + + +  +AL+ L  + W  NV+EL
Sbjct: 301 LSVVPVHAPPLRERKEDIPELATRFLAEACDRNGRRPMRLPREALAALQGHEWPGNVREL 360

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLL--SREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +N++ R  I      ++      +L  +R  + +R          +  G S      +L 
Sbjct: 361 RNLVERLAILCDGPEISAQDVAAVLPGARRPRPDR----------FRAGAS----FHDLV 406

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           +E+                E+EII  A+  +   +SE AR LG+ RS LY+K+R   +
Sbjct: 407 EEA----------------EREIILGALDAHDDNVSETARDLGLERSHLYKKMRALGV 448


>gi|222055856|ref|YP_002538218.1| Fis family transcriptional regulator [Geobacter sp. FRC-32]
 gi|221565145|gb|ACM21117.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. FRC-32]
          Length = 483

 Score =  172 bits (435), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 139/480 (28%), Positives = 234/480 (48%), Gaps = 22/480 (4%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           ++LI+D D + + ++K        +V + + SD  L  I   + NV    +         
Sbjct: 4   KLLILDDDPDILLMLKTVFHGEEMEVMLESESDAALKLILTERPNVAIFDISMPGKSGFQ 63

Query: 70  ILKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           +L+      P + II+    +TTQ+ I+ +    Y+ ++K F     R  +  ++ C L 
Sbjct: 64  VLQEAKKIDPGLSIIMTTGHKTTQNAIEAMKFGAYDYVTKPFDTNKLRSSVQKALECNLL 123

Query: 126 EGVVPSQEN------EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
              V   ++      E  A D +I  S  MI++  +  K  D    ++IQGE G GK+ L
Sbjct: 124 NRKVRYTKDTNQLKLEEDADDIMIGSSAEMIEIWKMVGKVADSDATVLIQGESGTGKELL 183

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R I+++ +R   PF  VNC  + +  +E  LFG +    T   A+ +GKF + NGGTI 
Sbjct: 184 ARAIYDNSRRKNRPFLAVNCAALPEALLESELFGHEKGAFTDAHARRIGKFEQCNGGTIF 243

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   + LA QG++   +E  + E       IR+DVR+I  T ++L+  VK   FR DL
Sbjct: 244 LDEIGEMSLANQGKLLRVLECQEFERVGGNDTIRVDVRIIAATNRSLVTSVKEKTFRMDL 303

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +YR+ V    +  L+ R+EDIP L+  F++ F  K       ++ +   LL K+PW  N+
Sbjct: 304 FYRLRVVNFFLPPLKDRAEDIPLLIDLFVKKFSRKYGKTIRRVAPETTDLLLKHPWEGNI 363

Query: 359 QELKNILLRAVIGLK-DSHLTEDRFVLLLSREGKKEREFHTETACTCYTE--GKSSDTIL 415
           +ELKN++  A +  K D  + ED    L ++ G KE +   + A   Y E   K  + + 
Sbjct: 364 RELKNVINSATVFCKSDVLMPEDLESFLTAKAGFKEVDL--DCAGDDYYEVFWKMLEPVF 421

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
           D +  ++   I +   +     +EK +I +AM+         A+ LGI R+TL  ++  Y
Sbjct: 422 DGICLKNKGTIYESVNM----GLEKALIHMAMEKSNNNQVFAAKLLGISRNTLRDRLERY 477


>gi|224585714|ref|YP_002639513.1| transcriptional regulator ZraR [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|224470242|gb|ACN48072.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
          Length = 441

 Score =  172 bits (435), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 126/466 (27%), Positives = 222/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRL+  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLVAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+ L   +++E    L ++    K       T C+                       
Sbjct: 367 RAVVLLTGEYISERELPLAIAATPIK-------TECS----------------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L ++EKE+I  A++      +E AR+LGI R TL  KI
Sbjct: 397 ---GEIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKI 439


>gi|162457508|ref|YP_001619875.1| sigma-54 dependent DNA-binding response regulator [Sorangium
           cellulosum 'So ce 56']
 gi|161168090|emb|CAN99395.1| sigma-54 dependent DNA-binding response regulator [Sorangium
           cellulosum 'So ce 56']
          Length = 468

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 130/471 (27%), Positives = 218/471 (46%), Gaps = 40/471 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           VL++D +   +  I+   +  G  V   + +   L  +   +V V+   L+        +
Sbjct: 27  VLVVDDEPSNVASIEKIFQRDGMRVITADSAKAALEIVRSRRVEVVLTDLMMPGVSGLEL 86

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSI-ICALREGVV 129
           L+ +    P   +++ T    ++     +      F    + R  +  S+   A R+ +V
Sbjct: 87  LRALKQLAPDTEVVMMTAYGTVETAVQAMREGAYDFVEKPLKRMTIIKSVRKAAERQSLV 146

Query: 130 PS-----QENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
                  QE +      ++  SP + +V+D+A +A   +  +++ GE G GK+ L+RFIH
Sbjct: 147 AENRSLRQEIKLLTKREIVGSSPTLRRVLDIATQAAPSSATVLVLGESGTGKELLARFIH 206

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPD 243
           E   R+  PF  VNC  I +  +E  LFG +    T   A+  G+F +A GGT+ L+E  
Sbjct: 207 ERSARSRGPFVAVNCAAIPETILEAELFGHERGAFTGALAKRDGRFAKAAGGTLFLDEIG 266

Query: 244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS 303
            L  AVQ ++   ++ G+ E       +R DVRL+  T K+L  +V +  FR+DL+YR++
Sbjct: 267 ELSPAVQVKLLRVLQEGEYEPVGG-DTVRADVRLVAATNKDLRAEVAAGRFREDLFYRLN 325

Query: 304 VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKN 363
           V  I    LR+R EDIP LV  FL  +CTKN   ++      L+ LT Y W  NV+EL+N
Sbjct: 326 VIAITAPPLRTRREDIPLLVDHFLGVYCTKNNRPRLEAPRDVLARLTDYTWPGNVRELEN 385

Query: 364 ILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESI 423
           ++ RAV+  +   L+ D     + RE         E +   ++ G               
Sbjct: 386 VIERAVVLCRGDQLSVDDLPDFI-REAAP-----AEPSSLTFSVGTP------------- 426

Query: 424 PAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
                      L ++E+ +I   ++  R   S  A+ LGI   T+YRK+ E
Sbjct: 427 -----------LDEVERRLIRETLRHARGDKSVAAQLLGISTRTIYRKLGE 466


>gi|197123810|ref|YP_002135761.1| Fis family transcriptional regulator [Anaeromyxobacter sp. K]
 gi|196173659|gb|ACG74632.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter sp. K]
          Length = 455

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 127/478 (26%), Positives = 228/478 (47%), Gaps = 45/478 (9%)

Query: 13  VLIIDKDDEQIKIIKDH---VESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           VL++D D+  I++       +E Y  +        L  I+ + V+V+ + +   + D   
Sbjct: 5   VLVVD-DERNIQVTLSRALSMEGYAVETASGGREALEKIAALPVDVVVMDVRMPDLDGLA 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNI-KILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
           +L+   +  P +PI++ +   +I  + + F           +  +++L  ++  AL    
Sbjct: 64  VLQRARETRPELPIVIMSGHGSIDTVRSAFKLGAFDYLEKPITEKEKLLVAVKNAL---A 120

Query: 129 VPSQENEHCALD--------SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
           + S   E+ AL          +I   PAM ++ DL R+       ++I GE G GK+ ++
Sbjct: 121 LESLRAENAALRRAAGQGQLEMIGGGPAMQRLFDLVRRTAPSEGRVLITGENGTGKELVA 180

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R IHE  +R   PF  +NC  +  + IE  LFG +    T   A   G+F +A+GGT+ L
Sbjct: 181 RAIHEQSRRRERPFVKLNCAAVPAELIESELFGHERGAFTGAVAARRGRFEQADGGTLFL 240

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P A+Q ++   ++ G++E    +  +R DVR++  T K+L  +V +  FR+DLY
Sbjct: 241 DEVGDMPAAMQAKVLRVLQEGELERVGGQQTLRCDVRVVAATNKDLQAEVAAGRFREDLY 300

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  I+   LR   ED+P L   FL   C +N  + + +  +A++ L  + W  NV+
Sbjct: 301 YRLNVVPIHTPALRDHKEDVPELAARFLGEACERNGRRAMRLGREAVAALQTHDWPGNVR 360

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           EL+N++ R  I      +  +  V +L   G +        A   + E          L 
Sbjct: 361 ELRNLVERLAILCDGPEIGAEDVVAMLP--GARRPRGDRLRAGAAFHE----------LV 408

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           +E+                E+EI+  A++ ++  +S+ AR LG+ RS LY+K+R   I
Sbjct: 409 EEA----------------EREIVLAALEAHQDNVSDTARALGLERSHLYKKMRALGI 450


>gi|255021371|ref|ZP_05293419.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Acidithiobacillus caldus ATCC 51756]
 gi|254969234|gb|EET26748.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Acidithiobacillus caldus ATCC 51756]
          Length = 447

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 133/467 (28%), Positives = 212/467 (45%), Gaps = 39/467 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           RVL+++ D +  +++ + +E  G +V         L+ +   Q ++I         D   
Sbjct: 7   RVLLVEDDVDFAEVLAEGLEEAGMEVQQAADGKEALNRLRDGQFDLILSDAQMQPMDGYG 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  +    P+++ T    I      L N    + +   + ++L   +     E + 
Sbjct: 67  LLAALRAQPGHPPVVMMTAWGTIDEAVRALQNGAVDYLVKPFAMQELLTKL--QRHERLQ 124

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
           P  E E       +A SP M++ +  AR+       +++ GE GVGK+ L+RFIH    R
Sbjct: 125 PGAELEP------LAHSPVMLETLIKARRVAQTEASVLLTGESGVGKEVLARFIHRESNR 178

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  VNC  I +  +E  LFG +    T  S    GKF +A GGT++L+E   + L 
Sbjct: 179 AREPFVAVNCAAIPESLLEATLFGHEKGAFTGASQSSPGKFEQAQGGTLLLDEVTEMALP 238

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E    R  IRLDVR+I  + ++L   V    FR+DLYYR+ V  + 
Sbjct: 239 LQAKLLRVLQERELERVGGRRTIRLDVRVIATSNRDLRQAVSEGKFREDLYYRLQVIPLC 298

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
           +  LR R EDI  L    L   C + AI   S+  +A ++L  YPW  NV+EL N L RA
Sbjct: 299 VPPLRQRREDILPLAQRLLAKHCERMAIAPKSLDPEAQAVLLSYPWPGNVRELDNALQRA 358

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
            I   D+ +  D   L +             T     +EG S   + D  S++       
Sbjct: 359 AIFSADTVIRSDDLGLEIR-----------GTLDDARSEGSSRPILEDVRSRQ------- 400

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
                     E+E I   ++  R   +E ARRLGI   TL  K++ Y
Sbjct: 401 ----------EQETIVSVLRECRGSRNEAARRLGISPRTLRHKLQRY 437


>gi|149177152|ref|ZP_01855759.1| probable response regulatory protein (atoC) [Planctomyces maris DSM
           8797]
 gi|148844044|gb|EDL58400.1| probable response regulatory protein (atoC) [Planctomyces maris DSM
           8797]
          Length = 476

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 133/489 (27%), Positives = 214/489 (43%), Gaps = 60/489 (12%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST--ISKIQVNVIFLSLINCEDDKEN 69
           RVLIID D+   + + + +E  G D  I    +     I     +++   L     D   
Sbjct: 17  RVLIIDDDEAHAQAVAESLERVGCDCKIATSGEQGAKLIESETADIVITDLRMDGVDGLA 76

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICA------ 123
           IL+   D++P   +IV T   +I      +      +    +   +L +++  A      
Sbjct: 77  ILRTAKDELPDAEVIVLTGHGSINSAVTAMQLGAYTYLTKPLDINELRNAVEKASTRVRL 136

Query: 124 -LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
             R   +  + +E    + +I  +P M ++VD  +        ++I+GE G GK+ ++R 
Sbjct: 137 MRRNAELHRRLDEKFGFEGVIGNTPQMHKIVDKLKNVASTNSTVLIEGESGTGKELVARA 196

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           IH++ +R   PF  +N   +    +E  LFG +    T    + +GKF  ANGGT+ L+E
Sbjct: 197 IHQNSERKSKPFVPLNISALPDSILESELFGHEPGAFTGAVGKRIGKFEHANGGTLFLDE 256

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +P+  Q ++   +E  KI        I L+VRL+  T  +LL  VK   FR+DLYYR
Sbjct: 257 VGEMPMQTQIKLLRVLEDRKIARLGMNEEISLNVRLVAATNADLLEMVKKGTFRQDLYYR 316

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           +SV  I +  LR R  DIP L   FL+   ++       +S  A   L  Y W  N+++L
Sbjct: 317 LSVVKIELPPLRERRGDIPLLTDHFLKELSSQYHKPYDGVSRAARRALMSYDWPGNIRQL 376

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQE 421
           KN   R               +L+L  +G  +                     LD+L +E
Sbjct: 377 KNAAER---------------MLVLDTDGILD---------------------LDDLPEE 400

Query: 422 SIPAIGQDGEV--------------RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRST 467
            +P  G +G+               R  S++E+  I  A+ L   +  E AR LGIG  T
Sbjct: 401 IVPMTGPEGDSSYISDRSGADFLIGRPFSEVERYYIERALDLADGKREEAARMLGIGERT 460

Query: 468 LYRKIREYN 476
           LYRK++EY 
Sbjct: 461 LYRKLKEYQ 469


>gi|110633970|ref|YP_674178.1| nitrogen metabolism transcriptional regulator, NtrC, Fis family
           [Mesorhizobium sp. BNC1]
 gi|110284954|gb|ABG63013.1| nitrogen metabolism transcriptional regulator, NtrC, Fis family
           [Chelativorans sp. BNC1]
          Length = 486

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 126/480 (26%), Positives = 227/480 (47%), Gaps = 20/480 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   G+ V +  N + L   ++  + +++   ++  +++  ++
Sbjct: 7   ILVADDDAAIRTVLNQALSRVGHQVRVTSNAATLWRWVAAGEGDLVITDVVMPDENAFDM 66

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P+IV + Q+     I+      Y  + K F +L     +    +   R 
Sbjct: 67  LPRIRKARPDLPVIVMSAQNTFMTAIRASEAGAYEYLPKPF-DLTELLGIVGRALAEPRS 125

Query: 127 GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES 186
             V ++ N+      LI  SPAM  +  +  +     + +MI GE G GK+ ++R +HE 
Sbjct: 126 KAVETRTNDTPEAMPLIGRSPAMQDIYRMLARMMQTDLTVMITGESGTGKELVARALHEF 185

Query: 187 GKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGTIVLEE 241
           G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +A GGT+ L+E
Sbjct: 186 GRRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQQRSS----GRFEQAEGGTLFLDE 241

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   +   +FR+DL+YR
Sbjct: 242 IGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIVAATNKDLRALINQGLFREDLFYR 301

Query: 302 ISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           ++V  + +  LR RSEDIP LV HFF Q    +  ++   I+   +  + KYPW  NV+E
Sbjct: 302 LNVVPLRLPPLRERSEDIPDLVRHFFAQ--AEREGLQPKRIATGGVDAMMKYPWPGNVRE 359

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L+N++ R         ++E+  +  L            + A      G+S +  L    +
Sbjct: 360 LENLVRRLAALYPQDEISEEIILGELHGGMPAANSPLNDGAGQDLPLGQSVEQYLQRYFR 419

Query: 421 ESIPAIGQDGEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
               A+   G   R L+++E  +I  A+          A  LG+ R+TL +KIR+ ++++
Sbjct: 420 GFGSALPPPGLYHRILAEVEYPLILAALAATHGNQIRAAELLGVNRNTLRKKIRDLSVDI 479


>gi|254719181|ref|ZP_05180992.1| nitrogen regulation protein NtrC [Brucella sp. 83/13]
 gi|265984178|ref|ZP_06096913.1| nitrogen metabolism transcriptional regulator [Brucella sp. 83/13]
 gi|306838174|ref|ZP_07471030.1| nitrogen regulation protein NR(I) [Brucella sp. NF 2653]
 gi|306841844|ref|ZP_07474526.1| nitrogen regulation protein NR(I) [Brucella sp. BO2]
 gi|264662770|gb|EEZ33031.1| nitrogen metabolism transcriptional regulator [Brucella sp. 83/13]
 gi|306288071|gb|EFM59468.1| nitrogen regulation protein NR(I) [Brucella sp. BO2]
 gi|306406764|gb|EFM62987.1| nitrogen regulation protein NR(I) [Brucella sp. NF 2653]
          Length = 491

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 133/490 (27%), Positives = 237/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKMRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF +    +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKR--AAEEGLPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|197248989|ref|YP_002149082.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197212692|gb|ACH50089.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 441

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 219/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++     +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALFRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S+               
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKAENSA--------------- 397

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
               E++ L D+EKEII  A++      +E AR+LGI R TL  K+
Sbjct: 398 ----EIQPLVDVEKEIILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|256061200|ref|ZP_05451352.1| nitrogen regulation protein NtrC [Brucella neotomae 5K33]
 gi|261325208|ref|ZP_05964405.1| nitrogen metabolism transcriptional regulator [Brucella neotomae
           5K33]
 gi|261301188|gb|EEY04685.1| nitrogen metabolism transcriptional regulator [Brucella neotomae
           5K33]
          Length = 491

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 133/490 (27%), Positives = 237/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF +    +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKR--AAEEGVPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|237799232|ref|ZP_04587693.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331022087|gb|EGI02144.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 470

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 129/475 (27%), Positives = 226/475 (47%), Gaps = 20/475 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVE--SYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKENI 70
           VL+++ D    + + + +E  SYGY         L  +     N++   +     D   +
Sbjct: 5   VLLVEDDRALREALGETLELASYGYKAVGSAEEALLAVEAQPFNLVVSDVNMPGMDGHQL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           L  +  + P +P+++ T    ++     +    + + +     K L  +++     G + 
Sbjct: 65  LSLLRSRHPQLPVLLMTAHGAVERAVDAMRQGAADYLVKPFEPKALI-ALVARHALGRLG 123

Query: 131 SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
             E+     D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  RA
Sbjct: 124 PAES-----DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPRA 178

Query: 191 FFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAV 249
             PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +P+ +
Sbjct: 179 DKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPMGL 238

Query: 250 QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINI 309
           Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF +  
Sbjct: 239 QAKLLRVLQEREVERVGARKPITLDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLAW 298

Query: 310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
             LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA+
Sbjct: 299 QALRQRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVGYPWPGNVRELDNAVQRAL 358

Query: 370 IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQD 429
           I  +   +    F L                +    +  ++++     +S ES+ A+G D
Sbjct: 359 ILQQGGVIQAQDFCLSGPVTSLPAAVVEAAASLPVMSVAENANA---GVSPESVGALGDD 415

Query: 430 GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
             +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 416 --LRRR---EFQMIIDTLRSERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 465


>gi|256044774|ref|ZP_05447678.1| nitrogen regulation protein NR(I) [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|260565623|ref|ZP_05836107.1| nitrogen regulation protein NtrC [Brucella melitensis bv. 1 str.
           16M]
 gi|265991198|ref|ZP_06103755.1| nitrogen metabolism transcriptional regulator [Brucella melitensis
           bv. 1 str. Rev.1]
 gi|260151691|gb|EEW86785.1| nitrogen regulation protein NtrC [Brucella melitensis bv. 1 str.
           16M]
 gi|263001982|gb|EEZ14557.1| nitrogen metabolism transcriptional regulator [Brucella melitensis
           bv. 1 str. Rev.1]
          Length = 491

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 133/490 (27%), Positives = 238/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF ++   +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKRA--AEEGVPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|197118370|ref|YP_002138797.1| sigma-54-dependent transcriptional response regulator [Geobacter
           bemidjiensis Bem]
 gi|197087730|gb|ACH39001.1| sigma-54-dependent transcriptional response regulator [Geobacter
           bemidjiensis Bem]
          Length = 509

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 150/518 (28%), Positives = 230/518 (44%), Gaps = 62/518 (11%)

Query: 8   DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCED 65
           D   R+LIID + +        +   GY V         LS +   Q +V  + L   + 
Sbjct: 3   DSSTRILIIDDERDVCTFFSRLLSRKGYQVVTAASEPEALSALEAAQFSVALVDLKLPDT 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQLCDSII 121
           D   +L+ I  + P   +I+ T    +K     +    Y  + K F ++   +QL     
Sbjct: 63  DGITLLEIIKSRQPACEVIIMTGYSTVKTAVAAMQLGAYEYLEKPFDDIDQIEQLVGR-- 120

Query: 122 CALREGVVPSQENEHCALDSL-------IAVSPAMIQVVDLARKAGDCAIPIMIQGEFGV 174
            A     +   +N H     +       +  SP+M ++V LA K     I ++IQG+ G 
Sbjct: 121 AAGSGASLLRGDNSHDEWAEVAQGVGFRVGSSPSMKRMVSLAYKVAGKDISVLIQGKTGT 180

Query: 175 GKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEAN 233
           GK+ L+RFIH +  RA  PF  VNCG + ++ +E  LFG        + Q   G F  AN
Sbjct: 181 GKEVLARFIHAASCRAGQPFIPVNCGALPENLLEGELFGHEKGAFTGANQTRRGIFELAN 240

Query: 234 GGTIVLEE-PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH 292
            GT++L+E  DA P  +Q ++   +ETG+         IR DVR+I  T  +L   +   
Sbjct: 241 NGTLLLDEIGDATP-QIQVKLLRVLETGEFMRVGGERPIRTDVRVIAATNVDLEQAIAEK 299

Query: 293 VFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY 352
            FR+DL+YR++V  + I +L +RSEDIP L   F+         +++ ++   L +L  Y
Sbjct: 300 SFREDLFYRLNVVRLEIPSLSARSEDIPLLAEHFVHQIN-----RELKLAAGTLRMLQGY 354

Query: 353 PWIDNVQELKNILLRAV-IGLKDSHLTEDRFVLLLSREGKKEREFHTET----------- 400
            W  N++EL N++ RAV I   D+ L E      L+     ER    +T           
Sbjct: 355 AWPGNIRELANVMRRAVVICNGDTILPEHLGGTFLAGPTAPERGSAAKTIQQPDRSRLQA 414

Query: 401 ----ACTCYTEGKSSDT-----ILDNLSQES------------IPAIGQDGEVRRLSDIE 439
                C    E +  D      +LD+L Q              +PA+        L D E
Sbjct: 415 TLLEHCDSAEELERLDAEELNRLLDSLRQAQSNLLGVMRKKKIVPAL------HALKDSE 468

Query: 440 KEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
            E I  A+  Y   ++E AR LGI R+TLYRKI+E  +
Sbjct: 469 AETIKEALAQYDGNITEAARALGIARNTLYRKIKELGL 506


>gi|147676843|ref|YP_001211058.1| transcriptional regulator [Pelotomaculum thermopropionicum SI]
 gi|146272940|dbj|BAF58689.1| transcriptional regulator [Pelotomaculum thermopropionicum SI]
          Length = 478

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 123/386 (31%), Positives = 192/386 (49%), Gaps = 33/386 (8%)

Query: 102 RISKFFLNLVSRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGD 161
           +  K F  LVS+  L + + C  RE  +          + +I  SP +I V DLA+K   
Sbjct: 113 KTKKEFAELVSK--LKEEVDCYKRE--LNEIYTSKWKFEDIITCSPNLIHVKDLAQKVAP 168

Query: 162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG--DVDLQT 219
             + +MI GE G GK+ L+  IH +  R+  PF  +NC  I ++ +E  LFG        
Sbjct: 169 VDVNVMILGESGSGKELLAHSIHSASTRSSKPFVCINCAAIPENIMESELFGYEPGAFTN 228

Query: 220 KNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIF 279
             S   LGK   AN GT+ L+E   +P  +Q ++  F++ G++E   S   + ++VR+I 
Sbjct: 229 AKSNGKLGKLEIANNGTVFLDEIGDMPPFMQAKLLRFLQEGELEKVGSVKPVSVNVRVIC 288

Query: 280 LTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI 339
            T +N+   V+  +FR DLYYR+S  ++ I  LR R EDI  L   FL+S   K AI   
Sbjct: 289 ATNRNIQKMVEDGIFRADLYYRLSSIILKIPPLRERPEDIELLCDHFLKSITEKWAIPLK 348

Query: 340 SISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTE 399
            I  +AL +L  Y W  NV+EL++ LL  +  + D ++ + +                  
Sbjct: 349 KIDKEALEILKNYYWPGNVRELQH-LLETLCCITDGNIIKAK------------------ 389

Query: 400 TACTCYTEGKSSDTILDN--LSQESIPAIGQDGEVRRL-SDI----EKEIIGLAMKLYRA 452
            A   Y  G+S   +L N  L + S+  I  DG  + + SD+    EKE++   ++    
Sbjct: 390 -ALPSYLFGQSDSAMLKNNELRRISLSNINSDGNNKYICSDVINSKEKELLEEVLRNTGG 448

Query: 453 QMSEVARRLGIGRSTLYRKIREYNIE 478
              + A  LGI R+TLY K+R+YN++
Sbjct: 449 NKRKAAEMLGIHRTTLYYKLRKYNMQ 474


>gi|94310726|ref|YP_583936.1| sigma-54 factor, interaction region [Cupriavidus metallidurans
           CH34]
 gi|93354578|gb|ABF08667.1| transcriptional regulator of phenol hydroxylase genes, Fis family
           [Cupriavidus metallidurans CH34]
          Length = 542

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 114/345 (33%), Positives = 175/345 (50%), Gaps = 43/345 (12%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
           +LI  SPA  +  +L   A D  I +++ GE G GK+  +R++H+ G R   PF  VNC 
Sbjct: 230 NLIGQSPAFREAFNLLSAAADSHITVLLTGETGAGKEMFARWLHDHGPRGEQPFVAVNCA 289

Query: 201 MIDQDKIEKFLFGDVDLQTKNSAQ--FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIE 258
            I  + IE  LFG V+      AQ    G+F  A+GGT+ L+E   LP A Q ++   ++
Sbjct: 290 AIPHELIESELFG-VEKGAYTGAQQSRPGRFERAHGGTLFLDEIGDLPPAAQVKLLRVLQ 348

Query: 259 TGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSED 318
             ++E      A +++VRLI  T  NL   +K   FR DL+YRIS + I+I  LR R ED
Sbjct: 349 NNEVERLGGVEARKVNVRLIAATNVNLAQAIKHGQFRADLFYRISTYPISIPALRERKED 408

Query: 319 IPWLVHFFLQSFCTKNAI--KQI-SISDKALSLLTKYPWIDNVQELKNILLRAVI----- 370
           IP L   F+Q F   NA+  KQ+  +S +A   L +YPW  N++EL+N++ R V+     
Sbjct: 409 IPELAQSFIQRF---NALYQKQVRGLSTRARDALVQYPWPGNIRELENMIERGVLLAPAT 465

Query: 371 GLKD-SHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQD 429
           G+ D +HL                  F ++ A       + +D +++ L  + +      
Sbjct: 466 GMIDVAHL------------------FASQQAAGSEEPSQDADALIEKLLNQQV------ 501

Query: 430 GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
                L  IE +++ LAM   R  +S  AR LGI R  L  ++++
Sbjct: 502 ----SLPQIEAKLMQLAMTTTRGNLSSAARMLGITRPQLAYRLKK 542


>gi|317484038|ref|ZP_07942971.1| sigma-54 interaction domain-containing protein [Bilophila
           wadsworthia 3_1_6]
 gi|316924682|gb|EFV45835.1| sigma-54 interaction domain-containing protein [Bilophila
           wadsworthia 3_1_6]
          Length = 648

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 110/351 (31%), Positives = 174/351 (49%), Gaps = 44/351 (12%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            D ++  +PA  +VV +AR A    +  +I GE G GK+  ++ IH  G+RA  PF +VN
Sbjct: 330 FDHIVGNAPATQEVVRMARMAAQSDVTTLILGESGTGKELFAQSIHNGGRRANAPFVVVN 389

Query: 199 CGMIDQDKIEKFLFGDVDLQTKNSAQFLGK---FIEANGGTIVLEEPDALPLAVQGRIYN 255
           CG + ++ ++  LFG  D  +   A  LGK   F  A+ GTI L+E   +PL  Q  +  
Sbjct: 390 CGALPRNLVQSELFG-YDEGSFTGASRLGKPGKFELADNGTIFLDEIGEMPLEAQVSLLR 448

Query: 256 FIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSR 315
            ++ G++     +    ++VR++  T +NL   ++ + FR+DLYYR++VF +N+  LR R
Sbjct: 449 LLQNGEVTRVGGKHTRLVNVRVLAATNRNLENAIRQNAFREDLYYRLNVFTLNVPPLRER 508

Query: 316 SEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDS 375
           S DI  L++ FL  F        + ++D+A+ +L  YPW  N++EL+N++          
Sbjct: 509 SSDIALLINHFLDHFVASLGRGPLRVTDRAMDVLLGYPWPGNIRELENVI---------- 558

Query: 376 HLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSS---DTILDN-LSQESIPAIGQDGE 431
                            ER  H        ++G  S   D +  N L+ E IP       
Sbjct: 559 -----------------ERMVH-------MSQGVPSIDIDVLPANILNHEGIPGGAPRPA 594

Query: 432 VRR--LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
           V R  LS  EKE I  A++     +   A+ LGI RS LY K+R + +  D
Sbjct: 595 VPRGLLSHQEKETIVRALQEAGGNIRATAKALGISRSGLYVKMRRFGLSPD 645


>gi|229591855|ref|YP_002873974.1| two-component response regulator [Pseudomonas fluorescens SBW25]
 gi|229363721|emb|CAY51116.1| two-component response regulator [Pseudomonas fluorescens SBW25]
          Length = 458

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 124/476 (26%), Positives = 224/476 (47%), Gaps = 32/476 (6%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           +VL+++ D    + + D +   G+D   V  ++  L  + +   +++   +     D   
Sbjct: 4   KVLLVEDDRALREALADTLLLAGHDYRAVGSAEDALEAVEQESFSLVVSDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    ++     +    + + +     K L + ++     GV+
Sbjct: 64  LLSLLRARQPQLPVLLMTAHGAVERAVDAMRQGAADYLVKPFEPKALIE-LVARHALGVI 122

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
           P+ + E       IA  PA  Q+++LA +       ++I GE G GK+ L+R+IH+   R
Sbjct: 123 PASDGE-----GPIAFEPASAQLLELAARVARSDSTVLISGESGTGKEVLARYIHQQSTR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL 
Sbjct: 178 AKQPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I+LD+R++  T ++L  +V +  FR+DL+YR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPIQLDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R  DI  L    L +   K    Q  +S +A + L  YPW  NV+EL N + RA
Sbjct: 298 WRPLRERPADIIPLAERLLNNHVKKMKHAQARLSAEAQACLISYPWPGNVRELDNAIQRA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           +I  +   +    F L +   G       T        E +++  + D+L +        
Sbjct: 358 LILQQGGLIQPQDFCLAM---GSGAAPLPTLAPAPIVAETETAGALGDDLRRR------- 407

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
                     E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 408 ----------EFQMIIDTLRSERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 453


>gi|154142|gb|AAA27149.1| hydrogenase G [Salmonella enterica subsp. enterica serovar
           Typhimurium]
          Length = 441

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVRPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ---GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|86159757|ref|YP_466542.1| two component sigma54 specific Fis family transcriptional regulator
           [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85776268|gb|ABC83105.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 453

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 125/477 (26%), Positives = 229/477 (48%), Gaps = 43/477 (9%)

Query: 13  VLIIDKDDEQIKIIKDH---VESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           VL++D D+  I++       +E Y  +        L  ++ + V+V+ + +   + D   
Sbjct: 5   VLVVD-DERNIQLTLSRALSMEGYAVETASGGREALEKLAALPVDVVVMDVRMPDLDGLA 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNI-KILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
           +L+   +  P +P+++ +   +I  + + F           +  +++L  ++  AL    
Sbjct: 64  VLQKARETRPELPVVIMSGHGSIDTVRSAFKLGAFDYLEKPITEKEKLLVAVKNAL---A 120

Query: 129 VPSQENEHCALD------SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
           + S   E+ AL        +I   PAM ++ DL R+       ++I GE G GK+ ++R 
Sbjct: 121 LQSLRAENAALRRAAGQLEMIGGGPAMQRLFDLVRRTAPSEGRVLITGENGTGKELVARA 180

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           IH+  +R   PF  +NC  +  + IE  LFG +    T   A   G+F +A+GGT+ L+E
Sbjct: 181 IHDQSRRRDRPFVKLNCAAVPAELIESELFGHERGAFTGAVAARRGRFEQADGGTLFLDE 240

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +P A+Q ++   ++ G++E    +  +R DVR++  T K+L  +V +  FR+DLYYR
Sbjct: 241 VGDMPAAMQAKVLRVLQEGELERVGGQQTLRCDVRVVAATNKDLQAEVAAGRFREDLYYR 300

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  I+   LR   ED+P L   FL   C +N  + + +  +A++ L  + W  NV+EL
Sbjct: 301 LNVVPIHTPALREHKEDVPELAARFLGEACERNGRRAMRLGREAIAALQTHDWPGNVREL 360

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQE 421
           +N++ R  I      +  D  V +L   G +        A   + E          L +E
Sbjct: 361 RNLVERLAILCDGPEIGADDVVAMLP--GARRPRGDRLRAGAAFHE----------LVEE 408

Query: 422 SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
           +                E+EI+  A++ ++  +S+ AR LG+ RS LY+K+R   I+
Sbjct: 409 A----------------EREIVLAALEAHQDNVSDTARALGLERSHLYKKMRALGIK 449


>gi|220918575|ref|YP_002493879.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219956429|gb|ACL66813.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 455

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 127/479 (26%), Positives = 228/479 (47%), Gaps = 45/479 (9%)

Query: 13  VLIIDKDDEQIKIIKDH---VESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           VL++D D+  I++       +E Y  +        L  I+ + V+V+ + +   + D   
Sbjct: 5   VLVVD-DERNIQLTLSRALSMEGYAVETASGGREALEKIAALPVDVVVMDVRMPDLDGLA 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNI-KILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
           +L+   +  P +PI++ +   +I  + + F           +  +++L  ++  AL    
Sbjct: 64  VLQRARETRPELPIVIMSGHGSIDTVRSAFKLGAFDYLEKPITEKEKLLVAVKNAL---A 120

Query: 129 VPSQENEHCALD--------SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
           + S   E+ AL          +I   PAM ++ DL R+       ++I GE G GK+ ++
Sbjct: 121 LESLRAENAALRRAAGQGQLEMIGGGPAMQRLFDLVRRTAPSEGRVLITGENGTGKELVA 180

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R IHE  +R   PF  +NC  +  + IE  LFG +    T   A   G+F +A+GGT+ L
Sbjct: 181 RAIHEQSRRRDRPFVKLNCAAVPAELIESELFGHERGAFTGAVAARRGRFEQADGGTLFL 240

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P A+Q ++   ++ G++E    +  +R DVR++  T K+L  +V +  FR+DLY
Sbjct: 241 DEVGDMPAAMQAKVLRVLQEGELERVGGQQTLRCDVRVVAATNKDLQAEVAAGRFREDLY 300

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  I+   LR   ED+P L   FL   C +N  + + +   A++ L  + W  NV+
Sbjct: 301 YRLNVVPIHTPALRDHKEDVPELAARFLAEACERNGRRAMRLGRDAVAALQTHDWPGNVR 360

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           EL+N++ R  I      +  +  V +L   G +        A   + E          L 
Sbjct: 361 ELRNLVERLAILCDGPEIGAEDVVAMLP--GARRPRGDRLRAGAAFHE----------LV 408

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
           +E+                E+EI+  A++ ++  +S+ AR LG+ RS LY+K+R   I+
Sbjct: 409 EEA----------------EREIVLAALEAHQDNVSDTARALGLERSHLYKKMRALGIK 451


>gi|17987149|ref|NP_539783.1| nitrogen assimilation regulatory protein [Brucella melitensis bv. 1
           str. 16M]
 gi|17982814|gb|AAL52047.1| nitrogen assimilation regulatory protein [Brucella melitensis bv. 1
           str. 16M]
          Length = 528

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 131/489 (26%), Positives = 233/489 (47%), Gaps = 37/489 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 47  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 106

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 107 LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 166

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 167 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 220

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 221 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 276

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 277 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 336

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF ++   +  + +  I++  L ++ +YPW 
Sbjct: 337 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKRA--AEEGVPEKRITNAGLEMMRRYPWP 394

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+EL+N++ R         +  +     L  E  K        A     E  S    +
Sbjct: 395 GNVRELENLVRRLAALYPQEEIAPEIIETELKAELAKP---DVVAAAGGEMENISISQAV 451

Query: 416 DNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
           +   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL +
Sbjct: 452 EQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLRK 511

Query: 471 KIREYNIEV 479
           KIRE  + +
Sbjct: 512 KIRELGVNI 520


>gi|23501995|ref|NP_698122.1| nitrogen regulation protein NtrC [Brucella suis 1330]
 gi|62290031|ref|YP_221824.1| nitrogen regulation protein NtrC [Brucella abortus bv. 1 str.
           9-941]
 gi|82699958|ref|YP_414532.1| response regulator receiver [Brucella melitensis biovar Abortus
           2308]
 gi|148560702|ref|YP_001259038.1| nitrogen regulation protein NR(I) [Brucella ovis ATCC 25840]
 gi|161619069|ref|YP_001592956.1| nitrogen regulation protein NR(I) [Brucella canis ATCC 23365]
 gi|189024271|ref|YP_001935039.1| nitrogen regulation protein NtrC [Brucella abortus S19]
 gi|254689343|ref|ZP_05152597.1| nitrogen regulation protein NtrC [Brucella abortus bv. 6 str. 870]
 gi|254697476|ref|ZP_05159304.1| nitrogen regulation protein NtrC [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254701860|ref|ZP_05163688.1| nitrogen regulation protein NtrC [Brucella suis bv. 5 str. 513]
 gi|254704406|ref|ZP_05166234.1| nitrogen regulation protein NtrC [Brucella suis bv. 3 str. 686]
 gi|254706698|ref|ZP_05168526.1| nitrogen regulation protein NtrC [Brucella pinnipedialis
           M163/99/10]
 gi|254710194|ref|ZP_05172005.1| nitrogen regulation protein NtrC [Brucella pinnipedialis B2/94]
 gi|254714192|ref|ZP_05176003.1| nitrogen regulation protein NtrC [Brucella ceti M644/93/1]
 gi|254717627|ref|ZP_05179438.1| nitrogen regulation protein NtrC [Brucella ceti M13/05/1]
 gi|254730373|ref|ZP_05188951.1| nitrogen regulation protein NtrC [Brucella abortus bv. 4 str. 292]
 gi|256031688|ref|ZP_05445302.1| nitrogen regulation protein NtrC [Brucella pinnipedialis M292/94/1]
 gi|256257589|ref|ZP_05463125.1| nitrogen regulation protein NtrC [Brucella abortus bv. 9 str. C68]
 gi|256369544|ref|YP_003107054.1| nitrogen regulation protein NtrC [Brucella microti CCM 4915]
 gi|260546583|ref|ZP_05822322.1| nitrogen regulation protein NtrC [Brucella abortus NCTC 8038]
 gi|260754860|ref|ZP_05867208.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           6 str. 870]
 gi|260758077|ref|ZP_05870425.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           4 str. 292]
 gi|260761901|ref|ZP_05874244.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           2 str. 86/8/59]
 gi|260883872|ref|ZP_05895486.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           9 str. C68]
 gi|261219464|ref|ZP_05933745.1| nitrogen metabolism transcriptional regulator [Brucella ceti
           M13/05/1]
 gi|261314159|ref|ZP_05953356.1| nitrogen metabolism transcriptional regulator [Brucella
           pinnipedialis M163/99/10]
 gi|261317752|ref|ZP_05956949.1| nitrogen metabolism transcriptional regulator [Brucella
           pinnipedialis B2/94]
 gi|261321960|ref|ZP_05961157.1| nitrogen metabolism transcriptional regulator [Brucella ceti
           M644/93/1]
 gi|261752423|ref|ZP_05996132.1| nitrogen metabolism transcriptional regulator [Brucella suis bv. 5
           str. 513]
 gi|261755083|ref|ZP_05998792.1| nitrogen metabolism transcriptional regulator [Brucella suis bv. 3
           str. 686]
 gi|265988783|ref|ZP_06101340.1| nitrogen metabolism transcriptional regulator [Brucella
           pinnipedialis M292/94/1]
 gi|297248431|ref|ZP_06932149.1| nitrogen regulation protein NR(I) [Brucella abortus bv. 5 str.
           B3196]
 gi|23347946|gb|AAN30037.1| nitrogen regulation protein NtrC [Brucella suis 1330]
 gi|62196163|gb|AAX74463.1| NtrC, nitrogen regulation protein NtrC [Brucella abortus bv. 1 str.
           9-941]
 gi|82616059|emb|CAJ11096.1| CbxX/CfqX superfamily:Response regulator receiver:Sigma-54 factor
           interaction domain:Helix-turn-helix, Fis-type:AAA ATPase
           [Brucella melitensis biovar Abortus 2308]
 gi|148371959|gb|ABQ61938.1| nitrogen regulation protein NR(I) [Brucella ovis ATCC 25840]
 gi|161335880|gb|ABX62185.1| nitrogen regulation protein NR(I) [Brucella canis ATCC 23365]
 gi|189019843|gb|ACD72565.1| nitrogen regulation protein NtrC [Brucella abortus S19]
 gi|255999706|gb|ACU48105.1| nitrogen regulation protein NtrC [Brucella microti CCM 4915]
 gi|260095633|gb|EEW79510.1| nitrogen regulation protein NtrC [Brucella abortus NCTC 8038]
 gi|260668395|gb|EEX55335.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           4 str. 292]
 gi|260672333|gb|EEX59154.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           2 str. 86/8/59]
 gi|260674968|gb|EEX61789.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           6 str. 870]
 gi|260873400|gb|EEX80469.1| nitrogen metabolism transcriptional regulator [Brucella abortus bv.
           9 str. C68]
 gi|260924553|gb|EEX91121.1| nitrogen metabolism transcriptional regulator [Brucella ceti
           M13/05/1]
 gi|261294650|gb|EEX98146.1| nitrogen metabolism transcriptional regulator [Brucella ceti
           M644/93/1]
 gi|261296975|gb|EEY00472.1| nitrogen metabolism transcriptional regulator [Brucella
           pinnipedialis B2/94]
 gi|261303185|gb|EEY06682.1| nitrogen metabolism transcriptional regulator [Brucella
           pinnipedialis M163/99/10]
 gi|261742176|gb|EEY30102.1| nitrogen metabolism transcriptional regulator [Brucella suis bv. 5
           str. 513]
 gi|261744836|gb|EEY32762.1| nitrogen metabolism transcriptional regulator [Brucella suis bv. 3
           str. 686]
 gi|264660980|gb|EEZ31241.1| nitrogen metabolism transcriptional regulator [Brucella
           pinnipedialis M292/94/1]
 gi|297175600|gb|EFH34947.1| nitrogen regulation protein NR(I) [Brucella abortus bv. 5 str.
           B3196]
          Length = 491

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 133/490 (27%), Positives = 237/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF +    +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKR--AAEEGLPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|225852618|ref|YP_002732851.1| nitrogen regulation protein NR(I) [Brucella melitensis ATCC 23457]
 gi|256113673|ref|ZP_05454484.1| nitrogen regulation protein NR(I) [Brucella melitensis bv. 3 str.
           Ether]
 gi|256263890|ref|ZP_05466422.1| nitrogen regulation protein NtrC [Brucella melitensis bv. 2 str.
           63/9]
 gi|265995034|ref|ZP_06107591.1| nitrogen metabolism transcriptional regulator [Brucella melitensis
           bv. 3 str. Ether]
 gi|225640983|gb|ACO00897.1| nitrogen regulation protein NR(I) [Brucella melitensis ATCC 23457]
 gi|262766147|gb|EEZ11936.1| nitrogen metabolism transcriptional regulator [Brucella melitensis
           bv. 3 str. Ether]
 gi|263094021|gb|EEZ17955.1| nitrogen regulation protein NtrC [Brucella melitensis bv. 2 str.
           63/9]
          Length = 491

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 133/490 (27%), Positives = 238/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF ++   +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKRA--AEEGLPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|256159844|ref|ZP_05457577.1| nitrogen regulation protein NtrC [Brucella ceti M490/95/1]
 gi|256255090|ref|ZP_05460626.1| nitrogen regulation protein NtrC [Brucella ceti B1/94]
 gi|261222284|ref|ZP_05936565.1| nitrogen metabolism transcriptional regulator [Brucella ceti B1/94]
 gi|265998248|ref|ZP_06110805.1| nitrogen metabolism transcriptional regulator [Brucella ceti
           M490/95/1]
 gi|260920868|gb|EEX87521.1| nitrogen metabolism transcriptional regulator [Brucella ceti B1/94]
 gi|262552716|gb|EEZ08706.1| nitrogen metabolism transcriptional regulator [Brucella ceti
           M490/95/1]
          Length = 491

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 133/490 (27%), Positives = 237/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF +    +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKR--AAEEGLPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNVQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|237815540|ref|ZP_04594537.1| nitrogen regulation protein NR(I) [Brucella abortus str. 2308 A]
 gi|237788838|gb|EEP63049.1| nitrogen regulation protein NR(I) [Brucella abortus str. 2308 A]
          Length = 528

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 131/489 (26%), Positives = 233/489 (47%), Gaps = 37/489 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 47  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 106

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 107 LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 166

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 167 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 220

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 221 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 276

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 277 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 336

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF ++   +  + +  I++  L ++ +YPW 
Sbjct: 337 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKRA--AEEGLPEKRITNAGLEMMRRYPWP 394

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+EL+N++ R         +  +     L  E  K        A     E  S    +
Sbjct: 395 GNVRELENLVRRLAALYPQEEIAPEIIETELKAELAKP---DVVAAAGGEMENISISQAV 451

Query: 416 DNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
           +   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL +
Sbjct: 452 EQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLRK 511

Query: 471 KIREYNIEV 479
           KIRE  + +
Sbjct: 512 KIRELGVNI 520


>gi|15639510|ref|NP_218960.1| response regulatory protein (atoC) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025749|ref|YP_001933521.1| response regulatory protein [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322811|gb|AAC65507.1| response regulatory protein (atoC) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018324|gb|ACD70942.1| response regulatory protein [Treponema pallidum subsp. pallidum
           SS14]
 gi|291059896|gb|ADD72631.1| acetoacetate metabolism regulatory protein AtoC [Treponema pallidum
           subsp. pallidum str. Chicago]
          Length = 458

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 133/483 (27%), Positives = 236/483 (48%), Gaps = 60/483 (12%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKENI 70
           +L++D +    + ++  +E  GY+VF      + +    K  +++I   L       E +
Sbjct: 5   ILVLDDEKNIREGLQMALEDEGYEVFTAEDGNTGVEIALKGDIDLIITDLKMPRMSGELV 64

Query: 71  LKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFF----LNLVSRKQLCD-SII 121
           L+++   +P +PII+     T ++ ++ ++   Y+ ++K      L+L+ R+ L +  +I
Sbjct: 65  LQHVHAVLPDIPIIILTGHGTVENAVEAMHKGAYDFLTKPLDLNRLSLLVRRALQNRELI 124

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              RE +   Q     + ++++  SPAM +V D+ +KA      ++I GE GVGK+ ++ 
Sbjct: 125 VQHRELI--KQIGNRTSFENIVGESPAMNKVFDMVKKAAASKASVLITGESGVGKELIAN 182

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            IH    R   P   V+C    +  +E  LFG +    T    +  G+F  A+ G++ L+
Sbjct: 183 AIHNLSPRKAKPLIKVHCASFAEGVLESELFGHERGAFTGAVNRMKGRFELAHEGSMFLD 242

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   + +AVQ ++   ++    E    R  I++DVR+I  T +NLL ++K ++FR+DLYY
Sbjct: 243 EIGEVSMAVQIKLLRVLQERSFERVGGRETIKVDVRVISATNRNLLEEIKRNLFREDLYY 302

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++V  I++  LR R ED+P L+  FL+    +N  K  SI  +A S L  Y W  N+++
Sbjct: 303 RLNVVHIHVPALRERKEDLPLLIATFLKEIAEENGKKITSIDPQAQSALHAYDWPGNIRQ 362

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI--LDNL 418
           L+N +  AVI                                       SS  +  +++L
Sbjct: 363 LRNCIESAVI--------------------------------------MSSGPVIHIEDL 384

Query: 419 SQESIPAIGQDGEVR-----RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
           S E I ++G+   +R      + D EKEII   ++  +   S+ A  LGIGR TLY K+ 
Sbjct: 385 S-EPIRSLGETSSIRIPIGVSMEDAEKEIILQTLEAQKGNKSKTADVLGIGRKTLYLKLD 443

Query: 474 EYN 476
           +Y 
Sbjct: 444 QYT 446


>gi|168264570|ref|ZP_02686543.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|205346966|gb|EDZ33597.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
          Length = 441

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 220/466 (47%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHVCS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S+               
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKAENSA--------------- 397

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
               E++ L D+EKEII  A++      +E AR+LGI R TL  K+
Sbjct: 398 ----EIQPLVDVEKEIILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|91203987|emb|CAJ71640.1| stongly similar to sigma 54 response regulator [Candidatus Kuenenia
           stuttgartiensis]
          Length = 466

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 127/427 (29%), Positives = 214/427 (50%), Gaps = 51/427 (11%)

Query: 66  DKENILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF-----LNLVSR--- 113
           D   +L N+ +  P   +IV T        I+ +    Y+ I+K F     L+++ R   
Sbjct: 65  DGLEVLSNVKEINPSTEVIVMTAFGTINSAIQAIRDGAYDYITKPFHLPDMLSVIERALE 124

Query: 114 KQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFG 173
           K+     +  L++G       EH   + +I  SP M++++++  +  +    ++I GE G
Sbjct: 125 KKRLSEKVNNLQKGT-----KEHYKFEGIIGNSPVMMRILNILAELTNSESTVLITGESG 179

Query: 174 VGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ-FLGKFIEA 232
            GK+ ++R IH +  R+  PF +VNCG + +   E   FG V      + +   G F EA
Sbjct: 180 TGKELVARSIHNNSPRSNKPFVVVNCGALPEYLQESEFFGHVMGSFTGAVKDKKGLFFEA 239

Query: 233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH 292
            GGT+ L+E     L+ Q ++  F++ G+I        + LDVR+I  T K+L    K+ 
Sbjct: 240 QGGTLFLDEIGEASLSTQVKLLRFLQNGEIRKVGDNKPVFLDVRVIVATNKDLEESTKNG 299

Query: 293 VFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI-SISDKALSLLTK 351
            FRKDL+YR++V  I++  LR R EDIP LV++F+ + C+    K+I  IS+ A+S L  
Sbjct: 300 GFRKDLFYRLNVIRIHVPPLRERKEDIPALVNYFVNA-CSHKLNKKIPEISETAMSTLLN 358

Query: 352 YPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSS 411
           Y W  N++EL+N++ RA+                LS+ G   R    + A          
Sbjct: 359 YSWYGNIRELENVIERAIT---------------LSKNG---RIMPADLA---------- 390

Query: 412 DTILDNLSQESIPAIGQDGEVR-RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
             I ++L  +SI  +   G +R  L+  E++ I  ++K +     + A  LGI  +TL+R
Sbjct: 391 --IQESLFHDSIDILHDSGGIRAALAQQERKTIVESLKKFAGNRKQAANNLGISTTTLWR 448

Query: 471 KIREYNI 477
           K++EY+I
Sbjct: 449 KMKEYHI 455


>gi|220903471|ref|YP_002478783.1| Fis family two component sigma-54 specific transcriptional
           regulator [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219867770|gb|ACL48105.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio desulfuricans subsp. desulfuricans
           str. ATCC 27774]
          Length = 457

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 125/477 (26%), Positives = 230/477 (48%), Gaps = 35/477 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           +L++D DD    +++  + S+ Y V      D  ++ + +   + +   +     +  + 
Sbjct: 5   ILVVDDDDAHRGMLRTMLRSWDYVVEEAADGDEAVALVREKAFDAVLTDVRMARMNGIHA 64

Query: 71  LKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           LK I+   P +P+I+ T     +  ++ L    Y+ + K  L+  S K      I   R 
Sbjct: 65  LKGILAYNPALPVILMTAYSSVETAVEALRLGAYDYLVKP-LDFESLKHSLQQGIERSRL 123

Query: 127 GV----VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
            V    +  Q +   A+  +I  SPA+  + ++          ++I GE G GK+ ++R 
Sbjct: 124 SVENRELRRQLSHAAAMPGIIGRSPAIRAMQEIMDTVAPTEATVLITGESGTGKELVARA 183

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEE 241
           +H    RA  P   VNC  + ++ +E  LFG      T    +  G+F +A+GGT+ L+E
Sbjct: 184 LHGKSLRADKPLVTVNCAALAENLLESELFGHEKGSFTGAERRREGRFAQAHGGTLFLDE 243

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +PL++Q ++   ++ G+++   S   + +DVR++  T ++L  +V    FR+DL++R
Sbjct: 244 VGEMPLSLQAKLLRALQQGEVQRVGSDTQLTVDVRVLAATNRDLRHEVAHRRFREDLFFR 303

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  + +  LR R+EDIP L  +FL++F ++N       S +AL ++ ++ W  NV+EL
Sbjct: 304 LNVISVEVPPLRERAEDIPVLAAYFLENFASRNRKAVRGFSAQALDIMLRHSWPGNVREL 363

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQE 421
           +N + RAVI      +T      +LS           ET         +      +LS  
Sbjct: 364 ENAVERAVILCTGDLITARELPSVLS-----------ETVAAAEA--PAEAPAEADLSLA 410

Query: 422 SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            +P          L ++E+ +I   ++      SE ARRLGI R+TL+ K+R+Y +E
Sbjct: 411 GLP----------LDEVERRVIEETLRQTGDNKSEAARRLGITRATLHNKLRKYELE 457


>gi|194442721|ref|YP_002043422.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194401384|gb|ACF61606.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
          Length = 441

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 130/466 (27%), Positives = 218/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVT 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I +  L  R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPALCQRREDIPLLAEHFLQRFAARNRKAVKGFTPQAMDLLIHYGWPGNIRELENAVE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S                
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKTEYS---------------- 396

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
              GE++ L ++EKE+I  A++      +E AR+LGI R TL  KI
Sbjct: 397 ---GEIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKI 439


>gi|296284394|ref|ZP_06862392.1| sigma-54 dependent DNA-binding response regulator [Citromicrobium
           bathyomarinum JL354]
          Length = 472

 Score =  171 bits (432), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 137/497 (27%), Positives = 221/497 (44%), Gaps = 56/497 (11%)

Query: 8   DRHKRVL-IIDKDDEQIKIIKDHVESYGYDVFIVN-----VSDLSTISKIQVNVIFLSLI 61
           D  +R+L +ID +  Q +++       G+   +VN     ++ L T   +Q++ I L   
Sbjct: 3   DHEERLLMLIDDEPAQSRLVTALAARDGWRTLVVNDAETAIATLGTRQGMQLSAIILDQW 62

Query: 62  NCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSII 121
              D   +++  +  + P +PI++ TT  +  +    +    + + +  V+ ++L  ++ 
Sbjct: 63  VPGDAACDLIAELKKRRPALPILMLTTSASPLLAVEAMRAGATDYLIKPVAPERLMRALR 122

Query: 122 CALREGVVPSQENEHCAL----------DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGE 171
            A R   V +  NE   L          D++I   P     +  A KA      ++I+GE
Sbjct: 123 SATR---VEASRNELQPLTEKMPAVLDFDAMIGTDPIFRIALARAAKAARSHGHVLIEGE 179

Query: 172 FGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE 231
            G GK+ L R I  +  R+  PF +VN   +  + IE  LFG           F G F  
Sbjct: 180 SGTGKEMLLRAIQATSPRSKAPFRLVNVAGVPVNSIESALFG------HEKGAFAGAFES 233

Query: 232 ANG-------GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN 284
             G       GT+VL+E D L    Q R+   +  G +    +    R+D RL+  + + 
Sbjct: 234 QMGALQHCDTGTLVLDEIDRLSADQQARLATTLNEGIVRPIGATHGFRIDTRLLSASNRP 293

Query: 285 LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK 344
           L        F +DL   IS   I++  LR R  DI  L   FL     +  ++ +S++D 
Sbjct: 294 LSELAAKGQFDQDLLAAISATRISLPPLRERPGDIASLARHFLARIGDEPGLRHLSLADS 353

Query: 345 ALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFH---TETA 401
           AL+LL  Y W  NV++L+ +L RA +      LT   F  L    G++    H       
Sbjct: 354 ALNLLCAYDWPGNVRQLQAVLFRAAVFCDAEMLTSSDFPQLSELIGEQAGSGHHVQEAVG 413

Query: 402 CTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRL 461
              YT+                     DG +R L +IE ++I LA+  YR +M+EVARRL
Sbjct: 414 VMLYTD---------------------DGNLRPLEEIEADVIRLAIGHYRGRMTEVARRL 452

Query: 462 GIGRSTLYRKIREYNIE 478
           GIGRSTLYRK+ +  I+
Sbjct: 453 GIGRSTLYRKLSDLGID 469


>gi|289627782|ref|ZP_06460736.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
 gi|289651627|ref|ZP_06482970.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. aesculi str. 2250]
 gi|330866442|gb|EGH01151.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 471

 Score =  171 bits (432), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 134/475 (28%), Positives = 224/475 (47%), Gaps = 19/475 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTIS-KIQVNVIFLSLINCED-DKENI 70
           VL+++ D    + + + +E  GY    V  +  + ++ + Q   + +S +N    D   +
Sbjct: 5   VLLVEDDRSLREALGETLELAGYGYQAVGSAKEALVAAEAQPFSLVISDVNMPGMDGHQL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           L  +  + P +P+++ T    +      +    + + +     K L   I    R  +  
Sbjct: 65  LSLLRSRHPQLPVLLMTAHGAVDRAVDAMRQGAADYLVKPFEPKAL---IALVARHALGR 121

Query: 131 SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
            +  E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  RA
Sbjct: 122 LEPAER---DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPRA 178

Query: 191 FFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAV 249
             PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL +
Sbjct: 179 DKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLGL 238

Query: 250 QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINI 309
           Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF +  
Sbjct: 239 QAKLLRVLQEREVERVGARKPIILDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLAW 298

Query: 310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
             LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA+
Sbjct: 299 QALRQRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVSYPWPGNVRELDNAVQRAL 358

Query: 370 IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQD 429
           I  +   +    F   LS             A        S D      + ES+ A+G D
Sbjct: 359 ILQQGGVIQAQDFC--LSGPVTSLPAAAVVEAVPSLPVTSSPDNAGAGANAESVGALGDD 416

Query: 430 GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
             +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 417 --LRRR---EFQMIIDTLRAERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 466


>gi|154253569|ref|YP_001414393.1| nitrogen metabolism transcriptional regulator NtrC [Parvibaculum
           lavamentivorans DS-1]
 gi|154157519|gb|ABS64736.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Parvibaculum lavamentivorans DS-1]
          Length = 480

 Score =  170 bits (431), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 132/484 (27%), Positives = 232/484 (47%), Gaps = 31/484 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY+V    N + L   +S+ + ++I   ++  +++  ++
Sbjct: 6   ILLADDDAAIRTVLNQALGRVGYEVRSTGNAATLWRWVSQGEGDLIITDVVMPDENAFDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKIL----NCFLYNRISKFF-LNLVSRKQLCDSIICALR 125
           +  I    P +PI+V + Q+ +K          Y  + K F LN + R  + D  + A R
Sbjct: 66  IPRIKRARPDLPIVVMSAQNTLKTAIMAAERGAYEYLPKPFDLNELIR--VVDRAMTAPR 123

Query: 126 EGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
           E  +  Q+ E      LI  SPAM  +  +  +     + +MI GE G GK+ ++R +H+
Sbjct: 124 EPAIGRQQPEEGEKIPLIGRSPAMQDIYRVLARLMQTDLTVMISGESGTGKELVARALHD 183

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
            G+R   PF  VN   I ++ IE  LFG +    T  S +  G+F +A GGT+ L+E   
Sbjct: 184 YGRRRNGPFVAVNMAAIPRELIESELFGHEKGAFTGASQRATGRFEQAEGGTLFLDEIGD 243

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+DL++R++V
Sbjct: 244 MPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIVAATNRDLRQLINQGLFREDLFFRLNV 303

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I +  LR R+EDI  L+  FL        +   +I  + + LL +Y W  NV+EL+N+
Sbjct: 304 VPIRLPPLRERTEDISDLIRHFLGQ-AEDEGLPPKNIDSEGMELLKRYRWPGNVRELENL 362

Query: 365 LLR-------AVIGLK--DSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
           + R         IG    ++ L E  F       GK   +   +       E ++ + I 
Sbjct: 363 VRRLAALYTEETIGASILETELAEPDF-------GKPSEQPSMDEPLAQSVE-RTLNRIF 414

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
                +  P    D   R L ++E+ +  +++   R    + A  LGI R+TL +KIRE 
Sbjct: 415 SGHGDDLPPPGLYD---RLLKEVERPLFSMSLAATRGNQIKAAHLLGINRNTLRKKIREL 471

Query: 476 NIEV 479
           +I+V
Sbjct: 472 DIQV 475


>gi|166710190|ref|ZP_02241397.1| two-component system regulatory protein [Xanthomonas oryzae pv.
           oryzicola BLS256]
          Length = 448

 Score =  170 bits (431), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 130/481 (27%), Positives = 226/481 (46%), Gaps = 52/481 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSD-LSTISKIQVNVIFLSLINCEDDKENI 70
           +LIID D      ++  + S+G+ V    N  D L+ +S+  +++ F+       D   +
Sbjct: 4   ILIIDDDAAFRTTLQATLRSFGHTVVAADNGPDGLARLSEGGIDMAFVDFRMPGMDGIAV 63

Query: 71  LKNIVD-----KIPIVPIIVQTTQDN-IKILNCFLYNRISKF-----FLNLVSRKQL--C 117
           L+  +D     ++P+V +    +  N I+ +    ++ + K       + +V R  L   
Sbjct: 64  LRARLDDAQARQVPLVMLTAHVSSGNTIEAMTLGAFDHLVKPVGRADIVEVVERALLSRA 123

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
           D+   A      P +++     D+L+  SPAM  V      A    +P++I GE G GK+
Sbjct: 124 DAQAAATETPQAPHEDD-----DALVGHSPAMRTVHKHIGLAAASDLPVLITGETGTGKE 178

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGT 236
             +R +H +  RA  PF  VNC  I  + +E  LFG      +  S+  LG   EA+GGT
Sbjct: 179 LAARALHRASPRAEAPFVAVNCAAIPLELMESELFGHRKGAFSGASSDRLGLIREADGGT 238

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +PL +Q ++  F++ G++      G+ ++DVR++  T ++L   V    FR 
Sbjct: 239 LFLDEIGDMPLPMQAKLLRFLQEGEVTPLGGSGSQKVDVRVLAATHRDLAACVADGRFRS 298

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DL YR++V  I +  LR R +DI  L     Q F + NA +  S+S  A   L  + W  
Sbjct: 299 DLRYRLNVVPIELPPLRERGQDILLLA----QHFLSTNAARAQSLSPAAQERLLAHRWPG 354

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           NV+EL+N++ R+ + ++ + +        L+  G+           T       + T+ +
Sbjct: 355 NVRELRNVMQRSQVMVRGASIDAADLDEALAEAGE----------ATADVASAMTGTLPE 404

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
            L++                 +EK++I  A++      +E ARRLGI R  LYRK+ EY 
Sbjct: 405 ALAR-----------------LEKQMIQSALEQSHGNRAEAARRLGIHRQLLYRKLEEYG 447

Query: 477 I 477
           +
Sbjct: 448 L 448


>gi|330995075|ref|ZP_08318992.1| Sigma-54 interaction domain protein [Paraprevotella xylaniphila YIT
           11841]
 gi|329576651|gb|EGG58154.1| Sigma-54 interaction domain protein [Paraprevotella xylaniphila YIT
           11841]
          Length = 449

 Score =  170 bits (430), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 139/491 (28%), Positives = 237/491 (48%), Gaps = 70/491 (14%)

Query: 13  VLIIDKDDEQI--KIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKE 68
           +LIID  DE I  K++   +E  GY+VF      S +  ++     ++   +   + +  
Sbjct: 5   ILIID--DEPIIRKLLARMMELEGYEVFQAADRASGMKQLTAKMPQLVLCDVFLPDGNGV 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNI----KILNCFLYNRISKF-----FLNLVSR--KQLC 117
            ++K I +  P   +I+ T   NI    + +    ++ I+K       + ++SR  +++ 
Sbjct: 63  EMVKEIKELQPEAEVILLTAHGNIPDGVQAIKNGAFDYITKGDDNNKIIPIISRAMEKIN 122

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              +      VVP +E+   A D+++  S  + QV+ LARK     +P+++ GE G GK+
Sbjct: 123 RRPVQPSGSAVVPVRES---AFDTVLGHSRGLQQVIRLARKVAVTDVPVLLTGETGTGKE 179

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGK-------FI 230
             ++ IH    RA  PF  +NC    ++ +E  +FG        +  F G        F 
Sbjct: 180 VFAQAIHHGSARAKQPFVAINCSAFSKELLESEIFG------HKAGAFTGALKDKKGLFE 233

Query: 231 EANGGTIVLEEPDALPLAVQGRIYNFIETGK-IEFFDSRGAIRLDVRLIFLTEKNLLPQV 289
           EAN GTI L+E   +   +Q ++   +ETG+ I+  D++   ++DVR++  T +NL  ++
Sbjct: 234 EANHGTIFLDEIGEMAYGLQAKLLRVLETGEYIKVGDTK-PTKIDVRIVSATNRNLKEEI 292

Query: 290 KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALS-L 348
           ++  FR+DLY+R+SVF +++  LR R EDIP L   FL+ F  K   KQ+   D A    
Sbjct: 293 ENSNFREDLYFRLSVFHLHLPPLRERREDIPELATAFLKLFSAKMG-KQVKGFDAACQDW 351

Query: 349 LTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEG 408
           +  Y W  NV+EL+N++ RA+I + D ++T D   L          +F + T        
Sbjct: 352 MQSYAWPGNVRELRNVIERALI-ICDDYITLDDMPL----------DFRSST-------- 392

Query: 409 KSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
                         +     DG+   L++ E   I   ++  +   +E AR L IG +TL
Sbjct: 393 --------------LSGSAADGDDFELAEAEHRHIQRVLQYTKGNKAEAARLLKIGLTTL 438

Query: 469 YRKIREYNIEV 479
           YRKI EY I +
Sbjct: 439 YRKIEEYGINI 449


>gi|86158661|ref|YP_465446.1| two component sigma54 specific Fis family transcriptional regulator
           [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85775172|gb|ABC82009.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 466

 Score =  170 bits (430), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 131/481 (27%), Positives = 219/481 (45%), Gaps = 42/481 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYD-VFIVNVSD-LSTISKIQVNVIFLSLINCEDDKEN 69
           RVL++D +      +K+ V+  G++ V   + S+ L  + +  V V   S+   E D   
Sbjct: 3   RVLLVDDEPSVRAALKELVQGRGWEPVLACSASEALEQLERADVLVTDFSM--PEMDGLA 60

Query: 70  ILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           +L+ + ++   +P+I+ T   +    ++ +    Y  + K F       +L  +I  AL 
Sbjct: 61  LLQAVRERDEWLPVILLTAHGSERLAVRAMKAGAYEYVPKPF----DVDELALAIGRAL- 115

Query: 126 EGVVPSQEN-----EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
           E  +  Q N     EH     L+  S  M QV+    +     I ++++GE G GK+ + 
Sbjct: 116 EARLLRQRNRQLTVEHAIGRRLVFESANMRQVLAATARVAAREITVLVRGETGTGKELIG 175

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEANGGTIVL 239
             +H   KRA  P    NC  I  +  E  LFG V      + Q   G F +A+GGT+VL
Sbjct: 176 TLLHALSKRAAGPLVRFNCSAIPAELAEAELFGHVRGAFTGAVQARPGFFAQADGGTLVL 235

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++ G+I+   S    R+DVR++  T ++L   V+   FR+DLY
Sbjct: 236 DEVGELPLGIQAKLLRTLQEGEIQPVGSGRVERVDVRIVACTHRDLRADVQEGRFREDLY 295

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R EDIP L H F   +  +   + + ++   +  L K  W  NV+
Sbjct: 296 YRLAVVELTVPPLRDRREDIPALAHEFALRYAERFGSEDVRLAPALVERLVKADWPGNVR 355

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N++ R V       +  D F      E                +EG+ + T+   L 
Sbjct: 356 QLENVVARMVALSGGGEIGPDAF------EATGAPAGGAGRPAAPPSEGEGTRTLRAQLD 409

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           +                 +E+ +I   M   R   SE ARRLGI R+TL  ++R Y +  
Sbjct: 410 E-----------------LERAVIARTMVAVRGNQSEAARRLGISRNTLTERLRRYELVT 452

Query: 480 D 480
           D
Sbjct: 453 D 453


>gi|311281441|ref|YP_003943672.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Enterobacter cloacae SCF1]
 gi|308750636|gb|ADO50388.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Enterobacter cloacae SCF1]
          Length = 440

 Score =  170 bits (430), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 127/454 (27%), Positives = 219/454 (48%), Gaps = 40/454 (8%)

Query: 25  IIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVP 82
           I++  +  +GY V I N     L  + +   +V+   +   E D  + LK I    P +P
Sbjct: 19  ILQALLRGWGYQVAIANSGKEALRQVREHVFDVVLCDVRMAEMDGIDTLKEIKALNPAIP 78

Query: 83  IIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQENE--HCALD 140
           +++ T   +++     + +    + +  +   +L +++  AL     P  E      A  
Sbjct: 79  VLIMTAFSSVETAVEAIKSGALDYLIKPLDFDRLQETLAQALAHTREPEGEPSPVSAAQC 138

Query: 141 SLIAVSPAMIQVV-DLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNC 199
            ++  SPAM  ++ D+A  A   A  ++I G+ G GK+ ++R +H S  R   P   +NC
Sbjct: 139 GMVGRSPAMQHLLNDIAMVAPSDAT-VLIHGDSGTGKELVARALHASSARGEKPLVTLNC 197

Query: 200 GMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIE 258
             +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   +   +Q R+   I+
Sbjct: 198 AALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRVIQ 257

Query: 259 TGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSED 318
             +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V  I + +LR R ED
Sbjct: 258 EREVQRVGSNQTISVDVRLIAATHRDLAQEVSAGRFRQDLYYRLNVVTIEMPSLRQRRED 317

Query: 319 IPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLT 378
           IP L   FLQ +  +N       + +A+ LL  Y W  N++EL+N + RAV+        
Sbjct: 318 IPLLAEHFLQRYAGRNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIERAVV-------- 369

Query: 379 EDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDI 438
                 LL+ E   ERE     A T                 +++P    + ++  L ++
Sbjct: 370 ------LLTGEFITERELPLAIAATPI---------------KALP----EHDILPLVEV 404

Query: 439 EKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
           EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 405 EKEVIQAALEKTGGNKTEAARQLGITRKTLLAKL 438


>gi|322419347|ref|YP_004198570.1| Fis family two component sigma54 specific transcriptional regulator
           [Geobacter sp. M18]
 gi|320125734|gb|ADW13294.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. M18]
          Length = 460

 Score =  170 bits (430), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 139/494 (28%), Positives = 229/494 (46%), Gaps = 62/494 (12%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
           K++LII+ +      +   +E+ GY V      D  +  I K + +V+   +     D  
Sbjct: 2   KKILIIEDELSMRLGLAYTLEAAGYAVTAAERGDEGIDLIGKQRFDVVVTDMRLPGADGL 61

Query: 69  NILKNIVDKIPIVPIIVQT----TQDNIKILNCFLYNRISKFF-----LNLVSRKQLCDS 119
            +LK +    P   ++V T     Q  ++ +    ++ I+K F     L+LV R  LC +
Sbjct: 62  EVLKAVRKAQPDTGVVVITGYADVQTAVEAMKLGAFDYIAKPFEPAHLLSLVERF-LCQT 120

Query: 120 IICA----LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
                   LRE V      EH   + +++ SP+M+ V +L + A      ++I GE G G
Sbjct: 121 AHVEDSQRLREEVA-----EHQRFEEIVSNSPSMLSVFNLIQMAAKTDSSVIIYGESGTG 175

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANG 234
           K+ ++  +H    R   PF  VNC  I ++ +E  + G +    T    +  GK   A+G
Sbjct: 176 KELVANAVHNRSPRLDKPFIKVNCAAIPENLLEAEMCGYEKGAFTGALQRKKGKLETADG 235

Query: 235 GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF 294
           GT   +E   +   +Q ++   +ET   E       + +D+R IF T + L  +++   F
Sbjct: 236 GTFFFDEIGDMSFPLQAKLLRVLETRSFERVGGTEPVHVDIRFIFATMRRLPDEIRKGKF 295

Query: 295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW 354
           R+DLYYRI+V  I +  LR R++DIP L+HFF+  FC K   + + I+ +A+ LL  YP+
Sbjct: 296 REDLYYRINVLPITLPPLRERADDIPLLLHFFVAHFCRKQGRQVLDIAPEAMELLRSYPY 355

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
             NV+ELK+ +  AV    D  +T                        +C          
Sbjct: 356 PGNVRELKHAVEMAVTFCSDRVITP-----------------------SC---------- 382

Query: 415 LDNLSQESIPAI-GQDGEVRRLSDIEKE-----IIGLAMKLYRAQMSEVARRLGIGRSTL 468
           L    +E  PA+ G  G+   L    KE     II +  K    +M+  A+ LGI R TL
Sbjct: 383 LPGEIREGSPALQGWRGDAGALESSRKETERQTIINVLKKTGGRKMA-AAKALGISRETL 441

Query: 469 YRKIREYNIEVDSL 482
           +RK++EYN++ D++
Sbjct: 442 WRKLKEYNVDTDAI 455


>gi|307942247|ref|ZP_07657598.1| nitrogen regulation protein [Roseibium sp. TrichSKD4]
 gi|307774533|gb|EFO33743.1| nitrogen regulation protein [Roseibium sp. TrichSKD4]
          Length = 479

 Score =  169 bits (429), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 136/489 (27%), Positives = 234/489 (47%), Gaps = 42/489 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY V +  N + L   +S    +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYTVRVTSNATTLWRWVSSGDGDLVITDVVMPDENIFDV 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  +    P +PI+V + Q+     IK      Y+ + K F      K++ + +  AL E
Sbjct: 66  LPRMKKARPDLPILVMSAQNTFMTAIKASEKGAYDYLPKPF----DLKEMINIVGRALEE 121

Query: 127 GVVPSQENEHCALD-----SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              P     H A D      L+  SPAM ++  +  +     + +MI GE G GK+ ++R
Sbjct: 122 ---PKASRPHVAEDLGEHMPLVGRSPAMQEIYRVLARLMQTDLTVMINGESGTGKELVAR 178

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H+ GKR   PF  +N   I +D IE  LFG +    T    +  G+F +A GGT+ L+
Sbjct: 179 ALHDYGKRRNGPFVAINMAAIPKDLIEAELFGHEKGAFTGAQHRSTGRFEQAEGGTLFLD 238

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +P+  Q R+   ++ G+      R  ++ DVR++  T K+L   +   +FR+DLY+
Sbjct: 239 EIGDMPMEAQTRLLRVLQQGEYTTVGGRTPLKTDVRIVAATNKDLRHLINQGLFREDLYF 298

Query: 301 RISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           R++V  I +  LR R +DIP LV HFF  S   +  +    I   AL+LL +Y W  N++
Sbjct: 299 RLNVVPIRLPPLRERVDDIPDLVRHFF--SLAEQEGLPPKQIDQAALALLRRYRWPGNIR 356

Query: 360 ELKNILLRA-------VIG--LKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKS 410
           EL+N++ R        VIG  L +  L++  F   +   G+         A   Y  G  
Sbjct: 357 ELENLIRRLAALYPQDVIGEALLEHELSQPEFSETVDDLGQVT---DLRGAVERYLGGYF 413

Query: 411 SDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
           ++        E++P  G    +  L D+E  +I  A+   R    + A  LG+ R+TL +
Sbjct: 414 ANF------GEALPPPGLYHRI--LRDVEHPLISAALTATRGNQIKAAELLGVNRNTLRK 465

Query: 471 KIREYNIEV 479
           KIR+ +++V
Sbjct: 466 KIRDLDVQV 474


>gi|256830705|ref|YP_003159433.1| Fis family two component sigma5-4 specific transcriptional
           regulator [Desulfomicrobium baculatum DSM 4028]
 gi|256579881|gb|ACU91017.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfomicrobium baculatum DSM 4028]
          Length = 451

 Score =  169 bits (429), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 129/478 (26%), Positives = 229/478 (47%), Gaps = 49/478 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           +LI+D D     +++  +  +G+    +   +  +S   +   ++I + +          
Sbjct: 8   ILIVDDDSGHRGMLRTLLADWGFVPHEIESGEAAVSLCRERAFDLILMDVRMAGISGIEA 67

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQLCDSII--CAL 124
           LK I    P +PI++ T   N++     +    Y+ ++K  L+    +   D  +   AL
Sbjct: 68  LKEIKAYNPAIPILIMTAYSNVETAVEAIKAGAYDYLTKP-LDFDDLRLTLDRALDHAAL 126

Query: 125 REGVVPSQENEHCALDS--LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
           R+     ++    + DS  +I  SPAM +++D+          IM+ GE G GK+ ++R 
Sbjct: 127 RDENKALRQTLSASFDSGGIIGQSPAMHRLMDMLATIAPSEATIMVTGESGTGKELIARA 186

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           +H +  R   P+  VNC  + +  +E  LFG +    T    +  G+F+ A+ GTI L+E
Sbjct: 187 VHANSPRRKGPYVAVNCAALTETLLESELFGHEKGAFTGADRRREGRFLAADKGTIFLDE 246

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +PL++Q ++   I+  +I+       I++DVR++  T ++LL +V++  FR+DLYYR
Sbjct: 247 IGEMPLSMQVKLLRVIQEREIQRVGGDQTIKVDVRIVAATNRDLLAEVEAGRFRQDLYYR 306

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  + +  LR R EDIP L   FL  F  KN  +    + +A+  L K+ W  NV+EL
Sbjct: 307 LNVVALALPPLREREEDIPLLASHFLTGFAVKNGKRIKGFTPEAMDRLLKHQWPGNVREL 366

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLS---REGKKEREFHTETACTCYTEGKSSDTILDNL 418
           +N + RAV+  +  +++E      LS    EG+ E  F                    NL
Sbjct: 367 ENAVERAVVLARGEYVSERELPPALSGGAGEGRPEGGFA-------------------NL 407

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
           + E         E+ RL+ ++      A++      SE ARRLGI R T++ K+ +Y 
Sbjct: 408 TLE---------ELERLAILD------ALEAAGGNKSEAARRLGITRKTMHAKLAKYG 450


>gi|197122042|ref|YP_002133993.1| Fis family transcriptional regulator [Anaeromyxobacter sp. K]
 gi|196171891|gb|ACG72864.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter sp. K]
          Length = 463

 Score =  169 bits (429), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 128/478 (26%), Positives = 219/478 (45%), Gaps = 45/478 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYD-VFIVNVSD-LSTISKIQVNVIFLSLINCEDDKEN 69
           RVL++D +      +K+ V+  G++ V   + S+ L  + +  V V   S+   E D   
Sbjct: 3   RVLLVDDEPSVRAALKELVQGRGWEPVLACSASEALEQLERADVLVTDFSM--PEMDGLA 60

Query: 70  ILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           +L+ + ++   +P+I+ T   +    ++ +    Y  + K F       +L  +I  AL 
Sbjct: 61  LLQAVRERDEWLPVILLTAHGSERLAVRAMKAGAYEYVPKPF----DVDELALAIGRAL- 115

Query: 126 EGVVPSQEN-----EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
           E  +  Q N     EH     L+  S  M QV+    +     I ++++GE G GK+ + 
Sbjct: 116 EARILRQRNRQLTVEHAIGRRLVFESANMRQVLAATARVAAREITVLVRGETGTGKELVG 175

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEANGGTIVL 239
             +H   KRA  P    NC  I  D  E  LFG V      + Q   G F +A+GGT+VL
Sbjct: 176 TLLHALSKRAAGPLVRFNCSAIPADLAEAELFGHVRGAFTGAVQARPGFFAQADGGTLVL 235

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++ G+I+   S    R+DVR++  T ++L   V++  FR+DLY
Sbjct: 236 DEIGELPLGIQAKLLRALQEGEIQPVGSGRVERVDVRIVACTHRDLRADVQAGRFREDLY 295

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R EDIP L H F   +  +   + + ++   +  L +  W  NV+
Sbjct: 296 YRLAVVELTVPPLRDRREDIPALAHEFALRYAERFGSEDVRLAPALIERLVEADWPGNVR 355

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N++ R V       +  D F         +      +        G+ + T+ + L 
Sbjct: 356 QLENVVARMVALSGGGEIGPDAF---------EATSVPADRPAAIARGGEETRTLREQLD 406

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           +                 +E+ +I   M   R   SE ARRLGI R+TL  ++R Y +
Sbjct: 407 E-----------------LERAVIARTMAAVRGNQSEAARRLGISRNTLTERLRRYEL 447


>gi|119505578|ref|ZP_01627649.1| two-component response regulator PilR [marine gamma proteobacterium
           HTCC2080]
 gi|119458521|gb|EAW39625.1| two-component response regulator PilR [marine gamma proteobacterium
           HTCC2080]
          Length = 463

 Score =  169 bits (429), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 122/413 (29%), Positives = 208/413 (50%), Gaps = 17/413 (4%)

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
            +++++ +  P VP+ + T   +++     L      F    ++ ++L + +  AL+   
Sbjct: 64  TLIEHMQNDYPDVPVAMITAHGSVESAIEALKLGAFDFVTKPLALEKLRELVAHALK--T 121

Query: 129 VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK 188
            P+  N     ++L+  +PAM ++ D  RK      P+ I GE G GK+ ++R IH+SG 
Sbjct: 122 TPA--NTDVTKETLVGETPAMGKLRDQIRKVARSQAPVHIHGESGTGKEVVARLIHQSGP 179

Query: 189 RAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPL 247
           R   PF  VNCG I  D +E  LFG      T   +   G F+ ANGGT++L+E   LPL
Sbjct: 180 RQDQPFIAVNCGAIPADLVESELFGHKKGAFTGAVSDKSGLFLAANGGTLLLDEVADLPL 239

Query: 248 AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLI 307
            +Q ++   I+   +    S   I +D+RL+  T KNL  +V++  FR DLYYRI+V  +
Sbjct: 240 PMQVKLLRVIQEKSVRPVGSETEIPIDIRLLSATHKNLAQEVQNRTFRDDLYYRINVIGL 299

Query: 308 NISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLR 367
            +  LR R +DIP LV   L       ++   +++D ALS L    +  N++EL+NIL R
Sbjct: 300 QVPALRERLDDIPVLVTHILMKIAEDQSVPARTLTDGALSQLMSQKFPGNIRELENILAR 359

Query: 368 AVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIG 427
           A      S LTE   + +       +++    TA     E  ++   L+  S   I  + 
Sbjct: 360 A------SALTETGHIDIDD----LDQQQDVSTADYAVPEAPAAPNQLEGESTAPITLLE 409

Query: 428 Q-DGEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
           + +G++   L+  E++I+  A+  +R   +  AR LGI   +L  ++++  +E
Sbjct: 410 EVNGDLETYLASRERQILTEALTAHRWNRTSAARSLGISFRSLRYRLKKLGLE 462


>gi|255038581|ref|YP_003089202.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Dyadobacter fermentans DSM 18053]
 gi|254951337|gb|ACT96037.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Dyadobacter fermentans DSM 18053]
          Length = 456

 Score =  169 bits (429), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 134/484 (27%), Positives = 219/484 (45%), Gaps = 65/484 (13%)

Query: 7   LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDD 66
           L RH + + I+K+ +++  +   V +  Y++ +++++             F   +N   +
Sbjct: 25  LKRHAKAVDIEKNPQKLPFL---VTNGDYNLILLDMN-------------FTRDVNSGRE 68

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
             + L  I+D  P   +I+ T   +I++    +      F L      +L  +I  AL  
Sbjct: 69  GFHWLDRILDINPAAKVIMITAYGDIEMAIRAIKAGAIDFVLKPWENDKLLATIATALEG 128

Query: 127 G---VVPSQE---------NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGV 174
           G   V P  E         N   A D+++A S +M QV+  A +       ++I GE G 
Sbjct: 129 GKDKVAPVAEEKTKDDPKKNSKAAADTIVATSDSMRQVLLTAERVASTDANVLILGENGT 188

Query: 175 GKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEAN 233
           GK +L+R +H+  KRA  PF  V+ G I +   E  LFG V    T       G+F EA 
Sbjct: 189 GKTQLARHVHQHSKRADKPFVAVDLGAISETLFESELFGHVKGAFTDAKEDRAGRFEEAK 248

Query: 234 GGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHV 293
           GGTI L+E   L L +Q ++   I+  K+    S   I LDVRLI  T  N+   V    
Sbjct: 249 GGTIFLDEIGNLTLPLQAKLLTVIQERKVTRVGSNKPIALDVRLICATNMNIEKMVTDKT 308

Query: 294 FRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP 353
           FR+DL YRI+   + +  LR R EDI  L  ++L+ +  K       IS+  +  + +Y 
Sbjct: 309 FRQDLLYRINTIELELPPLRDRPEDISALADYYLKQYAKKYNRPVNDISNALVKKMQQYN 368

Query: 354 WIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDT 413
           W  N++EL++ + RAVI  ++  L  D                               D 
Sbjct: 369 WPGNIRELQHAVERAVILSQEKTLQPD-------------------------------DL 397

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
            L + + +   A G D     L D+EK +I  A+K +   +++ AR LG+ R+ LYR++ 
Sbjct: 398 FLKSSAGQPATATGFD-----LEDMEKTMIIKALKRFNGNITDAARELGLSRAALYRRME 452

Query: 474 EYNI 477
           +Y +
Sbjct: 453 KYGL 456


>gi|66046688|ref|YP_236529.1| helix-turn-helix, Fis-type [Pseudomonas syringae pv. syringae
           B728a]
 gi|63257395|gb|AAY38491.1| Helix-turn-helix, Fis-type [Pseudomonas syringae pv. syringae
           B728a]
          Length = 471

 Score =  169 bits (429), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 134/478 (28%), Positives = 226/478 (47%), Gaps = 25/478 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNV-IFLSLINCED-DKENI 70
           VL+++ D    + + + +E  GYD   V  ++ + ++       + +S +N    D   +
Sbjct: 5   VLLVEDDRSLREALGETLELAGYDYKAVGSAEEALVAAEATPFSLVISDVNMPGMDGHQL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           L  +  + P +P+++ T    ++     +    + + +     K L   I    R  +  
Sbjct: 65  LSLLRSRHPQLPVLLMTAHGAVERAVDAMRQGAADYLVKPFEPKAL---IALVARHALGR 121

Query: 131 SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
            +  E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  RA
Sbjct: 122 LEPAER---DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPRA 178

Query: 191 FFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAV 249
             PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL +
Sbjct: 179 DKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLGL 238

Query: 250 QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINI 309
           Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF +  
Sbjct: 239 QAKLLRVLQEREVERVGARKPIVLDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLAW 298

Query: 310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
             LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA+
Sbjct: 299 QALRQRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVSYPWPGNVRELDNAVQRAL 358

Query: 370 IGLKDSHLTEDRFVL---LLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           I  +   +    F L   + S       E       T   E   +      +S ES+ A+
Sbjct: 359 ILQQGGVIQAQDFCLSGPVTSLPVAASVEAAVAVTGTTVAENAGA-----GVSPESVGAL 413

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           G D     L   E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 414 GDD-----LRRHEFQMIIDTLRSERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 466


>gi|154248319|ref|YP_001419277.1| nitrogen metabolism transcriptional regulator, NtrC, Fis family
           [Xanthobacter autotrophicus Py2]
 gi|154162404|gb|ABS69620.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Xanthobacter autotrophicus Py2]
          Length = 482

 Score =  169 bits (429), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 133/485 (27%), Positives = 229/485 (47%), Gaps = 33/485 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY+V    N + L   +S+   +++   ++  +++  ++
Sbjct: 8   ILVADDDAAIRTVLNQALSRAGYEVRSCGNAATLWRWVSQGDGDLVITDVVMPDENAFDL 67

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P+IV + Q+     I+      Y  + K F +L     +    +   ++
Sbjct: 68  LPRIKKARPDLPVIVMSAQNTFMTAIRASERGAYEYLPKPF-DLKELISIVGRALAEPKK 126

Query: 127 GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES 186
           G      +E      L+  SPAM ++  L  +     + +MI GE G GK+ ++R +H+ 
Sbjct: 127 GDGHHHSHEEQDNIPLVGRSPAMQEIYRLLARLMQTDLTVMIAGESGTGKELVARALHDY 186

Query: 187 GKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDAL 245
           GKR   PF  +N   I +D IE  LFG      T  + +  G+F +A GGT+ L+E   +
Sbjct: 187 GKRRTGPFVAINMAAIPRDLIESELFGHEKGSFTGATTRNPGRFEQAEGGTLFLDEIGDM 246

Query: 246 PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF 305
           P+  Q R+   ++ G+      R  I+ DVR+I  T K+L   ++  +FR+DL++R++V 
Sbjct: 247 PMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIIAATNKDLRTLIQQGLFREDLFFRLNVV 306

Query: 306 LINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
            + +  LR RSED+P LV HFFLQ+       KQI  +  AL  L +Y W  NV+EL+N 
Sbjct: 307 PLRLPPLRERSEDVPDLVRHFFLQAEREGLPAKQIDTA--ALDRLKRYRWPGNVRELEN- 363

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ---- 420
           L+R +  L    +     +         E E           EG    T+  ++ +    
Sbjct: 364 LVRRLAALYPQEVITPAII---------EAELSEPMPSALSEEGPVDATLAASVERHLNT 414

Query: 421 ------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
                 E +P  G    +  L D+E  ++  A+   R    + A  LG+ R+TL +KIR+
Sbjct: 415 YFSGFGEDLPPPGLYHRI--LKDVEYPLLSAALAATRGNQIKAAELLGLNRNTLRKKIRD 472

Query: 475 YNIEV 479
            +I+V
Sbjct: 473 LDIQV 477


>gi|307718254|ref|YP_003873786.1| transcriptional regulatory protein [Spirochaeta thermophila DSM
           6192]
 gi|306531979|gb|ADN01513.1| transcriptional regulatory protein [Spirochaeta thermophila DSM
           6192]
          Length = 453

 Score =  169 bits (429), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 139/477 (29%), Positives = 220/477 (46%), Gaps = 43/477 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST--ISKIQVNVIFLSLINCEDDKENI 70
           VL+ D +    + +K  +E  GY+VF+    D +   + +  ++++   L       + +
Sbjct: 5   VLVADDEKNIREGLKTFLEMEGYEVFLAEDGDRAKKILDEEDIDLVIADLKMPGMPGDEL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFF---LNLVSRKQLCDSIICALREG 127
           L+ +V   P VP+I+ T    I+     + +    F    LNL  R  L      + RE 
Sbjct: 65  LRYVVGGYPTVPVIILTGHGTIESAVQAMRDGAFDFLTKPLNL-DRLGLLVKRALSTREL 123

Query: 128 VVPSQE-----NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
           V+  +E             LI  SP M Q+ ++ ++       ++I GE GVGK+R++  
Sbjct: 124 VLQHRELQRELERQKKFGMLIGKSPQMKQIFEVIQQVAPTRASVLITGESGVGKERIADA 183

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           IH    R   P   V+C  + +  +E  LFG +    T   A   G+F  A+GGT+ L+E
Sbjct: 184 IHYFSNRRDKPLIKVHCAALAESLLESELFGHEKGAFTGAHATRRGRFELADGGTLFLDE 243

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +  AVQ ++   ++  K E       I +DVR+I  T K+L  +V+   FR+DLYYR
Sbjct: 244 IGEISPAVQVKLLRVLQEKKFERVGGERTIEVDVRIIAATNKDLKREVEEGRFREDLYYR 303

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  I++  LR R EDIP L+  FL+    +N  K   I  KA ++L  Y W  NV+EL
Sbjct: 304 LNVVHIHVPPLRERKEDIPLLIAAFLKELAEENGKKIEGIDPKARAILYNYSWPGNVREL 363

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQE 421
           +N +  AV+  K + +  +     +  E                 EG     I       
Sbjct: 364 RNCIESAVVMCKGTIILAEDLPPQIREE----------------AEGGGLIRI------- 400

Query: 422 SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
              A+G       L + EKEII   +   +   S  A+ LGIGR TL+RKI+EY +E
Sbjct: 401 ---AVGTS-----LEEAEKEIIRATLAYCKGNKSRAAQILGIGRKTLHRKIQEYGLE 449


>gi|229588672|ref|YP_002870791.1| putative two-component system response regulator [Pseudomonas
           fluorescens SBW25]
 gi|229360538|emb|CAY47395.1| putative two-component system, response regulator [Pseudomonas
           fluorescens SBW25]
          Length = 465

 Score =  169 bits (429), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 136/485 (28%), Positives = 228/485 (47%), Gaps = 41/485 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKENI 70
           +L++D + +   ++   +      VFI    +  L  + +  ++++         D   +
Sbjct: 5   ILVVDDEPKLCDLLASALGQNNVQVFIAGNGLHALKVLEQEDIDLVISDWRMPGMDGPAL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIK----ILNCFLYNRISKFF----LNLVSRKQLCDSIIC 122
           L  I  + P VP+IV T    +K     +    Y+ I+K F    L++   K L    I 
Sbjct: 65  LAEIKVRYPHVPVIVMTAYSTVKNAVQSMRNGAYDYIAKPFDIDELDITVAKALQFRDI- 123

Query: 123 ALREGV-VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            +R+   + ++ +EH   DSL+  SPA  +V+       D +  I++ GE G GK+ ++R
Sbjct: 124 -MRDNARLRAELDEHAQFDSLVGDSPAFRKVLQAVDSVRDSSATILLTGESGTGKEMVAR 182

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLE 240
            IH+ G RA  PF  VNC  I +  +E  +FG      T   A  +G+F +A+ GT+ L+
Sbjct: 183 AIHKHGSRADKPFVAVNCAAIPEGLLESEMFGHRKGAFTGAVADRVGRFQQADKGTLFLD 242

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PLA+Q +I   ++   IE        ++DVR+I  T KNLL  V +  FR+DLYY
Sbjct: 243 EVGDMPLALQAKILRALQERVIEPVGDPRERKVDVRVIAATNKNLLEAVANKEFREDLYY 302

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++VF I +  LR R EDI  L   F Q+       +    S +AL  +  Y W  N++E
Sbjct: 303 RLNVFPIPLPALRERVEDIAPLARHFAQTLSATAGKRITGFSPEALQAMAAYHWPGNIRE 362

Query: 361 LKNILLRAVIGLKDSHLTED---RFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           L+N + RA I +    + ED      L  SR                 +EG  +  + D 
Sbjct: 363 LQNCVERATI-VAAKPVIEDIDLPGYLFASRP----------------SEGGVTAILSDG 405

Query: 418 LSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
                 P I QD +   L+++EK  I  A++      +  A ++GI   + + ++++  I
Sbjct: 406 ------PGIPQDLDA-ALAEVEKAYILAALQESNGVQAAAAAKIGISERSFWYRLKKLGI 458

Query: 478 EVDSL 482
           +VD +
Sbjct: 459 QVDKI 463


>gi|118589889|ref|ZP_01547293.1| two-component response regulator [Stappia aggregata IAM 12614]
 gi|118437386|gb|EAV44023.1| two-component response regulator [Stappia aggregata IAM 12614]
          Length = 479

 Score =  169 bits (429), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 138/486 (28%), Positives = 229/486 (47%), Gaps = 36/486 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY V +  N S L   +S    +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYTVRLTSNASTLWRWVSSGDGDLVITDVVMPDENIFDV 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  +    P +P++V + Q+     IK      Y  + K F      K+L   +  AL E
Sbjct: 66  LPRMKKMRPELPVLVMSAQNTFMTAIKASEKGAYEYLPKPF----DLKELTSIVQRALEE 121

Query: 127 GVVPSQENEHCALD------SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
                ++     LD       L+  SPAM ++  +  +     + +MI GE G GK+ ++
Sbjct: 122 ----PKKRPAVDLDDAGEGMPLVGRSPAMQEIYRVLARLMQTDLTVMINGESGTGKELVA 177

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGG 235
           R +H+ GKR   PF  +N   I +D IE  LFG         Q ++S    G+F +A+GG
Sbjct: 178 RALHDYGKRRNGPFVAINMAAIPRDLIEAELFGHEKGAFTGAQNRSS----GRFEQADGG 233

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T+ L+E   +P+  Q R+   ++ G+      R  I+ DVR+I  T K+L   +   +FR
Sbjct: 234 TLFLDEIGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIIAATNKDLRHLINQGLFR 293

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPW 354
           +DLY+R++V  I +  LR R EDIP LV HFF  +   K  +    I   AL+LL +Y W
Sbjct: 294 EDLYFRLNVVPIRLPPLRERVEDIPDLVRHFF--ALVEKEGLPAKQIDQGALNLLRRYRW 351

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
             NV+EL+N++ R         ++E+     LS+      E  T+        G S +  
Sbjct: 352 PGNVRELENLVRRLAALYPQDVISENLLEQELSQPSVSPMEEETQETINL---GGSVERY 408

Query: 415 LDNLSQESIPAIGQDGEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
           L         A+   G   R L ++E  +I  A+   R    + A  LG+ R+TL +KIR
Sbjct: 409 LSGYFDTFGDALPPPGLYHRILREVEYPLISAALAATRGNQIKAAELLGVNRNTLRKKIR 468

Query: 474 EYNIEV 479
           + +I+V
Sbjct: 469 DLDIQV 474


>gi|317051506|ref|YP_004112622.1| sigma-54 factor interaction domain-containing protein
           [Desulfurispirillum indicum S5]
 gi|316946590|gb|ADU66066.1| sigma-54 factor interaction domain-containing protein
           [Desulfurispirillum indicum S5]
          Length = 487

 Score =  169 bits (428), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 128/488 (26%), Positives = 230/488 (47%), Gaps = 37/488 (7%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCED---DK 67
           K VL++D +D+    +++ +   GY+V I      + +SK+Q N I   + +      D 
Sbjct: 6   KTVLVVDDEDQMRLALRETLTRAGYEV-ITAFDGNNGLSKLQNNSIDAVITDLRMPVMDG 64

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQL--CDSII 121
              L+  + + P +PI++ T    +      +    ++ I K F   V    L       
Sbjct: 65  MEFLQKALQEKPGLPIVLMTAYATVNTAVDAMKSGAFDYIMKPFSPEVIESTLERVFQYH 124

Query: 122 CALREGV-VPSQENEHCA---LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
            AL +    P+Q+NE  A     ++I  S  M +++ LA      +  +++ GE G GK+
Sbjct: 125 GALEQNTPAPAQKNEAAANHKAPTIITRSKRMEELIHLATDVASSSANVLVNGESGTGKE 184

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
             +R +H +G R   PF  VNC  +  + +E  LFG +    T  + + +GKF  A+GGT
Sbjct: 185 LFARLLHYAGNRQDKPFVAVNCAALPDNLLESELFGYEKGAFTGAANRKIGKFEMADGGT 244

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           ++L+E   +P  +Q ++   ++ G+++       I +DVR++  T +++   +K   FR+
Sbjct: 245 LLLDEITEMPFHLQAKLLRVLQEGEVDRLGGSKPINVDVRIVATTNRDIQESIKEKTFRE 304

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DLYYR++V  ++I  LR R EDI  LV  F+  +  KN+    +++ + ++ L  + W  
Sbjct: 305 DLYYRLNVIPLHIPPLRRRKEDIALLVDHFIAKYNRKNSKSITAVTPEGMNALMNHQWHG 364

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI-- 414
           NV+EL+NI+ RAV+  +   LT                 F   T     T G    T+  
Sbjct: 365 NVRELENIIERAVVICRTQTLTPGNL-------------FLHGTLLDIPTAGDEGQTVCV 411

Query: 415 --LDNLSQESIPAIGQDGEV-----RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRST 467
               ++ +  +PA+  D  +       + ++EK +I   ++       + A  LGI   T
Sbjct: 412 EQAQSVEEGCMPALADDDPLLIEVGTSVHEMEKRLILQTLEKCSGNRKQAADMLGITSRT 471

Query: 468 LYRKIREY 475
           L  KI+EY
Sbjct: 472 LLNKIKEY 479


>gi|404256|emb|CAA47916.1| ntrC [Azospirillum brasilense]
          Length = 481

 Score =  169 bits (428), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 133/495 (26%), Positives = 237/495 (47%), Gaps = 49/495 (9%)

Query: 12  RVLIIDKDDEQIK-IIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKE 68
           R +++  DD  I+ ++   +   G++V    N S L   ++  Q ++I   ++  +++  
Sbjct: 4   RTILVADDDRAIRTVLTQALARLGHEVRTTGNASTLWRWVADGQGDLIITDVVMPDENGL 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDS 119
           +++  I    P + IIV + Q+     +K      +  + K F     +++V R    ++
Sbjct: 64  DLIPRIKKIRPDLRIIVMSAQNTLITAVKAAERGAFEYLPKPFDLKELVSVVERALNSNT 123

Query: 120 IICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
              AL     P+   E      LI  SPAM ++  +  +     + + I GE G GK+ +
Sbjct: 124 PPAAL-----PADAGEADEQLPLIGRSPAMQEIYRVLARLMGTDLTVTITGESGTGKELV 178

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R +H+ GKR   PF  +N   I ++ IE  LFG +    T  + +  G+F +A GGT+ 
Sbjct: 179 ARALHDYGKRRNGPFVAINMAAIPRELIESELFGHEKGAFTGATNRSTGRFEQAQGGTLF 238

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   +PL  Q R+   ++ G+      R  I+ DVR++  T ++L   ++  +FR+DL
Sbjct: 239 LDEIGDMPLEAQTRLLRVLQEGEYTTVGGRTPIKTDVRIVAATHRDLRTLIRQGLFREDL 298

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +YR+ V  I +  LR R+ED+P LV  FL   C+   +   SI   A+  L +Y W  NV
Sbjct: 299 FYRLCVVPIRLPPLRERTEDVPLLVRHFLNQ-CSAQGLPVKSIDQPAMDRLKRYRWPGNV 357

Query: 359 QELKNILLR-------AVIGLK--DSHLTEDRFVLLLSREGKKER-----EFHTETACTC 404
           +EL+N++ R        VIGL   ++ L +         E + E      E H +     
Sbjct: 358 RELENLVRRLAALYSQEVIGLDVVEAELADTTPAAQPVEEPQGEGLSAAVERHLKDYFAA 417

Query: 405 YTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIG 464
           + +G  S+ + D                R L ++E+ +I L++   R    + A+ LG+ 
Sbjct: 418 HKDGMPSNGLYD----------------RVLREVERPLISLSLSATRGNQIKAAQLLGLN 461

Query: 465 RSTLYRKIREYNIEV 479
           R+TL +KIR+ +I+V
Sbjct: 462 RNTLRKKIRDLDIQV 476


>gi|56416000|ref|YP_153075.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197364927|ref|YP_002144564.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56130257|gb|AAV79763.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197096404|emb|CAR62009.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
          Length = 441

 Score =  169 bits (428), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 132/467 (28%), Positives = 221/467 (47%), Gaps = 42/467 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE-PDAL 245
            R+  P   +N   +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E  D  
Sbjct: 187 ARSDKPLVTLNGAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEISDIS 246

Query: 246 PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF 305
           PL +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V 
Sbjct: 247 PL-MQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVV 305

Query: 306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNIL 365
            I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N +
Sbjct: 306 AIEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAI 365

Query: 366 LRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPA 425
            RAV+              LL+ E   ERE     A T      S               
Sbjct: 366 ERAVV--------------LLTGEYISERELPLAIAATPIKTEYS--------------- 396

Query: 426 IGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
               GE++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 397 ----GEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|283787323|ref|YP_003367188.1| two-component system response regulator [Citrobacter rodentium
           ICC168]
 gi|282950777|emb|CBG90453.1| two-component system response regulator [Citrobacter rodentium
           ICC168]
          Length = 441

 Score =  169 bits (428), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 126/470 (26%), Positives = 221/470 (47%), Gaps = 48/470 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    + K   +V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGREALEKASGHVFDLVLCDVRMAEMDGIE 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE--- 126
            L+ I    P +P+++ T   +++     L      + +  +   +L +++  +L     
Sbjct: 67  TLREIKALNPAIPVLIMTAFSSVETAVEALKTGALDYLIKPLDFDRLQETLEKSLAHAQE 126

Query: 127 --GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
             G +PS       +   +  SPAM Q++            ++I G+ G GK+ ++R +H
Sbjct: 127 VAGELPSVSASQSGM---VGKSPAMQQLLSEIAMVAPSDATVLIHGDSGTGKELVARALH 183

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE-P 242
            S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E  
Sbjct: 184 ASSARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIG 243

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
           D  PL +Q R+   I+  +++   S   + +DVRLI  T ++L  +  +  FR+DLYYR+
Sbjct: 244 DISPL-MQVRLLRAIQEREVQRVGSNQTLSVDVRLIAATHRDLAQEASAGRFRQDLYYRL 302

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           +V  I   +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+
Sbjct: 303 NVVTIETPSLRQRREDIPLLAEHFLQRFAARNRKAVKGFTPQAMDLLIHYAWPGNIRELE 362

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           N + RAV+ L   +++E    L ++                             N +   
Sbjct: 363 NAIERAVVLLTGEYISERELPLAIA-----------------------------NQAMPL 393

Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
           +PA      ++ L ++EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 394 MPAQA----IQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|260566347|ref|ZP_05836817.1| nitrogen regulation protein NtrC [Brucella suis bv. 4 str. 40]
 gi|260155865|gb|EEW90945.1| nitrogen regulation protein NtrC [Brucella suis bv. 4 str. 40]
          Length = 491

 Score =  169 bits (427), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 132/490 (26%), Positives = 237/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR +SED+P LV HFF +    +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLREQSEDVPDLVRHFFKR--AAEEGLPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|124267473|ref|YP_001021477.1| phenol-degradation regulator [Methylibium petroleiphilum PM1]
 gi|124260248|gb|ABM95242.1| phenol-degradation regulator [Methylibium petroleiphilum PM1]
          Length = 550

 Score =  169 bits (427), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 112/350 (32%), Positives = 180/350 (51%), Gaps = 38/350 (10%)

Query: 142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM 201
           LI VSP      +L R A   AI +++ GE GVGK+  +R++HE+G RA  PF  VNC  
Sbjct: 222 LIGVSPGFRAAFELLRSAAGSAITVLLLGETGVGKEMFARWLHENGPRAGGPFIAVNCAA 281

Query: 202 IDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
           I  + IE  LFG V+      AQ    G+F  A+GGT+ L+E   LPLA Q ++   ++T
Sbjct: 282 IPHELIEAELFG-VEKGAYTGAQLARAGRFERASGGTLFLDEVGDLPLAAQVKLLRALQT 340

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
            ++E   S  A ++DVR++  T  +L   +++  FR DL+YR+++F I I  LR R+ DI
Sbjct: 341 AEVERLGSEHATKIDVRIVAATNVDLQQAMQAGRFRSDLFYRLNIFPITIPPLRERTTDI 400

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
           P L+  FL+ +      K   ++DKA+  +  + W  N++EL+N++ RA           
Sbjct: 401 PALIERFLEKYGELYNKKLRGLTDKAMRQVLSHAWPGNIRELENVIERA----------- 449

Query: 380 DRFVLLLSREGKKEREFHTETACTCYTEG--KSSDTILDNLSQESIPAIGQDGEVR---- 433
              VLL    G  E       AC  + E   ++S+  LD  ++  +  +  D   R    
Sbjct: 450 ---VLLAPANGPIE-------ACHLFGEPALRASEGSLD--AKGRVTEVHPDALGRLCDE 497

Query: 434 ------RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
                  L  +E+ ++  AM+  +  +S+ AR LGI R  L  ++++  +
Sbjct: 498 AFEHHIDLESLERRMMQAAMQRAKGNLSQAARLLGITRPQLAYRLKKEGL 547


>gi|221068460|ref|ZP_03544565.1| sigma54 specific transcriptional regulator, Fis family [Comamonas
           testosteroni KF-1]
 gi|220713483|gb|EED68851.1| sigma54 specific transcriptional regulator, Fis family [Comamonas
           testosteroni KF-1]
          Length = 516

 Score =  169 bits (427), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 107/377 (28%), Positives = 185/377 (49%), Gaps = 35/377 (9%)

Query: 112 SRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGE 171
           +R++L      +L   V  S+ +++ +  S +  SPA ++V   AR+A     P+++ GE
Sbjct: 162 ARRELAAQRSRSLHASVQGSRRSKY-SFASFVGSSPAAVEVKRQARRAAQSMSPVLLLGE 220

Query: 172 FGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-------DVDLQTKNSAQ 224
            G GK+ L+  IH +  R+  PF  VN   I +  +E   FG         + +T++   
Sbjct: 221 TGTGKEVLAHAIHAASARSAGPFVSVNIAAIPETLLEAEFFGVAPGAFTGAERKTRD--- 277

Query: 225 FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN 284
             GKF  A+GGT+ L+E   +P ++Q ++   ++ G+IE   S   +  DVR++  T ++
Sbjct: 278 --GKFKLADGGTLFLDEIGDMPASLQAKLLRALQEGEIEPLGSNQIVHFDVRMVAATSRD 335

Query: 285 LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK 344
           LL  V+   FR+DL+YR+ V  + +  LR RS DIP LV    +    +N +    +   
Sbjct: 336 LLQMVRDGRFREDLFYRLHVLPVRVPPLRERSSDIPALVEMLCEDLALRNDMVPPELGKG 395

Query: 345 ALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTC 404
           AL LL    W  N++EL+N+L +A +   DSH+       +L   G + +  H +     
Sbjct: 396 ALELLVAQAWRGNIRELRNVLEQAAMRCDDSHIDAGLLAQVLRSSGVEPQAPHRQPP--- 452

Query: 405 YTEGKSSDTILDNLSQESIPAIGQDGEV-----RRLSDIEKEIIGLAMKLYRAQMSEVAR 459
                         +QE++ A+   G++      +++D+E   I  AM+ +      VAR
Sbjct: 453 --------------AQETMAAMPATGDLLKPLAEQIADLETRAIRAAMQAHGGNKLAVAR 498

Query: 460 RLGIGRSTLYRKIREYN 476
            LGI R+ LY ++   N
Sbjct: 499 TLGISRAKLYDRLETLN 515


>gi|16762283|ref|NP_457900.1| transcriptional regulator ZraR [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29143771|ref|NP_807113.1| transcriptional regulator ZraR [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|213022036|ref|ZP_03336483.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
 gi|213161649|ref|ZP_03347359.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213423580|ref|ZP_03356560.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
 gi|213428476|ref|ZP_03361226.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213580343|ref|ZP_03362169.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213612381|ref|ZP_03370207.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
 gi|213647189|ref|ZP_03377242.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855078|ref|ZP_03383318.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|20140998|sp|Q8Z333|ZRAR_SALTI RecName: Full=Transcriptional regulatory protein zraR
 gi|25301132|pir||AD0931 transcription regulatory protein STY3711 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16504587|emb|CAD09470.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|29139406|gb|AAO70973.1| transcriptional regulatory protein [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 441

 Score =  169 bits (427), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 128/466 (27%), Positives = 219/466 (46%), Gaps = 40/466 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +PI++ T   +++     L      + +  +   +L +++  AL     
Sbjct: 67  TLKEIKALNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDRLQETLEKALAHTRE 126

Query: 130 PSQE--NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
              E  +   A   +I  SPAM  +++           ++I G+ G GK+ ++R +H   
Sbjct: 127 TGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS 186

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
            R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   + 
Sbjct: 187 ARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDIS 246

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
             +Q R+   I+  +++   S   I +DV LI  T ++L  +V +  FR+DLYYR++V  
Sbjct: 247 PLMQVRLLRAIQEREVQRVGSNQTISVDVWLIAATHRDLAEEVSAGRFRQDLYYRLNVVA 306

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N + 
Sbjct: 307 IEMPSLRQRREDIPLLADHFLRRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAIE 366

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           RAV+              LL+ E   ERE     A T      S+               
Sbjct: 367 RAVV--------------LLTGEYISERELPLAIAATPIKAENSA--------------- 397

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
               E++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 398 ----EIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|332185237|ref|ZP_08386986.1| nitrogen regulation protein NR [Sphingomonas sp. S17]
 gi|332014961|gb|EGI57017.1| nitrogen regulation protein NR [Sphingomonas sp. S17]
          Length = 485

 Score =  169 bits (427), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 129/484 (26%), Positives = 230/484 (47%), Gaps = 30/484 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQV----NVIFLSLINCEDDKE 68
           VL++D D     ++   +   G++V    V  L+ + ++      +V+   +I  + D  
Sbjct: 4   VLVVDDDAAIRTVVGQALRRAGHEV--TTVETLARLDRLLAGGAPDVLVTDVILPDGDGI 61

Query: 69  NILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
           + ++ +  + P +PII+ + Q+     ++      Y  + K F        L +++  AL
Sbjct: 62  DHIRGVAARFPALPIIILSAQNTLTTAVRAAEVGAYEYLPKPF----DLDALTNAVAGAL 117

Query: 125 REGVVPSQEN--EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
             G V  ++   E      LI  S AM  V  +  +     + ++I GE G GK+ ++R 
Sbjct: 118 ARGGVLVEDGLGEDDRALPLIGRSQAMQSVYRIIARVVATDLTVLISGESGTGKELVARA 177

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF-LGKFIEANGGTIVLEE 241
           IH+ G R   PF  +N   I ++ IE  LFG        +AQ   G+F +A GGT+ L+E
Sbjct: 178 IHDLGPRRAAPFVAINMAAIPRELIEAELFGHERGAFTGAAQRNAGRFEQAAGGTLFLDE 237

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +P+  Q R+   +++G+         IR DVR++  T ++L  QV S  FR+DL+YR
Sbjct: 238 IGDMPMEAQTRLLRVLQSGEFTTVGGARTIRTDVRIVAATNRDLSQQVASGQFREDLFYR 297

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  I +  LR R +DIP L   FL++   +  + +  I  +AL +L  + W  NV+EL
Sbjct: 298 LNVVPIALPALRERRQDIPLLARHFLENAAAQG-LPRRKIDAQALDVLVVHDWPGNVREL 356

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTE----GKSSDTILDN 417
           +N++ R  +  +D  +  +    +L      E  FH+ TA +          +    L  
Sbjct: 357 ENLMRRLAVLARDEVIDAEAIRTMLG-----ETAFHSTTAGSGRAAVPDLAAAVRAYLAR 411

Query: 418 LSQESIPAIGQDGEV--RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
           L+ E  P +  DG +  R + ++E+ +I   +  +       AR +GI R+TL +++   
Sbjct: 412 LAIER-PLLLDDGTLYDRVIGEVERPLIEAMLARHGGNQLRTARAMGINRNTLRKRLDSL 470

Query: 476 NIEV 479
           NI V
Sbjct: 471 NISV 474


>gi|323171898|gb|EFZ57542.1| acetoacetate metabolism regulatory protein atoC [Escherichia coli
           LT-68]
          Length = 461

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 133/483 (27%), Positives = 226/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              IC L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEICHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEVKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|312959224|ref|ZP_07773742.1| sigma-54 dependent DNA-binding response regulator [Pseudomonas
           fluorescens WH6]
 gi|311286484|gb|EFQ65047.1| sigma-54 dependent DNA-binding response regulator [Pseudomonas
           fluorescens WH6]
          Length = 465

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 139/482 (28%), Positives = 228/482 (47%), Gaps = 35/482 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKENI 70
           +L++D + +   ++   +   G  VFI    +  L  + +  ++++         D   +
Sbjct: 5   ILVVDDEPKLCDLLASALGQNGIQVFIAGNGLHALKVLEQEDIDLVISDWRMPGMDGPAL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIK----ILNCFLYNRISKFF----LNLVSRKQLCDSIIC 122
           L  I  + P VP+IV T    +K     +    Y+ I+K F    L++   K L    I 
Sbjct: 65  LAEIKVRYPHVPVIVMTAYSTVKNAVQSMRNGAYDYIAKPFDIDELDITVAKALQFRDI- 123

Query: 123 ALREGV-VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            LR+   + ++ +EH   DSL+  SPA  +V+       D +  I++ GE G GK+ ++R
Sbjct: 124 -LRDNARLRAELDEHAQFDSLVGDSPAFRKVLHAVDSVRDSSATILLTGESGTGKEMVAR 182

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLE 240
            IH+ G RA  PF  VNC  I +  +E  +FG      T   A  +G+F++A+ GT+ L+
Sbjct: 183 AIHKHGSRADQPFVAVNCAAIPEGLLESEMFGHRKGAFTGAVADRVGRFMQADKGTLFLD 242

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PLA+Q +I   ++   IE        ++DVR+I  T KNLL  V    FR+DLYY
Sbjct: 243 EVGDMPLALQAKILRALQERVIEPVGDPRERKVDVRVIAATNKNLLDAVADKEFREDLYY 302

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++VF I +  LR R EDI  L   F Q+       +    S +AL  +  Y W  N++E
Sbjct: 303 RLNVFPIPLPPLRERVEDIAPLARHFAQTLSATACKRITGFSPEALQAMAAYHWPGNIRE 362

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L+N + RA I +  S + ED     +   G          A     EG  +  + D    
Sbjct: 363 LQNCVERATI-VAASPVIED-----IDLPGYL-------FASKPSGEGGVAAILSDG--- 406

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
              P I QD +   L+++EK  I LA       +   A ++GI   + + ++++  I+VD
Sbjct: 407 ---PGIPQDLDA-ALAEVEKAYI-LAALHESNGVQAAAAKIGISERSFWYRLKKLGIQVD 461

Query: 481 SL 482
            +
Sbjct: 462 KI 463


>gi|78187120|ref|YP_375163.1| two component Fis family transcriptional regulator [Chlorobium
           luteolum DSM 273]
 gi|78167022|gb|ABB24120.1| two component transcriptional regulator, Fis family [Chlorobium
           luteolum DSM 273]
          Length = 486

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 132/487 (27%), Positives = 226/487 (46%), Gaps = 31/487 (6%)

Query: 6   SLDRHKRVLIIDKDDEQIKIIKDHV-ESYGYDVFIV--NVSDLSTISKIQVNVIFLSLIN 62
           +L +  + +++  D   I+ +  H+ +  GY         S + T+ +  V+V+ L L  
Sbjct: 2   ALQKQPKTVLVADDSSVIRTLMQHLLKKLGYRAITAENGTSCIRTLEEEPVDVLLLDLNM 61

Query: 63  CEDDKENILKNIVDKIPIVPIIVQTTQDNI-KILNC-------FLYNRISKFFLNLVSRK 114
            E D   +L  + ++   +P+I+ T  +++ + + C       +L   +    L ++ R 
Sbjct: 62  PEKDGMEVLSWVREQGMTLPVIIITALEDVSQAVQCMKMGAYEYLTKPVENERLEIILRN 121

Query: 115 QLCDSIICALREGVVPSQENEHCALD---SLIAVSPAMIQVVDLARKAGDCAIPIMIQGE 171
            L +S  C L+E V    E E  A D    +   SPA+ + +D A +  +  + +++ GE
Sbjct: 122 ALSES--C-LKEKVA-VLEKELIAKDLFREIRGNSPALRRSIDQAMQVMETDMNVLLNGE 177

Query: 172 FGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFI 230
            G GK+  ++ IH   +R   PF  +NC  I  +  E  LFG      T  +A   G F 
Sbjct: 178 SGTGKELFAKAIHHGSRRKGGPFVTINCAAISSELAESLLFGHTKGAFTGATADHAGYFE 237

Query: 231 EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK 290
           +A+GGTI L+E   + L +Q ++   ++  KI     +    +D RL+  T ++    + 
Sbjct: 238 QADGGTIFLDEIGDMSLDIQAKVLRALQEKKIRRVGEKKERAVDFRLVSATHRDFSQSIT 297

Query: 291 SHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLT 350
              FR DLYYR+  + + I  LR R EDI  L   FLQ FC  N +    I+ +AL  L 
Sbjct: 298 DKSFRADLYYRLEEYPLYIPPLRERQEDIIPLAEHFLQEFCKANGLDTPVIAPEALLSLQ 357

Query: 351 KYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKS 410
            +PW  NV+EL+NI+ RAV+        E R    +  +G +++     ++       ++
Sbjct: 358 SHPWPGNVRELQNIIRRAVL-----TAGEGRIASFMP-QGSQQKSTPQPSSLPISVPAET 411

Query: 411 SDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
           + T     S    P  G + +   L DIE + I    +      S  A  LGI RSTL R
Sbjct: 412 TPT-----SAPVKPERGTENQA-ILKDIELQAIVDTYRECGGNQSRTAELLGISRSTLIR 465

Query: 471 KIREYNI 477
           K++ + +
Sbjct: 466 KMKRHGL 472


>gi|239832006|ref|ZP_04680335.1| nitrogen regulation protein NR(I) [Ochrobactrum intermedium LMG
           3301]
 gi|239824273|gb|EEQ95841.1| nitrogen regulation protein NR(I) [Ochrobactrum intermedium LMG
           3301]
          Length = 490

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 131/489 (26%), Positives = 225/489 (46%), Gaps = 28/489 (5%)

Query: 9   RHKRVLIIDKDDEQIKIIKDHVES-YGYDVFIV-NVSDLSTISKIQVNVIFLSLINCEDD 66
           R    +++  DD  I+ + +   S  GYDV +  N + L          + ++ +N  D+
Sbjct: 5   RPSGTILVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVITDVNMPDE 64

Query: 67  KE-NILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSII 121
              ++L  +    P +P++V + Q+     I+      Y  + K F +L     +    +
Sbjct: 65  NAFDLLPRVKKMRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPF-DLTELINIAGRAL 123

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              +     +  +E      L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 124 SEPKNKPAAALSDEQADNMPLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIRTDVRIVAATNKDLRQLIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+  LV HFF +    +  + +  IS   L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVADLVRHFFKR--AAEEGLPEKRISTAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+EL+N++ R         ++ +     L  E  K        A     E  S    +
Sbjct: 358 GNVRELENLVRRLAALYPQEEISPEIIETELRAELTKP---DVVPAGAGDIENISISQAV 414

Query: 416 DNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYR 470
           +   Q    + G D    G   R L+++E  +I   +   R    + A  LG+ R+TL +
Sbjct: 415 EQNMQRYFASFGSDLPPPGLYHRVLAELEYPLILACLTATRGNQIKAADLLGLNRNTLRK 474

Query: 471 KIREYNIEV 479
           KIRE  + +
Sbjct: 475 KIRELGVNI 483


>gi|83647863|ref|YP_436298.1| sigma 54-dependent transcriptional activator [Hahella chejuensis
           KCTC 2396]
 gi|83635906|gb|ABC31873.1| sigma 54-dependent transcriptional activator containing CheY-like
           receiver domain [Hahella chejuensis KCTC 2396]
          Length = 467

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 131/475 (27%), Positives = 227/475 (47%), Gaps = 27/475 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENI 70
           +LI++ D E +  +   +E  GYD   V+ +   LS + +  V++I   +     +   +
Sbjct: 6   LLIVEDDLELLDALTTTLEMNGYDYIGVDSAREALSVLEQRAVDMIISDVNMPGMNGFEL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           +  +  + P VP+++ T    I      + +  + + +     + L D+I     E  + 
Sbjct: 66  MLEVRRQYPGVPVVLMTAYGQISQAVAAMQSGAADYLVKPFEPQTLLDTI-----EKYMG 120

Query: 131 SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
               +  A D  +AV  A  ++  LA++       ++I GE G GK+ L+R+IH    R 
Sbjct: 121 GAGGDSNA-DEPVAVDGASKRIFQLAQRVAMTDSTVLISGESGTGKEVLARYIHRKSARK 179

Query: 191 FFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAV 249
             PF  +NC  I ++ +E  LFG +    T   A   GKF +A+GGTI+L+E   + L +
Sbjct: 180 NAPFVAINCAAIPENMLEAILFGHEKGAFTGAYASMPGKFEQADGGTILLDEISEMDLGL 239

Query: 250 QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINI 309
           Q ++   ++  ++E    R +IRLDVR++  T ++L   V+   FR+DLYYR+SVF I+ 
Sbjct: 240 QAKLLRVLQEREVERIGGRKSIRLDVRVLATTNRDLKTYVQEGRFREDLYYRLSVFPIHW 299

Query: 310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
             LR R  DI  L    L +   K  +  +   D A   L  + W  NV+EL N + RA+
Sbjct: 300 RPLRERRADIVPLAEHLLANHAQKMKLSFVRFDDSARQALYNHDWPGNVRELDNAIQRAL 359

Query: 370 IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ-ESIPAIGQ 428
           I  ++  +T     L    EG        ++       G +    +D + + + +  +GQ
Sbjct: 360 ILQQNGQITAADVCL----EG-----VSLDSLTAPMASGMTMSEPMDEMEEMDDVSGLGQ 410

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVD 480
           +  +R     E +II   +K    + ++VA +LGI   TL  KI   RE+ I++D
Sbjct: 411 EMRMR-----EFQIILDTLKSEGGRRNKVAEKLGISPRTLRYKIARMREFGIDID 460


>gi|326409136|gb|ADZ66201.1| nitrogen regulation protein NR(I) [Brucella melitensis M28]
 gi|326538844|gb|ADZ87059.1| nitrogen regulation protein NR(I) [Brucella melitensis M5-90]
          Length = 491

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 132/490 (26%), Positives = 237/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE   GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESSTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+P LV HFF ++   +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVPDLVRHFFKRA--AEEGLPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|254469521|ref|ZP_05082926.1| nitrogen regulation protein [Pseudovibrio sp. JE062]
 gi|211961356|gb|EEA96551.1| nitrogen regulation protein [Pseudovibrio sp. JE062]
          Length = 479

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 137/482 (28%), Positives = 232/482 (48%), Gaps = 28/482 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY V +  N + L   +S  + +++   ++  +++  ++
Sbjct: 6   ILVADDDSAIRTVLNQALSRAGYTVRLTSNATTLWRWVSSGEGDLVISDVVMPDENAFDV 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICAL-- 124
           L  I    P +P+I+ + Q+     IK      Y  + K F      K+L   +  AL  
Sbjct: 66  LPRIRKLRPELPVIIMSAQNTFMTAIKASEQGAYEYLPKPF----DLKELTGIVGRALAE 121

Query: 125 ---REGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              R+  +  + N++     L+  SPAM ++  +  +     + +MI GE G GK+ ++R
Sbjct: 122 PKGRQFDMGGEGNDNI---PLVGRSPAMQEIYRVLARLMQTDLTVMINGESGTGKEVVAR 178

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLE 240
            +H+ GKR   PF  VN   I +D IE  LFG      T   A+  G+F +A+GGT++L+
Sbjct: 179 ALHDYGKRRNGPFVAVNMAAIPKDLIESELFGHEKGSFTGAQARSSGRFEQADGGTLLLD 238

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +P+  Q R+   ++ G+      R  I+ DVR+I  T K+L   +   +FR+DLY+
Sbjct: 239 EIGDMPMEAQTRLLRVLQQGEYTSVGGRTPIQTDVRIIAATNKDLRQLINQGLFREDLYF 298

Query: 301 RISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           R++V  I +  LR R+EDIP LV HFF  +       KQI ++  AL  L +Y W  NV+
Sbjct: 299 RLNVVPIRLPPLRERTEDIPDLVRHFFAMAESEGLPAKQIEVA--ALDKLRRYRWPGNVR 356

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           EL+N++ R         +T     L LS+      E    +A      G     + D  S
Sbjct: 357 ELENLVRRLAALYPQDDITASLIDLELSQPSAAISEADAPSAQDL--SGSVERYLGDYFS 414

Query: 420 --QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
              E +P  G    +  L ++E  +I   +   R    + A  LG+ R+TL +KIR+ ++
Sbjct: 415 GFGEELPPPGLYHRI--LREVEYPLISAVLAATRGNQIKAAELLGVNRNTLRKKIRDLDV 472

Query: 478 EV 479
           +V
Sbjct: 473 QV 474


>gi|331011061|gb|EGH91117.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 471

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 134/476 (28%), Positives = 224/476 (47%), Gaps = 21/476 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVE--SYGYDVFIVNVSDLSTISKIQVNVIFLSLINCED-DKEN 69
           VL+++ D    + + + +E   YGY   + +  +    ++ Q   + +S +N    D   
Sbjct: 5   VLLVEDDRSLREALGETLELAGYGYQA-VCSAEEALVAAEAQPFSLVISDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    +      +    + + +     K L   I    R  + 
Sbjct: 64  LLSLLRSRHPQLPVLLMTAHGAVDRAVDAMRQGAADYLVKPFEPKAL---IALVARHALG 120

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
             +  E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  R
Sbjct: 121 RLEPAER---DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL 
Sbjct: 178 ADKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPIILDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA
Sbjct: 298 WQALRQRTADILPLAERLLAKHVNKMKHAPVRLSAQAQQCLVSYPWPGNVRELDNAVQRA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           +I  +   +    F   LS             A        S D      + ES+ A+G 
Sbjct: 358 LILQQGGVIQAQDF--FLSGPVTSLPAAAVVEAVPSLPVTSSPDNAGAGGNAESVGALGD 415

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           D  +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 416 D--LRRR---EFQMIIDTLRAERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 466


>gi|58583825|ref|YP_202841.1| two-component system regulatory protein [Xanthomonas oryzae pv.
           oryzae KACC10331]
 gi|84625628|ref|YP_453000.1| two-component system regulatory protein [Xanthomonas oryzae pv.
           oryzae MAFF 311018]
 gi|188574844|ref|YP_001911773.1| two-component system regulatory protein [Xanthomonas oryzae pv.
           oryzae PXO99A]
 gi|58428419|gb|AAW77456.1| two-component system regulatory protein [Xanthomonas oryzae pv.
           oryzae KACC10331]
 gi|84369568|dbj|BAE70726.1| two-component system regulatory protein [Xanthomonas oryzae pv.
           oryzae MAFF 311018]
 gi|188519296|gb|ACD57241.1| two-component system regulatory protein [Xanthomonas oryzae pv.
           oryzae PXO99A]
          Length = 448

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 129/481 (26%), Positives = 226/481 (46%), Gaps = 52/481 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSD-LSTISKIQVNVIFLSLINCEDDKENI 70
           +LIID D      ++  + S+G+ V    N  D L+ +S+  +++ F+       D   +
Sbjct: 4   ILIIDDDAAFRTTLQATLRSFGHTVVAADNGPDGLARLSEGGIDMAFVDFRMPGMDGIAV 63

Query: 71  LKNIVD-----KIPIVPIIVQTTQDN-IKILNCFLYNRISKF-----FLNLVSRKQL--C 117
           L+  +D     ++P+V +    +  N I+ +    ++ + K       + +V R  L   
Sbjct: 64  LRARLDDAQARQVPLVMLTAHVSSGNTIEAMTLGAFDHLVKPVGRADIVEVVERALLSRA 123

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
           D+   A      P +++     D+L+  SPAM  V      A    +P++I GE G GK+
Sbjct: 124 DAQAAATETPQAPHEDD-----DALVGHSPAMRTVHKHIGLAAASDLPVLITGETGTGKE 178

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGT 236
             +R +H +  RA  PF  VNC  I  + +E  LFG      +  S+  LG   EA+GGT
Sbjct: 179 LAARALHRASPRAEAPFVAVNCAAIPLELMESELFGHRKGAFSGASSDRLGLIREADGGT 238

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +PL +Q ++  F++ G++      G+ ++DVR++  T ++L   V    FR 
Sbjct: 239 LFLDEIGDMPLPMQAKLLRFLQEGEVTPLGGSGSQKVDVRVLAATHRDLAACVADGRFRS 298

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DL YR++V  I +  LR R +DI  L     Q F + NA +  S+S  A   L  + W  
Sbjct: 299 DLRYRLNVVPIELPPLRERGQDILLLA----QHFLSTNAARAQSLSPAAQERLLAHRWPG 354

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           NV+EL+N++ R+ + ++ + +        L+  G+           T       + T+ +
Sbjct: 355 NVRELRNVMQRSQVMVRGASIDAADLDEALAEAGE----------ATPDVASAMTGTLPE 404

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
            +++                 +EK++I  A++      +E ARRLGI R  LYRK+ EY 
Sbjct: 405 AVAR-----------------LEKQMIQSALEQSHGNRAEAARRLGIHRQLLYRKLEEYG 447

Query: 477 I 477
           +
Sbjct: 448 L 448


>gi|212711604|ref|ZP_03319732.1| hypothetical protein PROVALCAL_02679 [Providencia alcalifaciens DSM
           30120]
 gi|212685706|gb|EEB45234.1| hypothetical protein PROVALCAL_02679 [Providencia alcalifaciens DSM
           30120]
          Length = 482

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 120/437 (27%), Positives = 212/437 (48%), Gaps = 19/437 (4%)

Query: 56  IFLSLINCED-DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRK 114
           + LS I   D D   +L  +    P++PII+ T   ++        N       + + + 
Sbjct: 50  VLLSDIRMPDMDGLALLTQLKQSHPLLPIIIMTAHSDLDAA----VNAYQSGAFDYLPKP 105

Query: 115 QLCDSIICALREGVVPSQENEHCALD---------SLIAVSPAMIQVVDLARKAGDCAIP 165
              D  +  +   +  S+E  + A D         ++I  +PAM +V  +  +    +I 
Sbjct: 106 FDIDETVALVERALNHSREQNNTAGDKPQAAIVSSTMIGEAPAMQEVYRIIGRLSRSSIS 165

Query: 166 IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF 225
           ++I GE G GK+ ++  +H+   RA  PF  +N   I +D IE  LFG        ++Q 
Sbjct: 166 VLINGESGTGKELVAHALHQHSPRANEPFIALNMAAIPKDLIESELFGHEKGAFTGASQV 225

Query: 226 -LGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN 284
             G+F +AN G++ L+E   +PL VQ R+   +  G+         +++DVR+I  T +N
Sbjct: 226 RQGRFEQANRGSLFLDEIGDMPLDVQTRLLRVLAEGQFYRIGGYTPVKVDVRIIAATHQN 285

Query: 285 LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK 344
           L  +V+  +FR+DL++R++V  + +  LR R EDIP L H+FLQ+   +  ++   +   
Sbjct: 286 LEKRVEEGLFREDLFHRLNVIRVQLPPLRERVEDIPRLAHYFLQNTAKELGVESKVLHPD 345

Query: 345 ALSLLTKYPWIDNVQELKNIL-LRAVIGLKDSHLTEDRFVLLLSRE--GKKEREFHTETA 401
           ++ LL +YPW  NV++L+N+     V+      L +D    L  ++   K  ++ H+ + 
Sbjct: 346 SIKLLQRYPWSGNVRQLENVCRWLTVMAASQEVLPQDLPSDLFGKQESTKVAKDPHSLST 405

Query: 402 CTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRL 461
                     D +L+  +  ++ A  QD     +  +EK ++  A+K       E AR L
Sbjct: 406 NAVDPNITWCD-LLEKWTDLALHAGQQDLFNDAMPLLEKTMLNCALKYTDGHKQEAARLL 464

Query: 462 GIGRSTLYRKIREYNIE 478
           G GR+TL RK++E  IE
Sbjct: 465 GWGRNTLTRKLKELGIE 481


>gi|322419733|ref|YP_004198956.1| Fis family two component sigma54 specific transcriptional regulator
           [Geobacter sp. M18]
 gi|320126120|gb|ADW13680.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. M18]
          Length = 511

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 144/520 (27%), Positives = 232/520 (44%), Gaps = 62/520 (11%)

Query: 7   LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCE 64
           ++   ++LIID + +     +  +   GY+V         L+ +   + NV  + L   +
Sbjct: 2   IESQTQILIIDDERDVCTFFRRLLARRGYEVVTAANEPEALAALEAGRFNVALVDLKLPD 61

Query: 65  DDKENILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQLCDSI 120
            D   +L+ I  + P   +I+ T    +K     +    Y  + K F ++   +QL    
Sbjct: 62  TDGITLLEIIKSRQPSCEVIIMTGYSTVKTAVTAMQLGAYEYLEKPFDDIDQIEQLI--- 118

Query: 121 ICALREGVVPSQENEHCALDSL----------IAVSPAMIQVVDLARKAGDCAIPIMIQG 170
             A   G   S       +D            +  +P+M ++V LA K     I ++IQG
Sbjct: 119 --ARAAGAGASHRRGDAGVDEWAEVAQGVGFRVGAAPSMKRMVSLAYKVAGKDISVLIQG 176

Query: 171 EFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKF 229
           + G GK+ L+RFIH +  RA  PF  VNCG + ++ +E  LFG        + Q   G F
Sbjct: 177 KTGTGKEVLARFIHAASARAGQPFIPVNCGALPENLLESELFGHEKGAFTGANQTRRGIF 236

Query: 230 IEANGGTIVLEE-PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ 288
             AN GT++L+E  DA P  +Q ++   +ETG+         I+ DVR+I  T  +L   
Sbjct: 237 ELANNGTLLLDEIGDATP-QIQVKLLRVLETGEFMRVGGERPIKTDVRVIAATNVDLEQA 295

Query: 289 VKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSL 348
           ++   FR+DL+YR++V  + I +L +RSEDIP L   F++        + + +S   + L
Sbjct: 296 IREKTFREDLFYRLNVVRLEIPSLSARSEDIPLLAEHFVKQLN-----RDLRLSPGTVRL 350

Query: 349 LTKYPWIDNVQELKNILLRAV-IGLKDSHLTEDRFVLLLSREGKKER----------EFH 397
           L  Y W  N++EL N++ RAV I   D+ L E      L+      R          E  
Sbjct: 351 LQGYSWPGNIRELANVMRRAVVICTGDTILPEHLGGTFLAGPSAPSRIPGQLPQRAAELE 410

Query: 398 TETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRR--------------------LSD 437
             TA +   E   S  +L+ +  E +  +   G VR                     L D
Sbjct: 411 QVTAASDLIEQCQSCELLERMGAEELNRM--LGSVRHAQSNLLAVMRRKKIVPPLHALKD 468

Query: 438 IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
            E E I  A+  Y   ++E A+ LGI R+TLYRK++E  +
Sbjct: 469 SEAETIKEALTQYDGNITEAAKALGIARNTLYRKMKELEL 508


>gi|183219984|ref|YP_001837980.1| putative two-component sensor protein [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
 gi|189910106|ref|YP_001961661.1| transcriptional regulator [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167774782|gb|ABZ93083.1| Transcriptional regulator [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167778406|gb|ABZ96704.1| Putative two-component sensor protein [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
          Length = 705

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 121/344 (35%), Positives = 181/344 (52%), Gaps = 8/344 (2%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
           SLI  + +M ++ +  +   D    ++I GE G GK+ ++  IH +  R+  PF  +NC 
Sbjct: 363 SLIGKAASMEKMFEKIQLVADSRASVLITGESGTGKEMIANAIHYNSSRSENPFVKINCA 422

Query: 201 MIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            I ++ +E  LFG      T       GKF  A+ GTI L+E   + L +Q ++   ++ 
Sbjct: 423 AIPENLLESELFGHKKGSFTGAVTDKKGKFELADTGTIFLDEIGEMDLNLQSKLLRVLQE 482

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
            +IE   S  A ++DVR+I  T   L   V    FR DL+YR++V  IN   LR R EDI
Sbjct: 483 REIEAIGSTKAKKVDVRIIAATNAELEQLVAEKKFRADLFYRLNVVKINTPPLRDRVEDI 542

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
           P L++ FL+ +   N      IS +A  LL KY W  NV+EL+N++ RAV+  +D  L E
Sbjct: 543 PLLMNHFLEKYTKDNNKSIKGISREASRLLLKYRWPGNVRELENVIERAVVLAQDEILNE 602

Query: 380 DRFVLLLSREGKKEREFHT-ETACTCYTEGKSSDTILDNLSQE--SIPAIGQDGEVRRL- 435
           + F  +LS    +E   +T E + + + E  S    LD  S    S    G DG    + 
Sbjct: 603 EDFSDILS--NMEEMPDNTVEVSHSNHVESVSGAEPLDLGSGRLTSGQLDGLDGRAMEIV 660

Query: 436 -SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            S++E  +I  AMK +R   + VA+ LGI R+TL +KI+E NIE
Sbjct: 661 VSEVESRLIQYAMKKFRYTKTRVAKFLGINRNTLDKKIKELNIE 704


>gi|220916812|ref|YP_002492116.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219954666|gb|ACL65050.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 463

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 128/483 (26%), Positives = 221/483 (45%), Gaps = 45/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYD-VFIVNVSD-LSTISKIQVNVIFLSLINCEDDKEN 69
           RVL++D +      +K+ V+  G++ V   + S+ L  + +  V V   S+   E D   
Sbjct: 3   RVLLVDDEPSVRAALKELVQGRGWEPVLACSASEALEQLERADVLVTDFSM--PEMDGLA 60

Query: 70  ILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           +L+ + ++   +P+I+ T   +    ++ +    Y  + K F       +L  +I  AL 
Sbjct: 61  LLQAVRERDEWLPVILLTAHGSERLAVRAMKAGAYEYVPKPF----DVDELALAIGRAL- 115

Query: 126 EGVVPSQEN-----EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
           E  +  Q N     EH     L+  S  M QV+    +     I +++ GE G GK+ + 
Sbjct: 116 EARLLRQRNRQLTVEHAIGRRLVFESANMRQVLAATARVAAREITVLVCGETGTGKELIG 175

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEANGGTIVL 239
             +H   KRA  P    NC  I  +  E  LFG V      + Q   G F +A+GGT+VL
Sbjct: 176 TLLHALSKRAAGPLVRFNCSAIPAELAEAELFGHVRGAFTGAVQARPGFFAQADGGTLVL 235

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPL +Q ++   ++ G+I+   S    R+DVR++  T ++L   V++  FR+DLY
Sbjct: 236 DEVGELPLGIQAKLLRALQEGEIQPVGSGRVERVDVRIVACTHRDLRADVQAGRFREDLY 295

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R EDIP L H F   +  +   + + ++   +  L +  W  NV+
Sbjct: 296 YRLAVVELTVPPLRDRREDIPALAHEFALRYAERFGSEDVRLAPALIERLVEADWPGNVR 355

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N++ R V       +  D F         +      +        G+ + T+ + L 
Sbjct: 356 QLENVVARMVALSGGGEIGPDAF---------EATSVPADRPAAVARGGEETRTLREQLD 406

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           +                 +E+ +I   M   R   SE ARRLGI R+TL  ++R Y +  
Sbjct: 407 E-----------------LERAVIARTMAAVRGNQSEAARRLGISRNTLTERLRRYELVT 449

Query: 480 DSL 482
           D++
Sbjct: 450 DAV 452


>gi|134300113|ref|YP_001113609.1| two component sigma-54 specific Fis family transcriptional
           regulator [Desulfotomaculum reducens MI-1]
 gi|134052813|gb|ABO50784.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfotomaculum reducens MI-1]
          Length = 512

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 141/515 (27%), Positives = 237/515 (46%), Gaps = 55/515 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKENI 70
           VLIID +          ++  GY V +    V     ++K   +V  + L   + D  ++
Sbjct: 7   VLIIDDEQSVGTFFSRLLKPKGYRVGVACSGVQAHELVAKDHYDVAMVDLKLPDADGLSL 66

Query: 71  LKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L++I +  P   +I+     TT+  +K +    ++ I K F +++  ++L +    AL  
Sbjct: 67  LQHIKNVQPQCEVIIMTGYSTTRTAVKAIQYGAFDYIEKPFDDILLIEKLIEK---ALNF 123

Query: 127 GVVPSQENEHCALDSLIAV--------SPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
           G+   Q ++     S +A         +P MI++V +A +     I ++IQGE G GK+ 
Sbjct: 124 GMTDGQMDKETFSWSKVAEKIGFQVGRTPQMIKLVSIAERIAAKDINVLIQGETGTGKEV 183

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           L+RF+H + +R+  PF  +NCG + ++ +E  LFG +    T  S Q  G F  AN GT+
Sbjct: 184 LARFVHAASQRSDKPFLAINCGALPENLLESELFGHERGSFTGASVQRKGIFELANNGTL 243

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E     LA+Q ++   +ETG+         ++ +VR+I  T  +L   VK   FR+D
Sbjct: 244 FLDEIGEASLAIQVKLLRVLETGEFLRVGGEKPVKTNVRIIAATNVDLEEAVKQKQFRED 303

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR+ V  + +  L+ R EDIP  V  F+  F  +N     + +   +  +  Y W  N
Sbjct: 304 LFYRLDVIRLVLPPLKERLEDIPQFVEHFVNRFWERNDGPVPAFAPSCIEAMLNYHWPGN 363

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREF----HTETACTCYTEGKSSDT 413
           ++EL N + +A+       L +   VL     GK   +F     T+     Y  G S  T
Sbjct: 364 IRELANSVEQALA------LCDGNAVLPEHLSGKINGQFLNDERTDKKALSYHPGLSDAT 417

Query: 414 ILDNLSQESIPAIGQ----------DGEVR-----------------RLSDIEKEIIGLA 446
            + N+  E +  + Q          DG  R                  + ++E   I   
Sbjct: 418 SVLNVKPEDLDQLDQQALLDLYHKVDGLYRAIHRTMGKKGITTVFPLTIQELEARAIEET 477

Query: 447 MKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVDS 481
           ++ +   +S  AR LGIGR+TLYRK +EYNI +  
Sbjct: 478 LEFFNGNVSMSARALGIGRNTLYRKAKEYNINISG 512


>gi|322419277|ref|YP_004198500.1| Fis family two component sigma54 specific transcriptional regulator
           [Geobacter sp. M18]
 gi|320125664|gb|ADW13224.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. M18]
          Length = 484

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 137/484 (28%), Positives = 238/484 (49%), Gaps = 21/484 (4%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           ++LI+D D + + ++K       Y++ + + S+  L  +   + NV  + +   +     
Sbjct: 4   KLLILDDDHDILLMLKTIFAGEEYELLLESDSEGALKRVIAERPNVAIMDISLPQKSGIE 63

Query: 70  ILKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFF----LNLVSRKQL-CDSI 120
           +LK      P + +I+    +TTQ+ I+ +    ++ ++K F    L    +K L C+ +
Sbjct: 64  VLKEAKKIDPGLAVIMATGYKTTQNAIEAMKYGAFDYVTKPFDMNKLKGAVKKALECNLL 123

Query: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
              +R     +Q  E    D +I  SP MI++  +     D    ++IQGE G GK+ L+
Sbjct: 124 SRKVRYTKERAQVEEDLTEDLMIGSSPEMIEIWKMVGTVADSDATVLIQGESGTGKELLA 183

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R I+ + KR   PF  VNC  + +  +E  LFG +    T   ++ +GKF + NGGTI L
Sbjct: 184 RAIYNNSKRKNRPFLAVNCAALPEALLESELFGHEKGAFTDAHSRRIGKFEQCNGGTIFL 243

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +  A QG+    +E  + E       I++DVR+I  T ++LL  VK   FR DL+
Sbjct: 244 DEVGEMSPANQGKFLRVLENQEFERVGGNETIKVDVRVIAATNRSLLACVKDKSFRMDLF 303

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V    +  LR R EDIP LV  F++ F  K       ++   ++LL  + +  N++
Sbjct: 304 YRLRVVNFFLPPLRDRVEDIPLLVDLFVRKFSKKYGKNVKGVAPDTMALLANHQFDGNIR 363

Query: 360 ELKNILLRAVIGLKDSHLTEDRF-VLLLSREGKKEREFHTETACTCYTEGKSS--DTILD 416
           ELKN++  A++  +   L    F   L ++ G KE +   E+A   Y E   S  + + D
Sbjct: 364 ELKNVINSAIVFCRGDILVPGDFETFLTAKAGFKEVDL--ESAGDDYYEVFWSMLEPVFD 421

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
            + Q++  AI +   +     +EK +I +AM+         A+ LGI R+TL  ++  Y 
Sbjct: 422 GICQKNKGAIYESVNM----GLEKALIHMAMEKSNNNQVFAAKLLGISRNTLRDRLERYR 477

Query: 477 IEVD 480
           I ++
Sbjct: 478 IGMN 481


>gi|149369867|ref|ZP_01889718.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [unidentified eubacterium SCB49]
 gi|149356358|gb|EDM44914.1| two component, sigma54 specific, transcriptional regulator, Fis
           family protein [unidentified eubacterium SCB49]
          Length = 441

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 111/371 (29%), Positives = 201/371 (54%), Gaps = 11/371 (2%)

Query: 9   RHKRVLIIDKDDEQIKIIKDHVESYGYDVF-IVNVSDLSTISK-IQVNVIFLSLINCEDD 66
           + + +LI+D D   +++++ H++S+ Y  +  V+V +   I +  +++++   L   E D
Sbjct: 5   QKENILIVDDDINILELLQRHLQSWNYHTYKAVSVKEAVQILRDTKIDLLITDLKMPEVD 64

Query: 67  KENILKNIVDKIPIVPIIVQT----TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIIC 122
              ++K + +  P +P +V T     QD++  +   + + ++K F     +  +  SI+ 
Sbjct: 65  GSELIKFVSEHYPKLPKLVVTGYPSVQDSLVAIKSGVVDYLTKPFTKNELKTAIDASIVS 124

Query: 123 A--LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
           +  LR  V+P  E +      +I VS  + +V+ +  +  D    I ++GE G GK+ ++
Sbjct: 125 SEKLRSDVIPVSEEKPYG--DIIGVSDKIKKVIQIIERVKDNKATIFVKGESGTGKELVA 182

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVL 239
           R IH  GK +  PF  VNCG I ++ +E  LFG      T       G F  ANGGTI L
Sbjct: 183 RAIHYQGKFSRAPFIAVNCGGIPENLLESELFGYTKGAFTGAEKDRDGFFQAANGGTIFL 242

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E      AVQ R+   ++  ++    ++ A ++DVR+I  T  +LL  +K   FR+DL+
Sbjct: 243 DEIGNASKAVQSRLLRVLQEKEVLKVGAQKATKIDVRIIAATNSDLLEMIKKQTFREDLF 302

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + ++ LR R EDIP LV  FL  +  +   + + ++ +AL++L +Y W  N++
Sbjct: 303 YRLTVVEVEVAPLRERKEDIPLLVDKFLFKYGIEYKDRFVKMTPEALNILKRYNWPGNIR 362

Query: 360 ELKNILLRAVI 370
           EL+N++ RAVI
Sbjct: 363 ELENVIQRAVI 373


>gi|315186283|gb|EFU20044.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Spirochaeta thermophila DSM 6578]
          Length = 453

 Score =  168 bits (425), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 138/477 (28%), Positives = 220/477 (46%), Gaps = 43/477 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST--ISKIQVNVIFLSLINCEDDKENI 70
           VL+ D +    + +K  ++  GY+VF+    D +   + +  ++++   L       + +
Sbjct: 5   VLVADDEKNIREGLKTFLQMEGYEVFLAEDGDRAKKILDEEDIDLVIADLKMPGMPGDEL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFF---LNLVSRKQLCDSIICALREG 127
           L+ +V   P VP+I+ T    I+     + +    F    LNL  R  L      + RE 
Sbjct: 65  LRYVVGGYPTVPVIILTGHGTIESAVQAMRDGAFDFLTKPLNL-DRLGLLVKRALSTREL 123

Query: 128 VVPSQE-----NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
           V+  +E             LI  SP M Q+ ++ ++       ++I GE GVGK+R++  
Sbjct: 124 VLQHRELQRELERQKKFGMLIGKSPQMKQIFEVIQQVAPTRASVLITGESGVGKERIADA 183

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           IH    R   P   V+C  + +  +E  LFG +    T   A   G+F  A+GGT+ L+E
Sbjct: 184 IHYFSNRRDKPLIKVHCAALAESLLESELFGHEKGAFTGAHATRRGRFELADGGTLFLDE 243

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +  AVQ ++   ++  K E       I +DVR+I  T K+L  +V+   FR+DLYYR
Sbjct: 244 IGEISPAVQVKLLRVLQEKKFERVGGERTIEVDVRIIAATNKDLKREVEEGRFREDLYYR 303

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  I++  LR R EDIP L+  FL+    +N  K   I  KA ++L  Y W  NV+EL
Sbjct: 304 LNVVHIHVPPLRERKEDIPLLIAAFLKELAEENGKKIEGIDPKARAILYNYSWPGNVREL 363

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQE 421
           +N +  AV+  K + +  +     +  E                 EG     I       
Sbjct: 364 RNCIESAVVMCKGTIIVVEDLPPHIREE----------------AEGGGLIRI------- 400

Query: 422 SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
              A+G       L + EKEII   +   +   S  A+ LGIGR TL+RKI+EY +E
Sbjct: 401 ---AVGTS-----LEEAEKEIIRATLAYCKGNKSRAAQILGIGRKTLHRKIQEYGLE 449


>gi|150004891|ref|YP_001299635.1| two-component system response regulator [Bacteroides vulgatus ATCC
           8482]
 gi|294778456|ref|ZP_06743879.1| response regulator receiver domain protein [Bacteroides vulgatus
           PC510]
 gi|149933315|gb|ABR40013.1| two-component system response regulator [Bacteroides vulgatus ATCC
           8482]
 gi|294447718|gb|EFG16295.1| response regulator receiver domain protein [Bacteroides vulgatus
           PC510]
          Length = 451

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 112/409 (27%), Positives = 199/409 (48%), Gaps = 39/409 (9%)

Query: 79  PIVPIIVQTTQDNIKI----LNCFLYNRISKFFLN--LVSRKQLCDSIICALREGVVPSQ 132
           P VP+I+ T   +I++    +    ++ I+K + N  L+ R +    +    ++  VP +
Sbjct: 74  PDVPVILMTAWGSIQLAVQGMQAGAFDFITKPWNNVALMQRIETALELTSQDKKAAVPVE 133

Query: 133 ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF 192
           +N+      +I  S A++ V+   ++       ++I GE G GK+ ++  +H +  R+  
Sbjct: 134 DNDGFNRSHIIGKSKALMDVLATIKRIARTNASVLITGESGTGKELIAEAVHLNSSRSKK 193

Query: 193 PFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQG 251
           PF  VN G I     E  +FG      T  +A  +G+F  A+ GTI L+E   L L+ Q 
Sbjct: 194 PFVKVNLGGISHTLFESEMFGHKKGAFTDATADRVGRFELADKGTIFLDEIGDLDLSCQV 253

Query: 252 RIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIST 311
           ++   ++    E        ++D+R++  T  +L   V+ H FR+DL+YRI++  +++  
Sbjct: 254 KLLRVLQEQTFEVLGDSRPRKVDIRVVSATNADLRQMVQEHTFREDLFYRINLITVHLPA 313

Query: 312 LRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIG 371
           LR R EDIP LV  F    C  N + ++  + +A+  L++ P+  N++ELKN++ R ++ 
Sbjct: 314 LRERREDIPLLVRHFADKQCESNGLPKVEFTSEAMDYLSRLPYPGNIRELKNLVERTLLV 373

Query: 372 LKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGE 431
                LT D F        K + +   E   T   +G +                     
Sbjct: 374 SGKEILTADDF--------KSQYQHPIEQKMTTNLQGMT--------------------- 404

Query: 432 VRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
              L +IEK+ I   ++ Y   MS+VA  LGI R+ LYR++ +YNI+V+
Sbjct: 405 ---LEEIEKQTILQTLEKYNNNMSQVAIALGISRAALYRRLEKYNIQVN 450


>gi|119897516|ref|YP_932729.1| sigma-54 dependent transcriptional regulator [Azoarcus sp. BH72]
 gi|119669929|emb|CAL93842.1| Sigma-54 dependent transcriptional regulator [Azoarcus sp. BH72]
          Length = 686

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 114/372 (30%), Positives = 177/372 (47%), Gaps = 33/372 (8%)

Query: 110 LVSRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQ 169
           LV  + + +S +  L E    +     C  D+++  SPAM +  DL R+     +P++++
Sbjct: 327 LVPGRGVRNSPVARLAEQSSEADPRRSC-FDNILGRSPAMREATDLGRRLATKRVPVLVE 385

Query: 170 GEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV--DLQTKNSAQFLG 227
           GE GVGK+  +R +H  G+    PF   NCG   ++ I   LFG V        +    G
Sbjct: 386 GETGVGKELFARALH-GGEHLGGPFITYNCGAASKELIAADLFGHVRGAFTGATNDGRPG 444

Query: 228 KFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLP 287
           +F  ANGGT+ L+E   +PL +Q  +   +E G +         R+DVRLI +T +NL  
Sbjct: 445 RFELANGGTLCLDEIGEMPLDLQPVLLRALEEGIVYRLGDTQPRRVDVRLIAMTNRNLRE 504

Query: 288 QVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALS 347
           +V +  FR+DLYYRI V  + I  LR R  DIP L   F      ++ + +     + L 
Sbjct: 505 EVAAGRFRRDLYYRIGVTRLRIPPLRERDGDIPLLASHFCTQLAERHGVPRREFGPEVLD 564

Query: 348 LLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTE 407
            L  Y W  NV+EL+N++              +  +L+ S    +  E   E        
Sbjct: 565 ALQAYCWPGNVRELRNVV--------------ESLLLMDSTPQVRVDELPEE-------- 602

Query: 408 GKSSDTILDNLSQESIPAI-GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
                 IL ++ Q + PA  G + E   L   E+  I  A+  ++  +++ AR LGI RS
Sbjct: 603 ------ILASVPQAARPAAEGAEPECPSLEAAERRAIQKAVINFQGNLAQAARLLGISRS 656

Query: 467 TLYRKIREYNIE 478
           TLYRK+  Y +E
Sbjct: 657 TLYRKVERYALE 668


>gi|149927311|ref|ZP_01915567.1| transcriptional regulator, Fis family protein [Limnobacter sp.
           MED105]
 gi|149824025|gb|EDM83248.1| transcriptional regulator, Fis family protein [Limnobacter sp.
           MED105]
          Length = 554

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 104/348 (29%), Positives = 178/348 (51%), Gaps = 23/348 (6%)

Query: 140 DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNC 199
           D L+ VSPA +   +L ++A   +I +++ GE GVGK+  +R++H++  RA  PF  VNC
Sbjct: 223 DDLVGVSPAFMNAFELLQRAAQGSITVLLLGETGVGKEMFARWLHDNSPRAKGPFLAVNC 282

Query: 200 GMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIE 258
             I  + IE  LFG +    T       G+F  A+ GT+ L+E   LPL+ Q ++   ++
Sbjct: 283 AAIPHELIEAELFGVEKGAYTGAHTPRAGRFERADHGTLFLDEVGDLPLSTQVKLLRVLQ 342

Query: 259 TGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSED 318
           TG+ E   S    +++VR++  T   L   ++ + FR DLYYR++ F I I  LR R  D
Sbjct: 343 TGEFERLGSERVQKVNVRIVAATNVELQQAIRENKFRIDLYYRLNTFPIKIPPLRERQAD 402

Query: 319 IPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDS--- 375
           I  L++ F+  +C     K   ++DKA+  +  Y W  N++EL+N++ RAV+   D    
Sbjct: 403 ISPLINRFMTKYCASYNKKLQGLTDKAMQEVMSYEWPGNIRELENLIERAVVLAPDGGYV 462

Query: 376 ---HLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEV 432
              HL +DR       E  KE+            E +  D + + +  +++         
Sbjct: 463 EACHLFDDRI------EPCKEKSQLNAQGELAPVETRPIDDLCNEILTKNVG-------- 508

Query: 433 RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
             L  +E+ ++  A+K  +  +S+ AR LGI R  L  ++++  I ++
Sbjct: 509 --LDTLERRLMQTALKQAKGNLSQAARVLGITRPQLAYRLKKEGIPLE 554


>gi|303325765|ref|ZP_07356208.1| transcriptional regulatory protein ZraR [Desulfovibrio sp.
           3_1_syn3]
 gi|302863681|gb|EFL86612.1| transcriptional regulatory protein ZraR [Desulfovibrio sp.
           3_1_syn3]
          Length = 466

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 122/476 (25%), Positives = 222/476 (46%), Gaps = 44/476 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDV--FIVNVSDLSTISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D    ++++  +E +GY V   +     ++   K   +++ + +   +      
Sbjct: 4   ILVADDDATHREVLRTLLEEWGYAVREAVDGEHAVALCRKQPFDLVLMDVRMPKKSGLEA 63

Query: 71  LKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQLCDSIIC 122
           LK I    P VP+++ T        ++ +    Y+ ++K      L +V R       + 
Sbjct: 64  LKEIKVHNPAVPVLIMTAFSEVAAAVEAIKSGAYDYLTKPLDFEKLKVVLRNVFAH--VG 121

Query: 123 ALREGVVPSQENEHC-ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            +RE    S+      A   ++  S +M  + ++ R        ++I GE G GK+ +++
Sbjct: 122 LIRENATLSRSLAATEAQTGMVGRSESMRALWEMVRTIAPTDATVLITGESGTGKELVAK 181

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H + +RA  PF  VNC  + +  +   LFG +    T    +  G F++A+GGTI L+
Sbjct: 182 AVHAASRRARGPFVAVNCAALTESLLASELFGHEKGAFTGADKKHEGHFLKADGGTIFLD 241

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL++Q ++   I+  ++       A+ +DVR+I  T ++L  +V +  FR+DLYY
Sbjct: 242 EIGEMPLSMQVKLLRVIQEREVLSVGGNKAVPVDVRIIAATNRDLAKEVAAGTFRQDLYY 301

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++V  + +  LR R++DIP L   F+  F  KN       +  A+  L +Y W  NV+E
Sbjct: 302 RLNVVTLALPPLRERADDIPLLAQHFMARFADKNNKNIKGFTPGAMDRLVRYAWPGNVRE 361

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L+N++ RA I L   H++E              RE     A +        D + D L+ 
Sbjct: 362 LENVIERASILLLGEHISE--------------RELPERFAAS------QGDALTDALTT 401

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
           +  P          L D+E+ +I   +K +    +E A+ LGI R TL+ K+ +Y 
Sbjct: 402 D-CPT---------LEDVERAVILKTLKRFGGNKTEAAKALGITRKTLHAKLSKYQ 447


>gi|315187285|gb|EFU21041.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Spirochaeta thermophila DSM 6578]
          Length = 456

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 139/478 (29%), Positives = 229/478 (47%), Gaps = 40/478 (8%)

Query: 13  VLIIDKDDEQIKI-IKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           +L+ID D+E I++ ++D +   GY VF     +  L  + +  V+V+ L L         
Sbjct: 6   ILVID-DEENIRLALEDILTDEGYTVFTAEDGIEGLRLMDRYPVDVVLLDLWLPHRGGME 64

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           IL+ +  K P V I++ +    I+     +      F    +S +++   +  ALR   +
Sbjct: 65  ILEELRAKDPSVEIVIISGHGTIETAVRAVKQGAFDFLEKPLSLEKVLTVVRNALR---L 121

Query: 130 PSQENEHCAL-------DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
              +NE+  L       D +I  SPAM  + +   ++      I+I GE G GK+ ++R 
Sbjct: 122 RELQNENTRLRQRLYQEDEMIGTSPAMQVIRERIAQSAASDSRILILGENGTGKELVARE 181

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           IH   +RA  PF  VNC  I    +E  LFG +    T   +   GKF  A+ GT+ L+E
Sbjct: 182 IHRRSRRASGPFVEVNCAAIPDTLLESELFGHEKGAFTGALSSRRGKFELAHNGTLFLDE 241

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              + L+ Q ++   ++  +         I +DVRLI  T K+L  +VKS  FR+DLYYR
Sbjct: 242 VADMSLSAQAKVLRVLQELQFTRIGGERVITVDVRLIAATNKDLEGEVKSGRFREDLYYR 301

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  I +  LR R EDIP L+ +FL+ F       +  IS + L++L +YPW  N++EL
Sbjct: 302 LNVIPIYVPPLRERVEDIPTLIDYFLKKFTPPGETPK-RISREGLTMLKEYPWPGNIREL 360

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQE 421
           KN + R  I   ++ ++ +             +EF  E         ++  T+LD  S  
Sbjct: 361 KNFVERLCILSDEAEISPETI-----------KEFLGEA-----LHARTHSTVLDEYSHL 404

Query: 422 SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
            +      GE R     EK +I   ++ +   +S  A  LGI  S L+ KI+++ I++
Sbjct: 405 PL------GEAR--DAFEKRLIEKKLEEHDYNISRTAASLGIYPSNLHSKIKKFGIKI 454


>gi|78043414|ref|YP_360379.1| sigma-54 dependent transcriptional regulator [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77995529|gb|ABB14428.1| sigma-54 dependent transcriptional regulator [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 732

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 112/343 (32%), Positives = 174/343 (50%), Gaps = 31/343 (9%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
           LD +   +  +I+V  L  KA      ++IQGE GVGK+  +R IH   +RA  PF  +N
Sbjct: 419 LDGITGQTEKIIEVKKLIEKAAMSDGNVLIQGESGVGKEIAARTIHYLSERADKPFVAIN 478

Query: 199 CGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           C  I ++ +E  LFG  +            GK  +A+GGT+ L+E   +PL++Q ++  F
Sbjct: 479 CAAIPENLLESELFGYEEGAFTGAKRGGKAGKIEQADGGTLFLDEIGDMPLSMQVKLLRF 538

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           I+  + E   S    ++D+R+I  T + L   VK   FR DLYYR++VF INI  LR R 
Sbjct: 539 IQNREFERIGSNTPRKVDIRIIAATNQPLAKLVKEGRFRMDLYYRLNVFNINIPPLRERR 598

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           +DIP LV+ F+  FC +  +    ++ +A+++L  Y W  N++EL+N++ RA       +
Sbjct: 599 DDIPLLVNRFMNEFCERRKMAPKIVTSEAMNILMNYSWPGNIRELQNVIERAY------Y 652

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
           L E   +          +  H     T              LS E I  I    E   ++
Sbjct: 653 LAEGNLI----------KPEHLPAQLTS-----------KALSGERITKITTFKEA--VA 689

Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           ++EK++I   +K         A+ LGI R+TLY+KI+EY IE 
Sbjct: 690 EVEKKLIIEGLKATNYNKLACAKLLGIPRATLYQKIKEYGIEA 732


>gi|85858790|ref|YP_460992.1| response regulator [Syntrophus aciditrophicus SB]
 gi|85721881|gb|ABC76824.1| response regulator containing sigma 54 interaction domain
           [Syntrophus aciditrophicus SB]
          Length = 457

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 134/483 (27%), Positives = 223/483 (46%), Gaps = 45/483 (9%)

Query: 10  HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDK 67
            K +LI+D ++   K + D +   GY+V  V   +  +  + +    ++ L +     D 
Sbjct: 2   QKSILIVDDEESICKSLGDILVDEGYEVQTVQSGEEAIRLLDEDLPGIVLLDIWLPGIDG 61

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
             +LK I    P +P+++ +    I+        ++  F  + + +    + II  L+  
Sbjct: 62  MEVLKTIKSLHPKLPVVMMSGHGTIE--TAVKATKLGAF--DFIEKPLSLEKIILTLKHA 117

Query: 128 VVPSQ-ENEHCALD-------SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
           +  S+ E E+  L         L   SP +I+++++          I+I GE G GK+ +
Sbjct: 118 LDLSRLEEENVLLKQKINRDYELTGKSPPIIELMEMISIVAPTNAWILIMGENGTGKELV 177

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R IH   KRA  P   VNC  I ++ IE  LFG +    T  + +  GKF  A+ GTI 
Sbjct: 178 ARAIHRQSKRADKPMVEVNCAAIPEELIESELFGHEKGAFTGATEKKRGKFDIAHEGTIF 237

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   + L  Q +I   ++  K E       I+LDVR++  T K+L  +++   FR+DL
Sbjct: 238 LDEVADMSLKAQAKILRILQEKKFERVGGNKVIQLDVRVLAATNKDLEKEMEEGRFRQDL 297

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +YR++V  + +  LRSR EDIP L   FL  F  K      +I D AL+LL ++ W  NV
Sbjct: 298 FYRLNVIPLKVPPLRSRKEDIPLLAERFLSDFALKEGEPGKTIQDDALALLMEHSWPGNV 357

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHT---ETACTCYTEGKSSDTIL 415
           +ELKN + R  I +  S++     +  L R+G K   F     E     + E K      
Sbjct: 358 RELKNFIERLAI-MTTSNVITVHDIPPLPRDGHKVEPFREPGFELLAGSFREAK------ 410

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
                                D EK+ I   ++ +   +S+ A  +G+ RS L++KI+ Y
Sbjct: 411 --------------------MDFEKQYISRKLREFDGNISKTAESIGLERSNLHKKIKAY 450

Query: 476 NIE 478
            +E
Sbjct: 451 GLE 453


>gi|307719869|ref|YP_003875401.1| transcriptional regulatory protein [Spirochaeta thermophila DSM
           6192]
 gi|306533594|gb|ADN03128.1| transcriptional regulatory protein [Spirochaeta thermophila DSM
           6192]
          Length = 456

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 139/478 (29%), Positives = 229/478 (47%), Gaps = 40/478 (8%)

Query: 13  VLIIDKDDEQIKI-IKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           +L+ID D+E I++ ++D +   GY VF     +  L  + +  V+V+ L L         
Sbjct: 6   ILVID-DEENIRLALEDILTDEGYTVFTAEDGIEGLRLMDRYPVDVVLLDLWLPHRGGME 64

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           IL+ I  K P V I++ +    I+     +      F    +S +++   +  ALR   +
Sbjct: 65  ILEEIRAKDPSVEIVIISGHGTIETAVRAVKQGAFDFLEKPLSLEKVLTVVRNALR---M 121

Query: 130 PSQENEHCAL-------DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
              +NE+  L       D +I  SPAM  + +   ++      I+I GE G GK+ ++R 
Sbjct: 122 RELQNENTRLRQRLYQEDEMIGTSPAMQVIRERIAQSAASDSRILILGENGTGKELVARE 181

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           IH   +RA  PF  VNC  I    +E  LFG +    T   +   GKF  A+ GT+ L+E
Sbjct: 182 IHRRSRRASGPFVEVNCAAIPDTLLESELFGHEKGAFTGALSSRRGKFELAHNGTLFLDE 241

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              + L+ Q ++   ++  +         I +DVRLI  T K+L  +VK+  FR+DLYYR
Sbjct: 242 VADMSLSAQAKVLRVLQELQFTRIGGERVITVDVRLIAATNKDLEGEVKAGRFREDLYYR 301

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  I +  LR R EDIP L+ +FL+ F       +  IS + L++L +YPW  N++EL
Sbjct: 302 LNVIPIYVPPLRERVEDIPSLIDYFLKKFTPPGETPK-RISREGLTMLKEYPWPGNIREL 360

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQE 421
           KN + R  I   ++ ++ +             +EF  E         ++  T+LD  S  
Sbjct: 361 KNFVERLCILSDEAEISPETI-----------KEFLGEA-----LHARTHSTVLDEYSHL 404

Query: 422 SIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
            +      GE R     EK +I   ++ +   +S  A  LGI  S L+ KI+++ I++
Sbjct: 405 PL------GEAR--DAFEKRLIEKKLEEHDYNISRTAASLGIYPSNLHSKIKKFGIKI 454


>gi|1171795|sp|P45671|NTRC_AZOBR RecName: Full=Nitrogen assimilation regulatory protein
 gi|599602|emb|CAA86065.1| Nitrogen assimilation regulatory protein [Azospirillum brasilense]
          Length = 481

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 132/493 (26%), Positives = 234/493 (47%), Gaps = 48/493 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   G++V    N S L   ++  Q ++I   ++  +++  ++
Sbjct: 6   ILVADDDRAIRTVLTQALARLGHEVRTTGNASTLWRWVADGQGDLIITDVVMPDENGLDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           +  I    P + IIV + Q+     +K      +  + K F     +++V R    ++  
Sbjct: 66  IPRIKKIRPDLRIIVMSAQNTLITAVKAAERGAFEYLPKPFDLKELVSVVERALNSNTPP 125

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            AL     P+   E      LI  SPAM ++  +  +     + + I GE G GK+ ++R
Sbjct: 126 AAL-----PADAGEADEQLPLIGRSPAMQEIYRVLARLMGTDLTVTITGESGTGKELVAR 180

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H+ GKR   PF  +N   I ++ IE  LFG +    T  + +  G+F +A GGT+ L+
Sbjct: 181 ALHDYGKRRNGPFVAINMAAIPRELIESELFGHEKGAFTGATNRSTGRFEQAQGGTLFLD 240

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL  Q R+   ++ G+      R  I+ DVR++  T ++L   ++  +FR+DL+Y
Sbjct: 241 EIGDMPLEAQTRLLRVLQEGEYTTVGGRTPIKTDVRIVAATHRDLRTLIRQGLFREDLFY 300

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R+ V  I +  LR R+ED+P LV  FL   C+   +   SI   A+  L +Y W  NV+E
Sbjct: 301 RLCVVPIRLPPLRERTEDVPLLVRHFLNQ-CSAQGLPVKSIDQPAMDRLKRYRWPGNVRE 359

Query: 361 LKNILLR-------AVIGLK--DSHLTEDRFVLLLSREGKKER-----EFHTETACTCYT 406
           L+N++ R        VIGL   ++ L +         E + E      E H +     + 
Sbjct: 360 LENLVRRLAALYSQEVIGLDVVEAELADTTPAAQPVEEPQGEGLSAAVERHLKDYFAAHK 419

Query: 407 EGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
           +G  S+ + D                R L ++E+ +I L++   R    + A+ LG+ R+
Sbjct: 420 DGMPSNGLYD----------------RVLREVERPLISLSLSATRGNQIKAAQLLGLNRN 463

Query: 467 TLYRKIREYNIEV 479
           TL +KIR+ +I+V
Sbjct: 464 TLRKKIRDLDIQV 476


>gi|289207723|ref|YP_003459789.1| Fis family transcriptional regulator [Thioalkalivibrio sp. K90mix]
 gi|288943354|gb|ADC71053.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Thioalkalivibrio sp. K90mix]
          Length = 473

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 130/474 (27%), Positives = 217/474 (45%), Gaps = 26/474 (5%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLS--TISKIQVNVIFLSLINCEDDKEN 69
           RVL+++ D    +++ + +   GY V  V  ++ +   + +  V+++   L     D  +
Sbjct: 10  RVLVVEDDRGHRELLAEELAEVGYAVTAVETAEEAEQVLRQQTVSLVVSDLRLPGADGFH 69

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQL---CDSIICALRE 126
           +L+   D +P+   I+ T    I      L      F    V  + L    + +  A R 
Sbjct: 70  VLEVARDTVPVPGFIMLTGFGTIDQAVTALKAGADDFLTKPVDLEHLRLAAERVAEARRL 129

Query: 127 GVVPSQENEHCALD----SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
                Q  E  A D     +   SPAM+++ DL R+       ++I GE G GK+ ++R 
Sbjct: 130 RAEVRQYREALAGDESFHGMQGKSPAMLKLHDLIRRIAAADGSVLITGESGTGKELVARA 189

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEE 241
           +H    RA  PF  +NC  I +  +E  L G V    +       G F EA+GGT+ L+E
Sbjct: 190 LHAESARAEGPFIALNCAGIPETLLESELLGHVAGAFSGAKGARRGLFTEADGGTLFLDE 249

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +P+A+Q ++   ++ G++    S   I  DVR++  T ++L  +++   FR+DLYYR
Sbjct: 250 IAEMPVAMQSKLLRLLQDGRVRPVGSNEEIETDVRIVAATHQDLQERIRHEQFREDLYYR 309

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           +  F I I  LR R +DI  L   FL+       +    +S +A+  L +Y +  NV+EL
Sbjct: 310 LETFRIEIPPLRDRGDDIERLAQQFLREQALARGLPVRELSPEAMRALLRYGFPGNVREL 369

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETA-CTCYTEGKSSDTILDNLSQ 420
            +++ RA   L    + E R +         ER   + TA  +  + G  + T L     
Sbjct: 370 ASLMERAAT-LASGEVIELRDL--------PERVRQSGTAGGSGVSPGNVAGTDL----- 415

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
             IP  G D     L+++E+  +   ++         AR LGIGR TLYRK+ E
Sbjct: 416 -PIPGTGDDSHWPSLAEVEQAYLHRVLEHVEGNKQRAARILGIGRKTLYRKLGE 468


>gi|261339981|ref|ZP_05967839.1| transcriptional regulatory protein TyrR [Enterobacter cancerogenus
           ATCC 35316]
 gi|288317899|gb|EFC56837.1| transcriptional regulatory protein TyrR [Enterobacter cancerogenus
           ATCC 35316]
          Length = 513

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 103/346 (29%), Positives = 174/346 (50%), Gaps = 47/346 (13%)

Query: 138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV 197
           A   ++AVSP M  VVD ARK  +   P++I G+ G GK  L+  +H+S  RA  P+  +
Sbjct: 202 AFSQIVAVSPKMRHVVDQARKLANLTAPLLITGDTGTGKDLLAHAVHQSSPRAAKPYLAL 261

Query: 198 NCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
           NC  I +D +E  LFG      K      G F +ANGG+++L+E   +   +Q ++  F+
Sbjct: 262 NCASIPEDAVESELFGHAPEGKK------GFFEQANGGSVLLDEIGEMSPRMQAKLLRFL 315

Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
             G          + +DVR+I  T+KNL+  V+  VFR+DLYYR++V  +NI  LR   +
Sbjct: 316 NDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGVFREDLYYRLNVLTLNIPPLRDCPQ 375

Query: 318 DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHL 377
           DI  L   F+  F  +  + +  +S    ++LT+Y W  N+++LKN + RA+  L+   L
Sbjct: 376 DIMPLTELFVARFADEQGVPRPKLSADLGTVLTRYGWPGNIRQLKNAVYRALTQLEGYEL 435

Query: 378 TEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSD 437
                                          ++ D +L +    ++ ++G++     L D
Sbjct: 436 -------------------------------RAQDILLPDYDAGTV-SVGEEAMEGSLDD 463

Query: 438 I----EKEIIGLAMKLYRAQMS--EVARRLGIGRSTLYRKIREYNI 477
           I    E+ ++    +LYR+  S  ++A+RLG+  + +  K+REY +
Sbjct: 464 ITSRFERSVL---TQLYRSYPSTRKLAKRLGVSHTAIANKLREYGL 506


>gi|264677352|ref|YP_003277258.1| sigma54 specific transcriptional regulator, Fis [Comamonas
           testosteroni CNB-2]
 gi|262207864|gb|ACY31962.1| sigma54 specific transcriptional regulator, Fis [Comamonas
           testosteroni CNB-2]
          Length = 514

 Score =  167 bits (424), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 108/374 (28%), Positives = 184/374 (49%), Gaps = 32/374 (8%)

Query: 112 SRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGE 171
           +R++L      +L+  V  S+ +++ +  S +  SPA ++V   AR+A     P+++ GE
Sbjct: 163 ARRELAAQRSRSLQASVQGSRRSKY-SFASFVGSSPAAVEVKRQARRAAQSMSPVLLLGE 221

Query: 172 FGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-------DVDLQTKNSAQ 224
            G GK+ L+  IH +  R+  PF  VN   I +  +E   FG         D +T++   
Sbjct: 222 TGTGKEVLAHAIHAASARSAGPFVSVNIAAIPETLLEAEFFGVAPGAFTGADRKTRD--- 278

Query: 225 FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN 284
             GKF  A+GGT+ L+E   +P ++Q ++   ++ G+IE   S   +  DVR++  T ++
Sbjct: 279 --GKFKLADGGTLFLDEIGDMPASLQAKLLRALQEGEIEPLGSNQIVHFDVRVVAATSRD 336

Query: 285 LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK 344
           LL  V+   FR+DL+YR+ V  + +  LR RS DIP LV    +    +N +    +   
Sbjct: 337 LLQMVRDGRFREDLFYRLHVLPVRVPPLRERSSDIPALVEMLCEDLALRNDMVPPELGKG 396

Query: 345 ALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTC 404
           AL LL    W  N++EL+N+L +A +   DSH+       +L   G + +  H +     
Sbjct: 397 ALELLVAQAWRGNIRELRNVLEQAAMRCDDSHIDAGLLTQVLRSSGVELQVPHRQP---- 452

Query: 405 YTEGKSSDTILDNLSQESIPAIGQ--DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLG 462
                        L+QE + A G        +++++E   I  AM+ +      VAR LG
Sbjct: 453 -------------LAQEPVAAAGDLLKPLAEQMAELEARAIRAAMQAHGGNKLAVARTLG 499

Query: 463 IGRSTLYRKIREYN 476
           I R+ LY ++ + N
Sbjct: 500 ISRAKLYDRLEKLN 513


>gi|227821861|ref|YP_002825831.1| response regulator for gln [Sinorhizobium fredii NGR234]
 gi|227340860|gb|ACP25078.1| response regulator for gln [Sinorhizobium fredii NGR234]
          Length = 484

 Score =  167 bits (423), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 137/490 (27%), Positives = 232/490 (47%), Gaps = 41/490 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   I+    +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWIAAGDGDLVVTDVVMPDENAFDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 66  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALAE 121

Query: 127 GVVPSQENEHCALDS-----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              P +       DS     L+  S AM ++  +  +     + +MI GE G GK+ ++R
Sbjct: 122 ---PKRRPSKLDDDSQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVAR 178

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +H+ GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT
Sbjct: 179 ALHDYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGT 234

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+
Sbjct: 235 LFLDEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRSDVRIVAATNKDLKQSINQGLFRE 294

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DLYYR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  +PW  
Sbjct: 295 DLYYRLNVVPLRLPPLRDRAEDIPDLVRHFVQQ-AEKEGLDVKRFDQEALELMKAHPWPG 353

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTIL 415
           NV+EL+N++ R         +T +    ++  E + E  +   + A         S  + 
Sbjct: 354 NVRELENLVRRLTALYPQDVITRE----IIENELRSEVPDSPIDKAAARPGSMSISQAVE 409

Query: 416 DNLSQ------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           +N+ Q      E++P  G    V  L+++E  +I  A+   R    + A  LG+ R+TL 
Sbjct: 410 ENMRQYFASFGEALPPTGLYDRV--LAEMEYPLILAALTATRGNQIKAADLLGLNRNTLR 467

Query: 470 RKIREYNIEV 479
           +KIRE  + V
Sbjct: 468 KKIRELGVSV 477


>gi|153939902|ref|YP_001390983.1| signal-transduction and transcriptional-control protein
           [Clostridium botulinum F str. Langeland]
 gi|152935798|gb|ABS41296.1| sensory box sigma-54 dependent transcriptional regulator
           [Clostridium botulinum F str. Langeland]
 gi|295319042|gb|ADF99419.1| sensory box sigma-54 dependent transcriptional regulator
           [Clostridium botulinum F str. 230613]
          Length = 643

 Score =  167 bits (423), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 116/342 (33%), Positives = 177/342 (51%), Gaps = 32/342 (9%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            D++I V+  MI++++LA+KA      I+I+GE G GK+ +++ IH    RA  PF  VN
Sbjct: 332 FDNIITVNEKMIEIIELAKKASKSNCNILIEGESGTGKELIAQSIHNYSMRATGPFLAVN 391

Query: 199 CGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           C  I ++ +E  LFG         +     GKF  A+GGTI L+E   LPL +Q ++   
Sbjct: 392 CASIPRELVESELFGYEKGAFTGASKEGHPGKFELADGGTIFLDELGELPLDMQSKLLRV 451

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           ++  KI         +L+VR+I  T +NL  ++K   FR+DLYYR+ V  I I  LR R 
Sbjct: 452 LDNNKIIRVGGTYEKQLNVRVIGATNRNLKEEMKKKNFREDLYYRLGVINIKILPLRYRK 511

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           EDI  LV+ F+ +   KN  +   +    +  L +Y W  NV+EL+N++ R      D +
Sbjct: 512 EDIEVLVNSFVMNLNQKNLQQNKRVKKAYIDKLKEYDWPGNVRELRNVVER------DYY 565

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
           L++                  T T    Y E K    I    + E+     +D  +  + 
Sbjct: 566 LSD------------------TGTVSPYYIEKK----IFLETNNENYE--NKDINIIPME 601

Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            +EKE I  A++     +++VAR L IGRSTLYRKI++YNI+
Sbjct: 602 KLEKENIENAIEKCDGNLAKVARLLNIGRSTLYRKIKKYNIK 643


>gi|310820458|ref|YP_003952816.1| Fis family two component transcriptional regulator [Stigmatella
           aurantiaca DW4/3-1]
 gi|309393530|gb|ADO70989.1| Two component transcriptional regulator, Fis type [Stigmatella
           aurantiaca DW4/3-1]
          Length = 472

 Score =  167 bits (423), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 125/472 (26%), Positives = 213/472 (45%), Gaps = 42/472 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKENI 70
           VL++D D   +  +    +  G      +     L  + K +V+V+   L+    D + +
Sbjct: 6   VLVVDDDRANLDSVARIFQREGLATHCASNGTEALELLRKPEVSVMVTDLMMPGMDGQEL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           LK      P V +++ T    ++     + +    F    + R  L  ++  AL +  + 
Sbjct: 66  LKASRTIRPDVEVVLMTAYGTVETAVAAMKDGAYDFITKPLKRHALVKAVQKALEKQALV 125

Query: 131 SQ---------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           ++         E       +++  +PA   ++D  R+A      +++ GE G GK+  +R
Sbjct: 126 AENKVLKAKLAEMGASGGKAMVGQAPAFRAMMDTLRQAAPSTATVLLIGESGTGKELAAR 185

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +HE   RA   F  VNC  + +  +E  LFG +    T   A+  G+F  A+GGT+ L+
Sbjct: 186 ALHEHSSRAKTAFIAVNCAALPESILEAELFGVERGAYTGAVARREGRFERAHGGTLFLD 245

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL+ Q ++   ++ G+IE       +++DVRL+  T K+L  +V    FR+DLYY
Sbjct: 246 EVGEMPLSAQVKLLRVLQEGEIERLGGTQTVKVDVRLVAATNKDLQKEVAEGRFREDLYY 305

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++V  + +  L SR EDIP L   FL+ F  KN       S +AL +L  Y W  NV+E
Sbjct: 306 RLNVVEVRVPALASRREDIPLLADAFLRRFAAKNGKTVRGFSPEALQILENYAWPGNVRE 365

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L++ + RAV+  K   L        + R+G                        L +  Q
Sbjct: 366 LEHAVERAVVLAKGESLEAGDLPESV-RKGP-----------------------LGSAGQ 401

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
             IP IG       + +IE+ +I   ++  +   +  AR LGI   T+YRK+
Sbjct: 402 LVIP-IGTP-----MEEIERRVIHETLRHTKGDKTLAARLLGIAARTIYRKL 447


>gi|300855204|ref|YP_003780188.1| sigma-54- interacting transcriptional regulator [Clostridium
           ljungdahlii DSM 13528]
 gi|300435319|gb|ADK15086.1| sigma-54- interacting transcription regulator [Clostridium
           ljungdahlii DSM 13528]
          Length = 646

 Score =  167 bits (423), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 108/351 (30%), Positives = 177/351 (50%), Gaps = 38/351 (10%)

Query: 131 SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
           S    +   D++I    +  +V++ A+K  D    I++ GE G GK+  ++ IH    R 
Sbjct: 332 SNGQAYYTFDNIIGQDESFTKVINYAKKISDSKSTILVMGESGTGKEVFAQSIHNYSSRV 391

Query: 191 FFPFFIVNCGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
             PF  +NCG I +  IE  LFG  +           LGKF  A+GGTI+L+E   +PL 
Sbjct: 392 DGPFIALNCGAIPKQLIESELFGYEEGAFTGAKKGGNLGKFKLADGGTIMLDEIGEMPLD 451

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++ G I    S   I +DVR+I  T ++L  +V+   FRKDLYYR++V  + 
Sbjct: 452 MQTKLLRVVQEGVITTIGSSKPIPVDVRIIAATNRDLKKEVEVGRFRKDLYYRLNVLPLF 511

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
           + TL+ R +DIP L+ +F+++   K   K+  IS + L  + KY W  N++EL+N+    
Sbjct: 512 LPTLKERKKDIPLLIQYFVKNISQKLNKKEPVISKEYLKKMIKYNWPGNIRELENL---- 567

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
                         V L+   G    ++ TE  C         + +L ++S + +     
Sbjct: 568 --------------VELIVNTGSIPADYFTEEDC--------DNEVLVDVSDDCL----- 600

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
                +L  +EKE +   +K ++  ++  A  LGI R+TLY KI +YNI+V
Sbjct: 601 -----KLDYVEKEHVIKVLKKFKGNITHSAEALGIRRNTLYSKIEKYNIKV 646


>gi|108759510|ref|YP_630735.1| sigma-54 dependent DNA-binding response regulator [Myxococcus
           xanthus DK 1622]
 gi|108463390|gb|ABF88575.1| sigma-54 dependent DNA-binding response regulator [Myxococcus
           xanthus DK 1622]
          Length = 468

 Score =  167 bits (423), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 132/474 (27%), Positives = 214/474 (45%), Gaps = 46/474 (9%)

Query: 13  VLIIDKD----DEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKE 68
           VL++D D    D  I+I +   E             L  + + +V  +   L+    D +
Sbjct: 6   VLVVDDDRANLDSVIRIFQR--EGMATLAAANGTEALELLRRPEVAAMVTDLMMPNMDGQ 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL--RE 126
            +L+      P V +++ T    ++     + +    F    + R  L  +I  AL  R 
Sbjct: 64  ELLRAARAIRPDVEVVLMTAYGTVETAVAAMKDGAYDFITKPLKRHALVKAIQKALEKRA 123

Query: 127 GVVPSQ-------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
            V  +Q       E       S++  SPA   ++D  R+A      +++ GE G GK+  
Sbjct: 124 LVAENQSLKAKLAEMNAAGGRSMVGQSPAFRAMLDTIRQAAPSTATVLLLGESGTGKELA 183

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R +HE  +R   PF  VNCG + ++ +E  LFG +    T   A+  G+F  A+GGT+ 
Sbjct: 184 ARSVHEFSQRVRGPFVAVNCGALPENILEAELFGVERGAFTGAVARREGRFERAHGGTLF 243

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   +PL  Q ++   +  G+IE       +++DVRL+  T K+L  +V    FR+DL
Sbjct: 244 LDEVGEMPLPAQVKLLRALAEGEIERLGGTQTVKVDVRLVAATNKDLQKEVAEGRFREDL 303

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           YYR++V  I +  L SR EDIP L   FL+ F  KN       S +A+ +L  Y W  NV
Sbjct: 304 YYRLNVVEIRVPALASRREDIPLLADAFLRRFAAKNGKVLRGFSQEAMGVLENYAWPGNV 363

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNL 418
           +EL++ + RAV+ L    + +   +    R+G                        L + 
Sbjct: 364 RELEHAVERAVV-LARGEVLDASDLPESVRKGP-----------------------LGSA 399

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            Q  IP IG       + +IE+ +I   ++  R   +  AR LGI   T+YRK+
Sbjct: 400 GQLVIP-IGTP-----MEEIERRVIHETLRHTRGDKTLAARLLGIAARTIYRKL 447


>gi|115380039|ref|ZP_01467086.1| two component transcriptional regulator, Fis family [Stigmatella
           aurantiaca DW4/3-1]
 gi|115362956|gb|EAU62144.1| two component transcriptional regulator, Fis family [Stigmatella
           aurantiaca DW4/3-1]
          Length = 479

 Score =  167 bits (423), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 125/472 (26%), Positives = 213/472 (45%), Gaps = 42/472 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKENI 70
           VL++D D   +  +    +  G      +     L  + K +V+V+   L+    D + +
Sbjct: 13  VLVVDDDRANLDSVARIFQREGLATHCASNGTEALELLRKPEVSVMVTDLMMPGMDGQEL 72

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           LK      P V +++ T    ++     + +    F    + R  L  ++  AL +  + 
Sbjct: 73  LKASRTIRPDVEVVLMTAYGTVETAVAAMKDGAYDFITKPLKRHALVKAVQKALEKQALV 132

Query: 131 SQ---------ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           ++         E       +++  +PA   ++D  R+A      +++ GE G GK+  +R
Sbjct: 133 AENKVLKAKLAEMGASGGKAMVGQAPAFRAMMDTLRQAAPSTATVLLIGESGTGKELAAR 192

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +HE   RA   F  VNC  + +  +E  LFG +    T   A+  G+F  A+GGT+ L+
Sbjct: 193 ALHEHSSRAKTAFIAVNCAALPESILEAELFGVERGAYTGAVARREGRFERAHGGTLFLD 252

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL+ Q ++   ++ G+IE       +++DVRL+  T K+L  +V    FR+DLYY
Sbjct: 253 EVGEMPLSAQVKLLRVLQEGEIERLGGTQTVKVDVRLVAATNKDLQKEVAEGRFREDLYY 312

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++V  + +  L SR EDIP L   FL+ F  KN       S +AL +L  Y W  NV+E
Sbjct: 313 RLNVVEVRVPALASRREDIPLLADAFLRRFAAKNGKTVRGFSPEALQILENYAWPGNVRE 372

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L++ + RAV+  K   L        + R+G                        L +  Q
Sbjct: 373 LEHAVERAVVLAKGESLEAGDLPESV-RKGP-----------------------LGSAGQ 408

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
             IP IG       + +IE+ +I   ++  +   +  AR LGI   T+YRK+
Sbjct: 409 LVIP-IGTP-----MEEIERRVIHETLRHTKGDKTLAARLLGIAARTIYRKL 454


>gi|331683897|ref|ZP_08384493.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli H299]
 gi|331078849|gb|EGI50051.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli H299]
          Length = 461

 Score =  167 bits (423), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 133/483 (27%), Positives = 226/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSNETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +S LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILSPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|237710223|ref|ZP_04540704.1| two-component system response regulator [Bacteroides sp. 9_1_42FAA]
 gi|237727723|ref|ZP_04558204.1| two-component system response regulator [Bacteroides sp. D4]
 gi|229434579|gb|EEO44656.1| two-component system response regulator [Bacteroides dorei
           5_1_36/D4]
 gi|229455685|gb|EEO61406.1| two-component system response regulator [Bacteroides sp. 9_1_42FAA]
          Length = 451

 Score =  167 bits (423), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 112/409 (27%), Positives = 199/409 (48%), Gaps = 39/409 (9%)

Query: 79  PIVPIIVQTTQDNIKI----LNCFLYNRISKFFLN--LVSRKQLCDSIICALREGVVPSQ 132
           P VP+I+ T   +I++    +    ++ I+K + N  L+ R +    +    ++  VP +
Sbjct: 74  PDVPVILMTAWGSIQLAVQGMQAGAFDFITKPWNNVALMQRIETALELTSQDKKAEVPVE 133

Query: 133 ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF 192
           +N+      +I  S A++ V+   ++       ++I GE G GK+ ++  +H +  R+  
Sbjct: 134 DNDGFDRSHIIGKSKALMDVLATIKRIARTNASVLITGESGTGKELIAEAVHLNSPRSKK 193

Query: 193 PFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQG 251
           PF  VN G I     E  +FG      T  +A  +G+F  A+ GTI L+E   L L+ Q 
Sbjct: 194 PFVKVNLGGISHTLFESEMFGHKKGAFTDATADRVGRFELADKGTIFLDEIGDLDLSCQV 253

Query: 252 RIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIST 311
           ++   ++    E        ++D+R++  T  +L   V+ H FR+DL+YRI++  +++  
Sbjct: 254 KLLRVLQEQTFEVLGDSRPRKVDIRVVSATNADLRQMVQEHTFREDLFYRINLITVHLPA 313

Query: 312 LRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIG 371
           LR R EDIP LV  F    C  N + ++  + +A+  L++ P+  N++ELKN++ R ++ 
Sbjct: 314 LRERREDIPLLVRHFADKQCESNGLSKVEFTSEAMDYLSRLPYPGNIRELKNLVERTLLV 373

Query: 372 LKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGE 431
                LT D F        K + +   E   T   +G +                     
Sbjct: 374 SGKEILTADDF--------KSQYQHPIEQKVTTNLQGMT--------------------- 404

Query: 432 VRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
              L +IEK+ I   ++ Y   MS+VA  LGI R+ LYR++ +YNI+V+
Sbjct: 405 ---LEEIEKQTILQTLEKYNNNMSQVAVALGISRAALYRRLEKYNIQVN 450


>gi|91200751|emb|CAJ73803.1| strong similarity to sigma 54 response regulator protein
           [Candidatus Kuenenia stuttgartiensis]
          Length = 469

 Score =  167 bits (423), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 118/393 (30%), Positives = 192/393 (48%), Gaps = 46/393 (11%)

Query: 94  ILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVV 153
           +   F Y  + K   N + +K+L + +     EG V     E   L+ +I  S  M++V+
Sbjct: 104 VTKPFRYQEMLKVAKNALEKKELKERL--KYLEGEV----REKYKLEGIIGNSAVMVEVL 157

Query: 154 DLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG 213
            +          ++I GE G GK+ ++R IH +G R+ +PF ++NCG + ++  E  LFG
Sbjct: 158 KVTADVSRTESTVLITGESGTGKELIARAIHYNGPRSGYPFVVINCGALPENLQESELFG 217

Query: 214 DVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIR 272
                 T    + +G F  A+ GTI L+E      + Q ++  F++ G+I       +I 
Sbjct: 218 HAKGSFTGAVKEKVGLFHHAHKGTIFLDEIGETSASTQVKLLRFLQDGEIRQVGGNKSIH 277

Query: 273 LDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCT 332
           +DVR+I  T +NL   V    FRKDL+YRI+V  I++  L+ R EDIP LV++FL+ +  
Sbjct: 278 VDVRIIAATNENLERAVNQGRFRKDLFYRINVIRIHLPQLKERKEDIPLLVNYFLELYTD 337

Query: 333 KNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA-------VIGLKDSHLTEDRFVLL 385
           K    +   S  A+++L  Y W  N++EL+NI+ RA       VIG++   L    FV  
Sbjct: 338 KLKKDKRVFSGSAMAVLLNYDWPGNIRELQNIVERAVALSKNQVIGVEALPLPTGGFV-- 395

Query: 386 LSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGL 445
            +     ER+   +++                              V  LS+ EK  I  
Sbjct: 396 -AHNSNPERDVTVKSSI-----------------------------VETLSEQEKNAIVE 425

Query: 446 AMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
           AM  Y    ++V++ LGI  +TL+RKI++Y I+
Sbjct: 426 AMNKYGGNQTKVSQVLGISTTTLWRKIKKYKIK 458


>gi|71733300|ref|YP_275543.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|71553853|gb|AAZ33064.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|320325112|gb|EFW81181.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. glycinea str. B076]
 gi|320329371|gb|EFW85364.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330889063|gb|EGH21724.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. mori str. 301020]
 gi|330986487|gb|EGH84590.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 471

 Score =  167 bits (423), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 134/476 (28%), Positives = 224/476 (47%), Gaps = 21/476 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVE--SYGYDVFIVNVSDLSTISKIQVNVIFLSLINCED-DKEN 69
           VL+++ D    + + + +E   YGY   + +  +    ++ Q   + +S +N    D   
Sbjct: 5   VLLVEDDRSLREALGETLELAGYGYQA-VGSAEEALVAAEAQPFSLVISDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    +      +    + + +     K L   I    R  + 
Sbjct: 64  LLSLLRSRHPQLPVLLMTAHGAVDRAVDAMRQGAADYLVKPFEPKAL---IALVARHALG 120

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
             +  E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  R
Sbjct: 121 RLEPAER---DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL 
Sbjct: 178 ADKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPIILDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA
Sbjct: 298 WQALRQRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVSYPWPGNVRELDNAVQRA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           +I  +   +    F   LS             A        S D      + ES+ A+G 
Sbjct: 358 LILQQGGVIQAQDFC--LSGPVTSLPAAAVVEAVPSLPVTSSPDNAGAGGNAESVGALGD 415

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           D  +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 416 D--LRRR---EFQMIIDTLRAERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 466


>gi|254501466|ref|ZP_05113617.1| nitrogen regulation protein [Labrenzia alexandrii DFL-11]
 gi|222437537|gb|EEE44216.1| nitrogen regulation protein [Labrenzia alexandrii DFL-11]
          Length = 479

 Score =  167 bits (422), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 136/482 (28%), Positives = 226/482 (46%), Gaps = 28/482 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY V +  N S L   +S    +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYTVRLTSNASTLWRWVSAGDGDLVITDVVMPDENIFDV 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y  + K F      K+L   +  AL E
Sbjct: 66  LPRIKKMRPELPVLVMSAQNTFMTAIKASEKGAYEYLPKPF----DLKELTGIVQRALEE 121

Query: 127 GVV-PSQENEHCALD-SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
               P  + E       L+  SPAM ++  +  +     + +MI GE G GK+ ++R +H
Sbjct: 122 PKKRPVADLEESGEGMPLVGRSPAMQEIYRVLARLMQTDLTVMINGESGTGKELVARALH 181

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGTIVL 239
           + GKR   PF  +N   I +D IE  LFG         Q ++S    G+F +A+GGT+ L
Sbjct: 182 DYGKRRNGPFVAINMAAIPRDLIEAELFGHEKGAFTGAQNRSS----GRFEQADGGTLFL 237

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   +   +FR+DLY
Sbjct: 238 DEIGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIVAATNKDLRHLINQGLFREDLY 297

Query: 300 YRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +R++V  I +  LR R EDIP LV HFF  S   K  +    +   A++L+ +Y W  NV
Sbjct: 298 FRLNVVPIRLPPLRERVEDIPDLVRHFF--SIAEKEGLPAKQVDQSAMNLMRRYRWPGNV 355

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNL 418
           +EL+N++ R         + E      LS+      E  T         G S +  L   
Sbjct: 356 RELENLVRRLAALYPQDVIGEAMLDHELSQPSTNPLEDETSETVDL---GGSVEKYLSGY 412

Query: 419 SQESIPAIGQDGEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
            +    A+   G   R L ++E  +I  A+   R    + A  LG+ R+TL +KIR+ +I
Sbjct: 413 FETFGDALPPPGLYHRILREVEYPLISAALAATRGNQIKAAELLGVNRNTLRKKIRDLDI 472

Query: 478 EV 479
           +V
Sbjct: 473 QV 474


>gi|306843982|ref|ZP_07476577.1| nitrogen regulation protein NR(I) [Brucella sp. BO1]
 gi|306275737|gb|EFM57461.1| nitrogen regulation protein NR(I) [Brucella sp. BO1]
          Length = 491

 Score =  167 bits (422), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 132/490 (26%), Positives = 236/490 (48%), Gaps = 39/490 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           VL+ D D     ++   +   GYDV +  N + L   ++    +++   ++  +++  ++
Sbjct: 10  VLVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDL 69

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P++V + Q+     I+      Y  + K F     +N+V R        
Sbjct: 70  LPRIKKMRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQK 129

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R
Sbjct: 130 PAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+  LV HFF +    +  + +  I++  L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVRDLVRHFFKR--AAEEGLPEKRITNAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTI 414
            NV+EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    
Sbjct: 358 GNVRELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQA 413

Query: 415 LDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL 
Sbjct: 414 VEQNMQRYFASFGSDLPPPGLYQRILAEVEYPLILACLTATRGNQIKAADLLGLNRNTLR 473

Query: 470 RKIREYNIEV 479
           +KIRE  + +
Sbjct: 474 KKIRELGVNI 483


>gi|226310462|ref|YP_002770356.1| two-component response regulator [Brevibacillus brevis NBRC 100599]
 gi|226093410|dbj|BAH41852.1| two-component response regulator [Brevibacillus brevis NBRC 100599]
          Length = 468

 Score =  167 bits (422), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 135/492 (27%), Positives = 226/492 (45%), Gaps = 60/492 (12%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           +VLI+D +    + +   +   GY++      V  L  + +    V+ L L     D  +
Sbjct: 5   KVLIVDDEANVRRALSTTLRKMGYELLEAGSGVEALEQVERFCPQVMLLDLRMPHLDGMD 64

Query: 70  ILKNIVDKIPIVPIIVQTT-----QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICA- 123
            L+ + ++   +P +V  T      D ++ +    ++ + K F +L   KQ+    +   
Sbjct: 65  TLRQLNERKGRLPRVVMMTAYGSASDVMEAMKLGAFDYVQKPF-DLGQVKQVVAHALTQG 123

Query: 124 --LREGVVP---SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
             L +G V     +E  +    SLI +SPAM  V  L  K       ++I+GE G GK+ 
Sbjct: 124 ELLEQGEVGKVLQEEQANPNRTSLIGLSPAMQNVYKLVGKVAMSKATVLIEGESGTGKEL 183

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE-ANGGTI 237
           ++R IH +  RA  P   VNCG I ++ +E  LFG        +       +E ANGGT+
Sbjct: 184 IARAIHSNSPRADKPLIPVNCGAIPENLLESELFGYERGAFTGAVHRKQGLLELANGGTL 243

Query: 238 VLEEPDALPLAVQGRIYNF------IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKS 291
            L+E   L L++Q ++  F      I  G IE      AI +DVR+I  T ++L  +++ 
Sbjct: 244 FLDEVGELSLSLQVKLLRFLQDRVFIRVGGIE------AISVDVRVIAATNRDLQERIRQ 297

Query: 292 HVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTK 351
            +FR+DLYYR++V  I +  LR R EDIP L+  FL  +  +     + +S  A   L  
Sbjct: 298 ELFREDLYYRLNVVPIRMPPLRERKEDIPLLIRHFLAKYGKEAGKHDLCLSAAATEALIA 357

Query: 352 YPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSS 411
           Y W  NV++L+N + RAV+  + + +  +  +                            
Sbjct: 358 YHWPGNVRQLENTIERAVVLTRGAVIGHEHVL---------------------------- 389

Query: 412 DTILDNLSQESIPAIGQ---DGEVRR--LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
             I DN   E IP+ G+   +G   R  ++ +E+E I  A++  R    + A+RLGI R 
Sbjct: 390 SPIQDNKMSEQIPSHGKISYEGRTMREIIAQVEQEAIAHALRKERGNKLQTAKRLGISRR 449

Query: 467 TLYRKIREYNIE 478
            L  K++ Y ++
Sbjct: 450 ALLYKLQMYGLD 461


>gi|308274524|emb|CBX31123.1| Acetoacetate metabolism regulatory protein atoC [uncultured
           Desulfobacterium sp.]
          Length = 478

 Score =  167 bits (422), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 130/487 (26%), Positives = 231/487 (47%), Gaps = 34/487 (6%)

Query: 13  VLIIDKDDEQ----IKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKE 68
           +LIID DD+     +K++ +  E Y  D      + ++ +     +++ L +     +  
Sbjct: 4   ILIIDDDDQLRNSFVKLLTE--EGYNVDQAASGEAGVNIVKNKAPDIVILDMRLPGMNGF 61

Query: 69  NILKNIVDKIPIVPIIVQT----TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICA- 123
              + I +  P +P+I+ T    T   I+      ++ I K F ++ +   L    + A 
Sbjct: 62  ETFRAIHEVEPRLPVIIMTAFGTTDTAIEATKLGAFDYILKPF-DIPAMLSLIKQALSAS 120

Query: 124 --LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
             +R  V      +  + D++I  S  M +V     +       ++I+GE G GK+ + R
Sbjct: 121 RFMRSPVDMDTIPDKASRDAIIGRSAVMQEVYKAIGRVSPTDATVLIRGESGTGKELVVR 180

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            I++   RA  PF ++NC  I +  +E  LFG +    T  + + +GK  +A+GGTI+L+
Sbjct: 181 AIYQHSLRADKPFLVINCVAIPETLLESELFGYEKGAFTGAAHRRVGKIEQADGGTILLD 240

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL +Q ++   ++   IE    R  I  DVR+I  T ++L   +    FR+DLYY
Sbjct: 241 EIGDMPLNLQAKMLRLLQEKSIERVGGRENIATDVRIIAATNRDLEAAISEGRFREDLYY 300

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R+ V  I +  LR R  DIP L  +FL  +  +  IK   ISDKA +LL+ Y W  N++E
Sbjct: 301 RLKVVTIELPPLRERENDIPILTDYFLYKYSEEKGIKNPGISDKAKALLSGYSWPGNIRE 360

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L+N + +A+I  + + L+ D    +++ +               +T     + + D L Q
Sbjct: 361 LENTIQKALIFNRGAPLSPDDIAQVINEK--------------IHTSDLKKENVDDALRQ 406

Query: 421 ESIPAIGQDGEVRRL-----SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
                + +      L      D+   +I  A+ +     S+ A+ LG+ R TL+ KI +Y
Sbjct: 407 WIRKELTKKNNAEDLFDSCMDDMANAVISEALNICDGNRSKAAKLLGLSRPTLHSKIEKY 466

Query: 476 NIEVDSL 482
           NI +++L
Sbjct: 467 NIRMETL 473


>gi|332703870|ref|ZP_08423958.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio africanus str. Walvis Bay]
 gi|332554019|gb|EGJ51063.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio africanus str. Walvis Bay]
          Length = 459

 Score =  167 bits (422), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 133/481 (27%), Positives = 234/481 (48%), Gaps = 40/481 (8%)

Query: 12  RVLIIDKDDEQIKI-IKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
           R+LIID D+E I+  ++  +E  G++V      +  L  +     +++FL +     D  
Sbjct: 4   RILIID-DEESIRFSLRGVLEDEGHEVIEAGSGEQGLEMVENQGPDLVFLDIWLPGMDGL 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV 128
           ++L+ + +    VP+I+ +   N++     +      F    +S +++  ++  AL  G 
Sbjct: 63  HVLEKVREGQVDVPVIMISGHGNVETAVSAIKKGAFDFIEKPLSLEKVVITVNKALEFGK 122

Query: 129 VPSQENEHCA------LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
           +  +  E  A       +SL   +P+++++ +   +       ++I GE G GK+ ++R 
Sbjct: 123 LLRENLELRAQVNTDRAESLTGNAPSIVRLREQVARVAPTDAWVLITGENGTGKEIVARQ 182

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD--VDLQTKNSAQFLGKFIEANGGTIVLE 240
           +H   +RA  P   VNC  I ++ IE  LFG         + AQ  GKF  AN GT+ L+
Sbjct: 183 VHAGSRRAKRPMIAVNCAAIPEELIESELFGHEKGSFTGADKAQ-AGKFELANHGTLFLD 241

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   + L  Q +I   ++    E    R  I +DVR+I  T K+L  ++K+  FR+DLYY
Sbjct: 242 EIGDMSLKTQAKILRILQEQSFERIGGRKTITVDVRVIAATNKDLPTEIKAGNFREDLYY 301

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R+ VF + +  LR R+EDIP L+  FL      +  K ++ + +AL +L +YPW  NV+E
Sbjct: 302 RLKVFPLEVPPLRKRAEDIPLLIEEFLDLLVRAHNFKPLTFTPEALEILQRYPWPGNVRE 361

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL--DNL 418
           LKN +              +R +++ + +    RE   E      T G   D +L  D  
Sbjct: 362 LKNFV--------------ERMLIMYAGQMVGPRELPPEI-----TGGIDEDHVLGSDLA 402

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            Q  +     D +  R+   E   +   ++     +S++A  +G+ RS+LYRK++ YNI+
Sbjct: 403 CQPDL-----DLKTARMV-FETRFLEAKLRECSGSVSKLADAVGMERSSLYRKLKAYNIQ 456

Query: 479 V 479
           V
Sbjct: 457 V 457


>gi|222054817|ref|YP_002537179.1| Fis family transcriptional regulator [Geobacter sp. FRC-32]
 gi|221564106|gb|ACM20078.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. FRC-32]
          Length = 480

 Score =  167 bits (422), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 114/344 (33%), Positives = 179/344 (52%), Gaps = 15/344 (4%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
           ++I  SPAM ++     K     + +++QGE G GK+ ++R IH + KR   PF  +NC 
Sbjct: 144 TIIGNSPAMREIYKTIGKVAPSDVTVLVQGESGTGKELIARAIHFNSKRLGKPFVALNCA 203

Query: 201 MIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            I ++ +E  LFG +    T    + LGKF +AN GTI L+E   +P  +Q +I   ++ 
Sbjct: 204 AIPKELLESELFGFEKGAFTGAVERKLGKFEQANNGTIFLDEIGDMPFDLQSKILRVLQE 263

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
            ++        I +DVR++  T ++L   V+   FR+DL+YR++V  +++  LR RSEDI
Sbjct: 264 KEVTRTGGSQTISVDVRVVAATNQDLEEMVRKKQFREDLFYRLNVIPLHLVPLRERSEDI 323

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
           P LV +FL   C +  +   + S  A+ LLT Y W  NV+EL+N + RAVI   D  LT 
Sbjct: 324 PLLVDYFLAKVCAELEVPVKTCSPDAIRLLTSYNWPGNVRELENTIKRAVILSVDPLLTA 383

Query: 380 DRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIG--QDGEVRR--L 435
             F  L  ++G +             +E  S + I+D   + S   +   + G+V    L
Sbjct: 384 ADFSGLRVQKGGE----------PVQSEDLSLEGIVDIKLRGSFTNMEKMESGDVYTMVL 433

Query: 436 SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
             +E+ +I   ++  R      A  LGI R+TL +KI E  IEV
Sbjct: 434 EQVERPLIRFVLEKTRGNQVRAADILGINRNTLRKKITELGIEV 477


>gi|298291767|ref|YP_003693706.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Starkeya novella DSM 506]
 gi|296928278|gb|ADH89087.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Starkeya novella DSM 506]
          Length = 481

 Score =  167 bits (422), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 132/487 (27%), Positives = 229/487 (47%), Gaps = 36/487 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY+V    N + L   +S+   +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYEVRSCGNAATLWRWVSQGDGDLVITDVVMPDENAFDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P+IV + Q+     I+      Y  + K F      K+L   +  AL E
Sbjct: 66  LPRIKKVRPELPVIVMSAQNTFMTAIRASEKGAYEYLPKPF----DLKELISIVGRALSE 121

Query: 127 GVVPSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
              P         D+    L+  SPAM  +  +  +     + +MI GE G GK+ ++R 
Sbjct: 122 PKKPENALRTLGEDADNIPLVGRSPAMQDIYRVLARLMQTDLTVMIAGESGTGKELVARA 181

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           +H+ GKR   PF  +N   I +D IE  LFG +    T  +A+  G+F +A  GT+ L+E
Sbjct: 182 LHDYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGANARSAGRFEQAESGTLFLDE 241

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   ++  +FR+DL++R
Sbjct: 242 IGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIVAATNKDLRILIQQGLFREDLFFR 301

Query: 302 ISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           ++V  + +  LR R+ED+P L  HFFLQ    +  + +  I   AL  L +Y W  NV+E
Sbjct: 302 LNVVPLRLPPLRERTEDVPDLARHFFLQ--AEREGLPRKQIDAAALDRLKRYRWPGNVRE 359

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L+N L+R +  L    +     +         E E  T  A     E    +T+  ++ +
Sbjct: 360 LEN-LIRRLAALYPQEVITGSII---------EAELSTPVATNAPEETGQDETLSSSVER 409

Query: 421 ESIPAIGQDGEV--------RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
                 G  GE         R L D+E  ++  A+   R    + A  LG+ R+TL +KI
Sbjct: 410 HLNTYFGGFGENLPPPGLYHRILKDVEYPLLSAALAATRGNQIKAAELLGLNRNTLRKKI 469

Query: 473 REYNIEV 479
           R+ +I++
Sbjct: 470 RDLDIQI 476


>gi|153003833|ref|YP_001378158.1| two component sigma54 specific Fis family transcriptional regulator
           [Anaeromyxobacter sp. Fw109-5]
 gi|152027406|gb|ABS25174.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter sp. Fw109-5]
          Length = 466

 Score =  167 bits (422), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 118/483 (24%), Positives = 215/483 (44%), Gaps = 46/483 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKENI 70
           VL++D D    K+ K ++   G++V + +     L+ + +     +   L   + D   +
Sbjct: 12  VLLVDDDPGTRKVAKANLSLEGFEVLVASCGAEALARLGESDPLAVVSDLKMPDMDGIAL 71

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           +  +    P +P+++ T    ++         + K  L+ +++    D +   LR  V  
Sbjct: 72  MDRVHALRPSLPVVLVTAHATVETA----VEAMRKGALHYLTKPIRYDELALVLRHAVAH 127

Query: 131 SQENEHCA-----------LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
            ++    A            + ++  SPAM +V  +  +  D    ++++GE G GK+ +
Sbjct: 128 ERQRRDVARLRGELEQAAGFEEIVGTSPAMREVFSMVEQVADADATVLLRGETGTGKELV 187

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R IH    R   PF  VNC  I +D +E   FG +    T   A+ +G+F +A+G T+ 
Sbjct: 188 ARAIHRRSARRDRPFVAVNCTAIPRDLMESEFFGHEKGAFTGAVARRIGRFEQAHGSTLF 247

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   L L++Q ++   ++  ++    ++  +R+DVR++  T ++L   V+   FR DL
Sbjct: 248 LDEIGDLDLSIQAKLLRVLQEQELTRVGAQDPVRVDVRIVAATNRDLEALVREGRFRDDL 307

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           YYR++V  I +  LR R+ D+P L   FL SF  +            +     YPW  NV
Sbjct: 308 YYRLNVIPIRLPPLRERTSDLPALTEHFLGSFAKRYGRTAPIPPPDVIGAARAYPWPGNV 367

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI-LDN 417
           +EL+N+  RAV+                                     G  +DT+    
Sbjct: 368 RELRNLCERAVL-------------------------MGWAAVAPILGAGSRADTLGAAA 402

Query: 418 LSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           L   S+P +  D + R +   E+E +   +K +R ++ EVAR  GI    LY K++ Y +
Sbjct: 403 LVDPSLPLL--DAKQRLVERFEREYLTRLLKEHRGRIGEVARAAGIAERNLYEKMKAYGL 460

Query: 478 EVD 480
             D
Sbjct: 461 SRD 463


>gi|317484929|ref|ZP_07943816.1| sigma-54 interaction domain-containing protein [Bilophila
           wadsworthia 3_1_6]
 gi|316923805|gb|EFV45004.1| sigma-54 interaction domain-containing protein [Bilophila
           wadsworthia 3_1_6]
          Length = 488

 Score =  167 bits (422), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 110/342 (32%), Positives = 168/342 (49%), Gaps = 21/342 (6%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            ++++  +P +  +  L R+      PI++ GE G GK+ +++ +H + +R+  PF  VN
Sbjct: 158 FEAIVGEAPCIENMRCLGRRFAFSQEPILVCGESGTGKELVAQALHMASQRSDRPFVTVN 217

Query: 199 CGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           C  +  + +E  LFG               GKF  A+ GTI L+E   LPL +Q ++   
Sbjct: 218 CAALPPELMESELFGYETGAFTGAKVGGVKGKFEMADTGTIFLDEIGELPLPMQAKLLRV 277

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           +ETG+I+    +G +  D RLI  T +NL   V+   FR+DLY+R+SVF ++I  LR R 
Sbjct: 278 LETGEIQKIAHKGQLHSDFRLIGATNRNLAEMVRQGQFREDLYHRLSVFELDIPPLRDRV 337

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
            DIP LV  F+      N  K I I D       +YPW  NV+ELKN+L+ A+  L D  
Sbjct: 338 SDIPLLVRHFVTQSVGDNRQKDIRIDDALYDAFAQYPWRGNVRELKNVLVYALYSLGD-- 395

Query: 377 LTEDRFVLLLSREGKK-EREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRL 435
              D+ VL +     +  RE           + + S     N S+ S  A          
Sbjct: 396 ---DQSVLTVQHLPPRFMRELEAAAVAGTTPDAEDSRQDSQNFSEASARA---------- 442

Query: 436 SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
              E++++  A+   R      AR LGI RS LYRK+RE+ +
Sbjct: 443 ---ERKVLWDALVNSRYNKVLAARTLGISRSKLYRKLREHGL 481


>gi|212694141|ref|ZP_03302269.1| hypothetical protein BACDOR_03667 [Bacteroides dorei DSM 17855]
 gi|265751032|ref|ZP_06087095.1| two-component system response regulator [Bacteroides sp. 3_1_33FAA]
 gi|212663361|gb|EEB23935.1| hypothetical protein BACDOR_03667 [Bacteroides dorei DSM 17855]
 gi|263237928|gb|EEZ23378.1| two-component system response regulator [Bacteroides sp. 3_1_33FAA]
          Length = 451

 Score =  167 bits (422), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 112/409 (27%), Positives = 199/409 (48%), Gaps = 39/409 (9%)

Query: 79  PIVPIIVQTTQDNIKI----LNCFLYNRISKFFLN--LVSRKQLCDSIICALREGVVPSQ 132
           P VP+I+ T   +I++    +    ++ I+K + N  L+ R +    +    ++  VP +
Sbjct: 74  PDVPVILMTAWGSIQLAVQGMQAGAFDFITKPWNNVALMQRIETALELTSQDKKAEVPVE 133

Query: 133 ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF 192
           +N+      +I  S A++ V+   ++       ++I GE G GK+ ++  +H +  R+  
Sbjct: 134 DNDGFDRSHIIGKSKALMDVLATIKRIARTNASVLITGESGTGKELIAEAVHLNSPRSKK 193

Query: 193 PFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQG 251
           PF  VN G I     E  +FG      T  +A  +G+F  A+ GTI L+E   L L+ Q 
Sbjct: 194 PFVKVNLGGISHTLFESEMFGHKKGAFTDATADRVGRFELADKGTIFLDEIGDLDLSCQV 253

Query: 252 RIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIST 311
           ++   ++    E        ++D+R++  T  +L   V+ H FR+DL+YRI++  +++  
Sbjct: 254 KLLRVLQEQTFEVLGDSRPRKVDIRVVSATNADLRQMVQEHTFREDLFYRINLITVHLPA 313

Query: 312 LRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIG 371
           LR R EDIP LV  F    C  N + ++  + +A+  L++ P+  N++ELKN++ R ++ 
Sbjct: 314 LRERREDIPLLVRHFADKQCESNGLPKVEFTSEAMDYLSRLPYPGNIRELKNLVERTLLV 373

Query: 372 LKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGE 431
                LT D F        K + +   E   T   +G +                     
Sbjct: 374 SGKEILTADDF--------KSQYQHPIEQKVTTNLQGMT--------------------- 404

Query: 432 VRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
              L +IEK+ I   ++ Y   MS+VA  LGI R+ LYR++ +YNI+V+
Sbjct: 405 ---LEEIEKQTILQTLEKYNNNMSQVAVALGISRAALYRRLEKYNIQVN 450


>gi|226327583|ref|ZP_03803101.1| hypothetical protein PROPEN_01454 [Proteus penneri ATCC 35198]
 gi|225204109|gb|EEG86463.1| hypothetical protein PROPEN_01454 [Proteus penneri ATCC 35198]
          Length = 474

 Score =  166 bits (421), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 116/448 (25%), Positives = 220/448 (49%), Gaps = 20/448 (4%)

Query: 41  NVSDLSTISKIQVNVIFLSLINCED-DKENILKNIVDKIPIVPIIVQTTQDNI-KILNCF 98
           + +D+      ++  + LS I   D D  ++LK I +  P +P+I+ T   ++   +N +
Sbjct: 35  HANDVLNALNTEIPDVLLSDIRMPDIDGLSLLKIIKENYPTLPVIIMTAHSDLDAAVNAY 94

Query: 99  ---LYNRISKFFLNLVSRKQLCDSIICALREGVVP-SQENEHCALDSLIAVSPAMIQVVD 154
               ++ + K F ++     L D  I   RE   P + E    ++  +I  +PAM +V  
Sbjct: 95  QQGAFDYLPKPF-DIDETLALIDRAITHYREQKQPNTDETSLQSVTDMIGEAPAMQEVYR 153

Query: 155 LARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD 214
           +  +    +I ++I GE G GK+ ++  +H    RA  PF  +N   I +D IE  LFG 
Sbjct: 154 IIGRLSRSSISVLINGESGTGKELVAHALHRHSPRASSPFIALNMAAIPKDLIESELFGH 213

Query: 215 VDLQTKNSAQF-LGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRL 273
                  ++Q   G+F +ANGG++ L+E   +PL +Q R+   +  G+         +++
Sbjct: 214 EKGAFTGASQVRQGRFEQANGGSLFLDEIGDMPLDIQTRLLRVLAEGQFYRVGGYAPVKV 273

Query: 274 DVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTK 333
           DVR+I  T ++L  +V++  FR+DLY+R++V  I +  LR R+EDIP L  +FLQ    +
Sbjct: 274 DVRIIAATHQDLEKRVQAGDFREDLYHRLNVIRIQLPPLRDRTEDIPSLARYFLQKTAKE 333

Query: 334 NAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE 393
             ++   +  ++L ++ +Y W  NV++L+N+     +      +        + +  ++ 
Sbjct: 334 LGVEAKVLHQQSLQIMMEYNWSGNVRQLENVCRWLTVMTASQEIMPQDLPQEIRQPDERA 393

Query: 394 REFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGE---VRRLSDIEKEIIGLAMKLY 450
           +  +   +   +++         +LS  +  A+G+  E      L   E+ ++  A+   
Sbjct: 394 KNINRIASSQHWSQ---------HLSLWADEALGEGKENILTDALPQFERTLLLSALAYT 444

Query: 451 RAQMSEVARRLGIGRSTLYRKIREYNIE 478
           +    + AR LG GR+TL RK++E  IE
Sbjct: 445 QGHKQDAARLLGWGRNTLTRKLKELGIE 472


>gi|289669881|ref|ZP_06490956.1| two-component system regulatory protein [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 448

 Score =  166 bits (421), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 130/482 (26%), Positives = 225/482 (46%), Gaps = 52/482 (10%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSD-LSTISKIQVNVIFLSLINCEDDKEN 69
           R+LIID D      ++  + S G+ V    N  D L+ +S+  +++ F+       D   
Sbjct: 3   RILIIDDDAAFRTTLQATLRSLGHTVVAADNGPDGLARLSEGGIDMAFVDFRMPGMDGIA 62

Query: 70  ILKNIVD-----KIPIVPIIVQTTQDN-IKILNCFLYNRISKF-----FLNLVSRKQL-- 116
           +L+  +D     ++P+V +    +  N I+ +    ++ + K       + +V R  L  
Sbjct: 63  VLRARLDDAQARQVPLVMLTAYVSSGNTIEAMTLGAFDHLVKPVGRADIVEVVERALLSR 122

Query: 117 CDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
            D+   A      P +++     D+L+  SPAM  V      A    +P++I GE G GK
Sbjct: 123 ADAQAAATETPQAPPEDD-----DALVGHSPAMRTVHKRIGLAAASDLPVLITGETGTGK 177

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGG 235
           +  +R +H +  RA  PF  VNC  I  + +E  LFG      +  S+   G   EA+GG
Sbjct: 178 ELAARALHRASPRASAPFIAVNCAAIPLELMESELFGHRKGAFSGASSDRPGLIREADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T+ L+E   +PL +Q ++  F++ G++      G  ++DVR++  T ++L   V    FR
Sbjct: 238 TLFLDEIGDMPLPMQAKLLRFLQEGEVTPLGGSGPQKVDVRVLAATHRDLAACVADGRFR 297

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
            DL YR++V  I +  LR R +DI  L   FL    + NA +  S+S  A   L  + W 
Sbjct: 298 SDLRYRLNVVPIELPPLRERGQDILLLAQHFL----SANAARAQSLSPAAQERLLAHRWP 353

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+EL+N++ R+ + ++ + +        L+                    G++  T+ 
Sbjct: 354 GNVRELRNVMQRSQVMVRGASIDAADLDEALAE------------------AGEAPSTVA 395

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
             L+     A+ +         +EK++I  A++  +   +E ARRLGI R  LYRK+ EY
Sbjct: 396 SALTGTLPEAVAR---------LEKQMIQSALEQSQGNRAEAARRLGIHRQLLYRKLEEY 446

Query: 476 NI 477
            +
Sbjct: 447 GL 448


>gi|147678974|ref|YP_001213189.1| response regulator [Pelotomaculum thermopropionicum SI]
 gi|146275071|dbj|BAF60820.1| response regulator [Pelotomaculum thermopropionicum SI]
          Length = 512

 Score =  166 bits (421), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 146/515 (28%), Positives = 239/515 (46%), Gaps = 56/515 (10%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           +VL+ID + E    ++  ++  GY V +          I + + NV  + L   + D   
Sbjct: 5   QVLVIDDEVEVGTFLRRLLQKKGYAVSVAVSGAEAARLIVEKKFNVAMVDLKLPDADGLC 64

Query: 70  ILKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           +L+ I ++ P   +I+     TT+  +K +    ++ + K F ++   +++ +       
Sbjct: 65  LLQQIKNRQPDCEVIIMTGYSTTRTAVKAIQLGAFDYLEKPFEDIGEVEKIIERASEYRV 124

Query: 126 EGVVPSQENEHCA-----LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            G      N   A     +   +  S AM ++V +A K     I ++IQGE G GK+ L+
Sbjct: 125 RGYDGRPVNAEWAPIADRIGFQVGTSQAMQKLVSIAFKIAKKNINVLIQGETGTGKEVLA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           RFIH +  RA   F  VNCG + ++ +E  LFG +    T   A   G F  AN GT+ L
Sbjct: 185 RFIHAASNRADQIFIPVNCGALPENLLESELFGHEKGAFTGAGATRRGIFELANRGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E     L++Q ++   +ETG+         I+ DVR+I  T  +L   +K   FR+DL+
Sbjct: 245 DEVGESSLSIQVKLLRVLETGEFLRVGGEKPIKTDVRIIAATNVDLEQALKEKTFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + +  LR+R EDIP+L  +F++         ++ +S +A+ +L  YPW  NV+
Sbjct: 305 YRLDVVRLEVPPLRNRREDIPYLTEYFVKRLNP-----ELHVSVEAMRILYNYPWPGNVR 359

Query: 360 ELKNILLRAVIGLKDSH--LTEDRFVLLLSREGKKEREFHTETACTCYTEG------KSS 411
           EL N + +AV  L D    L E     L+S  G  E             EG      +S 
Sbjct: 360 ELANTISQAV-ALCDGKIILPEHLSGKLVS--GGSEPAAAGNPGGGAPPEGCSQLPPQSL 416

Query: 412 DTILDNLSQESI-------PAIGQDGEVRR---------------------LSDIEKEII 443
           + +L+  S ES+          G  G +RR                     L  +E E +
Sbjct: 417 EELLEYYSAESVLEAMEEGKLAGLKGLLRRLDASLSAAMRKKGIEVSPPPSLEKVEAEAV 476

Query: 444 GLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
             A+  YR  ++  AR LGIGR+TLYRK+++Y I+
Sbjct: 477 RNALNYYRGNITLAARALGIGRNTLYRKMKDYGIK 511


>gi|87308441|ref|ZP_01090582.1| acetoacetate metabolism regulatory protein atoC [Blastopirellula
           marina DSM 3645]
 gi|87288998|gb|EAQ80891.1| acetoacetate metabolism regulatory protein atoC [Blastopirellula
           marina DSM 3645]
          Length = 358

 Score =  166 bits (421), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 108/339 (31%), Positives = 183/339 (53%), Gaps = 5/339 (1%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
            LI  S AM++V +L R+       +++ GE GVGK+ ++  +H   +RA  PF  VNCG
Sbjct: 23  GLIGSSQAMMEVYNLTRRVAGSNASVLLLGETGVGKEMIASAVHRLSQRAAGPFVKVNCG 82

Query: 201 MIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            + +  +E  LFG +    T   +   G+F  A+GG+I L+E ++  L +Q ++   ++ 
Sbjct: 83  ALSESLLESELFGHMRGAFTGAVSNRTGRFEAAHGGSIFLDEINSTSLHLQVKLLRVLQE 142

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
            + E       IR+D R++  + ++L+ +V++  FR+DLY+R++V  I I  LR R EDI
Sbjct: 143 REFERVGDTQTIRVDTRVVAASNRDLMDEVEAERFREDLYWRLNVVPIRIPPLRERREDI 202

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
           P LV  FL  +   N    + I   A+  +  + W  NV+EL+N + RAV+  +   LT 
Sbjct: 203 PELVAHFLNVYSEANERHVVHIQRDAMDAMQDHDWPGNVRELQNYVERAVVLAESDELTV 262

Query: 380 DRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIE 439
           D     + R G K R     +A T   E  + + +   LS+    A  +D   R ++ +E
Sbjct: 263 DLLPPEM-RSGSK-RPSLGMSAQTLDLETLTQEVVQQGLSEADPNA--EDLHSRVVNRVE 318

Query: 440 KEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
           KE+I   M+      ++ A RLGI R+TL++K++EY+++
Sbjct: 319 KELIAQVMQSCSGVQTKAATRLGINRNTLHKKLKEYDLD 357


>gi|239904839|ref|YP_002951577.1| NtrC family two-component response regulator [Desulfovibrio
           magneticus RS-1]
 gi|239794702|dbj|BAH73691.1| NtrC family two-component response regulator [Desulfovibrio
           magneticus RS-1]
          Length = 443

 Score =  166 bits (421), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 116/340 (34%), Positives = 163/340 (47%), Gaps = 45/340 (13%)

Query: 142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM 201
           L+  SPA+ QV  L  K     +P++I GE G GK+  +  I    KRA  PFFI NC  
Sbjct: 144 LVGNSPAIKQVRYLIEKVAPTEVPVLITGESGAGKEVAAHLIQTLSKRADKPFFIKNCAT 203

Query: 202 IDQDKIEKFLFGDV----DLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
           + ++     LFG +        +NS  F+     AN GT+ L+E   LP+ VQ  +   +
Sbjct: 204 LQKELARSELFGHLRGSFTGAVENSEGFMAF---ANKGTLFLDEIGELPIEVQAALLRVL 260

Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
           E         +   R+D+RLIF T + L+ +V    F + L++RI+VF I + +LR R E
Sbjct: 261 ENKTYRRVGEKEERRVDIRLIFATNRELVREVAEGRFHEALFHRINVFNIEMPSLRERRE 320

Query: 318 DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHL 377
           DIP LV FFL       A     ISD+A+  LT Y W  NV+EL+N++ R++I  ++S +
Sbjct: 321 DIPLLVEFFLSRLTAGQA--PFRISDRAMKCLTSYDWPGNVRELRNVMERSIILSENSLI 378

Query: 378 TEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSD 437
           TE              REF                           PA  ++ E+  L  
Sbjct: 379 TEHAL----------PREFLE-------------------------PARAEE-EILTLEA 402

Query: 438 IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
            EKE I   +  Y    S  A  LGI R TLYRKIR+YN+
Sbjct: 403 KEKEHIAKVLNFYDNNRSLAAEALGICRKTLYRKIRQYNL 442


>gi|158424710|ref|YP_001526002.1| nitrogen assimilation regulatory protein ntrC [Azorhizobium
           caulinodans ORS 571]
 gi|172046081|sp|Q04848|NTRC_AZOC5 RecName: Full=Nitrogen assimilation regulatory protein ntrC
 gi|158331599|dbj|BAF89084.1| nitrogen assimilation regulatory protein ntrC [Azorhizobium
           caulinodans ORS 571]
          Length = 480

 Score =  166 bits (421), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 138/491 (28%), Positives = 233/491 (47%), Gaps = 45/491 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY+V    N + L   +S+   +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYEVRSCGNAATLWRWVSQGDGDLVITDVVMPDENAFDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P+IV + Q+     I+      Y  + K F      K+L   +  AL E
Sbjct: 66  LPRIKKARPDLPVIVMSAQNTFMTAIRASERGAYEYLPKPF----DLKELISIVGRALAE 121

Query: 127 GVVPSQENEHCALDS-------LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
                ++ E  AL S       L+  S AM ++  L  +     + +MI GE G GK+ +
Sbjct: 122 ----PKKAEKLALGSDEQENIPLVGRSAAMQEIYRLLARLMQTDLTVMIAGESGTGKELV 177

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIV 238
           +R +H+ GKR   PF  +N   I +D IE  LFG      T  + +  G+F +A GGT+ 
Sbjct: 178 ARALHDYGKRRNGPFVAINMAAIPRDLIESELFGHEKGSFTGATTRNAGRFEQAEGGTLF 237

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   +P+  Q R+   ++ G+      R  I+ DVR+I  T K+L   ++  +FR+DL
Sbjct: 238 LDEIGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIIAATNKDLRTLIQQGLFREDL 297

Query: 299 YYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           ++R++V  + +  LR RSED+P LV HFFLQ    +  +    +   AL  L +Y W  N
Sbjct: 298 FFRLNVVPLRLPPLRERSEDVPDLVRHFFLQ--AEREGLPAKQVDSAALDRLKRYRWPGN 355

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           V+EL+N L+R +  L    +     +         E E  +E A +  +E    D  L  
Sbjct: 356 VRELEN-LVRRLAALYPQEIITPSII---------EAEL-SEPAPSALSEDGPVDATLGA 404

Query: 418 LSQESI----PAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
             +  +       G+D    G   R L D+E  ++  A+   R    + A  LG+ R+TL
Sbjct: 405 SVERHLNGYFSGFGEDLPPPGLYHRILRDVEYPLLSAALAATRGNQIKAAELLGLNRNTL 464

Query: 469 YRKIREYNIEV 479
            +KIR+ +I+V
Sbjct: 465 RKKIRDLDIQV 475


>gi|213967563|ref|ZP_03395711.1| sigma-54 dependent transcriptional regulator/response regulator
           FleR [Pseudomonas syringae pv. tomato T1]
 gi|301385732|ref|ZP_07234150.1| sigma-54 dependent transcriptional regulator/response regulator
           FleR [Pseudomonas syringae pv. tomato Max13]
 gi|302059421|ref|ZP_07250962.1| sigma-54 dependent transcriptional regulator/response regulator
           FleR [Pseudomonas syringae pv. tomato K40]
 gi|302134814|ref|ZP_07260804.1| sigma-54 dependent transcriptional regulator/response regulator
           FleR [Pseudomonas syringae pv. tomato NCPPB 1108]
 gi|213927864|gb|EEB61411.1| sigma-54 dependent transcriptional regulator/response regulator
           FleR [Pseudomonas syringae pv. tomato T1]
          Length = 471

 Score =  166 bits (421), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 132/476 (27%), Positives = 229/476 (48%), Gaps = 21/476 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVE--SYGYDVFIVNVSDLSTISKIQVNVIFLSLINCED-DKEN 69
           VL+++ D    + + + +E   YGY   + +  +    ++ Q   + +S +N    D   
Sbjct: 5   VLLVEDDRSLREALGETLELAGYGYQA-VGSAEEALVAAEAQPFSLVISDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    +      +    + + +     K L  +++     G +
Sbjct: 64  LLSLLRSRHPQLPVLLMTAHGAVDRAVDAMRQGAADYLVKPFEPKALI-ALVARHALGRL 122

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
              E+     D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  R
Sbjct: 123 GPAES-----DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +P+ 
Sbjct: 178 ADKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPMG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPITLDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA
Sbjct: 298 WQALRQRTADILPLAERLLAKHVNKMKHAPVRLSAQAQQCLVSYPWPGNVRELDNAVQRA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           +I L+   + E +   L            +E A   +    S++     +  ES  A+G 
Sbjct: 358 LI-LQQGGVIEAQDFCLAGPVTSLPVAVPSE-AVPPHPVISSAENAGVGVGAESAGALGD 415

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           D  +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V+ 
Sbjct: 416 D--LRRR---EFQMIIDTLRAERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEG 466


>gi|161505338|ref|YP_001572450.1| transcriptional regulatory protein ZraR [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160866685|gb|ABX23308.1| hypothetical protein SARI_03483 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 441

 Score =  166 bits (421), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 130/469 (27%), Positives = 220/469 (46%), Gaps = 46/469 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V +   S    +++++  V  L L +    E D   
Sbjct: 8   ILVVDDDVSHCTILQALLRGWGYNVALA-YSGHDALAQVREKVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL---RE 126
            LK I    P +PI++ T   +++     L      + +  +    L +++  AL   RE
Sbjct: 67  TLKEIKLLNPAIPILIMTAFSSVETAVEALKAGALDYLIKPLDFDHLQETLEKALAHTRE 126

Query: 127 --GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
               +PS       +   I  SPAM  +++           ++I G+ G GK+ ++R +H
Sbjct: 127 TGAELPSASATQFGM---IGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALH 183

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPD 243
               R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E  
Sbjct: 184 ACSARSDKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIG 243

Query: 244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS 303
            +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++
Sbjct: 244 DISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLN 303

Query: 304 VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKN 363
           V  I + +LR R EDIP L   FL+ F  +N       + +A+ LL  Y W  N++EL+N
Sbjct: 304 VVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELEN 363

Query: 364 ILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESI 423
            + RAV+              LL+ E   ERE     A T      S+            
Sbjct: 364 AIERAVV--------------LLTGEYISERELPLTIAATPIKTENSAG----------- 398

Query: 424 PAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
                   ++ L D+EKE+I  A++      +E AR+LGI R TL  K+
Sbjct: 399 --------IQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439


>gi|152393|gb|AAA26346.1| ntrC [Sinorhizobium meliloti]
          Length = 482

 Score =  166 bits (421), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 137/490 (27%), Positives = 232/490 (47%), Gaps = 41/490 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   I+    +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWIAAGDGDLVVTDVVMPDENAFDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 66  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALAE 121

Query: 127 GVVPSQENEHCALDS-----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              P +       DS     L+  S AM ++  +  +     + +MI GE G GK+ ++R
Sbjct: 122 ---PKRRPSKLEDDSQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVAR 178

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +H+ GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT
Sbjct: 179 ALHDYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGT 234

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+
Sbjct: 235 LFLDEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRSDVRIVAATNKDLKQSINQGLFRE 294

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DLYYR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  +PW  
Sbjct: 295 DLYYRLNVVPLRLPPLRDRAEDIPDLVRHFVQQ-AEKEGLDVKRFDQEALELMKAHPWPG 353

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTIL 415
           NV+EL+N++ R         +T +    ++  E + E  +   E A         S  + 
Sbjct: 354 NVRELENLVRRLTALYPQDVITRE----IIENELRSEIPDSPIEKAAARSGSLSISQAVE 409

Query: 416 DNLSQ------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           +N+ Q      +++P  G    V  L+++E  +I  A+   R    + A  LG+ R+TL 
Sbjct: 410 ENMRQYFASFGDALPPSGLYDRV--LAEMEYPLILAALTATRGNQIKAADLLGLNRNTLR 467

Query: 470 RKIREYNIEV 479
           +KIRE  + V
Sbjct: 468 KKIRELGVSV 477


>gi|299533050|ref|ZP_07046436.1| sigma54 specific transcriptional regulator, Fis [Comamonas
           testosteroni S44]
 gi|298718935|gb|EFI59906.1| sigma54 specific transcriptional regulator, Fis [Comamonas
           testosteroni S44]
          Length = 514

 Score =  166 bits (421), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 108/374 (28%), Positives = 183/374 (48%), Gaps = 32/374 (8%)

Query: 112 SRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGE 171
           +R++L      +L+  V  S+ +++ +  S +  SPA ++V   AR+A     P+++ GE
Sbjct: 163 ARRELAAQRSRSLQASVQGSRRSKY-SFASFVGSSPAAVEVKRQARRAAQSMSPVLLLGE 221

Query: 172 FGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-------DVDLQTKNSAQ 224
            G GK+ L+  IH +  R+  PF  VN   I +  +E   FG         D +T++   
Sbjct: 222 TGTGKEVLAHAIHAASARSGGPFVSVNIAAIPETLLEAEFFGVAPGAFTGADRKTRD--- 278

Query: 225 FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN 284
             GKF  A+GGT+ L+E   +P ++Q ++   ++ G+IE   S   +  DVR++  T ++
Sbjct: 279 --GKFKLADGGTLFLDEIGDMPASLQAKLLRALQEGEIEPLGSNQIVHFDVRVVAATSRD 336

Query: 285 LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK 344
           LL  V+   FR+DL+YR+ V  + +  LR RS DIP LV    +    +N +    +   
Sbjct: 337 LLQMVRDGRFREDLFYRLHVLPVRVPPLRERSSDIPALVEMLCEDLALRNDMVPPELGKG 396

Query: 345 ALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTC 404
           AL LL    W  N++EL+N+L +A +   DSH+       +L   G + +  H       
Sbjct: 397 ALELLVAQAWRGNIRELRNVLEQAAMRCDDSHIDAGLLAQVLRSSGVELQVPHRPP---- 452

Query: 405 YTEGKSSDTILDNLSQESIPAIGQ--DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLG 462
                        L+QE + A G        +++++E   I  AM+ +      VAR LG
Sbjct: 453 -------------LAQEPVAAAGDLLKPLAEQMAELEARAIRAAMQAHGGNKLAVARTLG 499

Query: 463 IGRSTLYRKIREYN 476
           I R+ LY ++ + N
Sbjct: 500 ISRAKLYDRLEKLN 513


>gi|183597020|ref|ZP_02958513.1| hypothetical protein PROSTU_00252 [Providencia stuartii ATCC 25827]
 gi|188023676|gb|EDU61716.1| hypothetical protein PROSTU_00252 [Providencia stuartii ATCC 25827]
          Length = 481

 Score =  166 bits (420), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 114/426 (26%), Positives = 199/426 (46%), Gaps = 26/426 (6%)

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +    P +PII+ T   ++        N       + + +    D  +  +   + 
Sbjct: 65  LLNRLKQSHPSLPIIIMTAHSDLDAA----VNAYQSGAFDYLPKPFDIDETVALVERALS 120

Query: 130 PSQENEHCALDS----------LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
            S+E  H   DS          +I  +PAM +V  +  +    +I ++I GE G GK+ +
Sbjct: 121 HSREQNHLERDSKQKTESVSSTMIGEAPAMQEVYRIIGRLSRSSISVLINGESGTGKELV 180

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF-LGKFIEANGGTIV 238
           +  +H+   RA  PF  +N   I +D IE  LFG        + Q   G+F +ANGG++ 
Sbjct: 181 AHALHQHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGATQVRQGRFEQANGGSLF 240

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   +PL +Q R+   +  G+         +++DVR+I  T +NL  +VK  +FR+DL
Sbjct: 241 LDEIGDMPLDIQTRLLRVLAEGQFYRIGGYTPVKVDVRIIAATHQNLEKRVKEGLFREDL 300

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKAL-----SLLTKYP 353
           ++R++V  + +  LR R+EDIP L H+FLQ     N  K++ +  K L      +L +Y 
Sbjct: 301 FHRLNVIRVQLPPLRERTEDIPRLAHYFLQ-----NTAKELGVDSKVLHPDSEHILQRYH 355

Query: 354 WIDNVQELKNIL-LRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD 412
           W  NV++L+N+     V+      L +D    LL      +         +  +   S  
Sbjct: 356 WSGNVRQLENVCRWLTVMAASQEILPQDLPEDLLDSPQPDDASEEPAARQSVTSHHPSWF 415

Query: 413 TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +L+  +  ++    ++   + +  +E  ++  A+K       E AR LG GR+TL RK+
Sbjct: 416 ELLEQWTHSALAEGKENLLAQTVPLMEHTMLNCALKYTNGHKQEAARLLGWGRNTLTRKL 475

Query: 473 REYNIE 478
           +E  IE
Sbjct: 476 KELGIE 481


>gi|294852455|ref|ZP_06793128.1| nitrogen regulation protein NR(I) [Brucella sp. NVSL 07-0026]
 gi|294821044|gb|EFG38043.1| nitrogen regulation protein NR(I) [Brucella sp. NVSL 07-0026]
          Length = 480

 Score =  166 bits (420), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 133/487 (27%), Positives = 236/487 (48%), Gaps = 44/487 (9%)

Query: 19  DDEQIKIIKDHVES-YGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENILKNIV 75
           DD  I+ + +   S  GYDV +  N + L   ++    +++   ++  +++  ++L  I 
Sbjct: 4   DDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVISDVMMPDENAFDLLPRIK 63

Query: 76  DKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSR--KQLCDSIICAL 124
              P +P++V + Q+     I+      Y  + K F     +N+V R   +    +  AL
Sbjct: 64  KIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEPRQKLAVAL 123

Query: 125 REGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
                P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ ++R + 
Sbjct: 124 -----PDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELVARALR 175

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGTIVL 239
           E G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT+ L
Sbjct: 176 EYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGTLFL 231

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +FR+DLY
Sbjct: 232 DEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLFREDLY 291

Query: 300 YRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           YR++V  + +  LR RSED+P LV HFF +    +  + +  I++  L ++ +YPW  NV
Sbjct: 292 YRLNVVPLRLPPLRERSEDVPDLVRHFFKR--AAEEGLPEKRITNAGLEMMRRYPWPGNV 349

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTILDN 417
           +EL+N++ R    L   +  E+    ++  E K E  +     A     E  S    ++ 
Sbjct: 350 RELENLVRR----LAALYPQEEIAPEIIETELKAELAKPDVVAAAGGEMENISISQAVEQ 405

Query: 418 LSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
             Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL +KI
Sbjct: 406 NMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTLRKKI 465

Query: 473 REYNIEV 479
           RE  + +
Sbjct: 466 RELGVNI 472


>gi|15965212|ref|NP_385565.1| nitrogen assimilation regulatory protein [Sinorhizobium meliloti
           1021]
 gi|307309226|ref|ZP_07588897.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Sinorhizobium meliloti BL225C]
 gi|307321969|ref|ZP_07601350.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Sinorhizobium meliloti AK83]
 gi|7404399|sp|P10577|NTRC_RHIME RecName: Full=Nitrogen assimilation regulatory protein
 gi|15074392|emb|CAC46038.1| Nitrogen assimilation regulatory protein [Sinorhizobium meliloti
           1021]
 gi|306892393|gb|EFN23198.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Sinorhizobium meliloti AK83]
 gi|306900372|gb|EFN30988.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Sinorhizobium meliloti BL225C]
          Length = 484

 Score =  166 bits (420), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 137/490 (27%), Positives = 232/490 (47%), Gaps = 41/490 (8%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   I+    +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWIAAGDGDLVVTDVVMPDENAFDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 66  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALAE 121

Query: 127 GVVPSQENEHCALDS-----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              P +       DS     L+  S AM ++  +  +     + +MI GE G GK+ ++R
Sbjct: 122 ---PKRRPSKLEDDSQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVAR 178

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +H+ GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT
Sbjct: 179 ALHDYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGT 234

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+
Sbjct: 235 LFLDEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRSDVRIVAATNKDLKQSINQGLFRE 294

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DLYYR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  +PW  
Sbjct: 295 DLYYRLNVVPLRLPPLRDRAEDIPDLVRHFVQQ-AEKEGLDVKRFDQEALELMKAHPWPG 353

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTIL 415
           NV+EL+N++ R         +T +    ++  E + E  +   E A         S  + 
Sbjct: 354 NVRELENLVRRLTALYPQDVITRE----IIENELRSEIPDSPIEKAAARSGSLSISQAVE 409

Query: 416 DNLSQ------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
           +N+ Q      +++P  G    V  L+++E  +I  A+   R    + A  LG+ R+TL 
Sbjct: 410 ENMRQYFASFGDALPPSGLYDRV--LAEMEYPLILAALTATRGNQIKAADLLGLNRNTLR 467

Query: 470 RKIREYNIEV 479
           +KIRE  + V
Sbjct: 468 KKIRELGVSV 477


>gi|218261427|ref|ZP_03476248.1| hypothetical protein PRABACTJOHN_01914 [Parabacteroides johnsonii
           DSM 18315]
 gi|218224037|gb|EEC96687.1| hypothetical protein PRABACTJOHN_01914 [Parabacteroides johnsonii
           DSM 18315]
          Length = 446

 Score =  166 bits (420), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 134/481 (27%), Positives = 228/481 (47%), Gaps = 52/481 (10%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN-CEDDKENI 70
           +VLIID + + + ++   +   GYDVF    S  + I +++ N   + L + C  D   +
Sbjct: 3   KVLIIDDEKQILSLLSRIIGLEGYDVFQA-ASCKAGIKQLEQNDPEVVLCDVCLPDGSGV 61

Query: 71  LKNIVDKI----PIVPIIVQTTQDNI----KILNCFLYNRISKF-----FLNLVSRKQLC 117
              +V ++    P+  +I+ T   NI    + +    ++ I+K       L L++ K + 
Sbjct: 62  --ELVTELKRLRPLSEVILLTAHGNIPDGVQAIKNGAFDYITKGDDNNKILPLIA-KAME 118

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
            +     ++  V +   +  +  ++I  SPA+ + V LARK     +P+++ GE G GK+
Sbjct: 119 KATAAYQQQKAVGTAVGKQYSFATVIGRSPAIQEAVSLARKVAATDVPVLLTGETGTGKE 178

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-VDLQTKNSAQFLGKFIEANGGT 236
             ++ IH+   R+   F  +NC    +D +E  +FG      T    +  G F EA+ GT
Sbjct: 179 VFAQSIHQYSSRSDKTFVAINCSSFSRDLLESEMFGHKAGAFTGALKETKGLFEEADNGT 238

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           I L+E   +   +Q ++   +ETG+         I+++VR+I  T ++L  ++    FR+
Sbjct: 239 IFLDEIGEMAFDLQAKLLRILETGEFLKIGDTKPIKVNVRVIAATNRDLAKEIADGHFRE 298

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DL+YR+SVF I++  LR R +DIP  V  F+ +  +K      +IS   + +L +YPW  
Sbjct: 299 DLFYRLSVFQIHLPPLRERVDDIPLHVEAFVSALSSKMGKTIRTISPDYIRILKRYPWKG 358

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           NV+EL+N++ R++I      L  D   L +                   TEG  S     
Sbjct: 359 NVRELRNVVERSLIISDGDTLAADTLPLAMQ-------------TPQANTEGNYS----- 400

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
                     G D     LS +EK  I   +K      +E +R LGIG +TLYRKI EY 
Sbjct: 401 ----------GFD-----LSGVEKMHIQKVLKYTNGNKTETSRLLGIGLTTLYRKIEEYG 445

Query: 477 I 477
           +
Sbjct: 446 L 446


>gi|293410584|ref|ZP_06654160.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           B354]
 gi|291471052|gb|EFF13536.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           B354]
          Length = 461

 Score =  166 bits (420), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 133/483 (27%), Positives = 226/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++ +  N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETYCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSNETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K+S    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEVKTSPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|312889060|ref|ZP_07748620.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Mucilaginibacter paludis DSM 18603]
 gi|311298578|gb|EFQ75687.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Mucilaginibacter paludis DSM 18603]
          Length = 444

 Score =  166 bits (420), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 110/351 (31%), Positives = 168/351 (47%), Gaps = 48/351 (13%)

Query: 134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
           N H     ++  SPA  + + LA+K       +++ GE G GK+  ++ IHE+  R+  P
Sbjct: 135 NHHHTFGDILGNSPATAEAILLAQKVAHTPTTVLLMGETGTGKEIFAQAIHEASDRSNKP 194

Query: 194 FFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGK-------FIEANGGTIVLEEPDALP 246
           F  VNC     + ++  LFG V      +  F G        F EA+GGT+ L+E   + 
Sbjct: 195 FIAVNCSSFSNELLKSELFGHV------AGSFTGALKDKKGLFEEADGGTLFLDEIGEMN 248

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
           L +Q R+   +E G         +++++ R+I  T K+L  + ++++FR DLYYR++VF 
Sbjct: 249 LELQARLLRVLEDGTFNRVGDSKSMKVNARIIAATNKDLNYEAENNLFRLDLYYRLAVFT 308

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           I++  LR R EDI  L   FL  F TK   K   + D  L++LT + W  N++EL+N++ 
Sbjct: 309 IHLPPLRERREDIEVLAKHFLNEFSTKLNCKVKKMDDFFLNVLTHHHWKGNIRELRNVME 368

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           R VI      LT D            + +F T+                DN S       
Sbjct: 369 RVVIIAGSDTLTSDLL----------QFDFFTDDH--------------DNFSS------ 398

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
                   LS IE + I  AM   +   +E +R LGIG STLYRK+ EY +
Sbjct: 399 -----ALNLSGIESQYIRKAMARSKGNKAEASRLLGIGLSTLYRKLEEYKL 444


>gi|225851025|ref|YP_002731259.1| transcriptional regulatory protein ZraR [Persephonella marina
           EX-H1]
 gi|225645834|gb|ACO04020.1| transcriptional regulatory protein ZraR [Persephonella marina
           EX-H1]
          Length = 442

 Score =  166 bits (420), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 119/378 (31%), Positives = 199/378 (52%), Gaps = 13/378 (3%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKE 68
           KR+LI+D D + + ++K  +++YGY +F  +  V  L+ I     ++I +  +  E    
Sbjct: 3   KRILIVDDDRDILNLMKLKLKNYGYTIFTESSPVEALNRIKDEHFDLILVDQLMPELSGL 62

Query: 69  NILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
             +  + ++    P+I+ T     +D +  +    ++ I+K  +N    K + D    AL
Sbjct: 63  EFIDRLKERDIKTPVILMTAYGSLEDAVLAMKKGAFHYITKP-INFEELKIIIDQ---AL 118

Query: 125 REGVVPSQENEHCALDS--LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
               +  + NE  +L S  +IA SP M QV++ A+K       ++I GE G GK+ ++ F
Sbjct: 119 EVSDLKKELNELKSLLSTDIIAESPQMKQVLETAKKIAPFDTTVLITGESGTGKEMIANF 178

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           IH++  R   PF  +NCG I  + +E  LFG      T  +    G   EA GGT+ L+E
Sbjct: 179 IHKNSLRKERPFIAINCGAIPSELLESELFGYKKGAFTGANTDKKGLIEEAEGGTLFLDE 238

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              LPL +Q ++   ++  +I+   S    ++DVR I  T ++L   V+   FR+DLYYR
Sbjct: 239 IGELPLDLQVKLLRVLQENEIKPIGSNRPKKIDVRFIAATNRDLKKMVEEGKFREDLYYR 298

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           I+V  I+I  LR R EDI  L  +F+  FC++  I +  +S+KA   L  Y +  NV+EL
Sbjct: 299 INVIPIHIPPLRERKEDIIPLAQYFINKFCSRYGIPKKRLSEKAREKLLNYDYKGNVREL 358

Query: 362 KNILLRAVIGLKDSHLTE 379
           +NI+ RAV+  +   +T+
Sbjct: 359 ENIIERAVLTTEGEEITD 376


>gi|325104308|ref|YP_004273962.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Pedobacter saltans DSM 12145]
 gi|324973156|gb|ADY52140.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Pedobacter saltans DSM 12145]
          Length = 471

 Score =  166 bits (420), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 145/486 (29%), Positives = 226/486 (46%), Gaps = 59/486 (12%)

Query: 12  RVLIIDKDDEQIKIIKDHVESY-GYDVFIVNVSDLST-ISKIQ---VNVIFLSLINCEDD 66
           +VLIID D+E+I+ +   + S  G+DV  V   D+ T + K++   V+V+   +   +  
Sbjct: 26  KVLIID-DEEKIRTLLSKIISLEGFDV--VEAGDIKTGLKKLEIADVDVVICDVKLPDGS 82

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNI-----KILN-CFLY-------NRISKFFLNLVSR 113
                K+I DK P+  II+ T   NI      I N  F Y       N+I         +
Sbjct: 83  GVEATKDIKDKYPVTEIILLTAYGNIPDGVQAIKNGAFDYITKGDDNNKIIPLLYKATEK 142

Query: 114 KQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFG 173
             L   ++   R      Q     + D++I  S  +   +D A+K       +++ GE G
Sbjct: 143 VSLAKRVLQLER------QLANKYSFDNIIGKSKILNASIDAAKKVAGSETTVLLTGETG 196

Query: 174 VGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-VDLQTKNSAQFLGKFIEA 232
            GK+  ++ IH +  R+   F  VNC    +D +E  LFG      T       G F EA
Sbjct: 197 TGKEVFAQAIHNASNRSKQNFVAVNCSAFSKDLLENELFGHKAGAFTGAVKDSKGIFEEA 256

Query: 233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH 292
           N GT+ L+E   +PL +Q ++   +ETG+          +++VR+I  T +NL  +V+  
Sbjct: 257 NHGTVFLDEIGEMPLDLQAKLLRVLETGEFLKVGDSKPTKVNVRIIAATNRNLQQEVEEG 316

Query: 293 VFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY 352
            FR+DL+YRI+VF I++  LR R  DI  L  FFL++F  K   K   IS   L  L ++
Sbjct: 317 HFREDLFYRIAVFQISLPPLRERVIDIEELAIFFLRTFTNKTNKKINKISKNYLEALKQH 376

Query: 353 PWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD 412
            W  N++ELKN++ R+VI    + L ED   L L R G                      
Sbjct: 377 SWKGNIRELKNVIERSVILTGTTELEEDSLPLELQRLG---------------------- 414

Query: 413 TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
             LDN  ++++ A         L+ +EK  I   +       +E ++ L I  +TLYRKI
Sbjct: 415 -TLDN-REKTLSAF-------ELASVEKVHIQKVLNYTNGNKTETSKLLNIALTTLYRKI 465

Query: 473 REYNIE 478
            EY+I+
Sbjct: 466 DEYHIK 471


>gi|134299575|ref|YP_001113071.1| sigma-54 dependent trancsriptional regulator [Desulfotomaculum
           reducens MI-1]
 gi|134052275|gb|ABO50246.1| sigma54 specific transcriptional regulator, Fis family
           [Desulfotomaculum reducens MI-1]
          Length = 582

 Score =  166 bits (420), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 109/351 (31%), Positives = 170/351 (48%), Gaps = 39/351 (11%)

Query: 134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
            + CA + LI  S A+ +++   +K       ++++GE G GK+ L+R IH++  R   P
Sbjct: 260 GQDCAFNKLIGRSEAIQKLIVFGKKISVTEATVLLRGESGTGKELLARAIHQNSPRHMNP 319

Query: 194 FFIVNCGMIDQDKIEKFLFG-------DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
           F +VNCG I  +  E  LFG         D + K      G F  ANGGT+ L+E   +P
Sbjct: 320 FIVVNCGAIPNNLFESELFGYEGGAFTGADRKGKP-----GMFELANGGTLFLDEVGEMP 374

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
           + +Q ++   ++ G         ++ ++VR++  T +NL   +    FR+DLYYR++V  
Sbjct: 375 IEMQAKLLRVLQEGTFYRVGGSQSVHVNVRVLAATHRNLEDMINRRQFREDLYYRLNVVA 434

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           + I  LR R EDIP LVH F+Q FC K       I    ++    Y W  NV+ELKN + 
Sbjct: 435 LEIPPLRDRREDIPELVHLFMQEFCQKYDKNIKKIEPAVMTAFLDYTWPGNVRELKNAVE 494

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           R V+      LT+   +   +      R  +     +  ++GK     L N++ E+    
Sbjct: 495 RLVV------LTDGDIIDEAALPENLRRNTYISLVTSPVSQGK-----LMNVAVEA---- 539

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
                       EK++I   ++  R   SE AR LGI RSTLY K+R+  I
Sbjct: 540 ------------EKQLILKTLQQVRGNRSEAARVLGIPRSTLYYKLRQLGI 578


>gi|156933828|ref|YP_001437744.1| DNA-binding transcriptional regulator TyrR [Cronobacter sakazakii
           ATCC BAA-894]
 gi|156532082|gb|ABU76908.1| hypothetical protein ESA_01654 [Cronobacter sakazakii ATCC BAA-894]
          Length = 526

 Score =  166 bits (420), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 103/344 (29%), Positives = 169/344 (49%), Gaps = 36/344 (10%)

Query: 138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV 197
           A   +IAVSP M QVVD ARK      P++I G+ G GK  L+   H +  RA  P+  +
Sbjct: 208 AFSHIIAVSPRMKQVVDQARKLAMLNAPLLITGDTGTGKDLLAHACHLASPRADKPYLAL 267

Query: 198 NCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE-ANGGTIVLEEPDALPLAVQGRIYNF 256
           NC  I +D +E  LFG       N+ +    F E ANGG+++L+E   +   +Q ++  F
Sbjct: 268 NCASIPEDVVESELFGHAPGAYANAHEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRF 327

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           +  G          + +DVR+I  T+KNL+  V+   FR+DLYYR++V  +N+  LR R 
Sbjct: 328 LNDGTFRRVGEEHEVHVDVRVICATQKNLVELVQKGAFREDLYYRLNVLTLNLPPLRDRP 387

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           +DI  L   F+  F  +  + +  ++     +LT+Y W  NV++LKN + RA+  L+   
Sbjct: 388 QDIMPLTEMFVARFADEQGVPRPKLAGDLGQVLTRYGWPGNVRQLKNAIYRALTQLEGYE 447

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
           L                               +  D +L +    ++P +G++     L 
Sbjct: 448 L-------------------------------RPQDILLPDFDAAALP-VGEEAMEGSLD 475

Query: 437 DIEKEI-IGLAMKLYRAQMS--EVARRLGIGRSTLYRKIREYNI 477
           DI +     +  +LYR+  S  ++A+RLG+  + +  K+REY +
Sbjct: 476 DITRRFERSVLTQLYRSYPSTRKLAKRLGVSHTAIANKLREYGL 519


>gi|330880566|gb|EGH14715.1| sigma-54 dependent DNA-binding response regulator FleR [Pseudomonas
           syringae pv. glycinea str. race 4]
          Length = 425

 Score =  166 bits (419), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 115/351 (32%), Positives = 176/351 (50%), Gaps = 11/351 (3%)

Query: 135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPF 194
           E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  RA  PF
Sbjct: 77  EPAERDGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPRADKPF 136

Query: 195 FIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRI 253
             +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL +Q ++
Sbjct: 137 IAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLGLQAKL 196

Query: 254 YNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLR 313
              ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF +    LR
Sbjct: 197 LRVLQEREVERVGARKPIILDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLAWQALR 256

Query: 314 SRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK 373
            R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA+I  +
Sbjct: 257 QRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVSYPWPGNVRELDNAVQRALILQQ 316

Query: 374 DSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVR 433
              +    F   LS             A        S D      + ES+ A+G D  +R
Sbjct: 317 GGVIQAQDFC--LSGPVTSLPAAAVVEAVPSLPVTSSPDNAGAGGNAESVGALGDD--LR 372

Query: 434 RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           R    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 373 RR---EFQMIIDTLRAERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 420


>gi|323967662|gb|EGB63074.1| sigma-54 interaction domain-containing protein [Escherichia coli
           M863]
 gi|327252489|gb|EGE64148.1| acetoacetate metabolism regulatory protein atoC [Escherichia coli
           STEC_7v]
          Length = 461

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 132/483 (27%), Positives = 226/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C+   E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCSA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|146299737|ref|YP_001194328.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Flavobacterium johnsoniae UW101]
 gi|146154155|gb|ABQ05009.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Flavobacterium johnsoniae UW101]
          Length = 447

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 126/485 (25%), Positives = 228/485 (47%), Gaps = 59/485 (12%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           ++LIID +++   ++   ++S G++VF      S    + + +++V+   +   + +  +
Sbjct: 4   KILIIDDEEKLRSLLARIIKSEGFEVFEAKDLKSGFKKLEQTEIDVVLCDVKLPDGNGVD 63

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
            L+NI    P+  +I+ T      D ++ +    ++ I K   N        D II  L 
Sbjct: 64  FLQNIKGSFPLTEVILLTAFGNIPDGVQAMKNGAFDYIVKGDDN--------DKIIPMLY 115

Query: 126 EGV-----------VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGV 174
           + V           +  + N+  + +++I  S  + QV+DLA+K       +++ GE G 
Sbjct: 116 KAVEKVHLQKKVQQLEKRINDKYSFNTIIGKSKGIEQVIDLAQKVAKTDSTVLLMGETGT 175

Query: 175 GKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE-AN 233
           GK+  ++ IHE+  RA   F  +NC    ++ +E  LFG        + +    FIE AN
Sbjct: 176 GKEVFAQAIHENSNRAGKSFVALNCSTFTKEILESELFGHKQGAFTGAVKDKKGFIEEAN 235

Query: 234 GGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHV 293
           GGT+ L+E   +P+ +Q ++   +ET +          + + RLI  T ++L  +   H 
Sbjct: 236 GGTLFLDEIGEMPIDLQSKLLRVLETSEYIPVGDTTPKKSNFRLIAATNRDLKTESDEHR 295

Query: 294 FRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP 353
           FR DLY+R+++F I + +LR R +DIP L +++++ F  K   K + I+D  L  L  Y 
Sbjct: 296 FRSDLYFRLNIFEIKLPSLRERIKDIPLLANYYVKQFSEKTNKKALQIADDFLQKLENYS 355

Query: 354 WIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDT 413
           W  N++ELKN++ R+VI      LT D    +L  E + + E ++++             
Sbjct: 356 WPGNIRELKNVIERSVILSNGDILTSD----VLPYEMQHQAENNSKSMSAF--------- 402

Query: 414 ILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
                                +  +EK  I   +   +   +E AR L IG +TLYRK+ 
Sbjct: 403 --------------------SMQSVEKLHIQKVLNYTKGNKAETARLLEIGIATLYRKLE 442

Query: 474 EYNIE 478
           EY I+
Sbjct: 443 EYQIQ 447


>gi|323977582|gb|EGB72668.1| sigma-54 interaction domain-containing protein [Escherichia coli
           TW10509]
          Length = 461

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 133/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       PII+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPIILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|254882600|ref|ZP_05255310.1| two-component system response regulator [Bacteroides sp. 4_3_47FAA]
 gi|319642060|ref|ZP_07996726.1| two-component system response regulator [Bacteroides sp. 3_1_40A]
 gi|254835393|gb|EET15702.1| two-component system response regulator [Bacteroides sp. 4_3_47FAA]
 gi|317386326|gb|EFV67239.1| two-component system response regulator [Bacteroides sp. 3_1_40A]
          Length = 451

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 110/409 (26%), Positives = 199/409 (48%), Gaps = 39/409 (9%)

Query: 79  PIVPIIVQTTQDNIKI----LNCFLYNRISKFFLN--LVSRKQLCDSIICALREGVVPSQ 132
           P VP+++ T   +I++    +    ++ I+K + N  L+ R +    +    ++  VP +
Sbjct: 74  PDVPVVLMTAWGSIQLAVQGMQAGAFDFITKPWNNVALMQRIETALELTSQDKKAAVPVE 133

Query: 133 ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF 192
           +N+      +I  S A++ V+   ++       ++I GE G GK+ ++  +H +  R+  
Sbjct: 134 DNDGFNRSHIIGKSKALMDVLATIKRIARTNASVLITGESGTGKELIAEAVHLNSPRSKK 193

Query: 193 PFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQG 251
           PF  VN G I     E  +FG      T  ++  +G+F  A+ GTI L+E   L L+ Q 
Sbjct: 194 PFVKVNLGGISHTLFESEMFGHKKGAFTDATSDRVGRFELADKGTIFLDEIGDLDLSCQV 253

Query: 252 RIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIST 311
           ++   ++    E        ++D+R++  T  +L   V+ H FR+DL+YRI++  +++  
Sbjct: 254 KLLRVLQEQTFEVLGDSRPRKVDIRVVSATNADLRQMVQEHTFREDLFYRINLITVHLPA 313

Query: 312 LRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIG 371
           LR R EDIP LV  F    C  N + ++  + +A+  L++ P+  N++ELKN++ R ++ 
Sbjct: 314 LRERREDIPLLVRHFADKQCESNGLPKVEFTSEAMDYLSRLPYPGNIRELKNLVERTLLV 373

Query: 372 LKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGE 431
                LT D F        K + +   E   T   +G +                     
Sbjct: 374 SGKEILTADDF--------KSQYQHPIEQKMTTNLQGMT--------------------- 404

Query: 432 VRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
              L +IEK+ I   ++ Y   MS+VA  LGI R+ LYR++ +YNI+V+
Sbjct: 405 ---LEEIEKQTILQTLEKYNNNMSQVAIALGISRAALYRRLEKYNIQVN 450


>gi|13470632|ref|NP_102201.1| nitrogen assimilation regulatory protein ntrC [Mesorhizobium loti
           MAFF303099]
 gi|14021374|dbj|BAB47987.1| nitrogen assimilation regulatory protein; NtrC [Mesorhizobium loti
           MAFF303099]
          Length = 486

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 133/500 (26%), Positives = 230/500 (46%), Gaps = 60/500 (12%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   G++V +  N S L   ++  + +++   ++  +++  ++
Sbjct: 7   ILVADDDAAIRTVLNQALSRVGHEVRVTSNASTLWRWVAAGEGDLVITDVVMPDENAFDM 66

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P+IV + Q+     I+      Y  + K F     LN+V+R       +
Sbjct: 67  LPRIKKARPELPVIVMSAQNTFMTAIRASETGAYEYLPKPFDLTELLNIVNRA------L 120

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              R   + ++ +E      L+  S AM  +  +  +     + +MI GE G GK+ ++R
Sbjct: 121 SEPRRPKIDARPDEQPETMPLVGRSAAMQDIYRMLARMMQTDLTVMISGESGTGKELVAR 180

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +HE G+R   PF  +N   I +D IE  LFG +    T    +  G+F +A GGT+ L+
Sbjct: 181 ALHEYGRRRGGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSTGRFEQAEGGTLFLD 240

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   +   +FR+DL+Y
Sbjct: 241 EIGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIVAATNKDLRTLINQGLFREDLFY 300

Query: 301 RISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           R++V  + +  LR RSED+P LV HFF         ++   IS   + L+ +YPW  NV+
Sbjct: 301 RLNVVPLRLPALRERSEDVPDLVRHFF--KLGEMEGLQTKRISSGGIELMKRYPWPGNVR 358

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           EL+N++ R         ++ +            E E  T         G   + I D+LS
Sbjct: 359 ELENLVRRLAALYSQDEISAEII----------EAELKTGERPVVPGGG---NLIPDDLS 405

Query: 420 QESIPAIGQ-------------DGEV-------RRLSDIEKEIIGLAMKLYRAQMSEVAR 459
                 IGQ              GE+       R LS++E  ++  +M   R    + A 
Sbjct: 406 ------IGQAVEHFLQRYFASFAGELPPAGLYQRILSEVEYPLVLASMTATRGNQIKAAE 459

Query: 460 RLGIGRSTLYRKIREYNIEV 479
            LG+ R+TL +KIRE  + V
Sbjct: 460 LLGLNRNTLRKKIRELGVNV 479


>gi|197122377|ref|YP_002134328.1| Fis family transcriptional regulator [Anaeromyxobacter sp. K]
 gi|220917159|ref|YP_002492463.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
 gi|196172226|gb|ACG73199.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter sp. K]
 gi|219955013|gb|ACL65397.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 473

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 124/477 (25%), Positives = 223/477 (46%), Gaps = 30/477 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           VLI+D +    +++   ++  GY+V      +  L  + +  V+V+   L+        +
Sbjct: 4   VLIVDDEVNIRRVLAAMLKREGYEVTTAADGEQALGVLHRTPVHVVVTDLVMPRVGGMEL 63

Query: 71  LKNIVDKIPIVPIIVQTTQDNI----KILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L+ +    P VP+I+ T   ++      L    ++ I+K F     +++L   I  A R 
Sbjct: 64  LRRVSQDFPDVPVILITAHGSVDSAVAALKAGAFDYITKPF----EQEELKKVIAKAARA 119

Query: 127 GVVPSQENEHCALD-----SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
             +  Q N H  L+      LI  SP M  + D+  +  D    ++I GE G GK+ +++
Sbjct: 120 HDLERQ-NLHAMLNDGDGPPLIGQSPPMRAIYDMVARVADSPSTVLITGESGTGKELIAK 178

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H    R   P   VNC  I +D +E  LFG +    T       G+F  A+GGT+ L+
Sbjct: 179 ALHRGSSRRDKPLIKVNCAAIPKDLVESELFGYERGAFTGAVGSKPGRFELADGGTLFLD 238

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +P+ +Q ++   I+  + E       +++DVRLI  T ++L   +    FR+DLYY
Sbjct: 239 EIGEVPVEMQVKLLRAIQESEFERVGGIKTLQVDVRLIAATNRDLKQLIADGRFREDLYY 298

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++V  I +  LR R ED+P LV +F++ +  +   K   I D+AL LL  Y W  N++E
Sbjct: 299 RLAVVPIALPPLRDRREDVPLLVRYFIEKYDQRLGKKVEGIEDEALELLANYSWPGNIRE 358

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           L+N++ R+V+   D  L +   +    RE   +                 S   +  + +
Sbjct: 359 LENLMERSVL-FADGPLIQASALPDALREKGAQASVPIAAVGPLGAIAAPSGASMKEIVR 417

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           ++             +++E+E+I  A++     ++  A+RL I R +L  K++E  +
Sbjct: 418 QA------------QAELERELITRALEETGGNVTRAAKRLQISRKSLQVKMKELGL 462


>gi|298487837|ref|ZP_07005877.1| Flagellar regulatory protein fleQ [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298157562|gb|EFH98642.1| Flagellar regulatory protein fleQ [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 469

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 135/476 (28%), Positives = 224/476 (47%), Gaps = 23/476 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVE--SYGYDVFIVNVSDLSTISKIQVNVIFLSLINCED-DKEN 69
           VL+++ D    + + + +E   YGY   + +  +    ++ Q   + +S +N    D   
Sbjct: 5   VLLVEDDRSLREALGETLELAGYGYQA-VGSAEEALVAAEAQPFSLVISDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    +      +    + + +     K L   I    R  + 
Sbjct: 64  LLSLLRSRHPQLPVLLMTAHGAVDRAVDAMRQGAADYLVKPFEPKAL---IALVARHALG 120

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
             +  E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  R
Sbjct: 121 RLEPAER---DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL 
Sbjct: 178 ADKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPIILDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA
Sbjct: 298 WQALRQRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVNYPWPGNVRELDNAVQRA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           +I  +   +    F   LS             A        S D    N   ES+ A+G 
Sbjct: 358 LILQQGGVIQAQDFC--LSGPVTSLPAAAVVEAVPSLPVTSSPDNAGGN--AESVGALGD 413

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           D  +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 414 D--LRRR---EFQMIIDTLRAERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 464


>gi|291279231|ref|YP_003496066.1| two-component, sigma54 specific, transcriptional regulator
           [Deferribacter desulfuricans SSM1]
 gi|290753933|dbj|BAI80310.1| two-component, sigma54 specific, transcriptional regulator
           [Deferribacter desulfuricans SSM1]
          Length = 476

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 141/476 (29%), Positives = 234/476 (49%), Gaps = 28/476 (5%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFI-VNVSD-LSTISKIQVNVIFLSLINCEDDKE 68
           KRVL++D DD     +K  +   G DV + ++ +D      K   ++I   +   + D  
Sbjct: 5   KRVLVVDDDDNMRNGLKLTISRMGIDVDVAIDANDGFEKAMKTNYDLIISDIKMPKIDGI 64

Query: 69  N---ILKNIVDKIPIVPIIV-QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
               +LKN   K P+  I    T +  ++ L    ++ I K F   V  ++L + +    
Sbjct: 65  TFFKMLKNAGVKTPLCFITAYATVETAVEALKLGAFDYIIKPFPPEVI-EELIERVFS-- 121

Query: 125 REGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
              +   ++ +H      +  S  M ++ +LA         ++I GE G GK+ L++FIH
Sbjct: 122 ---INNLKQEDHNEDRKYVYKSRYMAEIFNLALDVASSDATVLITGESGTGKEVLAKFIH 178

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPD 243
           E+ +R   PF  VNC  I ++ +E   FG +    T    +  GKF  A+GGTI+L+E  
Sbjct: 179 ENSRRKAKPFVAVNCAAIPENLVESEFFGYEKGAFTGAEKRKPGKFEIADGGTILLDEIG 238

Query: 244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS 303
            +P+ +Q ++   ++  +IE       I +DVR+I  T ++LL +VK   FR+DLYYR++
Sbjct: 239 EIPINLQAKLLRVLQEKEIERLGGLKPIPVDVRIIATTNRDLLEEVKKGNFREDLYYRLN 298

Query: 304 VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKN 363
           V  ++I  LR R +DI  L  FF++ +   N  K  ++S+ A S L  Y W  NV+EL++
Sbjct: 299 VINLHIPPLRRRKDDILHLAEFFVEKYSKLNRKKAKNLSEDAKSTLVNYDWPGNVRELEH 358

Query: 364 ILLRAVIGLKDSHLT-EDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
            + RAVI  K   +T +D F+  L         FH E+      E K+ D+ + N     
Sbjct: 359 TIERAVILSKGDKITSKDLFLHGLV--------FHEESLV---EEVKTVDSDISNDEDSK 407

Query: 423 IP---AIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            P   +     + R ++D+EKE+I   +K      ++ A  LGI   TL  K++EY
Sbjct: 408 EPEKISFTNTLKNRSIADVEKELILNTLKDVGGNRTKAAEILGITVRTLRNKLKEY 463


>gi|297569043|ref|YP_003690387.1| Fis family transcriptional regulator [Desulfurivibrio alkaliphilus
           AHT2]
 gi|296924958|gb|ADH85768.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfurivibrio alkaliphilus AHT2]
          Length = 461

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 123/480 (25%), Positives = 228/480 (47%), Gaps = 34/480 (7%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKE 68
           K +L++D +   + I+ + +   GY+ F    ++  L       +++I   +     D  
Sbjct: 2   KTILVVDDEPNYLVILSELLRDEGYETFTAGSAEEGLEIARHTDLDLIITDMRMPGMDGL 61

Query: 69  NILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFFLN---LVSRKQLCDSII 121
            +LK I    P +P+I+ T        +  +    +N ++K F N   LVS ++  +   
Sbjct: 62  ELLKTIKGINPSLPVIMITAFGEVDKAVAAMRAGAFNYLTKPFDNDELLVSIRKALEHYE 121

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
                  + ++ +E  +  S++  S  M ++  L  K       ++I GE G GK+ ++R
Sbjct: 122 VVRENTRLRAEISERTSYASMVGKSHRMREIYGLIEKVAPTPTSVLITGESGTGKELVAR 181

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H +  R+  PF  +NC  + +  +E  LFG +    T   A   G+F  A+GGT+ L+
Sbjct: 182 AVHSNSPRSQAPFISINCAGLPESLLESELFGHEKGAFTGAVALRKGRFELADGGTLFLD 241

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL++Q ++   I+    E       IR++VRLI  T K+L  +V++  FR+DLYY
Sbjct: 242 EVGEMPLSLQAKLLRVIQERAFERVGGSRTIRVEVRLIAATNKDLKEEVEAGNFREDLYY 301

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R++V  I++  LR R++DIP L H F+  F  +     + I  + +S L+  PW  N++E
Sbjct: 302 RLNVVHIHLPPLRERTDDIPALAHHFVAKFARELHRPGLQIMPETISFLSTLPWEGNIRE 361

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNL-- 418
           L+N + RA +              L S+E     +   E++    + G   +  L+ L  
Sbjct: 362 LENTIERAAV--------------LCSKELITPADVQPESSGDQPSIGWGDNLQLEQLIP 407

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            +  +P I        ++ IEK+++  A+       +  A  LGI +S L  K+++Y ++
Sbjct: 408 PETPLPEI--------MNTIEKKMVAEALAKADHVQTRAADSLGITKSLLQYKMKKYGLQ 459


>gi|328952447|ref|YP_004369781.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfobacca acetoxidans DSM 11109]
 gi|328452771|gb|AEB08600.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfobacca acetoxidans DSM 11109]
          Length = 455

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 135/483 (27%), Positives = 215/483 (44%), Gaps = 63/483 (13%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVS----DLSTISKIQVNVIFLSLINCEDDKE 68
           +L++D D    + +   ++  G+ VF+        +L     +++ +I L L + E    
Sbjct: 4   ILVVDDDANTREALAGSLKKIGHQVFLAGAGAEALELVRQQPVELAIIDLKLPDMEGTDL 63

Query: 69  NILKNIVDKIPIVPIIVQ--TTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
                I+    I  +I    T  + +  L   +Y+ I+K F     R Q    ++    E
Sbjct: 64  FEAMRIIRPYTIAIMISARATVDEAVSALKLGIYDFITKDF-----RMQEIRKVVNKALE 118

Query: 127 GVVPSQEN--------EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
                QEN        E  A   +I  S A ++++    K       +++ GE GVGK+ 
Sbjct: 119 TQQLLQENQKLRQALQERLASGRIIGRSQAFLKIIHQVNKIAPLRSTVLLTGESGVGKEL 178

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++  IH    R   P   VNCG + +  IE  LFG +    T    Q  G+F  A+GGTI
Sbjct: 179 IAEAIHYGSPRRDKPLVKVNCGALPEGLIESELFGHEKGAFTGAHQQRKGRFELADGGTI 238

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   +PL+ Q ++   ++ G+ E       +++DVRL+  T +NL   V + VFRKD
Sbjct: 239 FLDEVAEMPLSTQVKLLRVLQEGEFERVGGARTLKVDVRLVAATNQNLEDMVAAGVFRKD 298

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           L+YR++V  + +  LR+R EDIP L   FL  FC +N    +  S +AL  L  Y W  N
Sbjct: 299 LFYRLNVIHLEVPPLRARDEDIPLLAQHFLDKFCLENERPPMGFSPEALKALKNYLWPGN 358

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           V+EL+N++ RAV                                CT  T G   D + D 
Sbjct: 359 VRELENVVERAV------------------------------ALCTGSTVG--LDDLPDE 386

Query: 418 LSQES------IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
           + Q+S      +  +G       + +IE+  I   +K         AR LGIG +TLYR+
Sbjct: 387 VRQQSQTEDHIVVQVGAS-----MEEIERLAIRQTLKKTGGDKEVAARILGIGLATLYRR 441

Query: 472 IRE 474
           ++E
Sbjct: 442 LKE 444


>gi|170760993|ref|YP_001787050.1| sensory box sigma-54 dependent transcriptional regulator
           [Clostridium botulinum A3 str. Loch Maree]
 gi|169407982|gb|ACA56393.1| sensory box sigma-54 dependent transcriptional regulator
           [Clostridium botulinum A3 str. Loch Maree]
          Length = 654

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 116/342 (33%), Positives = 178/342 (52%), Gaps = 32/342 (9%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            D++I V+  MI++++LA+KA      I+I+GE G GK+ +++ IH    RA  PF  VN
Sbjct: 332 FDNIITVNEKMIEIIELAKKASKSNCNILIEGESGTGKELIAQSIHNYSMRATGPFLAVN 391

Query: 199 CGMIDQDKIEKFLFG-DVDLQTKNSAQ-FLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           C  I ++ +E  LFG +    T  S +   GKF  A+GGTI L+E   LPL +Q ++   
Sbjct: 392 CASIPRELVESELFGYERGAFTGASKEGHPGKFELADGGTIFLDELGELPLDMQSKLLRV 451

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           ++  KI         +L+VR+I  T +NL  ++K   FR+DLYYR+ V  I I  LR R 
Sbjct: 452 LDNNKIIRVGGTYEKQLNVRVIGATNRNLKEEMKKKNFREDLYYRLGVINIKILPLRYRK 511

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           EDI  LV+ F+ +   +N  +   +    +  L  Y W  NV+EL+N++ R      D +
Sbjct: 512 EDIEALVNSFVMNLNQRNLQQNKRVKKAYIDKLKDYDWPGNVRELRNVVER------DYY 565

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
           L++                  T+T    Y E      I    + ES     +D  +  + 
Sbjct: 566 LSD------------------TDTVSPYYIE----KNIFLETNNESYE--NKDINIIPMG 601

Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            +EKE I  A++     +++ AR L IGRSTLYRKI++YNI+
Sbjct: 602 KLEKENIENAIEKCDGNLAKAARLLNIGRSTLYRKIKKYNIK 643


>gi|91202962|emb|CAJ72601.1| strongly similar to sigma 54 response regulatory protein
           [Candidatus Kuenenia stuttgartiensis]
          Length = 448

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 107/340 (31%), Positives = 171/340 (50%), Gaps = 36/340 (10%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
           S+I  SPA+  V  +  K     + ++IQGE G GK+  ++ IH+  KRA  PF IVNC 
Sbjct: 144 SMIGNSPAIKAVFKMIDKTAPSDVTVLIQGESGTGKELAAKMIHQYSKRADKPFVIVNCA 203

Query: 201 MIDQDKIEKFLFGDVDLQTKNSAQF-LGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            + +  +E  LFG V      +A+  +G F  A GGT+ L+E   L +  Q ++   I++
Sbjct: 204 TLQESLLESELFGHVKGAFTGAAESRVGLFEIAEGGTLFLDEIGELTVNTQAKLLRVIQS 263

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
           G+I        I +D R+I  T KNL  +VK   FR+DLY+R++V  + + +LR R +D+
Sbjct: 264 GEIRRVGDNRVITVDARIIAATHKNLPLEVKEGRFREDLYFRLNVITLRLPSLRERKDDL 323

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
             L+  FLQ FC     + + +  +AL  +T Y W  N++EL+N + R V+ L D ++  
Sbjct: 324 TALIQHFLQKFCKGE--RTMDMHPEALHAMTLYDWPGNIRELENTIERTVV-LADGNII- 379

Query: 380 DRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIE 439
                                         S + + DN+   +    G++GE+  LS++E
Sbjct: 380 ------------------------------SIEELPDNIRGRTYEHYGKNGEI-ALSEVE 408

Query: 440 KEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           K  I   +K         A+ LGI   TLY K++ YNI++
Sbjct: 409 KNHIIQVLKEKNWHKPLAAKTLGISLKTLYNKMKMYNIDL 448


>gi|85857963|ref|YP_460165.1| response regulator [Syntrophus aciditrophicus SB]
 gi|85721054|gb|ABC75997.1| response regulator with sigma 54 interaction domain [Syntrophus
           aciditrophicus SB]
          Length = 452

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 134/484 (27%), Positives = 229/484 (47%), Gaps = 48/484 (9%)

Query: 7   LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCE 64
           + +   VL++D D     ++K  +  +GYDV   +   S +  + +   ++I + +    
Sbjct: 1   MKKKSEVLVVDDDFAHRTMLKTLISGWGYDVSEADDGQSAIEAVHRRPFDLILMDIRMVR 60

Query: 65  DDKENILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL 116
                 L+ I    P +PII+ T     +  ++ L    Y+ ++K      L LV  + L
Sbjct: 61  ISGIEALEEIRRLNPAIPIILMTAYASVETAVEALKKGAYDYLTKPLDFDELRLVLERGL 120

Query: 117 CDSIICALREGVVPSQENEHCALD--SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGV 174
             +    L+E  +  +E      D  ++I  S +M +++DL  +       +++ GE G 
Sbjct: 121 EHT---RLKEENLLLKERLGIRFDRRNIIGRSESMTRLLDLVAQVAPSEATVLLSGESGT 177

Query: 175 GKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEAN 233
           GK+ ++  IH +  R   PF  +NC  I +  +E  LFG +    T    +  GKF +A+
Sbjct: 178 GKEVIAAAIHYNSLRKEKPFIKINCAAITETLLESELFGHEKGAFTGADRRKEGKFRQAD 237

Query: 234 GGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHV 293
           GGTI+L+E   + LA+Q ++   ++  +I        I +DVR+I  T ++L+ ++ +  
Sbjct: 238 GGTILLDEVSEMSLAMQVKLLRVLQEREITRVGGDEVIPIDVRVITATNRDLVREIAAGR 297

Query: 294 FRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP 353
           FR+DLYYR++V  + +  LR R EDIP L   FL+ F  KN  +    + +AL  + +Y 
Sbjct: 298 FREDLYYRLNVVTLQVPPLRERKEDIPLLAAHFLKEFAEKNRKELKGFTPRALDRMLRYS 357

Query: 354 WIDNVQELKNILLRAVIGLKDSHLTE-DRFVLLLSREGKKEREFHTETACTCYTEGKSSD 412
           W  NV+EL N + R V+  +  +L E D   +LL +E  +E        C     G SS 
Sbjct: 358 WPGNVRELMNTVERGVVLSRSDYLDESDLSPILLEKESPEE-----NPECAG---GNSS- 408

Query: 413 TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
                                 L  +EKE I   ++      SE ARRLGI R TL++K+
Sbjct: 409 ----------------------LEVVEKETILKTLEEAGGNKSEAARRLGITRRTLHQKL 446

Query: 473 REYN 476
           ++Y 
Sbjct: 447 KKYG 450


>gi|153954890|ref|YP_001395655.1| transcriptional regulator [Clostridium kluyveri DSM 555]
 gi|219855344|ref|YP_002472466.1| hypothetical protein CKR_2001 [Clostridium kluyveri NBRC 12016]
 gi|146347748|gb|EDK34284.1| Predicted transcriptional regulator [Clostridium kluyveri DSM 555]
 gi|219569068|dbj|BAH07052.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 656

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 102/344 (29%), Positives = 173/344 (50%), Gaps = 22/344 (6%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            D+++  +  M  +++ AR+       ++I GE G GK+  +  IH   KR   PF  +N
Sbjct: 331 FDNILTQNARMKGIIEDARRIAKNDCTVLITGESGTGKELFAHSIHNGSKRCSGPFVAIN 390

Query: 199 CGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           C  + +D +E  LFG         +     GKF  ANGGTI L+E   LPL +Q ++   
Sbjct: 391 CSALPKDLVESELFGYEKGSFTGASKEGNPGKFELANGGTIFLDEIGELPLEIQPKLLRV 450

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           ++   I     +    L+VR+I  T +NL  +VK   FR DLY+R++VF IN+  +R R 
Sbjct: 451 LDNHAITRIGGKYERDLNVRVIAATNRNLFKEVKLKNFRSDLYFRLNVFNINLIPVRERR 510

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           EDI   + FFL+    KN +K  +I ++ + ++  Y W+ NV+E++N++ R         
Sbjct: 511 EDIEMFIKFFLEKLAQKNKVKINNIDEEFMDVVKNYEWLGNVREIENVVQR--------- 561

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
                 V  LS +G+      T+     Y       +  D++   S        E++ L 
Sbjct: 562 ------VYYLSEKGR-----ITKALLPGYIMNYKKSSTEDDMKFSSDSYNEFKPEIQTLD 610

Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
            +EK++I  A++     +   ++ + +G+STLYRKI++YN+E +
Sbjct: 611 QVEKQLIIKALRYCNGNVVNASKLINMGKSTLYRKIKKYNLEFE 654


>gi|146311804|ref|YP_001176878.1| DNA-binding transcriptional regulator TyrR [Enterobacter sp. 638]
 gi|145318680|gb|ABP60827.1| transcriptional regulator, TyrR [Enterobacter sp. 638]
          Length = 514

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 104/346 (30%), Positives = 170/346 (49%), Gaps = 47/346 (13%)

Query: 138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV 197
           A   +IAVSP M  VVD ARK  +   P++I GE G GK  L+  +H +  RA  P+  +
Sbjct: 202 AFSQMIAVSPKMRHVVDQARKLANLTAPLLITGETGTGKDLLAHAVHTASPRAAKPYLAL 261

Query: 198 NCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
           NC  I +D +E  LFG      K      G F +A GG+++L+E   +   +Q ++  F+
Sbjct: 262 NCASIPEDAVESELFGHAPEGKK------GFFEQATGGSVLLDEIGEMSPRMQAKLLRFL 315

Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
             G          + +DVR+I  T+KNL+  V+  VFR+DLYYR++V  +NI  LR   +
Sbjct: 316 NDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGVFREDLYYRLNVLTLNIPPLRDCPQ 375

Query: 318 DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHL 377
           DI  L   F+  F  +  + +  +S    ++LT+Y W  N+++LKN + RA+  L+   L
Sbjct: 376 DIMPLTELFVARFADEQGVPRPKLSADLGTMLTRYNWPGNIRQLKNAVYRALTQLEGYEL 435

Query: 378 TEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSD 437
                                          +  D +L +    ++ A+G++     L D
Sbjct: 436 -------------------------------RPQDVLLPDYDAGTL-AVGEEAMEGSLDD 463

Query: 438 I----EKEIIGLAMKLYRAQMS--EVARRLGIGRSTLYRKIREYNI 477
           I    E+ ++    +LYR   S  ++A+RLG+  + +  K+REY +
Sbjct: 464 ITSRFERSVL---TQLYRNYPSTRKLAKRLGVSHTAIANKLREYGL 506


>gi|296447369|ref|ZP_06889296.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylosinus trichosporium OB3b]
 gi|296255148|gb|EFH02248.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Methylosinus trichosporium OB3b]
          Length = 490

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 127/491 (25%), Positives = 226/491 (46%), Gaps = 29/491 (5%)

Query: 10  HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDK 67
           H  +L+ D D     ++   +   GY+V     +      +   + +++   ++  +++ 
Sbjct: 3   HGEILVADDDAAIRTVVAQALSRAGYEVRTTGTAATLWRWVQSGEGDLVVTDVVMPDENA 62

Query: 68  ENILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICA 123
             +L  I    P +PIIV + Q+     I+      Y+ + K F      K+L   +  A
Sbjct: 63  FELLPRIKKLRPDLPIIVMSAQNTFMTAIRASERGAYDYLPKPF----DLKELVGIVGRA 118

Query: 124 LREGVVPSQENEHCALD-----SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
           + E   P ++ E    D      L+  SPAM ++     +     + +MI GE G GK+ 
Sbjct: 119 MAE---PRKKGEIDGPDEMEGMPLVGRSPAMQEIYRSLARLMQTDLTVMINGESGTGKEL 175

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTI 237
           ++R +H+ GKR   PF  +N   I +D IE  LFG      T  + + +G+F +A GGT+
Sbjct: 176 VARALHDYGKRKKGPFVAINMAAIPRDLIESELFGHEKGSFTGANQRSIGRFEQAEGGTL 235

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   +P+  Q R+   ++ G+      R  I+ +VR+I  T K+L   ++  +FR+D
Sbjct: 236 FLDEIGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTNVRIIAATNKDLRALIQQGLFRED 295

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LY+R++V  + +  LR R+ED+P LVH F +       + Q  I   AL  + +Y W  N
Sbjct: 296 LYFRLNVVPLRLPPLRERTEDVPDLVHHFFK-VAASEGLPQKYIEQAALDRMKRYRWPGN 354

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           ++EL+N++ R         +TE    L L  E ++        A          D  L  
Sbjct: 355 IRELENLIRRLAALHPQEVITEAVVELELEHEMRQASPGDRAAASAGGERPLDKDVTLST 414

Query: 418 LSQESIPAIGQD-GEV--------RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
             ++ +  + +D GE         R + +IE  +I  A+   R    + A  LG+ R+TL
Sbjct: 415 SVEQHLAKLFRDHGERLPPPGLYHRVIREIEVPLISAALAATRGNQIKAAELLGLNRNTL 474

Query: 469 YRKIREYNIEV 479
            +K+ + +I +
Sbjct: 475 RKKVNDLDIRL 485


>gi|258516115|ref|YP_003192337.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfotomaculum acetoxidans DSM 771]
 gi|257779820|gb|ACV63714.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfotomaculum acetoxidans DSM 771]
          Length = 513

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 117/368 (31%), Positives = 187/368 (50%), Gaps = 33/368 (8%)

Query: 143 IAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMI 202
           +  SPAM+++V +A K     I ++IQGE G GK+ L+ FIHE+G R  +PF  VNCG +
Sbjct: 148 VGNSPAMLRLVSMADKIARKNINVLIQGETGTGKEVLANFIHEAGNRTEYPFVAVNCGAL 207

Query: 203 DQDKIEKFLFGDVDLQTKNSA-QFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGK 261
            ++ +E  LFG        +A Q  G F  AN GT+ L+E     L++Q ++   +ETG+
Sbjct: 208 PENLLESELFGHEKGSFTGAANQRKGIFELANKGTLFLDEIGEASLSIQVKLLRVLETGE 267

Query: 262 IEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPW 321
                    I  DVR+I  T  +L   V+   FR+DL+YR+ V  + I +LR   +DIP 
Sbjct: 268 FMRVGGEKPIHTDVRVIAATNVDLEKAVRDKTFREDLFYRLDVVRLLIPSLREHKKDIPV 327

Query: 322 LVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKD------S 375
           LV++FL  F  K   + ++ S +A+ LL ++ W  N++EL N + ++ + L D      +
Sbjct: 328 LVNYFLNKFKNKYGSENMTFSKEAMELLLEHAWPGNIRELANTVDQS-MALCDGQIILPA 386

Query: 376 HLTE----DRFVLLLSREGKKEREFHTETACTCYTEGK-------SSDT--------ILD 416
           HL++     +  +     G    +         Y           S+DT        +L 
Sbjct: 387 HLSKKFSGKKLAVDSGANGDDSVKNIPVNEIKSYLGNSLSLIKILSADTENLPELLPVLR 446

Query: 417 NLSQESIPAIGQDGEV-----RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
            LS+E +  +  D EV       L ++E   +  A+   +  +S  A+ LGIGR+TLYRK
Sbjct: 447 ELSEE-LKKLCDDQEVCANYSLNLQEVESITVARALSRCKGNISVAAKLLGIGRNTLYRK 505

Query: 472 IREYNIEV 479
           I++Y + V
Sbjct: 506 IKDYGLSV 513


>gi|218700689|ref|YP_002408318.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           IAI39]
 gi|331653655|ref|ZP_08354656.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli M718]
 gi|218370675|emb|CAR18484.1| fused response regulator of ato opeon, in two-component system with
           AtoS: response regulator ; sigma54 interaction protein
           [Escherichia coli IAI39]
 gi|331048504|gb|EGI20580.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli M718]
          Length = 461

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 132/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSNETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|327191427|gb|EGE58450.1| two-component response regulator nitrogen regulation protein
           [Rhizobium etli CNPAF512]
          Length = 483

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 138/493 (27%), Positives = 231/493 (46%), Gaps = 47/493 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   IS  + +++   ++  +++  ++
Sbjct: 5   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWISAGEGDLVVTDVVMPDENAFDL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 65  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALAE 120

Query: 127 GVVPSQENEHCALDS--LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
                 + E    D   L+  S AM ++  +  +     + +MI GE G GK+ ++R +H
Sbjct: 121 PKRKPAKLEEDMQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVARALH 180

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGTIVL 239
           + GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT+ L
Sbjct: 181 DYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGTLFL 236

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+DLY
Sbjct: 237 DEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRTDVRIVAATNKDLKQAINQGLFREDLY 296

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  Y W  NV+
Sbjct: 297 YRLNVVPLRLPPLRDRAEDIPDLVRHFIQQ-AEKEGLGSKRFDQEALELMKAYAWPGNVR 355

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEG---KSSDTILD 416
           EL+N L+R ++ L    +     +         + E  ++   +   +G     S TI  
Sbjct: 356 ELEN-LIRRLMALYPQDVITREII---------DAELRSDVPDSPIDKGPIRNGSMTIAQ 405

Query: 417 NLSQ----------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
            + +          E++P  G    V  LS++E  +I  A+   R    + A  LG+ R+
Sbjct: 406 AVEENMRTYFAGFGENLPPPGLYDRV--LSEMEYPLILAALTATRGNQIKAADLLGLNRN 463

Query: 467 TLYRKIREYNIEV 479
           TL +KIRE  + V
Sbjct: 464 TLRKKIRELGVSV 476


>gi|317154217|ref|YP_004122265.1| sigma-54 factor interaction domain-containing protein
           [Desulfovibrio aespoeensis Aspo-2]
 gi|316944468|gb|ADU63519.1| sigma-54 factor interaction domain-containing protein
           [Desulfovibrio aespoeensis Aspo-2]
          Length = 452

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 124/478 (25%), Positives = 216/478 (45%), Gaps = 46/478 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           +L++D D+  +++++  + S G +  + + ++  L  ++   V+++   +         +
Sbjct: 9   ILVVDDDENILQVLEARLLSTGLNPLMADRAETALEMLACEPVDLVVSDVKMPGMGGHGL 68

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           L+ I++  P +P+I+ T    I      +    + +       K+L   I   L  G  P
Sbjct: 69  LREILEHWPHIPVIMLTAHGTIPDAVGSIQAGAADYLTKPFDGKELVRRIRAILEAGP-P 127

Query: 131 SQENEHCALDSLIAVS-------PAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
            +    CA D+  A +       PAM + + L  +       +++ GE G GK+  +R +
Sbjct: 128 DRGAPPCARDASAATASLWGGEAPAMARFLSLLDRVARSTAGVLLFGESGTGKELAARIL 187

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE-ANGGTIVLEEP 242
           HE+  RA  PF +V+CG      +E  LFG V     ++ +     IE A+GGT+ L+E 
Sbjct: 188 HEASPRAGGPFVVVDCGSTQPTLLESELFGHVKGAFTHALKDKKGLIEEADGGTLFLDEI 247

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             +   +Q R+  F++ G I          +  R++  T  NL  +V++  FR+DLYYR+
Sbjct: 248 GNISPEMQTRLLRFLQEGTIRRVGDTRERSVACRVVAATNANLPEKVRAGQFREDLYYRL 307

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
            V  + I  LR R+EDIP L   F+++ C +    +  +S K L  L  +PW  NV+ELK
Sbjct: 308 KVVTLTIPPLRERAEDIPVLARGFVRTMCNEQGRPEARLSAKGLERLKAHPWPGNVRELK 367

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           + L  A++                               C C T  ++ D  LD + + S
Sbjct: 368 HALEAALV------------------------------FCQCNTL-EADDIQLDPIPEGS 396

Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVD 480
            PA         L + EK+ I  A+ L+     + A  LGI R  ++ KIR+Y I  D
Sbjct: 397 -PA---SNAPLSLDESEKQAIIRALALHGGVRKDAADALGISRRAIHYKIRKYGIGSD 450


>gi|317051552|ref|YP_004112668.1| sigma-54 factor interaction domain-containing protein
           [Desulfurispirillum indicum S5]
 gi|316946636|gb|ADU66112.1| sigma-54 factor interaction domain-containing protein
           [Desulfurispirillum indicum S5]
          Length = 481

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 128/484 (26%), Positives = 239/484 (49%), Gaps = 31/484 (6%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKE 68
           K VLI+D D++ I+I+        + V + +     L+ +    V+++F+ +        
Sbjct: 6   KSVLIVD-DEKNIQIVMRRALDAQFRVHVASNAAEALTMLENTPVDLVFMDINMPGMSGL 64

Query: 69  NILKNI--VDKIPIVPIIVQTT-QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
             L+ I  +  IP++ +  +T+ Q  I  +    Y+ ++K F   +S+ +   S   +L+
Sbjct: 65  EALEKIHALYGIPVIIMTARTSMQSVIDAMKLSAYDFVTKPFE--ISQIRELASQATSLQ 122

Query: 126 EGVVPSQENEHCA--LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
            G    +  +      + +I  S AM +V  L  K     + ++I+GE G GK+ ++R I
Sbjct: 123 VGAFLRESTDGAPRRFEKIIGSSMAMREVFKLIGKVAPTRVTVLIEGESGTGKELVARVI 182

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEP 242
           H++   A  PF  VN   I ++ +E   FG      T  + Q +G F EA GGT+ L+E 
Sbjct: 183 HQNSLCADKPFIPVNLAAIPRELMESEFFGHEKGSFTGATDQRMGLFREAQGGTLFLDEL 242

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             +PL +Q ++   ++ G++    S     +DVR+I  T +NLL  VK ++FR+DLYYR+
Sbjct: 243 GHMPLDLQAKLLRVLQEGEVSPVGSSRIYHVDVRIIAATNRNLLEMVKKNLFREDLYYRL 302

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           +VF + +  LR R ED+  ++ +F+  +  +  + Q   + +AL+ L +Y W  NV+EL+
Sbjct: 303 NVFSLRLPPLRERMEDLKEILDYFIYRYSQEYRVPQKQPTPEALAKLRQYEWPGNVRELE 362

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           N++ RA++     +LT + F L             T+     +   +SS T+   +   +
Sbjct: 363 NVVRRALLLSNLPYLTPEDFPL-------------TDGDGVPFNAPESSQTLHQMIRSTA 409

Query: 423 IPAIGQ-----DGEVRRL--SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
           +P + Q      G +  L     EK +  + ++         A  LG+ R+T+ +KI++Y
Sbjct: 410 LPYLHQMMDHGTGNLHELIIGSAEKSLYEIVLEYTGGNQVSAASILGVNRNTVRKKIQDY 469

Query: 476 NIEV 479
           +I +
Sbjct: 470 DINM 473


>gi|170681202|ref|YP_001744414.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           SMS-3-5]
 gi|170518920|gb|ACB17098.1| sigma-54 dependent response regulator AtoC [Escherichia coli
           SMS-3-5]
          Length = 461

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 132/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRTLQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|258514260|ref|YP_003190482.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfotomaculum acetoxidans DSM 771]
 gi|257777965|gb|ACV61859.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfotomaculum acetoxidans DSM 771]
          Length = 459

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 135/483 (27%), Positives = 238/483 (49%), Gaps = 44/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDLSTISKIQV-NVIFLSLINCEDDKEN 69
           +VLI+D ++   +++KD +E  G+++ +  N  D   I + +  + + L +   + D   
Sbjct: 3   KVLIVDDEEGVCEMLKDVLEDEGFEITLAYNAKDALKIMETEFPDTVLLDIRLPDADGIE 62

Query: 70  ILKNIVDKIPIVPIIVQT----TQDNIKILNCFLYNRISKFFLNLVS---------RKQL 116
           ++  +      VP+I+ T    T+  I+ +    ++ ++K  LNL           + Q 
Sbjct: 63  VMDKLKQMGIEVPVILMTAFGTTEIAIQAMKQGAHDYLNKP-LNLDELVLAVQKSIKMQR 121

Query: 117 CDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
             S +  LRE +    + E  ++DS I  S  M  V     K  D  I ++IQGE G GK
Sbjct: 122 LVSEVAILREEL----DQETDSVDSFIGQSRHMQDVFKTIGKVVDSDITVLIQGESGTGK 177

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGG 235
           + ++R IH + +R+  PF  +NC  I +  +E  LFG      T   +Q  GKF  A+ G
Sbjct: 178 EVVARTIHSNSRRSSRPFIKINCATIPEQLMESELFGHEKGSFTGAVSQKAGKFEIAHNG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
            + L+E   LPL  Q ++   ++  + E      +I +DVR++  T +NL   V+   FR
Sbjct: 238 IVFLDEIGELPLHTQAKLLRVLQEKEFERVGGTKSIEVDVRILAATNRNLEDMVQEGKFR 297

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DLYYR++V  + +  LR R EDI  L+++F++ F  K       IS +A+    KY W 
Sbjct: 298 EDLYYRLNVVNVKLPPLRERKEDISLLINYFVKKFARKYNKNISGISQEAMIFAEKYAWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI- 414
            NV+E+KN+  +AV+  ++S L  D   L+ +  G              + E K++  I 
Sbjct: 358 GNVREIKNVCEQAVVMARNSVLMLDDMPLIGNGNG--------------FLEFKNNAKIS 403

Query: 415 LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
           LD   + S+  I        ++++EK++I  ++          A+ LG+ R +LY K++E
Sbjct: 404 LDTNDKRSLKDI--------VAEVEKQVILKSLNENNWNRQNTAKALGLNRRSLYAKMKE 455

Query: 475 YNI 477
           Y++
Sbjct: 456 YDL 458


>gi|26248609|ref|NP_754649.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           CFT073]
 gi|91211514|ref|YP_541500.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           UTI89]
 gi|110642430|ref|YP_670160.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           536]
 gi|117624414|ref|YP_853327.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           APEC O1]
 gi|191170007|ref|ZP_03031561.1| sigma-54 dependent response regulator AtoC [Escherichia coli F11]
 gi|218559138|ref|YP_002392051.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           S88]
 gi|218690383|ref|YP_002398595.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           ED1a]
 gi|227887278|ref|ZP_04005083.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           83972]
 gi|237704695|ref|ZP_04535176.1| acetoacetate metabolism regulatory protein AtoC [Escherichia sp.
           3_2_53FAA]
 gi|300936771|ref|ZP_07151664.1| response regulator receiver domain protein [Escherichia coli MS
           21-1]
 gi|300981267|ref|ZP_07175444.1| response regulator receiver domain protein [Escherichia coli MS
           200-1]
 gi|300983213|ref|ZP_07176490.1| response regulator receiver domain protein [Escherichia coli MS
           45-1]
 gi|301022434|ref|ZP_07186316.1| response regulator receiver domain protein [Escherichia coli MS
           69-1]
 gi|301048968|ref|ZP_07195957.1| response regulator receiver domain protein [Escherichia coli MS
           185-1]
 gi|306814666|ref|ZP_07448828.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           NC101]
 gi|331658300|ref|ZP_08359262.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli TA206]
 gi|26109014|gb|AAN81217.1|AE016763_176 Acetoacetate metabolism Regulatory protein atoC [Escherichia coli
           CFT073]
 gi|91073088|gb|ABE07969.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           UTI89]
 gi|110344022|gb|ABG70259.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           536]
 gi|115513538|gb|ABJ01613.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator/sigma54 interaction
           protein [Escherichia coli APEC O1]
 gi|190909523|gb|EDV69108.1| sigma-54 dependent response regulator AtoC [Escherichia coli F11]
 gi|218365907|emb|CAR03649.1| fused response regulator of ato opeon, in two-component system with
           AtoS: response regulator ; sigma54 interaction protein
           [Escherichia coli S88]
 gi|218427947|emb|CAR08718.1| fused response regulator of ato opeon, in two-component system with
           AtoS: response regulator ; sigma54 interaction protein
           [Escherichia coli ED1a]
 gi|222033982|emb|CAP76723.1| acetoacetate metabolism regulatory protein atoC [Escherichia coli
           LF82]
 gi|226901061|gb|EEH87320.1| acetoacetate metabolism regulatory protein AtoC [Escherichia sp.
           3_2_53FAA]
 gi|227835628|gb|EEJ46094.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           83972]
 gi|294494076|gb|ADE92832.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           IHE3034]
 gi|300299219|gb|EFJ55604.1| response regulator receiver domain protein [Escherichia coli MS
           185-1]
 gi|300307631|gb|EFJ62151.1| response regulator receiver domain protein [Escherichia coli MS
           200-1]
 gi|300397535|gb|EFJ81073.1| response regulator receiver domain protein [Escherichia coli MS
           69-1]
 gi|300408614|gb|EFJ92152.1| response regulator receiver domain protein [Escherichia coli MS
           45-1]
 gi|300458101|gb|EFK21594.1| response regulator receiver domain protein [Escherichia coli MS
           21-1]
 gi|305852060|gb|EFM52512.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           NC101]
 gi|307554287|gb|ADN47062.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           ABU 83972]
 gi|307626241|gb|ADN70545.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           UM146]
 gi|312946842|gb|ADR27669.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           O83:H1 str. NRG 857C]
 gi|315285840|gb|EFU45280.1| response regulator receiver domain protein [Escherichia coli MS
           110-3]
 gi|315292172|gb|EFU51524.1| response regulator receiver domain protein [Escherichia coli MS
           153-1]
 gi|315298046|gb|EFU57315.1| response regulator receiver domain protein [Escherichia coli MS
           16-3]
 gi|323955988|gb|EGB51741.1| sigma-54 interaction domain-containing protein [Escherichia coli
           H263]
 gi|324006598|gb|EGB75817.1| response regulator receiver domain protein [Escherichia coli MS
           57-2]
 gi|324013105|gb|EGB82324.1| response regulator receiver domain protein [Escherichia coli MS
           60-1]
 gi|331056548|gb|EGI28557.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli TA206]
          Length = 461

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 132/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|220926309|ref|YP_002501611.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Methylobacterium nodulans ORS 2060]
 gi|219950916|gb|ACL61308.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Methylobacterium nodulans ORS 2060]
          Length = 485

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 133/490 (27%), Positives = 235/490 (47%), Gaps = 39/490 (7%)

Query: 14  LIIDKDDEQIKIIKDHVES-YGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +I+  DD  I+ + +   S  GY+V    N + L   +++   +++   ++  +++  ++
Sbjct: 6   IIVADDDAAIRTVLNQALSRAGYEVRSTGNAATLWRWVAQGDGDLVITDVVMPDENAFDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +PIIV + Q+     I+      Y  + K F +L     +    +   R 
Sbjct: 66  LPRIKRVRPDLPIIVMSAQNTFMTAIRASERGAYEYLPKPF-DLKELTAIVGRALSRPRG 124

Query: 127 GVVPS--QENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
              P    ENE      L+  SPAM ++     +     + +MI GE G GK+ ++R +H
Sbjct: 125 NAAPGAGPENEDI---PLVGRSPAMQEIYRSLARLMPTDLTVMITGESGTGKELVARALH 181

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPD 243
           + G+R   PF  VN   I +D IE  LFG +    T  +A+  G+F +A GGT+ L+E  
Sbjct: 182 DYGRRRAGPFVPVNMAAIPRDLIESELFGHEKGAFTGATARSAGRFEQAEGGTLFLDEIG 241

Query: 244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS 303
            +P+  Q R+   ++ G+      R  I+ +VR+I  T K+L   ++  +FR+DL++R++
Sbjct: 242 DMPMEAQTRLLRVLQQGEYTTVGGRVPIKTNVRIIAATNKDLRVSIQQGIFREDLFFRLN 301

Query: 304 VFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           V  + +  LR R+ED+P LV HFF  +   +  + +  +   A+  L +Y W  NV+EL+
Sbjct: 302 VVPLRLPALRERTEDVPDLVRHFF--TLVEREGLSRKQLDADAMERLKRYRWPGNVRELE 359

Query: 363 NILLRAVIGLKDSHLTE-------DRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
           N++ R         +T        D   L     G   R+   E       EG S+  + 
Sbjct: 360 NLVRRLAALYPQETITGPVIEAELDTLPLAAPAPGGPPRKGAAE------AEGLSA-AVE 412

Query: 416 DNLSQ------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY 469
            +L++      +++P  G    V  L +IE  +IG A+   R      A  LG+ R+TL 
Sbjct: 413 RHLAEYFSGFRDTLPPPGLYHRV--LREIEGPLIGAALAATRGNQIRAAELLGVNRNTLR 470

Query: 470 RKIREYNIEV 479
           +K+R+ +++V
Sbjct: 471 KKVRDLDLQV 480


>gi|92114525|ref|YP_574453.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Chromohalobacter salexigens DSM 3043]
 gi|91797615|gb|ABE59754.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Chromohalobacter salexigens DSM 3043]
          Length = 461

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 123/485 (25%), Positives = 227/485 (46%), Gaps = 58/485 (11%)

Query: 13  VLIIDKDDEQIKIIKDH-VESYGY--DVFIVNVSDLSTISKIQVNVIFLSLINCEDDKEN 69
           V+++D D+  ++I     +E  GY  +V+    + LS +      V+   +     D   
Sbjct: 9   VMLVD-DEAHLRITASQTLELAGYVPEVYESAEAALSALRADFPGVLVSDIRMPGMDGMA 67

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L+ I  + P +P+++ T   +I      + +    F     + ++L + +    R G+ 
Sbjct: 68  LLREIRQRDPDLPVVLITGHGDISTAVEAMRDGAWDFLEKPFAGERLVEVV----RRGIE 123

Query: 130 P---SQENEHCALD----------SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
               S EN H   +           L+  +PA+ Q+  + ++       +++ GE G GK
Sbjct: 124 KRRLSLENRHLKAELEAQQSTPGPRLVGRTPAIQQLASMVQRISQVETDVLLFGETGTGK 183

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGG 235
             ++R IHE   R   PF  +NCG + +  IE  LFG +    T    + +GKF  ANGG
Sbjct: 184 DLVARAIHERSARGGKPFVAINCGAVPESTIESELFGHEKGAFTGAVERRVGKFEHANGG 243

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T+ L+E +++PL++Q ++   ++   +E   S   I LD+R+I  T+ +L     +  FR
Sbjct: 244 TVFLDEIESMPLSLQVKLLRVLQERAVERLGSNTLIPLDIRVIAATKTDLKAAADTGGFR 303

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DLYYR++V  + I +LR R EDIP L   F+    +++ ++   +    +S L  + W 
Sbjct: 304 EDLYYRLNVVTLPIPSLRERREDIPLLFQHFIAVSASRSGLEAPPLDGHGISALLAHDWP 363

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+EL+N+               +R+VLL                      G + D  L
Sbjct: 364 GNVRELRNV--------------AERYVLL----------------------GATCDYRL 387

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
           + L Q +    G+    +++   EK +I  A+  Y+  + ++  RLG+ R TLY K++++
Sbjct: 388 ETLLQGAQKDSGELPLAQQVELFEKSVINHALVRYQGCVPDICERLGVPRKTLYDKLKKH 447

Query: 476 NIEVD 480
            ++ D
Sbjct: 448 GLKAD 452


>gi|62184798|ref|YP_219583.1| putative sigma-54 dependent response regulator [Chlamydophila
           abortus S26/3]
 gi|62147865|emb|CAH63611.1| putative sigma-54 dependent response regulator [Chlamydophila
           abortus S26/3]
          Length = 386

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 117/394 (29%), Positives = 196/394 (49%), Gaps = 32/394 (8%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDLSTISKIQVNVIFLSLINCEDDKE- 68
           ++VLI+D +      + + + + G   F   NV       K +   + +S +N  D    
Sbjct: 4   EKVLIVDDEPLLRDFLSELLLTRGLSPFTADNVKQGCHKIKTEKYDLIISDMNMPDGTGL 63

Query: 69  NILKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFF-----LNLVSRKQLCDS 119
           +I+K   +  P  P++V     T ++ +K ++   +N ++K F        +++ +   +
Sbjct: 64  DIIKTSKEFAPHTPVLVITAYGTIENAVKAMHHGAFNYLTKPFSSEALFAFIAKAEELQN 123

Query: 120 IICALREGVVPSQENEHCALDS--------LIAVSPAMIQVVDLARKAGDCAIPIMIQGE 171
           ++            NE+  L S        LIA SPAM  ++  ARKA D +  I I GE
Sbjct: 124 LV------------NENLLLKSQISSESHPLIAESPAMKDLLSKARKAADSSANIFIHGE 171

Query: 172 FGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFI 230
            G GK+ LS FIH +  RA  P+  VNC  I +  +E   FG +    T  + +  G+F 
Sbjct: 172 SGCGKEVLSFFIHRNSPRASCPYIKVNCAAIPETLLESEFFGHEKGAFTGATGKKAGRFE 231

Query: 231 EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK 290
            A+ GT++L+E   +P+ +Q ++   I+  + E       + +DVR++  + +NL   V 
Sbjct: 232 LAHTGTLLLDEITEVPINLQAKLLRAIQEKEFEHLGGTKTLSVDVRILATSNRNLKEAVD 291

Query: 291 SHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLT 350
             +FR+DL+YR++V  + +  LR R +DI  L  +FL+ FC  N     ++S+ A S L 
Sbjct: 292 QKIFRQDLFYRLNVIPLYLPPLRERKDDILPLSQYFLEKFCRLNNKPMKTLSESAKSALL 351

Query: 351 KYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVL 384
            YPW  N++EL N+L RAVI    +HLTE    L
Sbjct: 352 DYPWPGNIRELSNVLERAVILESPTHLTETMLAL 385


>gi|331647875|ref|ZP_08348967.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli M605]
 gi|281179312|dbj|BAI55642.1| two-component response regulator [Escherichia coli SE15]
 gi|330912051|gb|EGH40561.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           AA86]
 gi|331043599|gb|EGI15737.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli M605]
          Length = 461

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 132/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRVIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|168701204|ref|ZP_02733481.1| cetoacetate metabolism regulatory protein atoC [Gemmata
           obscuriglobus UQM 2246]
          Length = 475

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 101/349 (28%), Positives = 174/349 (49%), Gaps = 14/349 (4%)

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
           P    +      +I   PAM++V     +     +P++I GE G GK+ ++R +H+  +R
Sbjct: 130 PDPGTDDGGTGPIIGSCPAMMEVYKAVGRVAPQDVPVLITGESGTGKELVARAVHQYSRR 189

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I +  +E  LFG +    T    + +G+F + +GGT+ L+E   +PLA
Sbjct: 190 AGRPFVALNCAAIPEQLLESELFGHEKGAFTGADRRRIGRFEQCDGGTLFLDEIGDMPLA 249

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++    E       +R DVR+I  T ++L  +  +  FR DLYYR+ VF + 
Sbjct: 250 LQSKLLRVLQEQAFERVGGGETVRTDVRIISATHRDLKARAAAGTFRPDLYYRLGVFTMR 309

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
           +  LR R+ED+P LV  FL  F  +   +   IS +AL+ LT+Y W  N++EL+++L +A
Sbjct: 310 LPPLRDRAEDLPLLVRHFLGRFNRELGRRVSDISAEALARLTQYAWPGNLRELQSVLKQA 369

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           ++    + L       +         E         +   + SD   +NL +E+      
Sbjct: 370 LLRTTGTVLLPSALADMAGPSAAPASEPPARADLHQFVRRRLSDGS-ENLLEEA------ 422

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
                RL ++++ ++ + M+L R      AR LG+ R TL R++ E  I
Sbjct: 423 -----RL-ELDRFLLPMVMELTRGNQVRAARVLGVARLTLRRRLHELGI 465


>gi|317484439|ref|ZP_07943352.1| sigma-54 interaction domain-containing protein [Bilophila
           wadsworthia 3_1_6]
 gi|316924299|gb|EFV45472.1| sigma-54 interaction domain-containing protein [Bilophila
           wadsworthia 3_1_6]
          Length = 459

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 129/482 (26%), Positives = 230/482 (47%), Gaps = 45/482 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ---VNVIFLSLINCEDDKEN 69
           +LI+D D     +++  +  +GY     +  D + + K++    + +   +     D  +
Sbjct: 7   ILIVDDDSSHRAMLRTVLRGWGYATDEADDGD-TAVEKVKERAYDAVLSDVRMARMDGIS 65

Query: 70  ILKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFF----LNLVSRKQLCDSII 121
            ++ I+   P +P++V    Q+ +  +  L    Y+ + K      L+L   + L  + +
Sbjct: 66  AIREILHHNPSIPVLVMTAWQSVETAVAALRLGAYDYLEKPLDFDLLHLTLERALDHTRL 125

Query: 122 CA----LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
            A    LRE +  S          L+  SP M +++++          ++I GE G GK+
Sbjct: 126 AAENRELREYIRESP-------SGLLGRSPRMRELIEMVNTVAPTEATVLITGESGTGKE 178

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
           R++R I E+  R    F  VNC  +++  +E  LFG +    T    +  G+F +A+GGT
Sbjct: 179 RVARAIQEASARRGKAFVTVNCAALNESLLESELFGHEKGAFTGADKRREGRFSQADGGT 238

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   LPL +Q ++   ++ G+++   S   I +DVR+I  T +NL  +V    FR+
Sbjct: 239 LFLDEIGELPLLLQAKLLRALQQGEVQRVGSDTPIIVDVRVIAATNRNLREEVSEGRFRE 298

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DLYYR++V  + + +LR R EDIP L   FL+ F   N  +    + +A+  L KY W  
Sbjct: 299 DLYYRLNVIGVEVPSLRERREDIPVLATAFLERFALANRKEIKGFTPQAMDALLKYSWPG 358

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           NV+EL+N + RA I     +++E    + +S   K     + +       +G        
Sbjct: 359 NVRELENAVERAAILCLGEYISERELPMAVSSAPK-----NNDAPTLAELQG-------- 405

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
                   A G++     L ++E+  I   ++      SE ARRLGI R+TL+ K+R Y+
Sbjct: 406 --------AAGEEPISMTLDEMERAAILRTLQDTGDNKSEAARRLGITRATLHNKLRRYD 457

Query: 477 IE 478
           +E
Sbjct: 458 ME 459


>gi|302039215|ref|YP_003799537.1| sigma-54 dependent response regulator [Candidatus Nitrospira
           defluvii]
 gi|300607279|emb|CBK43612.1| Sigma-54 dependent response regulator [Candidatus Nitrospira
           defluvii]
          Length = 459

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 131/474 (27%), Positives = 217/474 (45%), Gaps = 43/474 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           VL++D D +   ++ D ++  G+    V   D  L  +S+    V+   L         +
Sbjct: 8   VLVVDDDADMRSLLCDVLQGRGHQCTGVGSGDDALQQLSEEDYAVVLTDLRMKGMLGTEL 67

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           L  +  + P + +I+ T   +++     + +  S +    V  ++L   +  A+RE  + 
Sbjct: 68  LAEVKQRYPDIGVILMTAFGSVETAVEAIRHGASDYLTKPVKTEELVRVVERAIREAALR 127

Query: 131 -------SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
                   + ++  +   ++  S  M  V DL R+  D    ++I GE G GK+ +++ I
Sbjct: 128 REVSRLRKEVHKEYSFHQILGKSKPMQAVFDLIRRVADSPTNVLITGESGTGKELVAKAI 187

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEP 242
           H +  R   PF  VNC  I +  +E  LFG +    T       G F EA  GT+ L+E 
Sbjct: 188 HYNSDRRDAPFVPVNCAAIPEQLLESELFGHMRGSFTDAKMDKRGLFEEAQKGTLFLDEI 247

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             LPL +Q ++   I+  +I    +  +I +DVR+I  T  NL  +VK+  FR+D YYR+
Sbjct: 248 SELPLMLQAKLLRAIQEREIRRVGATKSIPVDVRIIAATNLNLAEEVKNKRFREDFYYRL 307

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQI-SISDKALSLLTKYPWIDNVQEL 361
           +V  + +  LR R EDIP LV  FL+  C  +  KQ+  +S+ AL++L  Y W  NV+EL
Sbjct: 308 NVIELRLPPLRERREDIPILVDAFLKK-CADSRGKQVKGLSESALAMLADYAWPGNVREL 366

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD-TILDNLSQ 420
           +N++ RAV       +  D                          +G   D  ILD  ++
Sbjct: 367 ENVIERAVTLSHGDMIGADDL--------------------PVQVQGSRGDRRILDEAAE 406

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
            ++P          L ++EKE I   ++       + A  LGI R TLYRK+ E
Sbjct: 407 RTLP----------LHEVEKEYIVKILEKTGGNKYQAAHVLGIDRKTLYRKLAE 450


>gi|332704004|ref|ZP_08424092.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio africanus str. Walvis Bay]
 gi|332554153|gb|EGJ51197.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio africanus str. Walvis Bay]
          Length = 444

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 135/478 (28%), Positives = 218/478 (45%), Gaps = 52/478 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST--ISKIQVNVIFLSLINCEDDKENI 70
           VL++D ++  +K+ K  + +   ++      + +   + K Q +VI L +   + D   +
Sbjct: 7   VLVVDDEESILKLFKKELSNSERNIHTTMSGNQARALLQKNQYDVILLDIRLPDADGIEL 66

Query: 71  LKNIVDKIPIVPIIVQTTQDNI----KILNCFLYNRISK-FFLN----LVSRKQLCDSII 121
           L     + P V II+ T   NI    + +    Y+ ++K F L+    L+ R        
Sbjct: 67  LMEWKQRFPDVEIIMITGHGNIDTAVEAMKIGAYDYVTKPFHLDKIELLIERAY---QRA 123

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           C  RE            L  L+  S  + QV  L RK     +P++I GE GVGK  ++R
Sbjct: 124 CLQRENRGFRHSQSSTRLPQLVGRSAGIEQVRFLIRKVAPTEVPVLITGESGVGKDVVAR 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLE 240
            IH    RA  P  + NC  +++      LFG +    T  +    G    A+ GT+ L+
Sbjct: 184 TIHALSPRAEKPLIVKNCATLEKTLARSELFGHLRGSFTGATENRDGLMTFAHSGTLFLD 243

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   LPL VQ  +   +E+        +   + D+RLI  T +NL  +V++  F   L++
Sbjct: 244 EIGELPLEVQASLLRVLESKAYRRVGEKEERKTDIRLICATNRNLAKEVEAGRFHDALFH 303

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           RI+VF   +  LR R+EDIP LV +FL S   +   K+ SI+D+AL  L +Y W  N++E
Sbjct: 304 RINVFSFKVPALRERAEDIPLLVEYFLGSLGRE---KRCSITDRALECLMRYDWPGNIRE 360

Query: 361 LKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQ 420
           LKN++ R++I L D+ +  D+ +           E   E   +    G S D+       
Sbjct: 361 LKNVIERSII-LSDNGVIMDQAL---------PPEMIEEADSSSSERGLSLDS------- 403

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
                            +E++ I   + L+     + A  LGIGR TLYRKI +Y I+
Sbjct: 404 -----------------MERDHISKVLALHEGNRQKTAEVLGIGRKTLYRKIEKYKIQ 444


>gi|145220040|ref|YP_001130749.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Prosthecochloris vibrioformis DSM 265]
 gi|145206204|gb|ABP37247.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Chlorobium phaeovibrioides DSM 265]
          Length = 487

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 133/490 (27%), Positives = 225/490 (45%), Gaps = 31/490 (6%)

Query: 2   PRKKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLS 59
           P  ++  + ++VLI D D+   ++    V   GY+  +VN     +  +++   +V+ L 
Sbjct: 11  PNSRAGIQKRKVLIADDDETSRRVFGHFVSKMGYEAIMVNDGRECVQAMAEESPDVVLLD 70

Query: 60  LINCEDDKENILKNIVDKIPIVPIIVQTTQDNI----KILNCFLYNRISKFF----LNLV 111
           +     D   ++++   +    PII+ T    I    K +    Y  ++K      L +V
Sbjct: 71  INMPVLDGFEVMQHAKSQNDTTPIIIITASHEIPSAVKCIKLGAYEYLTKPLNIDRLEIV 130

Query: 112 SRKQLCDSIICALREGV-VPSQENEHCAL-DSLIAVSPAMIQVVDLARKAGDCAIPIMIQ 169
            R  L DS   +L+  V +  +E + C L +++I  SPA+   +  A +  +  + ++I 
Sbjct: 131 MRNALQDS---SLQSQVKMLKKELKSCKLFENIIGKSPAIKAAMTQAMQVMETGLNVLIL 187

Query: 170 GEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGK 228
           GE G GK+  +  IH   +R+  PF  VNC  I     +  LFG      T   +  +G 
Sbjct: 188 GESGTGKELFAEAIHRGSRRSSGPFVSVNCAAISSSLADSILFGHAKGSFTGAGSDHMGY 247

Query: 229 FIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ 288
           F +A+ GTI L+E   +   +Q ++   I+  KI     +   + D R+I  T +N    
Sbjct: 248 FEQADQGTIFLDEIGDMGSDIQAKVLRVIQERKIRRVGEKQERKTDFRVISATNRNFNDA 307

Query: 289 VKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSL 348
           ++   FR+DLYYR+  F + +  LR R EDIP L   FL  F + N + +I++SD ALS 
Sbjct: 308 IRDGQFREDLYYRLEEFPLFLPALRERPEDIPLLCRHFLDEFSSANNLGKITMSDTALSA 367

Query: 349 LTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEG 408
              + W  N++ELKN + RA +  KD  + E     ++    K                 
Sbjct: 368 SENHRWPGNIRELKNAVQRAAVTRKDD-VIETLEPNIIPGSMKPAYAPPALLPPAAEYGL 426

Query: 409 KSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
           + SD+               D     L + E+E I  A K     +++ A  LGIGR+TL
Sbjct: 427 QPSDS--------------PDTNSYSLEEHEREAILKAYKAALGNLTKTAGILGIGRATL 472

Query: 469 YRKIREYNIE 478
           YRK+ ++ +E
Sbjct: 473 YRKLDKFGLE 482


>gi|28869160|ref|NP_791779.1| sigma-54 dependent transcriptional regulator/response regulator
           FleR [Pseudomonas syringae pv. tomato str. DC3000]
 gi|28852400|gb|AAO55474.1| sigma-54 dependent transcriptional regulator/response regulator
           FleR [Pseudomonas syringae pv. tomato str. DC3000]
          Length = 471

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 132/476 (27%), Positives = 228/476 (47%), Gaps = 21/476 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVE--SYGYDVFIVNVSDLSTISKIQVNVIFLSLINCED-DKEN 69
           VL+++ D    + + + +E   YGY   + +  +    ++ Q   + +S +N    D   
Sbjct: 5   VLLVEDDRSLREALGETLELAGYGYQA-VGSAEEALVAAEAQPFSLVISDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    +      +    + + +     K L  +++     G +
Sbjct: 64  LLSLLRSRHPQLPVLLMTAHGAVDRAVDAMRQGAADYLVKPFEPKALI-ALVARHALGRL 122

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
              E+     D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  R
Sbjct: 123 GPAES-----DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +P+ 
Sbjct: 178 ADKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPMG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPITLDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA
Sbjct: 298 WQALRQRTADILPLAERLLAKHVNKMKHAPVRLSAQAQQCLVSYPWPGNVRELDNAVQRA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           +I L+   + E +   L            +E A        S++     +  ES  A+G 
Sbjct: 358 LI-LQQGGVIEAQDFCLAGPVTSLPVAVPSE-AVPPQPVISSAENAGVGVGAESAGALGD 415

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           D  +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V+ 
Sbjct: 416 D--LRRR---EFQMIIDTLRAERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEG 466


>gi|128602|sp|P28787|NTRC_PROVU RecName: Full=Nitrogen regulation protein NR(I)
 gi|45902|emb|CAA48236.1| NR I [Proteus vulgaris]
          Length = 473

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 119/433 (27%), Positives = 212/433 (48%), Gaps = 21/433 (4%)

Query: 56  IFLSLINCED-DKENILKNIVDKIPIVPIIVQTTQDNI-KILNCF---LYNRISKFFLNL 110
           + LS I   D D  ++LK I ++ P +P+I+ T   ++   +N +    ++ + K F ++
Sbjct: 50  VLLSDIRMPDMDGLSLLKIIKEQYPTLPVIIMTAHSDLDAAVNAYQQGAFDYLPKPF-DI 108

Query: 111 VSRKQLCDSIICALREGVVPSQ-ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQ 169
                L +  I   RE   P+  EN   ++  +I  +PAM +V  +  +    +I ++I 
Sbjct: 109 DETLALIERAITHYREQKQPNNAENILQSVSDMIGEAPAMQEVYRIIGRLSRSSISVLIN 168

Query: 170 GEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF-LGK 228
           GE G GK+ ++  +H    RA  PF  +N   I +D IE  LFG        ++Q   G+
Sbjct: 169 GESGTGKELVAHALHRHSPRALAPFIALNMAAIPKDLIESELFGHEKGAFTGASQVRQGR 228

Query: 229 FIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ 288
           F +ANGG++ L+E   +PL +Q R+   +  G+         +++DVR+I  T ++L  +
Sbjct: 229 FEQANGGSLFLDEIGDMPLDIQTRLLRVLAEGQFYRVGGYAPVKVDVRIIAATHQDLEKR 288

Query: 289 VKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSL 348
           V    FR+DLY+R++V  I +  LR R+EDIP L  +FLQ    +  ++  S+ +++L  
Sbjct: 289 VNEGDFREDLYHRLNVIRIQLPPLRDRTEDIPSLARYFLQKTAKELGVETKSLHEQSLKT 348

Query: 349 LTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEG 408
           + +Y W  NV++L+N+     +      +        +    +K +  +  T        
Sbjct: 349 MMEYVWSGNVRQLENVCRWLTVMTASQEIMPQDLPSEIRLADEKAKNINRLT-------- 400

Query: 409 KSSDTILDNLSQESIPAIGQDGE---VRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGR 465
             S     +LS  +  A+G+  E      L   E+ ++  A+   +    + AR LG GR
Sbjct: 401 --SQHWSQHLSLWADEALGEGKENILNDALPQFERTLLLSALAYTQGHKQDAARLLGWGR 458

Query: 466 STLYRKIREYNIE 478
           +TL RK++E  IE
Sbjct: 459 NTLTRKLKELGIE 471


>gi|209549218|ref|YP_002281135.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Rhizobium leguminosarum bv. trifolii WSM2304]
 gi|209534974|gb|ACI54909.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Rhizobium leguminosarum bv. trifolii WSM2304]
          Length = 483

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 137/493 (27%), Positives = 231/493 (46%), Gaps = 47/493 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   IS  + +++   ++  +++  ++
Sbjct: 5   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWISAGEGDLVVTDVVMPDENAFDL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 65  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALAE 120

Query: 127 GVVPSQENEHCALDS--LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
                 + E    D   L+  S AM ++  +  +     + +MI GE G GK+ ++R +H
Sbjct: 121 PKRKPAKLEEDMQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVARALH 180

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGTIVL 239
           + GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT+ L
Sbjct: 181 DYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGTLFL 236

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+DLY
Sbjct: 237 DEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRTDVRIVAATNKDLKQAINQGLFREDLY 296

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  Y W  NV+
Sbjct: 297 YRLNVVPLRLPPLRDRAEDIPDLVRHFIQQ-AEKEGLGSKRFDQEALDLMKAYAWPGNVR 355

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEG---KSSDTILD 416
           EL+N L+R ++ L    +     +         + E  ++   +   +G     S TI  
Sbjct: 356 ELEN-LIRRLMALYPQDIITREII---------DAELRSDVPDSPIDKGPMRSGSMTIAQ 405

Query: 417 NLSQ----------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
            + +          E++P  G    V  L+++E  +I  A+   R    + A  LG+ R+
Sbjct: 406 AVEENMRTYFSGFGENLPPPGLYDRV--LTEMEYPLILAALTATRGNQIKAADLLGLNRN 463

Query: 467 TLYRKIREYNIEV 479
           TL +KIRE  + V
Sbjct: 464 TLRKKIRELGVSV 476


>gi|289664989|ref|ZP_06486570.1| two-component system regulatory protein [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 448

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 130/482 (26%), Positives = 224/482 (46%), Gaps = 52/482 (10%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSD-LSTISKIQVNVIFLSLINCEDDKEN 69
           R+LIID D      ++  + S G+ V    N  D L+ +S+  +++ F+       D   
Sbjct: 3   RILIIDDDAAFRTTLQATLRSLGHTVVAADNGPDGLARLSEGGIDMAFVDFRMPGMDGIA 62

Query: 70  ILKNIVD-----KIPIVPIIVQTTQDN-IKILNCFLYNRISKF-----FLNLVSRKQL-- 116
           +L+  +D     ++P+V +    +  N I+ +    ++   K       + +V R  L  
Sbjct: 63  VLRARLDDAQARQVPLVMLTAYVSSGNTIEAMTLGAFDHRVKPVGRADIVEVVERALLSR 122

Query: 117 CDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
            D+   A      P +++     D+L+  SPAM  V      A    +P++I GE G GK
Sbjct: 123 ADAQAAATETPQAPPEDD-----DALVGHSPAMRTVHKRIGLAAASDLPVLITGETGTGK 177

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGG 235
           +  +R +H +  RA  PF  VNC  I  + +E  LFG      +  S+   G   EA+GG
Sbjct: 178 ELAARALHRASPRASAPFIAVNCAAIPLELMESELFGHRKGAFSGASSDRPGLIREADGG 237

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T+ L+E   +PL +Q ++  F++ G++      G  ++DVR++  T ++L   V    FR
Sbjct: 238 TLFLDEIGDMPLPMQAKLLRFLQEGEVTPLGGSGPQKVDVRVLAATHRDLAACVADGRFR 297

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
            DL YR++V  I +  LR R +DI  L   FL    + NA +  S+S  A   L  + W 
Sbjct: 298 SDLRYRLNVVPIELPPLRERGQDILLLAQHFL----SANAARAQSLSPAAQERLLAHRWP 353

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+EL+N++ R+ + ++ + +        L+                    G++  T+ 
Sbjct: 354 GNVRELRNVMQRSQVMVRGASIDAADLDEALAE------------------AGEAPSTVA 395

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
             L+     A+ +         +EK++I  A++  +   +E ARRLGI R  LYRK+ EY
Sbjct: 396 SALTGTLPEAVAR---------LEKQMIQSALEQSQGNRAEAARRLGIHRQLLYRKLEEY 446

Query: 476 NI 477
            +
Sbjct: 447 GL 448


>gi|331017006|gb|EGH97062.1| sigma-54 dependent transcriptional regulator/response regulator
           FleR [Pseudomonas syringae pv. lachrymans str.
           M302278PT]
          Length = 471

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 132/476 (27%), Positives = 229/476 (48%), Gaps = 21/476 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVE--SYGYDVFIVNVSDLSTISKIQVNVIFLSLINCED-DKEN 69
           VL+++ D    + + + +E   YGY   + +  +    ++ Q   + +S +N    D   
Sbjct: 5   VLLVEDDRSLREALGETLELAGYGYQA-VGSAEEALVAAEAQPFSLVISDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    +      +    +++ +     K L  +++     G +
Sbjct: 64  LLSLLRSRHPQLPVLLMTAHGAVDRAVDAMRQGAAEYLVKPFEPKALI-ALVARHALGRL 122

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
              E+     D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  R
Sbjct: 123 GPAES-----DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +P+ 
Sbjct: 178 ADKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPMG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPITLDIRVVATTNRDLAGEVVAGRFREDLFYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA
Sbjct: 298 WQALRQRTADILPLAERLLAKHVNKMKHAPVRLSAQAQQCLVSYPWPGNVRELDNAVQRA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           +I L+   + E +   L            +E A        S++     +  ES  A+G 
Sbjct: 358 LI-LQQGGVIEAQDFCLAGPVTSLPVAVPSE-AVPPQPVISSAENAGVGVGAESAGALGD 415

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           D  +RR    E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V+ 
Sbjct: 416 D--LRRR---EFQMIIDTLRAERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEG 466


>gi|153009402|ref|YP_001370617.1| nitrogen metabolism transcriptional regulator NtrC [Ochrobactrum
           anthropi ATCC 49188]
 gi|151561290|gb|ABS14788.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Ochrobactrum anthropi ATCC 49188]
          Length = 490

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 130/498 (26%), Positives = 228/498 (45%), Gaps = 46/498 (9%)

Query: 9   RHKRVLIIDKDDEQIKIIKDHVES-YGYDVFIV-NVSDLSTISKIQVNVIFLSLINCEDD 66
           R    +++  DD  I+ + +   S  GYDV +  N + L          + ++ +N  D+
Sbjct: 5   RPTGTILVADDDAAIRTVLNQALSRAGYDVRVTSNAASLWRWVAAGDGDLVITDVNMPDE 64

Query: 67  KE-NILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSII 121
              ++L  I    P +P++V + Q+     I+      Y  + K F +L     +    +
Sbjct: 65  NAFDLLPRIKKMRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPF-DLTELINIVGRAL 123

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              +   + +  +E      L+  SPAM ++  +  +     + +M+ GE G GK+ ++ 
Sbjct: 124 SEPKHKPIAALSDEQADNMPLVGRSPAMQEIYRVLARMMQTDLTVMVTGESGTGKELVAS 183

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANGGT
Sbjct: 184 ALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANGGT 239

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   +   +FR+
Sbjct: 240 LFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNKDLRQLIAQGLFRE 299

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR RSED+  LV HFF +    +  + +  IS   L ++ +YPW 
Sbjct: 300 DLYYRLNVVPLRLPPLRERSEDVADLVRHFFKR--AAEEGLPEKRISTAGLEMMRRYPWP 357

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            NV+EL+N++ R         ++ +            E E  +E A          D  +
Sbjct: 358 GNVRELENLVRRLAALYPQEEISPEII----------ETELKSELAKPDIVPAGGGD--M 405

Query: 416 DNLS---------QESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRL 461
           +N+S         Q    + G D    G   R L+++E  +I   +   R    + A  L
Sbjct: 406 ENISISQAVEQNMQRYFASFGADLPPPGLYHRVLAELEYPLILACLTATRGNQIKAADLL 465

Query: 462 GIGRSTLYRKIREYNIEV 479
           G+ R+TL +KIRE  + +
Sbjct: 466 GLNRNTLRKKIRELGVNI 483


>gi|157144822|ref|YP_001452141.1| acetoacetate metabolism regulatory protein AtoC [Citrobacter koseri
           ATCC BAA-895]
 gi|157082027|gb|ABV11705.1| hypothetical protein CKO_00549 [Citrobacter koseri ATCC BAA-895]
          Length = 461

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 129/489 (26%), Positives = 224/489 (45%), Gaps = 51/489 (10%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    +   + L   +    +V+ + +   E +   
Sbjct: 6   RILIVDDEDNVRRMLATAFSLQGHETQCASNGQTALQHFADAPPDVVLMDIRMPEMNGIE 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRK----QLC 117
            LK +  + P VPII+ T     +  ++ L    ++ + K F    LNL+ ++    Q  
Sbjct: 66  ALKVMRAQHPRVPIILMTAYAEVETAVEALRSGAFDYVIKPFDLDELNLLIQRALQLQAM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I +L + +  S +  H     ++  SP M+ +     K       ++I GE G GK+
Sbjct: 126 KQEIRSLHQALSTSWQWGH-----ILTNSPGMMDICKDTAKIALSQANVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            ++R IH + +RA  PF  +NC  + +  +E  LFG +    T    +  G F  A+ GT
Sbjct: 181 LIARAIHYNSRRANGPFIKINCAALPESLLESELFGHEKGAFTGAQTRRQGLFERAHQGT 240

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           ++L+E   +PL +Q ++   ++  + E       I++D+R++  T +NL   VK   FR+
Sbjct: 241 LLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIQVDIRIVAATNRNLQEMVKEGTFRE 300

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DL+YR++V  + +  LR R EDIP L + FLQ F ++N    I I   A+SLLT +PW  
Sbjct: 301 DLFYRLNVIHLTLPPLRERREDIPLLANHFLQKFSSENQRDIIEIDPSAMSLLTAWPWPG 360

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           N++EL N++ RAV+                             T    + E   +     
Sbjct: 361 NIRELSNVIERAVV---------------------------MNTGAVIFAEDLPTQ-FRQ 392

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKE---IIGLAMKLYRAQMSEVARRLGIGRSTLYRKIR 473
           ++S  S     Q GE     +I++E   II   ++      +  A  LGI R  L  K++
Sbjct: 393 SVSHASGIKPAQPGERNLKEEIKREERRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQ 452

Query: 474 EYNIEVDSL 482
           EY I+   L
Sbjct: 453 EYGIDPAGL 461


>gi|331663726|ref|ZP_08364636.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli TA143]
 gi|284922212|emb|CBG35294.1| acetoacetate metabolism regulator (two-component system response
           regulator) [Escherichia coli 042]
 gi|331059525|gb|EGI31502.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli TA143]
          Length = 461

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 133/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K+S    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEVKTSPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|85859693|ref|YP_461895.1| response regulator [Syntrophus aciditrophicus SB]
 gi|85722784|gb|ABC77727.1| response regulator containing CheY-like receiver, AAA-type ATPase,
           and DNA-binding domains [Syntrophus aciditrophicus SB]
          Length = 456

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 88/238 (36%), Positives = 138/238 (57%), Gaps = 1/238 (0%)

Query: 134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
           ++    D++I  S  M  +  +A +       +++QGE G GK+ L+R IH+   R+  P
Sbjct: 137 DQGVTTDAIIFTSQKMAALTSMAARVASSRATVLLQGESGTGKELLARLIHQLSPRSTRP 196

Query: 194 FFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGR 252
              VNCG + +  IE  LFG +    T  +++ +G+F EA+GGT+ L+E   L + VQ +
Sbjct: 197 IITVNCGALPESLIESELFGHEKGAFTGATSRRIGRFEEADGGTLFLDEIGELTMPVQVK 256

Query: 253 IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTL 312
           +  F++  + +       IR DVR+I  T ++L   VK   FR+DLYYR++V +++I  L
Sbjct: 257 LLRFLQEREFQRVGGNTNIRADVRIISATNRDLETMVKEEKFREDLYYRLNVVVMSIPPL 316

Query: 313 RSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI 370
           R R EDIP L+  FL+ F  +N  K   IS +A  LL KY +  NV+EL+NI+ RAV+
Sbjct: 317 RERREDIPALIDHFLERFAAENGKKISGISSEARDLLMKYDYPGNVRELENIIERAVV 374


>gi|297617412|ref|YP_003702571.1| PAS modulated sigma54 specific transcriptional regulator, Fis
           family [Syntrophothermus lipocalidus DSM 12680]
 gi|297145249|gb|ADI02006.1| PAS modulated sigma54 specific transcriptional regulator, Fis
           family [Syntrophothermus lipocalidus DSM 12680]
          Length = 467

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 120/401 (29%), Positives = 197/401 (49%), Gaps = 47/401 (11%)

Query: 91  NIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE--GVVPSQENEHCALDSLIAVSPA 148
           N  ++ CF ++     F+++   K L ++++  L      V +  + H    S+I  SP 
Sbjct: 95  NQTVVGCFAFS----LFMDIWDAKDLVENLMFELNSYRNEVRNLYSAHYTFASIIGSSPK 150

Query: 149 MIQVVDLARKAG-DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKI 207
           M  V  LA++A    +  ++I GE G GK+  +  IH   +R+  PF  VNC  I +  +
Sbjct: 151 MQNVKFLAQQAALHSSTTVLITGESGTGKELFAHAIHNCSQRSRLPFVRVNCAAIPESLL 210

Query: 208 EKFLFGDVDLQTKNSAQF--LGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFF 265
           E  LFG V+     + +   LGKF  ANGGT+ L+E   +PL++Q ++   ++  + E  
Sbjct: 211 EAELFGYVEGAYTGARKGGNLGKFELANGGTVFLDEIGEMPLSMQSKLLVVLQEKEFEKL 270

Query: 266 DSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHF 325
                +R++VR+   T  +L  +VK + FR+DLYYR++V  + I  LR R EDIP LV+ 
Sbjct: 271 GGSRPVRVNVRVTAATNCDLEAKVKQNGFREDLYYRLNVLRLEIPPLRERREDIPELVYH 330

Query: 326 FLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI--GLKDSHLTEDRFV 383
           F+     +   K   IS +A+ +L+ Y W  NV+EL+N L RA+I   ++  ++ E   +
Sbjct: 331 FIDKLNARLKTKVNEISTRAMQMLSNYHWPGNVRELENTLERAMILADMQGGNILEPSHL 390

Query: 384 LLL--SREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRR-----LS 436
            L   +R G              +  G +                 QDG+  R     L 
Sbjct: 391 PLPHDNRNG-------------TFPNGNAF----------------QDGDAHRTLKTALE 421

Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           + EKE I   +K       + A+ LGI  S LY+K++++NI
Sbjct: 422 EFEKEYIANTLKNTGYDKEKAAKALGIDVSWLYKKLKKHNI 462


>gi|88704289|ref|ZP_01102003.1| Transcriptional regulatory protein zraR [Congregibacter litoralis
           KT71]
 gi|88701340|gb|EAQ98445.1| Transcriptional regulatory protein zraR [Congregibacter litoralis
           KT71]
          Length = 445

 Score =  164 bits (416), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 130/481 (27%), Positives = 221/481 (45%), Gaps = 44/481 (9%)

Query: 7   LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCE 64
           +++  RVLI++ DD     + D +E  GY           LS +     +++   +   E
Sbjct: 1   MNQATRVLIVEDDDTLRDALCDTIEFGGYSAVAAGNGREALSRMDAESFDMVISDVQMDE 60

Query: 65  DDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL 124
            D   +L+ +  + P +P ++ T   +++     + +  + + L     + L D +    
Sbjct: 61  LDGHGLLREVRSRKPEMPFVMITAHGSVRDAVSAMRDGATDYLLKPFEAQVLLDMVAR-- 118

Query: 125 REGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
              + P  E +       IAV PA  Q+  LA++       +++ GE G GK+ L+R+IH
Sbjct: 119 ---MQPPAEADL----PFIAVDPASQQLSVLAKRIAPSDATVLVSGESGCGKEVLARYIH 171

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPD 243
               RA  PF  VNC  I ++ +E  LFG +    T       GKF +ANGGT++L+E  
Sbjct: 172 SESARASRPFLAVNCAAIPENMLESMLFGYEKGAYTGAYQSRPGKFEQANGGTLLLDEIS 231

Query: 244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS 303
            + L +Q ++   ++  ++E       I LDVR+I  T + L  +V+   FR+DLYYR++
Sbjct: 232 EMDLGLQAKLLRVLQEREVERLGGNKLIPLDVRVIATTNRLLEEEVRDGHFREDLYYRLN 291

Query: 304 VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKN 363
           V  +N+  LR R  DI  L   FL  +  K      + ++KAL    +Y W  NV+EL+N
Sbjct: 292 VLPLNLPPLRQRPGDILPLARLFLDRYAPKPGASFDASAEKALE---QYSWRGNVRELEN 348

Query: 364 ILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESI 423
            + RAVI  +   L+E   +L        ++   +    +    G+              
Sbjct: 349 CVQRAVILARSDVLSEADLLL-------GDQLCASAEPLSPVPAGR-------------- 387

Query: 424 PAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK---IREYNIEVD 480
           PA+  D ++R     E+E+I  A++       + A RLGI   TL  K   +RE  I + 
Sbjct: 388 PALEGDLKIR-----EQELILQALESTGGNRKDTAERLGISPRTLRYKLARLREQGISLP 442

Query: 481 S 481
           +
Sbjct: 443 A 443


>gi|168184702|ref|ZP_02619366.1| pyruvate carboxylase [Clostridium botulinum Bf]
 gi|237794987|ref|YP_002862539.1| signal-transduction and transcriptional-control protein
           [Clostridium botulinum Ba4 str. 657]
 gi|182672222|gb|EDT84183.1| pyruvate carboxylase [Clostridium botulinum Bf]
 gi|229263062|gb|ACQ54095.1| signal-transduction and transcriptional-control protein
           [Clostridium botulinum Ba4 str. 657]
          Length = 643

 Score =  164 bits (416), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 114/343 (33%), Positives = 176/343 (51%), Gaps = 34/343 (9%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            D++I V+  MI++++LA+KA      I+I+GE G GK+ +++ IH    R+  PF  VN
Sbjct: 332 FDNIITVNEKMIEIIELAKKASKSNCNILIEGESGTGKELIAQSIHNYSMRSTGPFLAVN 391

Query: 199 CGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           C  I ++ +E  LFG         +     GKF  A+GGTI L+E   LPL +Q ++   
Sbjct: 392 CASIPRELVESELFGYERGAFTGASKEGHPGKFELADGGTIFLDELGELPLDMQSKLLRV 451

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           ++  KI         +L+VR+I  T +NL  ++K   FR+DLYYR+ V  I I  LR R 
Sbjct: 452 LDNNKIIRVGGTYEKQLNVRVIGATNRNLKEEMKKKNFREDLYYRLGVINIKILPLRYRK 511

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           EDI  LV+ F+ +   +N  +   +    +  L  Y W  NV+EL+N++ R      D +
Sbjct: 512 EDIEVLVNSFVMNLNQRNLQQNKRVKKSYIDKLKDYDWPGNVRELRNVVER------DYY 565

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGK-SSDTILDNLSQESIPAIGQDGEVRRL 435
           L++                  T+T  + Y E     +T  +N   E I  I        +
Sbjct: 566 LSD------------------TDTISSYYIEKNIFLETNNENHGNEDINIIS-------M 600

Query: 436 SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
             +EKE I  A++     +++ AR L IGRSTLYRKI++YNI+
Sbjct: 601 GKLEKENIENAIEKCDGNLTKAARLLNIGRSTLYRKIKKYNIK 643


>gi|168180303|ref|ZP_02614967.1| sensory box sigma-54 dependent transcriptional regulator
           [Clostridium botulinum NCTC 2916]
 gi|182668711|gb|EDT80689.1| sensory box sigma-54 dependent transcriptional regulator
           [Clostridium botulinum NCTC 2916]
          Length = 654

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 114/342 (33%), Positives = 173/342 (50%), Gaps = 32/342 (9%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            D++I V+  MI++++LA+KA      I+I+GE G GK+ +++ IH    RA  PF  VN
Sbjct: 332 FDNIITVNEKMIEIIELAKKASKSNCNILIEGESGTGKELIAQSIHNYSMRATGPFLAVN 391

Query: 199 CGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           C  I ++ +E  LFG         +     GKF  A+GGTI L+E   LPL +Q ++   
Sbjct: 392 CASIPRELVESELFGYEKGAFTGASKEGHPGKFELADGGTIFLDELGELPLDMQSKLLRV 451

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           ++  KI         +L+VR+I  T +NL  ++K   FR+DLYYR+ V  I I  LR R 
Sbjct: 452 LDNNKIIRVGGTYEKQLNVRVIGATNRNLKEEMKKKNFREDLYYRLGVINIKILPLRYRK 511

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           EDI  LV+ F+ +   KN  +   +    +  L +Y W  NV+EL+N++ R    L D+ 
Sbjct: 512 EDIEVLVNSFVMNLNQKNLQQNKRVKKAYIDKLKEYDWPGNVRELRNVVERDYY-LSDTG 570

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
                ++         E+    ET    Y          +N     IP          + 
Sbjct: 571 TVSPYYI---------EKNIFLETNNENY----------ENKDINIIP----------ME 601

Query: 437 DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            +EKE I  A++     +++ AR L IGRSTLYRKI++YNI+
Sbjct: 602 KLEKENIENAIEKCDGNLAKAARLLDIGRSTLYRKIKKYNIK 643


>gi|170767484|ref|ZP_02901937.1| sigma-54 dependent response regulator AtoC [Escherichia albertii
           TW07627]
 gi|170123818|gb|EDS92749.1| sigma-54 dependent response regulator AtoC [Escherichia albertii
           TW07627]
          Length = 461

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 132/483 (27%), Positives = 226/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGHTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +      +P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRIPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDIFKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEVKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRHALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|319783401|ref|YP_004142877.1| nitrogen regulation protein NR(I) [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317169289|gb|ADV12827.1| nitrogen regulation protein NR(I) [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 486

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 126/485 (25%), Positives = 227/485 (46%), Gaps = 30/485 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   G++V +  N S L   ++  + +++   ++  +++  ++
Sbjct: 7   ILVADDDAAIRTVLNQALSRVGHEVRVTSNASTLWRWVAAGEGDLVITDVVMPDENAFDM 66

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P+IV + Q+     I+      Y  + K F     LN+V+R       +
Sbjct: 67  LPRIKKARPELPVIVMSAQNTFMTAIRASETGAYEYLPKPFDLTELLNIVNRA------L 120

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              R   + ++  E      L+  S AM  +  +  +     + +MI GE G GK+ ++R
Sbjct: 121 SEPRRPKIDARPEEQPDAMPLVGRSAAMQDIYRMLARMMQTDLTVMISGESGTGKELVAR 180

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +HE G+R   PF  +N   I +D IE  LFG +    T    +  G+F +A GGT+ L+
Sbjct: 181 ALHEYGRRRGGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSTGRFEQAEGGTLFLD 240

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   +   +FR+DL+Y
Sbjct: 241 EIGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIVAATNKDLRTLINQGLFREDLFY 300

Query: 301 RISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           R++V  + +  LR RSED+P LV HFF         ++   IS   + L+ +YPW  NV+
Sbjct: 301 RLNVVPLRLPALRERSEDVPDLVRHFF--KLGEMEGLQTKRISSGGIELMKRYPWPGNVR 358

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           EL+N++ R         ++ +    ++  E K               +  S    +++  
Sbjct: 359 ELENLVRRLAALYSQDEISAE----VIEAELKTGERPVVPGGGNLIPDDLSIGQAVEHFL 414

Query: 420 QESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
           Q    +   D    G  +R LS++E  ++  +M   R    + A  LG+ R+TL +KIRE
Sbjct: 415 QRYFASFAGDLPPAGLYQRILSEVEFPLVLASMTATRGNQIKAAELLGLNRNTLRKKIRE 474

Query: 475 YNIEV 479
             + V
Sbjct: 475 LGVNV 479


>gi|40787322|gb|AAR90235.1| NtrC mutant form [Azospirillum brasilense]
          Length = 481

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 131/493 (26%), Positives = 233/493 (47%), Gaps = 48/493 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   G++V    N S L   ++  Q ++I   ++  +++  ++
Sbjct: 6   ILVADDDRAIRTVLTQALARLGHEVRTTGNASTLWRWVADGQGDLIITDVVMPDENGLDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           +  I    P + IIV + Q+     +K      +  + K F     +++V R    ++  
Sbjct: 66  IPRIKKIRPDLRIIVMSAQNTLITAVKAAERGAFEYLPKPFDLKELVSVVERALNSNTPP 125

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            AL     P+   E      LI  SPAM ++  +  +     + + I GE G  K+ ++R
Sbjct: 126 AAL-----PADAGEADEQLPLIGRSPAMQEIYRVLARLMGTDLTVTITGESGTDKELVAR 180

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H+ GKR   PF  +N   I ++ IE  LFG +    T  + +  G+F +A GGT+ L+
Sbjct: 181 ALHDYGKRRNGPFVAINMAAIPRELIESELFGHEKGAFTGATNRSTGRFEQAQGGTLFLD 240

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL  Q R+   ++ G+      R  I+ DVR++  T ++L   ++  +FR+DL+Y
Sbjct: 241 EIGDMPLEAQTRLLRVLQEGEYTTVGGRTPIKTDVRIVAATHRDLRTLIRQGLFREDLFY 300

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R+ V  I +  LR R+ED+P LV  FL   C+   +   SI   A+  L +Y W  NV+E
Sbjct: 301 RLCVVPIRLPPLRERTEDVPLLVRHFLNQ-CSAQGLPVKSIDQPAMDRLKRYRWPGNVRE 359

Query: 361 LKNILLR-------AVIGLK--DSHLTEDRFVLLLSREGKKER-----EFHTETACTCYT 406
           L+N++ R        VIGL   ++ L +         E + E      E H +     + 
Sbjct: 360 LENLVRRLAALYSQEVIGLDVVEAELADTTPAAQPVEEPQGEGLSAAVERHLKDYFAAHK 419

Query: 407 EGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
           +G  S+ + D                R L ++E+ +I L++   R    + A+ LG+ R+
Sbjct: 420 DGMPSNGLYD----------------RVLREVERPLISLSLSATRGNQIKAAQLLGLNRN 463

Query: 467 TLYRKIREYNIEV 479
           TL +KIR+ +I+V
Sbjct: 464 TLRKKIRDLDIQV 476


>gi|260459489|ref|ZP_05807744.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Mesorhizobium opportunistum WSM2075]
 gi|259035043|gb|EEW36299.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Mesorhizobium opportunistum WSM2075]
          Length = 486

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 133/500 (26%), Positives = 229/500 (45%), Gaps = 60/500 (12%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   G++V +  N S L   ++  + +++   ++  +++  ++
Sbjct: 7   ILVADDDAAIRTVLNQALSRVGHEVRVTSNASTLWRWVAAGEGDLVITDVVMPDENAFDM 66

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           L  I    P +P+IV + Q+     I+      Y  + K F     LN+V+R       +
Sbjct: 67  LPRIKKARPELPVIVMSAQNTFMTAIRASETGAYEYLPKPFDLTELLNIVNRA------L 120

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              R   + ++  E      L+  S AM  +  +  +     + +MI GE G GK+ ++R
Sbjct: 121 SEPRRPKIDARPEEQPDAMPLVGRSAAMQDIYRMLARMMQTDLTVMISGESGTGKELVAR 180

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +HE G+R   PF  +N   I +D IE  LFG +    T    +  G+F +A GGT+ L+
Sbjct: 181 ALHEYGRRRGGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSTGRFEQAEGGTLFLD 240

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   +   +FR+DL+Y
Sbjct: 241 EIGDMPMEAQTRLLRVLQQGEYTTVGGRTPIKTDVRIVAATNKDLRTLINQGLFREDLFY 300

Query: 301 RISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           R++V  + +  LR RSED+P LV HFF         ++   IS   + L+ +YPW  NV+
Sbjct: 301 RLNVVPLRLPALRERSEDVPDLVRHFF--KLGEMEGLQTKRISSGGIELMKRYPWPGNVR 358

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           EL+N++ R         ++ +            E E  T         G   + I D+LS
Sbjct: 359 ELENLVRRLAALYSQDEISAEII----------EAELKTGERPVVPDGG---NLIPDDLS 405

Query: 420 QESIPAIGQ-------------DGEV-------RRLSDIEKEIIGLAMKLYRAQMSEVAR 459
                 IGQ              GE+       R LS++E  ++  +M   R    + A 
Sbjct: 406 ------IGQAVEHFLQRYFASFAGELPPAGLYQRILSEVEYPLVLASMTATRGNQIKAAE 459

Query: 460 RLGIGRSTLYRKIREYNIEV 479
            LG+ R+TL +KIRE  + V
Sbjct: 460 LLGLNRNTLRKKIRELGVNV 479


>gi|312884914|ref|ZP_07744604.1| flagellar regulatory protein FleQ [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309367391|gb|EFP94953.1| flagellar regulatory protein FleQ [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 469

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 133/487 (27%), Positives = 238/487 (48%), Gaps = 45/487 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           +VLI++ D+   + + D +   GY     + ++  L  +    ++++   +         
Sbjct: 7   KVLIVEDDEGLREALVDTLALAGYSWLEADSAEDALVKLKSHHIDIVVSDVQMAGMGGLA 66

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF-----LNLVSRKQLCDSI 120
           +L+NI    P +P+++ T     +D +  +     + ++K F     LN+VSR       
Sbjct: 67  LLRNIKQHWPHLPVLLMTAYANIEDAVSAMKEGAIDYMAKPFAPEVLLNMVSR------- 119

Query: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
                    P++ +++   D+++A   + I+++ LA K       +M+ G  G GK+ +S
Sbjct: 120 -------YAPTKSDDNG--DAVVADEKS-IKLLSLAEKVAKTDANVMVLGPSGSGKEVMS 169

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEANGGTIVL 239
           R+IH +  R   PF  +NC  I  + +E  LFG        + Q   GKF +A GGTI+L
Sbjct: 170 RYIHNASPRKSGPFVAINCAAIPDNMLEATLFGYEKGAFTGAVQACPGKFEQAQGGTILL 229

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   + L++Q ++   ++  ++E   SR +++LDVR++  + ++L   V+   FR+DLY
Sbjct: 230 DEISEMDLSLQAKLLRVLQEREVERLGSRKSVKLDVRVLATSNRDLKQYVREGNFREDLY 289

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++VF I    L  R  DI  LV+   +  C K  + +  IS  A+  L+ Y W  NV+
Sbjct: 290 YRLNVFPIAWPALCDRKGDIEPLVYHLTERHCKKLGMPRPDISSSAIEKLSSYSWPGNVR 349

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETAC----TCYTEGKSSDTIL 415
           EL N++ RA+I L D HL +   +LL   EG    +  +  A      C      +  ++
Sbjct: 350 ELDNVIQRALI-LCDKHLLDSEHILL---EGLDWHDASSLQAVLDTGDCVVPNVKTSHLV 405

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL-YR--KI 472
           D     S   +G  GE+R   + E  II   ++  R +  E+A +LGI   TL Y+  K+
Sbjct: 406 DEKHLASPSGLG--GELR---EQEYAIILETLEECRGRRKEMAEKLGISPRTLRYKLAKM 460

Query: 473 REYNIEV 479
           R+  I++
Sbjct: 461 RDAGIDI 467


>gi|313673766|ref|YP_004051877.1| two component, sigma54 specific, transcriptional regulator, fis
           family [Calditerrivibrio nitroreducens DSM 19672]
 gi|312940522|gb|ADR19714.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Calditerrivibrio nitroreducens DSM 19672]
          Length = 470

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 115/345 (33%), Positives = 182/345 (52%), Gaps = 25/345 (7%)

Query: 146 SPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQD 205
           SP M Q+  +A+   +    ++I GE G GK+ L+RFIHE+ KR    F  +NC  I + 
Sbjct: 136 SPYMSQIFSIAKDVAESEATVLITGESGTGKEVLARFIHENSKRKG-DFVAINCAAIPES 194

Query: 206 KIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEF 264
            IE  LFG +    T    +  GKF  ANGGT++L+E   +P+ +Q ++   ++  +IE 
Sbjct: 195 LIESELFGYERGAFTGAINRKEGKFELANGGTLLLDEIGEIPINLQAKLLRVLQEKEIER 254

Query: 265 FDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVH 324
                  ++DVR+I  T +NL  +VK+  FR+DL+YR++V  I I  LR R EDI  L  
Sbjct: 255 LGGTKKQKVDVRIIATTNRNLREEVKNGNFREDLFYRLNVINIEIPPLRERKEDIEPLAL 314

Query: 325 FFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE-DRFV 383
           FF+  +C  N   Q  +S +AL LL  Y W  NV+EL++ + RAVI  KD ++T  + F+
Sbjct: 315 FFIDKYCNLNKKPQKKLSREALDLLKSYDWPGNVRELEHTIERAVILSKDQYITPLNLFL 374

Query: 384 LLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVR-----RLSDI 438
             +S    KE           Y   K    I + ++ E+     +D  ++      ++++
Sbjct: 375 HGISLNSYKE-----------YINNKDKIEITEIVNSET---TDEDKPIKISAGMTIAEM 420

Query: 439 EKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY---NIEVD 480
           E+E+I   ++  +   ++ A  LGI   TL  K+ EY    I+VD
Sbjct: 421 ERELILNTLRETKGNRTKAAELLGITVRTLRNKLHEYREQGIQVD 465


>gi|114776795|ref|ZP_01451838.1| putative transcriptional regulator, Fis family protein
           [Mariprofundus ferrooxydans PV-1]
 gi|114552881|gb|EAU55312.1| putative transcriptional regulator, Fis family protein
           [Mariprofundus ferrooxydans PV-1]
          Length = 465

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 133/478 (27%), Positives = 235/478 (49%), Gaps = 34/478 (7%)

Query: 12  RVLIIDKDDEQIKIIKDHV-ESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKE 68
           R LI+D DDE I+ I D V +  G DV          + ++    +V FL +   + +  
Sbjct: 4   RALIVD-DDEGIRWILDKVLQEEGVDVVQAGSIAEAKAALADGDFSVTFLDVYLPDGNGM 62

Query: 69  NILKNIVDKIPIVPIIVQTT-QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG 127
           ++L + +  +P+V +  +TT     +         + K F +L   +QL   +  A ++ 
Sbjct: 63  DLLASGL-SMPVVMLTAETTFGHAAEAYRMGAMEYLPKPF-DLDEVRQLLSRVRPA-QKA 119

Query: 128 VVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
             P+Q+    A   +I  SPAM Q+     +     + ++I GE G GK+ +++ +HE  
Sbjct: 120 SAPAQK---MADGLIIGRSPAMQQMFRTLGRVASSDLTVLITGESGTGKEMVAKTLHERS 176

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEANGGTIVLEEPDALP 246
           +RA   F  +N   I  D +E  LFG        + +   G+F++A+GGT+ L+E   +P
Sbjct: 177 QRADKAFVAINTAAIPADLLESELFGHEKGSFTGADKMREGRFVQADGGTLFLDEIGDMP 236

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
           LA+Q ++   +E G+++      +  ++VRL+  T +NL  ++    FR+DLYYR++V  
Sbjct: 237 LALQAKLLRVLEEGRVQRVGGSESKVVNVRLLAATHQNLNTKIAKGEFREDLYYRLNVIP 296

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           + I  LR R +DIP L +F L+    +  ++Q  + D A+ LL+++ W  NV+ELKN++ 
Sbjct: 297 VQIPPLRDRRDDIPELANFLLEQAVKELGMEQPILLDDAMDLLSRHDWPGNVRELKNVMR 356

Query: 367 RAVIGLKDSHLTEDRFVLLL----SREGKKEREFHTETACT---CYTEGKSSDTILDNLS 419
           R  +    + +T     L L    +  G++E      T CT    +  G +S T   NL 
Sbjct: 357 RLAVLTPGATITLTDVALALGNVDNHTGEEETLADAVTRCTRQYLHQLGYASAT---NLH 413

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           Q              L  IE  ++ LA++       +V+  LG+ R+T+ + + +YNI
Sbjct: 414 QH------------LLEQIEPPLLVLALEQCNGNQLKVSEMLGLNRNTVRKLLNKYNI 459


>gi|258591620|emb|CBE67921.1| putative Nitrogen assimilation transcription regulatory protein
           (ntrC)(synonyms:glnT, glnG) [NC10 bacterium 'Dutch
           sediment']
          Length = 487

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 130/486 (26%), Positives = 232/486 (47%), Gaps = 34/486 (6%)

Query: 11  KRVLIIDKDDEQIK-IIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCEDDK 67
           + +L++D D+E I+  ++  +E  GY V +    V  L+  +   ++++ + +     + 
Sbjct: 5   RHILVVD-DEESIRWALRKALEREGYQVVLAADGVEGLARATDPSIDLVLMDIKMPGAEG 63

Query: 68  ENILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF-----LNLVSR----K 114
              L  I +  P +P+I+ T     Q  ++ +    Y+ I+K F       LV R    +
Sbjct: 64  LETLSRIKETRPELPVIIMTAFGTLQAAVQAMKRGAYDYITKPFDFGELTILVQRVFEIR 123

Query: 115 QLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGV 174
           +L + +      G  P           ++ + PAM Q+  L  K     + ++++GE G 
Sbjct: 124 ELTERVAQMEALGGRPFD------FGGVVGLCPAMQQIFKLVGKMAASDLTVLVRGESGT 177

Query: 175 GKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEAN 233
           GK+ L++ +H + +R+  PF  VNC  I ++ +E  LFG +    T  SA   GKF  A 
Sbjct: 178 GKELLAKAVHYNSRRSARPFVAVNCAAIPRELLESELFGHERGAFTGASALRRGKFELAE 237

Query: 234 GGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHV 293
           GGTI L+E   + + +Q +I   ++  + E      ++  DVR+I  T +NL   V    
Sbjct: 238 GGTIFLDEIGDMDIGLQAKILRVLQERQFERVGGERSLSADVRVIAATNQNLETAVAQKG 297

Query: 294 FRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP 353
           FR+DLYYR++V  IN+  LR R EDIP LV+ FL  F  +   +  ++    L L+  Y 
Sbjct: 298 FREDLYYRLNVVAINLPPLRERVEDIPLLVNHFLHRFAEEQKQEPKTLPPDTLELMLAYR 357

Query: 354 WIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDT 413
           W  N++EL+N + RA +    S +  +     L +  + +      +     ++G + + 
Sbjct: 358 WPGNIRELENAVKRACVLAPTSLILPEHLPTALRQVDEVDGSGGRSSFERLLSQGITGE- 416

Query: 414 ILDNLSQESIPAIGQDGEVRR--LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
            L  L QE      +DG++    L+ +E+ ++   ++         A  LGI R+TL +K
Sbjct: 417 -LSRLKQE------RDGQLYAYFLAALERPLLLRVLERTGGNQLRAAELLGINRNTLRKK 469

Query: 472 IREYNI 477
           +RE  I
Sbjct: 470 LRELGI 475


>gi|262276059|ref|ZP_06053868.1| gAF modulated sigma54 specific transcriptional regulator Fis family
           [Grimontia hollisae CIP 101886]
 gi|262219867|gb|EEY71183.1| gAF modulated sigma54 specific transcriptional regulator Fis family
           [Grimontia hollisae CIP 101886]
          Length = 672

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 105/353 (29%), Positives = 175/353 (49%), Gaps = 38/353 (10%)

Query: 137 CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFI 196
            +L+ ++  SP +++ +  AR+     +P+++ GE GVGK+  ++ IH++ +    PF +
Sbjct: 347 ASLNGIVGQSPQLVEALTKARQLAKARVPVLLLGETGVGKELFAKGIHQASQDEKEPFVV 406

Query: 197 VNCGMIDQDKIEKFLFGDVD--LQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIY 254
           +NCG + +D +   LFG  D            GK   A+GGT+ L+E   +P+ +Q  + 
Sbjct: 407 LNCGGLSKDLLSSELFGYADGAFTGARKGGLAGKIEAADGGTLFLDEIGEMPMDIQPHLL 466

Query: 255 NFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRS 314
             +E+G+I         R+  RLI  T ++L   V   VFR DL+YRI+V  I I  LR 
Sbjct: 467 RVLESGEIYRLGENTPRRVRFRLIAATNRDLRVSVDEGVFRMDLFYRIAVTSIRIPPLRD 526

Query: 315 RSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKD 374
           RS DIP L  + +Q  C  + +   S+S +A S+L  Y W  NV+EL+NI+         
Sbjct: 527 RSGDIPLLTDWLIQHLCQHHELPLQSLSAEARSMLEAYSWPGNVRELRNII--------- 577

Query: 375 SHLTEDRFVLLLSREGKKEREFHTETA---CTCYTEGKSSDTILDNLSQESIPAIGQDGE 431
                +  +L+ + +     +   E A   CTC +  +S       LS  S         
Sbjct: 578 -----ESMLLMSTSDTLSVEDLPPEIANPFCTCSSVNES------GLSGRS--------- 617

Query: 432 VRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY--NIEVDSL 482
              L  +E   I   +      ++ VA++LGI +STLY K+++Y  N EV+++
Sbjct: 618 --PLEQVESHQIRTTLHQCEGNLTLVAQKLGIAKSTLYLKLKKYGLNQEVNAI 668


>gi|289548170|ref|YP_003473158.1| Fis family transcriptional regulator [Thermocrinis albus DSM 14484]
 gi|289181787|gb|ADC89031.1| transcriptional regulator, NifA subfamily, Fis Family [Thermocrinis
           albus DSM 14484]
          Length = 502

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 147/247 (59%), Gaps = 3/247 (1%)

Query: 134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
           +E   L+ +I  S AM  +++L +K     I ++I GE G GK  L++ IH   +R   P
Sbjct: 188 SERYNLEGIIGRSTAMRNIMELVKKVAPTDITVLITGESGTGKSLLAKVIHFLSRRKDKP 247

Query: 194 FFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGR 252
           F  +NC  I +  +E  LFG +    T       GKF  A+GGT+ L+E   +PL++Q +
Sbjct: 248 FVTINCSAIPETLLEAELFGYEKGAFTGAYTSKKGKFELADGGTVFLDEIGDMPLSLQPK 307

Query: 253 IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTL 312
           +   I+  ++E       +++DVR+I  T ++L   VK+ +FR+DLYYR++VF ++I  L
Sbjct: 308 LLRVIQDKEVEKLGGERTVKVDVRVIAATNRDLGQLVKNGLFREDLYYRLNVFPLHIPPL 367

Query: 313 RSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGL 372
           R R EDIP L+  FL+    +   K++SIS +A+ L+ +YPW  NV+EL+N+L R VI L
Sbjct: 368 RERREDIPLLIDHFLRVLSARYN-KKVSISPRAVELMMEYPWYGNVRELENLLERLVI-L 425

Query: 373 KDSHLTE 379
           K+  +TE
Sbjct: 426 KEGTITE 432


>gi|190891642|ref|YP_001978184.1| two-component response regulator nitrogen regulation protein
           [Rhizobium etli CIAT 652]
 gi|190696921|gb|ACE91006.1| two-component response regulator nitrogen regulation protein
           [Rhizobium etli CIAT 652]
          Length = 483

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 137/493 (27%), Positives = 231/493 (46%), Gaps = 47/493 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   IS  + +++   ++  +++  ++
Sbjct: 5   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWISAGEGDLVVTDVVMPDENAFDL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 65  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALAE 120

Query: 127 GVVPSQENEHCALDS--LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
                 + E    D   L+  S AM ++  +  +     + +MI GE G GK+ ++R +H
Sbjct: 121 PKRKPAKLEEDMQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVARALH 180

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGTIVL 239
           + GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT+ L
Sbjct: 181 DYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGTLFL 236

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+DLY
Sbjct: 237 DEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRTDVRIVAATNKDLKQAINQGLFREDLY 296

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  Y W  NV+
Sbjct: 297 YRLNVVPLRLPPLRDRAEDIPDLVRHFIQQ-AEKEGLGSKRFDQEALELMKAYAWPGNVR 355

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEG---KSSDTILD 416
           EL+N L+R ++ L    +     +         + E  ++   +   +G     S TI  
Sbjct: 356 ELEN-LIRRLMALYPQDVITREII---------DAELRSDVPDSPIDKGPIRNGSMTIAQ 405

Query: 417 NLSQ----------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
            + +          E++P  G    V  L+++E  +I  A+   R    + A  LG+ R+
Sbjct: 406 AVEENMRTYFAGFGENLPPPGLYDRV--LTEMEYPLILAALTATRGNQIKAADLLGLNRN 463

Query: 467 TLYRKIREYNIEV 479
           TL +KIRE  + V
Sbjct: 464 TLRKKIRELGVSV 476


>gi|8573370|gb|AAF01466.2| FlbD [Azospirillum brasilense]
          Length = 504

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 94/285 (32%), Positives = 159/285 (55%), Gaps = 11/285 (3%)

Query: 120 IICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
           +I A+ E V    E  H    +++   PAM+  + LA +       ++I GE G GK+ +
Sbjct: 105 LIAAVLEAVA---EESH----AIVCQDPAMLATLRLADQVAPSDASVLITGESGTGKELM 157

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R+IH   +R+  PF  VNC  I ++ +E  LFG +    T   A+ LG+F EANGGT++
Sbjct: 158 ARYIHRKSRRSDAPFVAVNCAAIPENLLESELFGHEKGAFTGAVARRLGRFEEANGGTLL 217

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   +   +Q ++   I+  +I+   S   ++++VRL+  + +NL  +V++  FR+DL
Sbjct: 218 LDELSEMHPRLQAKLLRAIQEKEIDRIGSSQPVKVNVRLVATSNRNLENEVRAGNFREDL 277

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           Y+R++VF + I +LR R  DIP +   FL+ +   N + +  +SD AL +L  + W  NV
Sbjct: 278 YFRLNVFSVAIPSLRERPADIPMIADHFLKKYAQANGLGEKRLSDDALLMLRAHHWRGNV 337

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVL---LLSREGKKEREFHTET 400
           +EL+N + RAV+  K   +  D  +L   LL+ EG  +    T +
Sbjct: 338 RELENTMHRAVLLSKSETVGPDAIMLTSQLLAPEGSAQASIPTNS 382


>gi|94987521|ref|YP_595454.1| response regulator [Lawsonia intracellularis PHE/MN1-00]
 gi|94731770|emb|CAJ55133.1| Response regulator containing CheY-like receiver, AAA-type ATPase,
           and DNA-binding domains [Lawsonia intracellularis
           PHE/MN1-00]
          Length = 471

 Score =  164 bits (415), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 135/482 (28%), Positives = 237/482 (49%), Gaps = 32/482 (6%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQ---VNVIFLSLINCEDDKEN 69
           +LI+D DD    ++   ++ +GY+    +  D++ I+K +    + I   L     D   
Sbjct: 6   ILIVDDDDVHRSMLSALLKGWGYETDEASDGDIA-ITKAKEHAYDTILSDLKMARVDGIK 64

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           +L+ I++  P +PII+ T     +  ++ L    Y+ ++K       +K L  ++     
Sbjct: 65  MLECILNYNPSIPIIIMTAWSSVETAVQALRMGAYDYLTKPLDFDALKKTLQKALTHLQV 124

Query: 126 EGVVPSQENEHCALD-------SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
             +V   E+ H            ++  SP M++++ +          I+I GE G GK+ 
Sbjct: 125 HPIVRDNESFHKVNTKIEQSNLGILGRSPCMLELIQMVSTVAPSEATILIVGESGTGKEL 184

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTI 237
           ++R I ++  R+  PF  VNC  +    +E  LFG +    T    +  G+F +A+GGT+
Sbjct: 185 VARAIRQASHRSDAPFVTVNCAALSPALLESELFGHEKGAFTGADRRREGRFKQADGGTL 244

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL +Q ++   I+ G+I+   S   I ++VR+I  T ++L  +V +  FR+D
Sbjct: 245 FLDEIGELPLLLQAKLLRAIQQGEIQRVGSDTPITVNVRVIAATNRDLPEEVIAGRFRED 304

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LYYR++V  I +  LR+R EDIP L  FFL+ F   N       + +++ +L +Y W  N
Sbjct: 305 LYYRLNVIGIEVPPLRNRIEDIPLLATFFLEKFALSNRKVIKGFTPQSMDVLLRYNWPGN 364

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKE-REFHTETACTCYTEGKSSDTILD 416
           V+EL+N + RAVI     +++E    ++++   +       ++     Y      DT+  
Sbjct: 365 VRELENAIERAVILTTGDYISERELPMVMTSPSQPNVLSSQSDKEIVQY-----KDTV-K 418

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
           +LSQE         +   L ++EK  I   +       SE ARRLGI R+TL+ K++ Y 
Sbjct: 419 HLSQE---------QTLTLEELEKRAIINMLHETSENKSEAARRLGITRATLHNKLKRYG 469

Query: 477 IE 478
           IE
Sbjct: 470 IE 471


>gi|262199013|ref|YP_003270222.1| Fis family transcriptional regulator [Haliangium ochraceum DSM
           14365]
 gi|262082360|gb|ACY18329.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Haliangium ochraceum DSM 14365]
          Length = 466

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 132/479 (27%), Positives = 229/479 (47%), Gaps = 39/479 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+L++D +     +  D +   G++V + +   + L+     + ++IF  +     D   
Sbjct: 15  RILVVDDERGIRALCSDVLRRAGHEVEVADTGTAGLAAAKAKRFDLIFCDINLPGVDGLT 74

Query: 70  ILKNIVDK--IPIVPIIVQ--TTQDNIKILNCFLYNRISKFF----LNLVSRKQLCDSII 121
           +L +++++   P V +I    + +  ++ +     + ++K F    L +V R+ L +  +
Sbjct: 75  MLPSLLEREDPPTVILITAFPSVETAVRGMKLGARDYLTKPFTPDELRMVCRRALSEDAM 134

Query: 122 CALREGVVPSQENEHC-ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
              RE    + E  H  A  +L+  SPAM+Q+     K     I +++ GE G GK+ ++
Sbjct: 135 --RRE----NAELRHALAYGNLVGQSPAMLQLKKTVAKVAGADINVLVMGESGTGKELVA 188

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF-LGKFIEANGGTIVL 239
           R +H  G RA   F  VNCG +    +E  LFG V      + Q   G F+ A+GGT+ L
Sbjct: 189 RALHYQGARAGRAFVPVNCGALVDSLLESELFGHVRGAFTGAEQAKRGLFLAADGGTLFL 248

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   LPLA+Q ++   ++ G+I+        R+DVR++  T ++L   V    FR+DL+
Sbjct: 249 DEIGELPLALQPKLLRALQDGEIKPVGGLEPQRVDVRVVAATNRDLQEAVAQGSFREDLF 308

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  I +  LR R ED+P L   F  S   +       IS  AL  L   PW  NV+
Sbjct: 309 YRLNVITIEVPALRERREDVPVLAQHFAASAARRARRACPDISPAALEWLAAQPWPGNVR 368

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           +L+N + RAV+    + L  + F       G        E+A    T G+  D+  D LS
Sbjct: 369 QLENAIERAVVLAAGNTLGIEDFQPRAGVAG-----LAAESAPGRRTGGR-GDSADDLLS 422

Query: 420 QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
                          L ++E+  I   ++    Q ++ +  LGI R+TL++K+R+Y +E
Sbjct: 423 ---------------LDELERLHILRVLEACGGQKTKASAVLGINRTTLWKKLRQYGLE 466


>gi|74312742|ref|YP_311161.1| acetoacetate metabolism regulatory protein AtoC [Shigella sonnei
           Ss046]
 gi|73856219|gb|AAZ88926.1| response regulator of ato [Shigella sonnei Ss046]
 gi|323168621|gb|EFZ54301.1| acetoacetate metabolism regulatory protein atoC [Shigella sonnei
           53G]
          Length = 461

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 132/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSASWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEVKTASVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|288960025|ref|YP_003450365.1| two-component response regulator [Azospirillum sp. B510]
 gi|288912333|dbj|BAI73821.1| two-component response regulator [Azospirillum sp. B510]
          Length = 517

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 94/285 (32%), Positives = 159/285 (55%), Gaps = 11/285 (3%)

Query: 120 IICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
           +I A+ E V    E  H    S++   PAM+  + LA +       +MI GE G GK+ +
Sbjct: 105 LIAAVLEAVA---EESH----SIVCSDPAMLATLRLAEQVAPSDASVMITGESGTGKELM 157

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +RFIH   +R+  PF  VNC  I ++ +E  LFG +    T   A+ LGKF EAN GT++
Sbjct: 158 ARFIHRKSRRSGEPFVAVNCAAIPENLLESELFGHEKGAFTGAVARRLGKFEEANNGTLL 217

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   +   +Q ++   I+  +I+   S   +R++VRLI  + +NL  +V+S  FR+DL
Sbjct: 218 LDELSEMHPRLQAKLLRAIQEKEIDRIGSSQPVRVNVRLIATSNRNLEAEVRSGNFREDL 277

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           Y+R++VF + I +LR R  DIP +   FL+ +   N + +  +++ AL +L  + W  NV
Sbjct: 278 YFRLNVFSVAIPSLRERPADIPLIADHFLKKYAEANGLGEKRLTEDALLMLKTHHWRGNV 337

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVL---LLSREGKKEREFHTET 400
           +EL+N + RAV+  +   +  +  +L   +L+ EG  +    +++
Sbjct: 338 RELENTMHRAVLLSRGEEVGPEAIMLTSKMLAPEGSAQASIPSDS 382


>gi|224025445|ref|ZP_03643811.1| hypothetical protein BACCOPRO_02185 [Bacteroides coprophilus DSM
           18228]
 gi|224018681|gb|EEF76679.1| hypothetical protein BACCOPRO_02185 [Bacteroides coprophilus DSM
           18228]
          Length = 455

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 114/409 (27%), Positives = 200/409 (48%), Gaps = 38/409 (9%)

Query: 79  PIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQLCDSI-ICALREGVVPSQE 133
           P VP+I+ T   +I++    +    ++ I+K + N    +++  ++ + A ++    S +
Sbjct: 74  PDVPVILMTAWGSIRLAVQGMQAGAFDFITKPWNNAALMQRIETALELTAPQKETPGSAD 133

Query: 134 NEHCALDS--LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF 191
            +H   D   +I  S A+ +V+D   +      P++I GE G GK+ ++  +H + +RA 
Sbjct: 134 QKHAGFDRHRIIGKSRALNEVLDTLCRIAPTNAPVLITGESGTGKELIAEALHVNSRRAS 193

Query: 192 FPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQ 250
            PF  VN G I Q   E  +FG      T      +G+F  A+ GTI L+E   L L+ Q
Sbjct: 194 GPFVKVNLGGISQSLFESEMFGHRKGAFTDAVTDRIGRFEMADRGTIFLDEIGELDLSCQ 253

Query: 251 GRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIS 310
            ++   ++    E        ++D+R++  T  +L   V+ H FR+DL+YRI++  +++ 
Sbjct: 254 VKLLRVLQDQTFEVLGDSRPRKVDIRVVCATNADLPQMVREHTFREDLFYRINLITVHLP 313

Query: 311 TLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI 370
            LR R EDIP L   F    C +N +  +  +  AL  L+  P+  N++ELKN++ R ++
Sbjct: 314 ALRERREDIPLLARHFADRQCEQNQLPPVDFTSDALDFLSSLPYPGNIRELKNLVERTLL 373

Query: 371 GLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDG 430
               + LTE  F L                   CY +      + ++ ++  +P      
Sbjct: 374 VSGKTRLTEADFRL-------------------CYQQ-----PVHNSAAKLQVP------ 403

Query: 431 EVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           +   L +IEK+ I  AMK     +S+VA  LGI R  LYR++ +YN+ V
Sbjct: 404 QGMTLEEIEKQTILQAMKECGNNLSQVAALLGISRGALYRRLEKYNLPV 452


>gi|295095720|emb|CBK84810.1| Transcriptional regulator of aromatic amino acids metabolism
           [Enterobacter cloacae subsp. cloacae NCTC 9394]
          Length = 513

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 102/346 (29%), Positives = 172/346 (49%), Gaps = 47/346 (13%)

Query: 138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV 197
           A   +IAVSP M  V+D ARK  +   P++I G+ G GK  L+  +H +  RA  P+  +
Sbjct: 202 AFSQIIAVSPKMRHVIDQARKLANLTAPLLITGDTGTGKDLLAHAVHMASPRAAKPYLAL 261

Query: 198 NCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
           NC  I +D +E  LFG      K      G F +ANGG+++L+E   +   +Q ++  F+
Sbjct: 262 NCASIPEDAVESELFGHAPEGKK------GFFEQANGGSVLLDEIGEMSPRMQAKLLRFL 315

Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
             G          + +DVR+I  T+KNL+  V+  VFR+DLYYR++V  +NI  LR   +
Sbjct: 316 NDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGVFREDLYYRLNVLTLNIPPLRDCPQ 375

Query: 318 DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHL 377
           DI  L   F+  F  +  + +  +S    ++LT+Y W  N+++LKN + RA+  L+   L
Sbjct: 376 DIMPLTELFVARFADEQGVPRPKLSADLGTVLTRYGWPGNIRQLKNAVYRALTQLEGYEL 435

Query: 378 TEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSD 437
                                          +  D +L +    ++ ++G++     L D
Sbjct: 436 -------------------------------RPQDILLPDYDAGTV-SVGEEAMEGSLDD 463

Query: 438 I----EKEIIGLAMKLYRAQMS--EVARRLGIGRSTLYRKIREYNI 477
           I    E+ ++    +LYR+  S  ++A+RLG+  + +  K+REY +
Sbjct: 464 ITSRFERSVL---TQLYRSYPSTRKLAKRLGVSHTAIANKLREYGL 506


>gi|40787320|gb|AAR90234.1| NtrC mutant form [Azospirillum brasilense]
          Length = 481

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 131/493 (26%), Positives = 233/493 (47%), Gaps = 48/493 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   G++V    N S L   ++  Q ++I   ++  +++  ++
Sbjct: 6   ILVADDDRAIRTVLTQALARLGHEVRTTGNASTLWRWVADGQGDLIITDVVMPDENGLDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDSII 121
           +  I    P + IIV + Q+     +K      +  + K F     +++V R    ++  
Sbjct: 66  IPRIKKIRPDLRIIVMSAQNTLITAVKAAERGAFEYLPKPFDLKELVSVVERALNSNTPP 125

Query: 122 CALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
            AL     P+   E      LI  SPAM ++  +  +     + + I GE   GK+ ++R
Sbjct: 126 AAL-----PADAGEADEQLPLIGRSPAMQEIYRVLARLMGTDLTVTITGESETGKELVAR 180

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            +H+ GKR   PF  +N   I ++ IE  LFG +    T  + +  G+F +A GGT+ L+
Sbjct: 181 ALHDYGKRRNGPFVAINMAAIPRELIESELFGHEKGAFTGATNRSTGRFEQAQGGTLFLD 240

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   +PL  Q R+   ++ G+      R  I+ DVR++  T ++L   ++  +FR+DL+Y
Sbjct: 241 EIGDMPLEAQTRLLRVLQEGEYTTVGGRTPIKTDVRIVAATHRDLRTLIRQGLFREDLFY 300

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R+ V  I +  LR R+ED+P LV  FL   C+   +   SI   A+  L +Y W  NV+E
Sbjct: 301 RLCVVPIRLPPLRERTEDVPLLVRHFLNQ-CSAQGLPVKSIDQPAMDRLKRYRWPGNVRE 359

Query: 361 LKNILLR-------AVIGLK--DSHLTEDRFVLLLSREGKKER-----EFHTETACTCYT 406
           L+N++ R        VIGL   ++ L +         E + E      E H +     + 
Sbjct: 360 LENLVRRLAALYSQEVIGLDVVEAELADTTPAAQPVEEPQGEGLSAAVERHLKDYFAAHK 419

Query: 407 EGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
           +G  S+ + D                R L ++E+ +I L++   R    + A+ LG+ R+
Sbjct: 420 DGMPSNGLYD----------------RVLREVERPLISLSLSATRGNQIKAAQLLGLNRN 463

Query: 467 TLYRKIREYNIEV 479
           TL +KIR+ +I+V
Sbjct: 464 TLRKKIRDLDIQV 476


>gi|150396309|ref|YP_001326776.1| nitrogen metabolism transcriptional regulator, NtrC, Fis family
           [Sinorhizobium medicae WSM419]
 gi|150027824|gb|ABR59941.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Sinorhizobium medicae WSM419]
          Length = 484

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 139/496 (28%), Positives = 232/496 (46%), Gaps = 53/496 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   I+    +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWIAAGDGDLVVTDVVMPDENAFDL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 66  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALAE 121

Query: 127 GVVPSQENEHCALDS-----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              P +       DS     L+  S AM ++  +  +     + +MI GE G GK+ ++R
Sbjct: 122 ---PKRRPSKLDDDSQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVAR 178

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +H+ GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT
Sbjct: 179 ALHDYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGT 234

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+
Sbjct: 235 LFLDEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRSDVRIVAATNKDLKQSINQGLFRE 294

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DLYYR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  +PW  
Sbjct: 295 DLYYRLNVVPLRLPPLRDRAEDIPDLVRHFVQQ-AEKEGLDVKRFDQEALELMKAHPWPG 353

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCY--TEGKS---- 410
           NV+EL+N L+R +  L    +     +         E E  +E   +    T  +S    
Sbjct: 354 NVRELEN-LIRRLTALYPQDVITREII---------ENELRSEIPDSPIEKTAARSGSLS 403

Query: 411 -SDTILDNLSQ------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGI 463
            S  + +N+ Q      + +P  G    V  L+++E  +I  A+   R    + A  LG+
Sbjct: 404 ISQAVEENMRQYFASFGDGLPPSGLYDRV--LAEMEYPLILAALTATRGNQIKAADLLGL 461

Query: 464 GRSTLYRKIREYNIEV 479
            R+TL +KIRE  + V
Sbjct: 462 NRNTLRKKIRELGVSV 477


>gi|118579322|ref|YP_900572.1| Fis family GAF modulated sigma54 specific transcriptional regulator
           [Pelobacter propionicus DSM 2379]
 gi|118502032|gb|ABK98514.1| GAF modulated sigma54 specific transcriptional regulator, Fis
           family [Pelobacter propionicus DSM 2379]
          Length = 661

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 110/366 (30%), Positives = 178/366 (48%), Gaps = 41/366 (11%)

Query: 121 ICALREG--VVPSQENEHCAL-----DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFG 173
           +  LR+    + S+  +H +L     D +I  SPA+ +  + AR A +    I++ GE G
Sbjct: 320 VAVLRQARDALKSRRAQHSSLPRYSFDDIIGESPAISEAKEWARIAANSGSTILLSGESG 379

Query: 174 VGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD--LQTKNSAQFLGKFIE 231
            GK+  ++ IH        PF  +NC  I +  +E  LFG  +            GKF  
Sbjct: 380 TGKELFAQSIHNVSSFRNGPFIAINCAAIPEALVESELFGYAEGTFTGAKKGGSPGKFES 439

Query: 232 ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKS 291
           A+ GT+ L+E   +PL VQ ++   I+  KI    S    ++++R+I  T KNL  +V +
Sbjct: 440 ADRGTLFLDEIGDMPLTVQAKVLRVIQEKKISRVGSSEERQVEIRIIASTHKNLRTEVLN 499

Query: 292 HVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTK 351
             FR+DL+YR++V ++ +  LR R  DIP +    ++    +   ++I   D     L  
Sbjct: 500 GNFREDLFYRLNVLVVQVPPLRDRGGDIPLVACHLVEKISARMGKQRIVGEDAFWGKLAS 559

Query: 352 YPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSS 411
           + W  NV+EL+N + +AV+   DS        +LL+R                     + 
Sbjct: 560 HNWPGNVRELENAIEQAVVRSDDSG-------VLLARH-------------------LTF 593

Query: 412 DTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
           D +      ES+   G   E+  L+++EK+ I  A+ LY   + + A +LGIGR+TLYRK
Sbjct: 594 DVV------ESVAPTGGRAEIVSLTEMEKQAITAALHLYDGNIQKAASKLGIGRNTLYRK 647

Query: 472 IREYNI 477
           IREY I
Sbjct: 648 IREYGI 653


>gi|56384259|gb|AAV85778.1| FlbD [Azospirillum brasilense]
          Length = 512

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 94/285 (32%), Positives = 159/285 (55%), Gaps = 11/285 (3%)

Query: 120 IICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
           +I A+ E V    E  H    +++   PAM+  + LA +       ++I GE G GK+ +
Sbjct: 105 LIAAVLEAVA---EESH----AIVCQDPAMLATLRLADQVAPSDASVLITGESGTGKELM 157

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           +R+IH   +R+  PF  VNC  I ++ +E  LFG +    T   A+ LG+F EANGGT++
Sbjct: 158 ARYIHRKSRRSDAPFVAVNCAAIPENLLESELFGHEKGAFTGAVARRLGRFEEANGGTLL 217

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   +   +Q ++   I+  +I+   S   ++++VRL+  + +NL  +V++  FR+DL
Sbjct: 218 LDELSEMHPRLQAKLLRAIQEKEIDRIGSSQPVKVNVRLVATSNRNLENEVRAGNFREDL 277

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           Y+R++VF + I +LR R  DIP +   FL+ +   N + +  +SD AL +L  + W  NV
Sbjct: 278 YFRLNVFSVAIPSLRERPADIPMIADHFLKKYAQANGLGEKRLSDDALLMLRAHHWRGNV 337

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVL---LLSREGKKEREFHTET 400
           +EL+N + RAV+  K   +  D  +L   LL+ EG  +    T +
Sbjct: 338 RELENTMHRAVLLSKSETVGPDAIMLTSQLLAPEGSAQASIPTNS 382


>gi|163843385|ref|YP_001627789.1| nitrogen regulation protein NR(I) [Brucella suis ATCC 23445]
 gi|163674108|gb|ABY38219.1| nitrogen regulation protein NR(I) [Brucella suis ATCC 23445]
          Length = 440

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 121/431 (28%), Positives = 205/431 (47%), Gaps = 35/431 (8%)

Query: 69  NILKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFF-----LNLVSRKQLCDS 119
           ++L  I    P +P++V + Q+     I+      Y  + K F     +N+V R      
Sbjct: 17  DLLPRIKKIRPDLPVVVMSAQNTFMTAIRASEAGAYEYLPKPFDLTELINIVGRALSEHR 76

Query: 120 IICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
              A+    +P ++ E+     L+  SPAM ++  L  +     + +M+ GE G GK+ +
Sbjct: 77  QKPAV---ALPDEQGENM---PLVGRSPAMQEIYRLLARMMQTDLTVMVTGESGTGKELV 130

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANG 234
           +R +HE G+R   PF  +N   I +D IE  LFG         Q ++S    G+F +ANG
Sbjct: 131 ARALHEYGRRRKGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSS----GRFEQANG 186

Query: 235 GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF 294
           GT+ L+E   +P+  Q R+   ++ G+      R  I+ DVR++  T ++L   +   +F
Sbjct: 187 GTLFLDEIGDMPMEAQTRLLRVLQQGEYMTVGGRTPIKTDVRIVAATNRDLRQIIAQGLF 246

Query: 295 RKDLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYP 353
           R+DLYYR++V  + +  LR RSED+P LV HFF      +  + +  I++  L ++ +YP
Sbjct: 247 REDLYYRLNVVPLRLPPLRERSEDVPDLVRHFF--KHAAEEGLPEKRITNAGLEMMRRYP 304

Query: 354 WIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDT 413
           W  NV+EL+N++ R         +  +     L  E  K        A     E  S   
Sbjct: 305 WPGNVRELENLVRRLAALYPQEEIAPEIIETELKAELAKP---DVVAAAGGEMENISISQ 361

Query: 414 ILDNLSQESIPAIGQD----GEVRR-LSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL 468
            ++   Q    + G D    G  +R L+++E  +I   +   R    + A  LG+ R+TL
Sbjct: 362 AVEQNMQRYFASFGSDLPPPGLYQRVLAEVEYPLILACLTATRGNQIKAADLLGLNRNTL 421

Query: 469 YRKIREYNIEV 479
            +KIRE  + +
Sbjct: 422 RKKIRELGVNI 432


>gi|253700850|ref|YP_003022039.1| Fis family transcriptional regulator [Geobacter sp. M21]
 gi|251775700|gb|ACT18281.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. M21]
          Length = 509

 Score =  164 bits (414), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 148/518 (28%), Positives = 229/518 (44%), Gaps = 62/518 (11%)

Query: 8   DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLSTISKIQVNVIFLSLINCED 65
           D   R+LIID + +        +   GY V         L+ +   Q +V  + L   + 
Sbjct: 3   DSPTRILIIDDERDVCTFFSRLLSRKGYQVVTAASEPEALAALEAAQFSVALVDLKLPDT 62

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQLCDSII 121
           D   +L+ I  + P   +I+ T    +K     +    Y  + K F ++   +QL     
Sbjct: 63  DGITLLEIIKSRQPACEVIIMTGYSTVKTAVAAMQLGAYEYLEKPFDDIDQIEQLVGR-- 120

Query: 122 CALREGVVPSQENEHCALDSL-------IAVSPAMIQVVDLARKAGDCAIPIMIQGEFGV 174
            A     +   +N H     +       +  SP+M ++V LA K     I ++IQG+ G 
Sbjct: 121 AAGSGASLLRGDNSHDEWAEVAQGVGFRVGSSPSMKRMVSLAYKVAGKDISVLIQGKTGT 180

Query: 175 GKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEAN 233
           GK+ L+RFIH +  RA  PF  VNCG + ++ +E  LFG        + Q   G F  AN
Sbjct: 181 GKEVLARFIHAASCRAGQPFIPVNCGALPENLLESELFGHEKGAFTGANQTRRGIFELAN 240

Query: 234 GGTIVLEE-PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH 292
            GT++L+E  DA P  +Q ++   +ETG+         I+ DVR+I  T  +L   +   
Sbjct: 241 NGTLLLDEIGDATP-QIQVKLLRVLETGEFMRVGGERPIKTDVRVIAATNVDLEQAIAEK 299

Query: 293 VFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY 352
            FR+DL+YR++V  + I +L SRSEDIP L   F+         + + ++   + +L  Y
Sbjct: 300 SFREDLFYRLNVVRLEIPSLSSRSEDIPLLAEHFVHQLN-----RDLKLAAGTVRMLQGY 354

Query: 353 PWIDNVQELKNILLRA-VIGLKDSHLTEDRFVLLLSREGKKEREFHTET----------- 400
            W  N++EL N++ RA VI   D+ L E      L+     ER    +T           
Sbjct: 355 AWPGNIRELANVMRRAVVICNGDTILPEHLGGTFLAGPTAPERGSAAKTIQQPDRGRLQS 414

Query: 401 ----ACTCYTEGKSSDT-----ILDNLSQES------------IPAIGQDGEVRRLSDIE 439
                C    E +  D      +LD+L Q              +PA+        L D E
Sbjct: 415 TLLEHCGSAEELERLDADELNRLLDSLRQAQSNLLGVMRKKKIVPAL------HALKDSE 468

Query: 440 KEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
            E I  A+  Y   ++E AR LGI R+TLYRKI+E  +
Sbjct: 469 AETIKEALAQYDGNITEAARALGIARNTLYRKIKELGL 506


>gi|323701779|ref|ZP_08113450.1| PAS modulated sigma54 specific transcriptional regulator, Fis
           family [Desulfotomaculum nigrificans DSM 574]
 gi|323533315|gb|EGB23183.1| PAS modulated sigma54 specific transcriptional regulator, Fis
           family [Desulfotomaculum nigrificans DSM 574]
          Length = 581

 Score =  163 bits (413), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 110/351 (31%), Positives = 165/351 (47%), Gaps = 39/351 (11%)

Query: 134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
            + CA   L   S AM  +++  +K       ++++GE G GK+  +R IH++  R   P
Sbjct: 260 GQDCAFSKLTGRSLAMQNLINFGKKVSTTDATVLLRGESGTGKELFARAIHQNSNRHLRP 319

Query: 194 FFIVNCGMIDQDKIEKFLFG-------DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP 246
           F +VNCG I  +  E  LFG         D + K      G F  ANGGTI L+E   LP
Sbjct: 320 FIVVNCGAIPNNLFESELFGYEGGAFTGADRKGKP-----GMFELANGGTIFLDEVGELP 374

Query: 247 LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL 306
           L +Q ++   ++ G          ++++VR++  T ++L   +    FR+DLYYR++V  
Sbjct: 375 LEMQVKLLRVLQEGSFYRVGGSEPVQVNVRVLAATHRDLEAMISRRQFREDLYYRLNVVS 434

Query: 307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL 366
           + I  LR R EDIP LVH FLQ FC K       I    ++    Y W  N++ELKN + 
Sbjct: 435 LEIPPLRERREDIPELVHQFLQEFCQKYQKSISKIEPAVMTAFLDYSWPGNIRELKNAVE 494

Query: 367 RAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI 426
           R V+      LTE   +   S      R  +         +GK     L +++ E+    
Sbjct: 495 RLVV------LTEGEVIDEQSLPENLRRNTYISLVTAPTAQGK-----LMSVAVEA---- 539

Query: 427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
                       EK++I   ++  +   SE AR LGI RSTLY K+R+  I
Sbjct: 540 ------------EKQLILKTLQQVKGNRSEAARVLGIPRSTLYYKLRQLGI 578


>gi|163781746|ref|ZP_02176746.1| transcriptional regulator (NifA family) protein [Hydrogenivirga sp.
           128-5-R1-1]
 gi|159882966|gb|EDP76470.1| transcriptional regulator (NifA family) protein [Hydrogenivirga sp.
           128-5-R1-1]
          Length = 506

 Score =  163 bits (413), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 110/342 (32%), Positives = 183/342 (53%), Gaps = 31/342 (9%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
           ++ ++  S  ++ V+++  +    +  ++++GE GVGK+  +R IH    RA  PF  VN
Sbjct: 193 VEGIVGRSREILGVLEIVHRVAPTSATVLLRGESGVGKEVFARAIHFLSPRADKPFIAVN 252

Query: 199 CGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI 257
           CG I ++ +E  LFG +    T   +   GKF  ANGGT+ L+E   LPL +Q ++   +
Sbjct: 253 CGAIPENLLEAELFGYEKGAFTGAYSSKKGKFELANGGTLFLDEVGELPLHLQVKLLRVL 312

Query: 258 ETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE 317
           +  ++E   S   +++DVR++  T ++L   V+   FR+DLYYR++V  I I  LR R +
Sbjct: 313 QEKEVERLGSSKPVKVDVRIVAATNRDLENMVREGKFREDLYYRLNVVPIFIPPLRERRD 372

Query: 318 DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHL 377
           DIP LV  FL+ F  K   K++SIS + +    +Y W  NV+EL+NIL R VI   D  L
Sbjct: 373 DIPVLVQHFLERF-KKEYGKEVSISAEVMDAFMEYEWKGNVRELQNILERMVILDSDGKL 431

Query: 378 TEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSD 437
           TE+     L R+ K+ER+ H       +T G+S                        + D
Sbjct: 432 TEEDLPPELRRK-KEERKTHR----PIFTNGES------------------------IWD 462

Query: 438 IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           +E+++I  A++     + E A+RLG+    +  +I++Y I++
Sbjct: 463 VERQLIEKALEDSGFVIKEAAKRLGMTPRQVSYRIQKYGIKL 504


>gi|322805963|emb|CBZ03528.1| transcriptional activator of acetoin dehydrogenase operon AcoR
           [Clostridium botulinum H04402 065]
          Length = 643

 Score =  163 bits (413), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 116/343 (33%), Positives = 178/343 (51%), Gaps = 34/343 (9%)

Query: 139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN 198
            D++I V+  MI++++LA+KA      I+I+GE G GK+ +++ IH    RA  PF  VN
Sbjct: 332 FDNIITVNEKMIEIIELAKKASKSNCNILIEGESGTGKELIAQSIHNYSMRAEGPFLAVN 391

Query: 199 CGMIDQDKIEKFLFG-DVDLQTKNSAQ-FLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           C  I ++ +E  LFG +    T  S +   GKF  A+GGTI L+E   LPL +Q ++   
Sbjct: 392 CASIPRELVESELFGYERGAFTGASKEGHPGKFELADGGTIFLDELGELPLDMQSKLLRV 451

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           ++  KI         +L+VR+I  T +NL  ++K   FR+DLYYR+ V  I I  LR R 
Sbjct: 452 LDNNKIIRVGGTYEKQLNVRVIGATNRNLKEEMKKKNFREDLYYRLGVINIKILPLRYRK 511

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           EDI  LV+ F+ +   +N  +   +    +  L  Y W  N++EL+N++ R      D +
Sbjct: 512 EDIEVLVNSFVMNLNQRNLQQNKRVKKSYIDKLKDYDWPGNIRELRNVVER------DYY 565

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGK-SSDTILDNLSQESIPAIGQDGEVRRL 435
           L++                  T T    Y E    S+T  +N   + I  I        +
Sbjct: 566 LSD------------------TGTVSPYYIEKNIFSETNNENYENKDINII-------PM 600

Query: 436 SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
             +EKE I  A++     +++ AR L IGRSTLYRKI++YNI+
Sbjct: 601 EKLEKENIENAIEKCNGNLAKAARLLDIGRSTLYRKIKKYNIK 643


>gi|16130157|ref|NP_416724.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator/sigma54 interaction
           protein [Escherichia coli str. K-12 substr. MG1655]
 gi|89109039|ref|AP_002819.1| fused response regulator of ato opeon, in two-component system with
           AtoS [Escherichia coli str. K-12 substr. W3110]
 gi|157161704|ref|YP_001459022.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           HS]
 gi|170081840|ref|YP_001731160.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator and sigma 54 interaction
           protein [Escherichia coli str. K-12 substr. DH10B]
 gi|188494177|ref|ZP_03001447.1| sigma-54 dependent response regulator AtoC [Escherichia coli 53638]
 gi|238901395|ref|YP_002927191.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator/sigma54 interaction
           protein [Escherichia coli BW2952]
 gi|253772856|ref|YP_003035687.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162232|ref|YP_003045340.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli B
           str. REL606]
 gi|256022097|ref|ZP_05435962.1| acetoacetate metabolism regulatory protein AtoC [Escherichia sp.
           4_1_40B]
 gi|300903602|ref|ZP_07121520.1| response regulator receiver domain protein [Escherichia coli MS
           84-1]
 gi|300931434|ref|ZP_07146763.1| response regulator receiver domain protein [Escherichia coli MS
           187-1]
 gi|300948915|ref|ZP_07162977.1| response regulator receiver domain protein [Escherichia coli MS
           116-1]
 gi|300958905|ref|ZP_07171009.1| response regulator receiver domain protein [Escherichia coli MS
           175-1]
 gi|301024238|ref|ZP_07187933.1| response regulator receiver domain protein [Escherichia coli MS
           196-1]
 gi|301306547|ref|ZP_07212610.1| response regulator receiver domain protein [Escherichia coli MS
           124-1]
 gi|301647689|ref|ZP_07247483.1| response regulator receiver domain protein [Escherichia coli MS
           146-1]
 gi|307138879|ref|ZP_07498235.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           H736]
 gi|312973526|ref|ZP_07787698.1| acetoacetate metabolism regulatory protein atoC [Escherichia coli
           1827-70]
 gi|331642850|ref|ZP_08343985.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli H736]
 gi|1168553|sp|Q06065|ATOC_ECOLI RecName: Full=Acetoacetate metabolism regulatory protein AtoC;
           AltName: Full=Ornithine decarboxylase antizyme; AltName:
           Full=Ornithine/arginine decarboxylase inhibitor
 gi|619917|gb|AAA60332.1| NtrC/NifA-like protein regulator [Escherichia coli]
 gi|1736875|dbj|BAA16016.1| fused response regulator of ato opeon, in two-component system with
           AtoS [Escherichia coli str. K12 substr. W3110]
 gi|1788550|gb|AAC75280.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator/sigma54 interaction
           protein [Escherichia coli str. K-12 substr. MG1655]
 gi|157067384|gb|ABV06639.1| sigma-54 dependent response regulator AtoC [Escherichia coli HS]
 gi|169889675|gb|ACB03382.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator and sigma 54 interaction
           protein [Escherichia coli str. K-12 substr. DH10B]
 gi|188489376|gb|EDU64479.1| sigma-54 dependent response regulator AtoC [Escherichia coli 53638]
 gi|238861249|gb|ACR63247.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator/sigma54 interaction
           protein [Escherichia coli BW2952]
 gi|242377856|emb|CAQ32623.1| AtoC transcriptional activator; Az protein inhibitor of ODC
           [Escherichia coli BL21(DE3)]
 gi|253323900|gb|ACT28502.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253974133|gb|ACT39804.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator/sigma54 interaction
           protein [Escherichia coli B str. REL606]
 gi|253978300|gb|ACT43970.1| fused response regulator of ato operon, in two-component system
           with AtoS: response regulator/sigma54 interaction
           protein [Escherichia coli BL21(DE3)]
 gi|260448686|gb|ACX39108.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli DH1]
 gi|299880501|gb|EFI88712.1| response regulator receiver domain protein [Escherichia coli MS
           196-1]
 gi|300314468|gb|EFJ64252.1| response regulator receiver domain protein [Escherichia coli MS
           175-1]
 gi|300404338|gb|EFJ87876.1| response regulator receiver domain protein [Escherichia coli MS
           84-1]
 gi|300451611|gb|EFK15231.1| response regulator receiver domain protein [Escherichia coli MS
           116-1]
 gi|300460804|gb|EFK24297.1| response regulator receiver domain protein [Escherichia coli MS
           187-1]
 gi|300838207|gb|EFK65967.1| response regulator receiver domain protein [Escherichia coli MS
           124-1]
 gi|301074219|gb|EFK89025.1| response regulator receiver domain protein [Escherichia coli MS
           146-1]
 gi|309702531|emb|CBJ01858.1| acetoacetate metabolism regulator (two-component system response
           regulator) [Escherichia coli ETEC H10407]
 gi|310332121|gb|EFP99356.1| acetoacetate metabolism regulatory protein atoC [Escherichia coli
           1827-70]
 gi|315136852|dbj|BAJ44011.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           DH1]
 gi|315255155|gb|EFU35123.1| response regulator receiver domain protein [Escherichia coli MS
           85-1]
 gi|315615482|gb|EFU96114.1| acetoacetate metabolism regulatory protein atoC [Escherichia coli
           3431]
 gi|320199815|gb|EFW74404.1| Acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           EC4100B]
 gi|323936835|gb|EGB33120.1| sigma-54 interaction domain-containing protein [Escherichia coli
           E1520]
 gi|323941085|gb|EGB37272.1| sigma-54 interaction domain-containing protein [Escherichia coli
           E482]
 gi|323961526|gb|EGB57134.1| sigma-54 interaction domain-containing protein [Escherichia coli
           H489]
 gi|323973079|gb|EGB68273.1| sigma-54 interaction domain-containing protein [Escherichia coli
           TA007]
 gi|331039648|gb|EGI11868.1| acetoacetate metabolism regulatory protein AtoC
           (Ornithine/argininedecarboxylase inhibitor) (Ornithine
           decarboxylase antizyme) [Escherichia coli H736]
          Length = 461

 Score =  163 bits (413), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 132/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEVKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|260598095|ref|YP_003210666.1| DNA-binding transcriptional regulator TyrR [Cronobacter turicensis
           z3032]
 gi|260217272|emb|CBA31212.1| Transcriptional regulatory protein tyrR [Cronobacter turicensis
           z3032]
          Length = 520

 Score =  163 bits (413), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 102/344 (29%), Positives = 168/344 (48%), Gaps = 36/344 (10%)

Query: 138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV 197
           A   +IAVSP M QVVD ARK      P++I G+ G GK  L+   H +  RA  P+  +
Sbjct: 202 AFSHIIAVSPRMKQVVDQARKLAMLNAPLLITGDTGTGKDLLAHACHLASPRADKPYLAL 261

Query: 198 NCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE-ANGGTIVLEEPDALPLAVQGRIYNF 256
           NC  I +D +E  LFG       N+ +    F E ANGG+++L+E   +   +Q ++  F
Sbjct: 262 NCASIPEDVVESELFGHAPGAYANAHEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRF 321

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           +  G          + +DVR+I  T+KNL+  V+   FR+DLYYR++V  +N+  LR R 
Sbjct: 322 LNDGTFRRVGEEHEVHVDVRVICATQKNLVELVQKGAFREDLYYRLNVLTLNLPPLRDRP 381

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           +DI  L   F+  F  +  + +  ++     +L +Y W  NV++LKN + RA+  L+   
Sbjct: 382 QDIMPLTEMFVARFADEQGVPRPKLASDLGQVLIRYGWPGNVRQLKNAVYRALTQLEGYE 441

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
           L                               +  D +L +    ++P +G++     L 
Sbjct: 442 L-------------------------------RPQDILLPDFDAAALP-VGEEAMEGSLD 469

Query: 437 DIEKEI-IGLAMKLYRAQMS--EVARRLGIGRSTLYRKIREYNI 477
           DI +     +  +LYR+  S  ++A+RLG+  + +  K+REY +
Sbjct: 470 DITRRFERSVLTQLYRSYPSTRKLAKRLGVSHTAIANKLREYGL 513


>gi|323188052|gb|EFZ73347.1| acetoacetate metabolism regulatory protein atoC [Escherichia coli
           RN587/1]
          Length = 461

 Score =  163 bits (413), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 131/483 (27%), Positives = 224/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SP M+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPTMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKKGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|215487439|ref|YP_002329870.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           O127:H6 str. E2348/69]
 gi|215265511|emb|CAS09913.1| fused response regulator of ato operon, in two-component system
           with AtoS [Escherichia coli O127:H6 str. E2348/69]
          Length = 461

 Score =  163 bits (413), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 131/483 (27%), Positives = 224/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SP M+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPTMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K++    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEAKTAPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|146307849|ref|YP_001188314.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Pseudomonas mendocina ymp]
 gi|145576050|gb|ABP85582.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Pseudomonas mendocina ymp]
          Length = 470

 Score =  163 bits (413), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 130/489 (26%), Positives = 239/489 (48%), Gaps = 46/489 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNV-IFLSLINCED-DKEN 69
           +VL+++ D    + + D +   G+D   V+ ++ + ++  +    + +S +N    D   
Sbjct: 4   KVLLVEDDRALREALADTLCLGGHDYRAVDCAEAALVALTEEPFGLVVSDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF-----LNLVSRKQLCDSI 120
           +L  I  + P +P+++ T     +  +  +     + + K F     L LV+R  L    
Sbjct: 64  LLAQIRARYPQLPVLLMTAFGAVERAVDAIRQGAADYLVKPFEPRTLLELVARHAL---- 119

Query: 121 ICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
                 G +P+ +      D  +A+ PA +Q+++LA +       +MI GE G GK+ L+
Sbjct: 120 ------GKLPAGDR-----DGPVALEPASVQLLELAARVAQSDSTVMITGESGTGKEVLA 168

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVL 239
           R+IH+   R+  PF  +NC  I  + +E  LFG +    T       GKF  A+GGTI+L
Sbjct: 169 RYIHQQSPRSSRPFIAINCAAIPDNMLEATLFGHEKGAFTGAVTSQPGKFELADGGTILL 228

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +PL +Q ++   ++  ++E   +R  I LD+R++  + ++L  +V +  FR+DLY
Sbjct: 229 DEISEMPLGLQAKLLRVLQEREVERVGARKPITLDIRVLATSNRDLASEVAAGRFREDLY 288

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+SVF +    LR R  DI  L    L     K     + +S+ A   L ++PW  NV+
Sbjct: 289 YRLSVFPLAWRPLRERPADILPLAERLLAKHVKKMNQAPVRLSESAAQSLVQHPWPGNVR 348

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS 419
           EL N + RA+I L+   + + + + L +  G+  +      A         S  +   ++
Sbjct: 349 ELDNAIQRALI-LQQGGVIQAQDLCLHAPIGQSVQGTAPRLAVV------PSAPVAPPVA 401

Query: 420 QESI----PAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI--- 472
           +E++     A+G+D  +RR    E ++I   ++  R +  E A RLGI   TL  K+   
Sbjct: 402 EEAMVADGGALGED--LRRR---EFQVIIDTLRAERGRRKEAAERLGISPRTLRYKLAQM 456

Query: 473 REYNIEVDS 481
           R+  ++V++
Sbjct: 457 RDAGMDVEA 465


>gi|222085891|ref|YP_002544422.1| nitrogen regulation protein [Agrobacterium radiobacter K84]
 gi|221723339|gb|ACM26495.1| nitrogen regulation protein [Agrobacterium radiobacter K84]
          Length = 483

 Score =  163 bits (412), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 143/496 (28%), Positives = 230/496 (46%), Gaps = 53/496 (10%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   +S  + +++   ++  +++  ++
Sbjct: 5   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWVSAGEGDLVVTDVVMPDENAFDL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 65  LPRIKKARPELPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIAIIGRALSE 120

Query: 127 GVVPSQENEHCALD-----SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
              P ++      D      L+  S AM ++  +  +     + +MI GE G GK+ ++R
Sbjct: 121 ---PKRKPAKLDDDMQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVAR 177

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGT 236
            +H+ GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT
Sbjct: 178 ALHDYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGT 233

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+
Sbjct: 234 LFLDEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRTDVRIVAATNKDLKQAINQGLFRE 293

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLV-HFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           DLYYR++V  + +  LR R+EDIP LV HF  Q    K  +       +AL L+  YPW 
Sbjct: 294 DLYYRLNVVPLRLPPLRDRAEDIPDLVRHFITQ--AEKEGLGSKRFDQEALELMKAYPWP 351

Query: 356 DNVQELKNILLRAVIGLK----------DSHLTEDRFVLLLSREGKKEREFHTETACTCY 405
            NV+EL+N L+R ++ L           DS L  D   +  S   K      T T     
Sbjct: 352 GNVRELEN-LIRRLMALYPQDVITREIIDSELRAD---VPDSPIEKGPVRTGTMTIAQAV 407

Query: 406 TEGKSS--DTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGI 463
            E   S   +  DNL    +         R L+++E  +I  A+   R    + A  LG+
Sbjct: 408 EENMRSYFSSFGDNLPPPGL-------YDRVLTEMEYPLILAALTATRGNQIKAADLLGL 460

Query: 464 GRSTLYRKIREYNIEV 479
            R+TL +KIRE  + V
Sbjct: 461 NRNTLRKKIRELGVSV 476


>gi|222055651|ref|YP_002538013.1| Fis family transcriptional regulator [Geobacter sp. FRC-32]
 gi|221564940|gb|ACM20912.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter sp. FRC-32]
          Length = 452

 Score =  163 bits (412), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 128/480 (26%), Positives = 230/480 (47%), Gaps = 51/480 (10%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           ++L+ID D+   ++++ +++  GY+V   +  +  L    + Q +++   +     D   
Sbjct: 4   KILVIDDDNSLRRVLEYNLKEEGYEVQAASSGEEGLFLFGQSQPDLVITDMKMSGMDGLM 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           +LK+I ++ P   +I+ T    + I    +    Y+ I+K F    +R +L   ++ AL+
Sbjct: 64  VLKSIKERSPETLVIIITAFGTVNIAVEAMKAGAYDYITKPF----NRDELKLIVLKALQ 119

Query: 126 -EGV------VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKR 178
             G+      + SQ ++     ++I  S  M +V D+ RK  D    I+I GE G GK+ 
Sbjct: 120 FNGLAEENKRLKSQLSDKTDFRTIIGTSKEMEKVFDVIRKVADTEAAILITGESGTGKEL 179

Query: 179 LSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTI 237
           ++R IH +  R   PF  +NC  I +D +E  LFG V    T       GKF  A+GGT+
Sbjct: 180 VARSIHANSSRREAPFIAINCAAIPRDLLESELFGHVKGAFTGALRDKTGKFQLADGGTL 239

Query: 238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD 297
            L+E   LPL +Q ++   ++  ++E        ++DVR++  T  N+   + +  FR+D
Sbjct: 240 FLDEVGELPLELQPKLLRALQEKEVEPVGGTKVQKIDVRVVSATNVNIDKAIANGSFRED 299

Query: 298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN 357
           LYYR++V  +++ +LR R +DIP L+ +    FC K+  + +++ + AL  L  + W  N
Sbjct: 300 LYYRLAVIPVHLPSLRERRKDIPLLIKY----FCGKHGSENVTLENSALETLVMHSWPGN 355

Query: 358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDN 417
           V+EL+N + R                LL+ R G        +       E ++  T +  
Sbjct: 356 VRELENTIER----------------LLIMRNGDM---ISVDDLPDKLREKRAQGTAVIK 396

Query: 418 LSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
           L  E  P          L  +E+E++  A++      +  AR L I R TL  ++ +Y I
Sbjct: 397 LPDEGYP----------LEQLEREVVVAALERSSWNQTAAARFLRIPRHTLIYRMEKYGI 446


>gi|258404306|ref|YP_003197048.1| PAS modulated sigma54 specific transcriptional regulator, Fis
           family [Desulfohalobium retbaense DSM 5692]
 gi|257796533|gb|ACV67470.1| PAS modulated sigma54 specific transcriptional regulator, Fis
           family [Desulfohalobium retbaense DSM 5692]
          Length = 462

 Score =  163 bits (412), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 103/344 (29%), Positives = 168/344 (48%), Gaps = 34/344 (9%)

Query: 141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG 200
            ++  +PAM  +  L  K      P+M++GE G GK+  +R +HE   R   PF  +NC 
Sbjct: 146 GMVGTAPAMRHLFSLLEKVAQSEAPVMVRGESGTGKELAARAVHECSPRREGPFIQLNCA 205

Query: 201 MIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
            +++  +E  LFG V    T       G+F  A GGT+ L+E   +PL+VQ ++   +ET
Sbjct: 206 ALNEALLESELFGHVKGAFTGAYRARPGRFEVATGGTLFLDEVGDIPLSVQAKLLRVLET 265

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
            +IE       I +DVR++  T ++L   V    FR+DLYYRI+   + +  LR R EDI
Sbjct: 266 KQIERVGDHRPIEVDVRIVSATNRDLDRLVAEGEFREDLYYRINALPVAMPALRERPEDI 325

Query: 320 PWLVHFFLQSFCTKNAIKQIS-ISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLT 378
           PWL   FL     +N+ K ++ ++ +AL  +  YPW  NV+ELK+ L             
Sbjct: 326 PWLASHFL-GLVRQNSGKALTGLTPEALRSVVAYPWPGNVRELKSAL------------- 371

Query: 379 EDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDI 438
              +  +L+  G+ +            TE         N S +  PA    GE    +D 
Sbjct: 372 --EYASVLAETGRLK------------TEHLPPHITAANPSAQ--PAASHSGE--ETADA 413

Query: 439 EKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVDSL 482
           +++ +  A++      S  A+ LG+ R T+Y ++R+Y + V ++
Sbjct: 414 QRQALIEALRQSGGNQSRAAQLLGVSRVTVYNRMRKYGLTVQTV 457


>gi|134287852|ref|YP_001110017.1| sigma-54 dependent trancsriptional regulator [Burkholderia
           vietnamiensis G4]
 gi|134132502|gb|ABO60485.1| sigma54 specific transcriptional regulator, Fis family
           [Burkholderia vietnamiensis G4]
          Length = 611

 Score =  163 bits (412), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 117/381 (30%), Positives = 184/381 (48%), Gaps = 43/381 (11%)

Query: 127 GVVPSQENEH----CALDSL------IAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGK 176
           G  P+   +H    C LD +      I  S     V+    +    +  +++ GE GVGK
Sbjct: 237 GPAPTDSTDHECVPCKLDEVPVKEGPIGASAGFNAVMHKIFRVAPTSATVLLMGESGVGK 296

Query: 177 KRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGG 235
              +R +H    R   PF  +NC  I    IE  LFG +    T  S   +G+F  AN G
Sbjct: 297 SLFARELHNRSSRVGKPFVELNCAAIPDSLIESELFGAERGAFTGASDARVGRFESANEG 356

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           TI L+E   L L  Q ++   ++TG++E   S   ++++VR+I  T  NL   +KS  FR
Sbjct: 357 TIFLDEIGTLSLTAQAKLLRVLQTGEMERLGSSKTVKVNVRVITATNDNLKQAIKSGRFR 416

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++VF I I  LR R +DIP L+ FF++ F  ++      +S++AL LL  Y W 
Sbjct: 417 EDLFYRLNVFPIFIPPLRERKDDIPVLLEFFIKKFSRRHGRPLKGLSNRALHLLLDYSWP 476

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD--- 412
            N++E++N+L R VI L ++  T D   L           F ++    C      SD   
Sbjct: 477 GNIREMENVLERGVI-LAEAGGTLDVCHL-----------FSSDDTVECKGAFGLSDLGS 524

Query: 413 TILDNLSQESIP-AIGQDGEVRR----------------LSDIEKEIIGLAMKLYRAQMS 455
            +LD++S  + P  IG+ GE                   L ++E  ++  A+K     +S
Sbjct: 525 LVLDSISTSAPPETIGKSGEGPEGLEDWAALAVQMNKATLREVEDALVRAALKAANGNIS 584

Query: 456 EVARRLGIGRSTLYRKIREYN 476
           E AR LG+ R+ L  ++++ N
Sbjct: 585 EAARLLGLTRAQLDYRVKKSN 605


>gi|258514266|ref|YP_003190488.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfotomaculum acetoxidans DSM 771]
 gi|257777971|gb|ACV61865.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfotomaculum acetoxidans DSM 771]
          Length = 442

 Score =  163 bits (412), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 128/469 (27%), Positives = 223/469 (47%), Gaps = 38/469 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKENIL 71
           ++LIID D    + ++  ++  GY   I+  ++   +S +   + +L  +  E D  + L
Sbjct: 5   KILIIDNDISSCRTMERAIQQEGYQA-IIATNEPDAVSLLIKEMFYLVFLGLETDNNDPL 63

Query: 72  KNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCD--SIICALREGVV 129
            NI    P VPII+   Q  I+     L      +    V+ ++L +    + A  +  +
Sbjct: 64  INIKSFSPSVPIIMLAHQGTIEKAIDALKKGAMDYMTKPVNPEKLKNILKTLSASHKNKL 123

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
            S ++     + ++  +PA+I++  L  K       ++I GE G GK+  +  IH + +R
Sbjct: 124 SSTQD----YNYILGETPAIIEINRLIEKVAATNATVLITGESGTGKEVAAMSIHRASQR 179

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
              PF  VNC  + +  +E  LFG +    T    +  G+F  A+ GT+ L+E   +PL 
Sbjct: 180 CNNPFVTVNCVALPEQLLESELFGHEKGAFTGAFTKRQGRFELAHTGTVFLDEIGDMPLT 239

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++    E       + +DVR+I  T KNL   V + +FR+DLYYR++V  I+
Sbjct: 240 MQAKLLRILQEKSFERVGGTETLNIDVRVIAATNKNLSDAVMNGMFREDLYYRLNVIHIH 299

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
           +  LR R EDIP LV  FL         K+  +S +A+ LL  Y W  N++E++NI+ RA
Sbjct: 300 LPPLRERKEDIPLLVSHFLDKLSHTYQAKK--VSGEAMRLLYNYCWPGNIREMQNIIERA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           VI      +++D  +L +        E    +A T                    P I  
Sbjct: 358 VI------ISQDLEILPVHLPP----ELQKSSAATVE------------------PIIRL 389

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
             E   L ++EK++I +A++  +   ++ A+ LGI RS L  + ++Y I
Sbjct: 390 PDEGISLVEVEKQLIIMALQKSKGNQTKAAQLLGITRSALLYRTQKYGI 438


>gi|147678773|ref|YP_001212988.1| transcriptional regulator [Pelotomaculum thermopropionicum SI]
 gi|146274870|dbj|BAF60619.1| transcriptional regulator [Pelotomaculum thermopropionicum SI]
          Length = 485

 Score =  163 bits (412), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 117/385 (30%), Positives = 183/385 (47%), Gaps = 30/385 (7%)

Query: 108 LNLVSRKQLCDSIICALREG---------VVPSQENEHCALDSLIAVSPAMIQVVDLARK 158
           +N    KQL D++   L++G         V+    + +   ++ +A SP M +++     
Sbjct: 119 INTALDKQLYDNLKMTLKDGKATNETFKKVIDYLSDANIPYETPVAESPQMREIIKNIDT 178

Query: 159 AGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD-- 216
                  I+I GE G GK+ ++R+IH+   +A  PF  +NC  I  + +E   FG V   
Sbjct: 179 IAKTHSTILITGESGTGKEVIARYIHKHSLQAEGPFIPINCASIPHELLESEFFGYVGGA 238

Query: 217 LQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR 276
               N     G F  AN GT+ L+E   LPL +Q ++   +E+G+I+       IR +VR
Sbjct: 239 FTGANPQGKPGLFEIANNGTLFLDEIAELPLTMQPKLLRVLESGEIKRVGGTDIIRTNVR 298

Query: 277 LIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAI 336
           LI  T K+L   V+ ++FR DLYYR++V  INI  LR R EDI  L   FL+    K  +
Sbjct: 299 LIAATNKDLKTMVRQNLFRNDLYYRLNVLPINIPPLRERPEDIVALSKRFLEYINKKYNL 358

Query: 337 KQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREF 396
           K+   +++A++    Y W  NV+EL+N++ R  I   D ++      LLL  +G    E 
Sbjct: 359 KK-RFTEQAINAFLNYSWPGNVRELRNVVERLAITSPDDNIGNINIHLLL--DGNSLEES 415

Query: 397 HTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSE 456
           +  T      E K     L +                 L  +E E I   + +   ++ E
Sbjct: 416 NITTGTYLPHENKIYQGTLKSF----------------LKKVEAEYIKQVLDICNGKVGE 459

Query: 457 VARRLGIGRSTLYRKIREYNIEVDS 481
            A+ LGI R+ LYRKI+     +DS
Sbjct: 460 AAKLLGIHRTMLYRKIKNNTKAIDS 484


>gi|218705751|ref|YP_002413270.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           UMN026]
 gi|293405687|ref|ZP_06649679.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           FVEC1412]
 gi|298381369|ref|ZP_06990968.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           FVEC1302]
 gi|300897713|ref|ZP_07116110.1| response regulator receiver domain protein [Escherichia coli MS
           198-1]
 gi|218432848|emb|CAR13742.1| fused response regulator of ato opeon, in two-component system with
           AtoS: response regulator ; sigma54 interaction protein
           [Escherichia coli UMN026]
 gi|291427895|gb|EFF00922.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           FVEC1412]
 gi|298278811|gb|EFI20325.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           FVEC1302]
 gi|300358553|gb|EFJ74423.1| response regulator receiver domain protein [Escherichia coli MS
           198-1]
          Length = 461

 Score =  163 bits (412), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 133/483 (27%), Positives = 225/483 (46%), Gaps = 47/483 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL--GKFIEANGG 235
            ++R IH + +RA  PF  VNC  + +  +E  LFG  +      AQ L  G F  AN G
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH-EKGAFTGAQTLRQGLFERANEG 239

Query: 236 TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFR 295
           T++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR
Sbjct: 240 TLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFR 299

Query: 296 KDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI 355
           +DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W 
Sbjct: 300 EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWP 359

Query: 356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTIL 415
            N++EL N++ RAV+         +   ++ S +   +     +  C    E K+S    
Sbjct: 360 GNIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEVKTSPVGE 407

Query: 416 DNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
            NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY
Sbjct: 408 RNLKEE-------------IKRVEKCIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454

Query: 476 NIE 478
            I+
Sbjct: 455 GID 457


>gi|104779399|ref|YP_605897.1| alginate biosynthesis response regulator AlgB [Pseudomonas
           entomophila L48]
 gi|95108386|emb|CAK13080.1| alginate biosynthesis response regulator AlgB [Pseudomonas
           entomophila L48]
          Length = 448

 Score =  163 bits (412), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 139/481 (28%), Positives = 221/481 (45%), Gaps = 49/481 (10%)

Query: 8   DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVN-VSDLSTISKIQV-NVIFLSLINCED 65
           D   R+L++D +   ++  +  +E  GY V   N  +   T+ + QV ++ FL L   ED
Sbjct: 6   DNQGRILLVDDESAILRTFRYCLEDEGYSVATANSAAQAETLLQRQVFDLCFLDLRLGED 65

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKIL--------NCFLYNRISKFFLNLVSRKQLC 117
           +  ++L  +  + P + +++ T    I             +L    S   L L + KQL 
Sbjct: 66  NGLDVLAQMRIQAPWMRVVIVTAHSAIDTAVDAIQAGAADYLVKPCSPDQLRLATAKQLE 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              + A  E +          LDS    SPAM+ V++ AR+       I+I GE G GK 
Sbjct: 126 VRQLSARLEALEGEVRKPKDGLDSH---SPAMMAVLETARQVATTDANILILGESGTGKG 182

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGT 236
            L+R IH   KRA      +NC  ++ + +E  LFG      T  S   LG+  +A+GGT
Sbjct: 183 ELARAIHGWSKRARKACVTINCPSLNAELMESELFGHTRGAFTGASESTLGRVSQADGGT 242

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E    PL +Q ++  FI+  + E        R DVR++  T  NL   V+ + FR+
Sbjct: 243 LFLDEIGDFPLTLQPKLLRFIQDKEYERVGDPVTRRADVRILAATNLNLEEMVRENRFRE 302

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DL YR++V  +++  LR RSEDI  L   FL  F  + +    + SD+A + L  Y W  
Sbjct: 303 DLLYRLNVITLHLPPLRERSEDILTLADRFLARFVKEYSRPAKAFSDEARAALLNYRWPG 362

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           N++EL+N++ RA I                     +ER    E +     E  + +T   
Sbjct: 363 NIRELRNVVERASIIC------------------PQER---VEISHLGMGEQPAGNT--- 398

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
                  P +G       L ++E+  IG A+      + + A+ LGI  STLYRK ++YN
Sbjct: 399 -------PRVGA---ALSLEELERAHIG-AVLATSDTLDQAAKTLGIDASTLYRKRKQYN 447

Query: 477 I 477
           +
Sbjct: 448 L 448


>gi|77457761|ref|YP_347266.1| two component, sigma-54 specific, Fis family transcriptional
           regulator [Pseudomonas fluorescens Pf0-1]
 gi|12056608|gb|AAG47966.1|AF312695_6 FleR [Pseudomonas fluorescens]
 gi|77381764|gb|ABA73277.1| two-component response regulator [Pseudomonas fluorescens Pf0-1]
          Length = 463

 Score =  163 bits (412), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 103/362 (28%), Positives = 178/362 (49%), Gaps = 9/362 (2%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           +VL+++ D    + + D +   G+D   V  ++  L+ + +   +++   +     D   
Sbjct: 4   KVLLVEDDRSLREALADTLLLAGHDYHAVGSAEEALNAVEREAFSLVVSDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    ++     +    + + +     K L D +       +V
Sbjct: 64  LLGLLRARQPQLPVLLMTAHGAVERAVDAMRQGAADYLVKPFEPKALLDLVARHALGSLV 123

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
            S        +  +AV PA  Q++DLA +       ++I GE G GK+ L+R+IH+   R
Sbjct: 124 ASDA------EGPVAVEPASAQLLDLAARVARSDSTVLISGESGTGKEVLARYIHQQSHR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL 
Sbjct: 178 ASQPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DLYYR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPITLDIRVVATTNRDLAGEVAAGRFREDLYYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R+ DI  L    L     K        S +A + L  YPW  NV+EL N + RA
Sbjct: 298 WRPLRERTADILPLAERLLAKHVNKMKHAMAKFSSEAQACLIGYPWPGNVRELDNAVQRA 357

Query: 369 VI 370
           +I
Sbjct: 358 LI 359


>gi|329942475|ref|ZP_08291285.1| response regulator [Chlamydophila psittaci Cal10]
 gi|332287112|ref|YP_004422013.1| putative sigma-54 dependent response regulator [Chlamydophila
           psittaci 6BC]
 gi|313847707|emb|CBY16697.1| putative sigma-54 dependent response regulator [Chlamydophila
           psittaci RD1]
 gi|325506544|gb|ADZ18182.1| putative sigma-54 dependent response regulator [Chlamydophila
           psittaci 6BC]
 gi|328815385|gb|EGF85373.1| response regulator [Chlamydophila psittaci Cal10]
 gi|328914351|gb|AEB55184.1| sigma-54 dependent response regulator [Chlamydophila psittaci 6BC]
          Length = 386

 Score =  163 bits (412), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 119/386 (30%), Positives = 191/386 (49%), Gaps = 16/386 (4%)

Query: 11  KRVLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDLSTISKIQVNVIFLSLINCEDDKE- 68
           ++VLI+D +      + + + + G   F   NV       K +   + +S +N  D    
Sbjct: 4   EKVLIVDDEPLLRDFLSELLLTRGLSPFTADNVKQGCHKIKTEKYDLIISDMNMPDGTGI 63

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-EG 127
           +I+K   +  P  P++V T    I+     +Y+    +     S + L   I  A   + 
Sbjct: 64  DIIKTAKECAPHTPVLVITAYGTIENAVKAMYHGAFNYLTKPFSSEALFAFIAKAEELQN 123

Query: 128 VVPSQENEHCALDS--------LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
           +V    NE+  L S        LIA SPAM  ++  ARKA D +  I I GE G GK+ L
Sbjct: 124 LV----NENLLLKSQISSESHPLIAESPAMKDLLSKARKAADSSANIFIHGESGCGKEVL 179

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIV 238
           S FIH +  RA  P+  VNC  I +  +E   FG +    T  + +  G+F  A+ GT++
Sbjct: 180 SFFIHRNSPRAARPYIKVNCAAIPETLLESEFFGHEKGAFTGATGKKAGRFELAHTGTLL 239

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E   +P+ +Q ++   I+  + E       + +DVR++  + +NL   V   +FR+DL
Sbjct: 240 LDEITEVPINLQAKLLRAIQEKEFEHLGGTKTLSVDVRILATSNRNLKEAVDQKIFRQDL 299

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           +YR++V  + +  LR R +DI  L  +FL+ FC  N     ++S+ A S L  YPW  N+
Sbjct: 300 FYRLNVIPLYLPPLRERKDDILPLSQYFLEKFCRLNNKPMKTLSESAKSALLDYPWPGNI 359

Query: 359 QELKNILLRAVIGLKDSHLTEDRFVL 384
           +EL N+L RAVI    +HLT+    L
Sbjct: 360 RELSNVLERAVILESPTHLTDAMLAL 385


>gi|86140887|ref|ZP_01059446.1| sigma-54 dependent DNA-binding response regulator [Leeuwenhoekiella
           blandensis MED217]
 gi|85832829|gb|EAQ51278.1| sigma-54 dependent DNA-binding response regulator [Leeuwenhoekiella
           blandensis MED217]
          Length = 440

 Score =  163 bits (412), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 113/372 (30%), Positives = 192/372 (51%), Gaps = 14/372 (3%)

Query: 9   RHKRVLIIDKDDEQIKIIKDHVESYGYDVF-IVNVSDLSTISK-IQVNVIFLSLINCEDD 66
           R + +LI+D D   +++++ H+ S+ Y  +  V+V +   I K   ++++   L   + D
Sbjct: 4   RKENILIVDDDLHILELLQRHLHSWNYHTYRAVSVKEAVAILKDTHIDLLITDLKMPQID 63

Query: 67  KENILKNIVDKIPIVPIIVQT----TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIIC 122
              ++K + +  P +P +V T     QD++K +   +   ++K F     +  +  ++  
Sbjct: 64  GFELIKFVSEHYPDLPKLVVTGFPSVQDSLKAIKSGVVEYLTKPFTKGELQAAVAKALPK 123

Query: 123 ALREGV---VPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRL 179
           A +E V   VP  +++      +I  S  + +V+ +  +  D    I I GE G GK+ +
Sbjct: 124 ASKEPVKNTVPKSKHQ----GEIIGASEKIEEVLQIIDRVKDNKATIFINGESGTGKELV 179

Query: 180 SRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIV 238
           +R IH  GK +  PF  VNCG I ++ +E  LFG      T       G F  A GGTI 
Sbjct: 180 ARAIHYEGKFSSAPFIPVNCGGIPENLLEAELFGYTKGAFTGADKDRKGAFQAAQGGTIF 239

Query: 239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL 298
           L+E     LAVQ R+   ++  ++    ++   ++DVR+I  T  NL   +K   FR+DL
Sbjct: 240 LDEIGNASLAVQARLLRVLQEKEVVRVGAQKPEKIDVRVIAATNNNLPEMIKKQTFREDL 299

Query: 299 YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV 358
           YYR+SV  I +  LR+R  DIP LV  FL  +  +   + + I  +AL +L +Y W  N+
Sbjct: 300 YYRLSVVEIPLPALRARMSDIPLLVDKFLFKYGVEYKDRFVRIDPEALEVLKRYSWPGNI 359

Query: 359 QELKNILLRAVI 370
           +EL+N++ RAVI
Sbjct: 360 RELENVIQRAVI 371


>gi|238794559|ref|ZP_04638167.1| Nitrogen regulation protein NR(I) [Yersinia intermedia ATCC 29909]
 gi|238726139|gb|EEQ17685.1| Nitrogen regulation protein NR(I) [Yersinia intermedia ATCC 29909]
          Length = 470

 Score =  163 bits (412), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 122/478 (25%), Positives = 225/478 (47%), Gaps = 25/478 (5%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENI 70
           V I+D D     +++  +   G +    +  +  L  ++    +V+   +     D   +
Sbjct: 6   VWIVDDDSSIRWVLERALTGAGLNCATFDTGNQVLDALATQTPDVLLSDIRMPGMDGLAL 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           LK I  + P++P+I+ T   +    +       ++ + K F ++     L D  I   +E
Sbjct: 66  LKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPF-DIDEAVALVDRAISHYQE 124

Query: 127 GVVPSQENEHCALDS-LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
              P++        + +I  +PAM  V  +  +    +I ++I GE G GK+ ++  +H 
Sbjct: 125 QQQPARSQPASGPTADIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHR 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF-LGKFIEANGGTIVLEEPDA 244
              RA  PF  +N   I +D IE  LFG        + Q   G+F +A+GGT+ L+E   
Sbjct: 185 HSPRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANQVRQGRFEQADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +PL VQ R+   +  G+         +++DVR+I  T +NL  +V+   FR+DL++R++V
Sbjct: 245 MPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLELRVQEGKFREDLFHRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             +++  LR R EDIP L  +FLQ    +  ++  ++  +    LT+ PW  NV++L+N 
Sbjct: 305 IRVHLPPLRERREDIPRLARYFLQVAAKELGVEAKNLHPETEVALTRLPWQGNVRQLENT 364

Query: 365 L-LRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD---TILDNLSQ 420
                V+      LT+D    L             ET+    +  ++ D   T+L   ++
Sbjct: 365 CRWLTVMAAGQEVLTQDLPSELF------------ETSTPDASGQRTPDNWATLLAQWAE 412

Query: 421 ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
            ++ +  QD       ++E+ ++  A++  +    E AR LG GR+TL RK++E  +E
Sbjct: 413 RALRSGHQDLLSEAQPEMERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLKELGME 470


>gi|158521660|ref|YP_001529530.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Desulfococcus oleovorans Hxd3]
 gi|158510486|gb|ABW67453.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfococcus oleovorans Hxd3]
          Length = 479

 Score =  162 bits (411), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 119/379 (31%), Positives = 186/379 (49%), Gaps = 27/379 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVF--IVNVSDLSTISKIQVNVIFLSL----INCEDD 66
           +LIID D+  +  ++   +  GYDV   +     L+ I K   ++I L      IN  D 
Sbjct: 4   ILIIDDDEGLVHFLRRFFQRKGYDVTACLTGREALAAIPKQSFDLILLDYKMPDINGLDM 63

Query: 67  KENILKNIVDKIPIVPIIVQTTQD-NIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL- 124
              I + I  K P++ +    T D  I+ +    Y+ ++K F     RK L   +  AL 
Sbjct: 64  LAEI-RRIEIKTPVILMTAYGTTDLAIETMKLGAYDYLTKPF----DRKDLSRIVTEALA 118

Query: 125 ---------REGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCA---IPIMIQGEF 172
                    R G  P    E     S+  V     Q+ ++ ++ G  A   +P++I GE 
Sbjct: 119 VNRQMKERVRIGTGPFTAAEAVDSRSIRMVGHGK-QMQEIFKRIGQVAANDVPVLITGES 177

Query: 173 GVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIE 231
           G GK+ ++R ++    R   PF  VNC  I  +  E  LFG +    T     ++GK   
Sbjct: 178 GTGKELVARALYHHSHRNDRPFIAVNCAAIPDNLFESELFGHERGAFTGADRTYIGKMER 237

Query: 232 ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKS 291
            + GT+ L+E   L   VQ ++   ++ G+IE     G I++DVR+I  T +NL  ++++
Sbjct: 238 CDHGTLFLDEISELAPGVQAKLLRALQEGEIERVGGSGPIKVDVRVIAATNRNLEQEIET 297

Query: 292 HVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTK 351
             FRKDLY+R+ V  I++  LR R EDIP L  +FL  FC +    Q  +S+ AL+ LT 
Sbjct: 298 GGFRKDLYWRLKVITIDLPPLRRRREDIPHLADYFLARFCAEYNRPQCYLSESALTKLTA 357

Query: 352 YPWIDNVQELKNILLRAVI 370
           Y W  NV+EL+N + RAV+
Sbjct: 358 YSWPGNVRELENCIRRAVL 376


>gi|163760107|ref|ZP_02167190.1| two component response regulator nitrogen regulation protein NR(I)
           [Hoeflea phototrophica DFL-43]
 gi|162282506|gb|EDQ32794.1| two component response regulator nitrogen regulation protein NR(I)
           [Hoeflea phototrophica DFL-43]
          Length = 483

 Score =  162 bits (411), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 133/488 (27%), Positives = 233/488 (47%), Gaps = 38/488 (7%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY+V I  N + L   +S  + +++   ++  +++  ++
Sbjct: 6   ILVADDDAAIRTVLNQALTRAGYEVRITSNAATLWRWVSAGEGDLVITDVVMPDENAFDM 65

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       ++  +I  AL E
Sbjct: 66  LPRIRRARPDLPVLVMSAQNTFMTAIKASEGGAYDYLPKPF----DLTEMIGTIGRALSE 121

Query: 127 G-VVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
              V +Q  +      L+  S AM ++  +  +     + +MI GE G GK+ ++R +H+
Sbjct: 122 PRKVAAQPEDTTEGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVARALHD 181

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
            GKR   PF  +N   I +D IE  LFG +    T    +  G+F +A GGT+ L+E   
Sbjct: 182 YGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQNRSTGRFEQAEGGTLFLDEIGD 241

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +P+  Q R+   ++ G+      R  I+ DVR++  T K+L   +   +FR+DL+YR++V
Sbjct: 242 MPMDAQTRLLRVLQQGEYTTVGGRTPIKSDVRIVAATNKDLKILINQGLFREDLFYRLNV 301

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             + +  LR R+ED+P LV  F++       +        AL LL  YPW  NV+EL+N+
Sbjct: 302 VPLRLPALRDRAEDVPDLVRHFVR-HAVGEGLDAKRFDGDALDLLKAYPWPGNVRELENV 360

Query: 365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKS-------SDTILDN 417
            +R V+ L            ++SRE   + E   ET      +G +       + ++ +N
Sbjct: 361 -VRRVMALYPQD--------VISRE-IIDNELRIETPEQSSPQGGAPMAQATIAQSVEEN 410

Query: 418 LSQ------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
           + +      E +P  G    V  L ++E  +I  A+   R    + A  LG+ R+TL +K
Sbjct: 411 MRRYFSGFGEDLPPPGLYHRV--LEEVEYPLILAALTATRGNQIKAADLLGLNRNTLRKK 468

Query: 472 IREYNIEV 479
           IRE  + V
Sbjct: 469 IRELGVTV 476


>gi|315288330|gb|EFU47729.1| response regulator receiver domain protein [Escherichia coli MS
           110-3]
          Length = 417

 Score =  162 bits (411), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 109/383 (28%), Positives = 191/383 (49%), Gaps = 11/383 (2%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +I+     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSIETAVEALKTGALDYLIKPLDFDNLQSTLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L   FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLS 387
           + RAV+ L   +++E    L ++
Sbjct: 365 VERAVVLLTGEYISERELPLAIA 387


>gi|302185564|ref|ZP_07262237.1| helix-turn-helix, Fis-type [Pseudomonas syringae pv. syringae 642]
          Length = 471

 Score =  162 bits (411), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 133/476 (27%), Positives = 224/476 (47%), Gaps = 21/476 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVE--SYGYDVFIVNVSDLSTISKIQVNVIFLSLINCED-DKEN 69
           VL+++ D    + + + +E   YGY   + +  +    ++ Q   + +S +N    D   
Sbjct: 5   VLLVEDDRSLREALGETLELAGYGYQA-VGSAEEALVAAEAQPFSLVISDVNMPGMDGHQ 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
           +L  +  + P +P+++ T    ++     +    + + +     K L   I    R  + 
Sbjct: 64  LLSLLRSRHPQLPVLLMTAHGAVERAVDAMRQGAADYLVKPFEPKAL---IALVGRHALG 120

Query: 130 PSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR 189
             +  E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  R
Sbjct: 121 RLEPAER---DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPR 177

Query: 190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLA 248
           A  PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL 
Sbjct: 178 ADKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLG 237

Query: 249 VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN 308
           +Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF + 
Sbjct: 238 LQAKLLRVLQEREVERVGARKPIILDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLA 297

Query: 309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA 368
              LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA
Sbjct: 298 WQALRQRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVSYPWPGNVRELDNAVQRA 357

Query: 369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQ 428
           +I  +   +    F   LS             A    T    ++     +S ES  A+G 
Sbjct: 358 LILQQGGVIQAQDFC--LSGPVTSLPVAAPIEAAAAVTVTTVAENAGAGVSPESAGALGD 415

Query: 429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
           D     L   E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 416 D-----LRRHEFQMIIDTLRSERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 466


>gi|170019466|ref|YP_001724420.1| acetoacetate metabolism regulatory protein AtoC [Escherichia coli
           ATCC 8739]
 gi|169754394|gb|ACA77093.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Escherichia coli ATCC 8739]
          Length = 461

 Score =  162 bits (411), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 130/482 (26%), Positives = 223/482 (46%), Gaps = 45/482 (9%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI+D +D   +++       G++    N   + L   + I  +V+ + +   E D   
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 70  ILKNIVDKIPIVPIIVQTT----QDNIKILNCFLYNRISKFF----LNLVSRKQL----C 117
            LK +       P+I+ T     +  ++ L C  ++ + K F    LNL+ ++ L     
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSM 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              I  L + +  S +  H     ++  SPAM+ +     K       ++I GE G GK+
Sbjct: 126 KKEIRHLHQALSTSWQWGH-----ILTNSPAMMDICKDTAKIALSQASVLISGESGTGKE 180

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGT 236
            ++R IH + +RA  PF  VNC  + +  +E  LFG +    T       G F  AN GT
Sbjct: 181 LIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTSRQGLFERANEGT 240

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           ++L+E   +PL +Q ++   ++  + E       I++D+R+I  T ++L   VK   FR+
Sbjct: 241 LLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFRE 300

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DL+YR++V  + +  LR R EDI  L + FLQ F ++N    I I   A+SLLT + W  
Sbjct: 301 DLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPG 360

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           N++EL N++ RAV+         +   ++ S +   +     +  C    E K++     
Sbjct: 361 NIRELSNVIERAVV--------MNSGPIIFSEDLPPQIR---QPVCNA-GEVKTAPVGER 408

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
           NL +E             +  +EK II   ++      +  A  LGI R  L  K++EY 
Sbjct: 409 NLKEE-------------IKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYG 455

Query: 477 IE 478
           I+
Sbjct: 456 ID 457


>gi|283853390|ref|ZP_06370636.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio sp. FW1012B]
 gi|283571203|gb|EFC19217.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio sp. FW1012B]
          Length = 482

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 120/413 (29%), Positives = 202/413 (48%), Gaps = 23/413 (5%)

Query: 79  PIVPIIVQT----TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICA---LREGVVPS 131
           P +P+I+ T    T   I+      Y+ I K F ++    +L +  + A   +R  V   
Sbjct: 76  PRLPVIIMTAFGTTDIAIEATKMGAYDYILKPF-DIPEILKLIEKAVAAGRSMRSRVAVG 134

Query: 132 QENEHC-ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
           +E E   A D++I  S AM  +     +A      ++I+GE G GK+ ++R +++   RA
Sbjct: 135 EEGEAAVAADAIIGRSQAMQDLYKAIGRAAPTDATVLIRGESGTGKELVARAVYQHSLRA 194

Query: 191 FFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAV 249
             PF ++NC  I +  +E  LFG +    T  + + +GK  +AN GT+ L+E   +PL++
Sbjct: 195 DKPFLVINCVAIPETLLESELFGYEKGAFTGATGRKVGKIEQANRGTVFLDEIGDMPLSI 254

Query: 250 QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINI 309
           Q +I   ++   +E    R  I +DVR+I  T ++L   V++  FR+DLYYR+ V  + +
Sbjct: 255 QAKILRLLQEQNVERLGGRQVIPVDVRIIAATNRDLEAAVRAGQFREDLYYRLKVVTMAM 314

Query: 310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
             LR R  DIP LV +FL  +  +       +SD+A++LLT  PW  NV+EL N + +A+
Sbjct: 315 PPLRERPGDIPLLVRYFLARYSREMGQPDPGVSDEAMALLTTQPWPGNVRELGNTVKKAL 374

Query: 370 IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQD 429
           I    + L  D            ++            E    D++   + +E   A G++
Sbjct: 375 IFNLGAPLGPDEV----------QKASGEPLRGGGPAEADPGDSLARYVRREL--ASGRE 422

Query: 430 GEVRRLSD-IEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVDS 481
                L D     +I  A++      S+ AR LG+ R TL  KI +Y + ++S
Sbjct: 423 SLFEDLMDRFGLLVIREALEATGGNRSQAARLLGLSRPTLLAKIEKYGLRIES 475


>gi|332982072|ref|YP_004463513.1| Fis family two component sigma-54 specific transcriptional
           regulator [Mahella australiensis 50-1 BON]
 gi|332699750|gb|AEE96691.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Mahella australiensis 50-1 BON]
          Length = 449

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 118/382 (30%), Positives = 193/382 (50%), Gaps = 19/382 (4%)

Query: 12  RVLIIDKDDEQIKII---KDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKE 68
           R+LIID D+E+++ +       ESY  +     +  L  + K  ++++ L +     D  
Sbjct: 4   RILIID-DEERMRWVLCKALEQESYEAEAAGDGIEGLKMLDKHSIDLVLLDMRLPIMDGM 62

Query: 69  NILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR-EG 127
            +LK I +  P +P+I+ T   +I++    +    + +        +L   I  AL    
Sbjct: 63  EVLKRIKELYPSLPVIIITAYGSIEMAVAAVKAGATDYITKPFDIDELVIQIKKALDVHR 122

Query: 128 VVPSQENEHCALDS------LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR 181
           +V   E     L        L + SP M +V +L R+  D    +++ GE G GK+ ++R
Sbjct: 123 LVDEVEFLRSELSQRYQDMLLSSKSPCMQEVYELVRRIADSDATVLLTGESGTGKEVIAR 182

Query: 182 FIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLE 240
            IH S +RA  PF  +NC  +  + +E  LFG +    T   A+  G+F  A+GGT+ L+
Sbjct: 183 TIHYSSRRADKPFVAINCAAVPDNLLESELFGYEKGAFTGAVARKAGRFEVADGGTVFLD 242

Query: 241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY 300
           E   + + +Q ++   ++    E       I +DVR+I  T K+L   +KS  FR+DLYY
Sbjct: 243 EIGEMSMNMQAKLLRVLQERSFEHLGGNDVISVDVRIIAATNKDLQYAMKSGYFREDLYY 302

Query: 301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE 360
           R+SV  IN+  LR R EDIP L  +F+  F  + AIK   IS +A+ +L  Y W  N++E
Sbjct: 303 RLSVIPINLPPLRERKEDIPDLALYFVNKFDKRKAIK--GISKQAMDILRLYSWPGNIRE 360

Query: 361 LKNILLRAVI-----GLKDSHL 377
           L+N + RAVI      ++ +HL
Sbjct: 361 LENAIERAVIICDTNAIQPAHL 382


>gi|317052124|ref|YP_004113240.1| sigma-54 factor interaction domain-containing protein
           [Desulfurispirillum indicum S5]
 gi|316947208|gb|ADU66684.1| sigma-54 factor interaction domain-containing protein
           [Desulfurispirillum indicum S5]
          Length = 454

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 106/338 (31%), Positives = 173/338 (51%), Gaps = 24/338 (7%)

Query: 142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM 201
           ++  SPA+ Q+ ++ ++A      ++IQGE G GK+ ++R IH   +RA  PF  VNC  
Sbjct: 140 IVGSSPAIRQMQEVIKRAAPSNGRVLIQGENGTGKELIARNIHFGSRRAAGPFVAVNCAA 199

Query: 202 IDQDKIEKFLFGDVDLQTKNSAQ-FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETG 260
           I ++ IE  LFG        +AQ   GKF  A+GGT+ L+E   + L  Q ++   +E  
Sbjct: 200 IPENLIESELFGHEKGAFTGAAQKRQGKFELADGGTLFLDEIADMSLNTQAKVLRVLEDQ 259

Query: 261 KIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIP 320
            +          +DVR+I  + K L   V+   FR+DLYYR++V  I I  LR R EDI 
Sbjct: 260 MVVRLGGSEVFPVDVRIISASNKKLTELVQRGEFREDLYYRLNVIPIEIPPLRERHEDIE 319

Query: 321 WLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTED 380
           +L++ FL+  C    + + ++S +A+ +L +YPW  NV+ELKN++ R VI ++DS +   
Sbjct: 320 FLLNHFLEVICADEGVPRKTVSSQAIEVLLRYPWPGNVRELKNLVERLVIMVQDSTID-- 377

Query: 381 RFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEK 440
             +  L  E ++     +  + T   EG      +DN  Q                D EK
Sbjct: 378 --IGDLPEEYRQTEGDRSAGSLTGAVEG------IDNFRQAR-------------EDFEK 416

Query: 441 EIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE 478
             I   ++     +++ A  + I R  L++KI++Y I+
Sbjct: 417 LFIAAKLRECEGNVTKAAELMEIDRVHLHKKIKQYGIK 454


>gi|189426125|ref|YP_001953302.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter lovleyi SZ]
 gi|189422384|gb|ACD96782.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Geobacter lovleyi SZ]
          Length = 454

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 129/483 (26%), Positives = 226/483 (46%), Gaps = 50/483 (10%)

Query: 10  HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDK 67
           H  +LIID D    ++++  ++  GY+V      +  L+  S +   ++   +     D 
Sbjct: 2   HPTILIIDDDASLRRVLEYQLQEAGYEVATAASGEEGLARFSDLAPQLVISDMQMPGMDG 61

Query: 68  ENILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSRKQLCDSIICA 123
             +LK + ++ P  P+I+ T   ++ +    +    Y+ I+K F    +R +L  ++  A
Sbjct: 62  MQVLKTVKERSPETPVIIITAFGSVDVAVQAMKQGAYDYITKPF----NRDELHLTVARA 117

Query: 124 LREGVVPSQEN----EHCALD----SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVG 175
           L    + ++EN    +  A D    S++  S A+ +V  + RK  D    +++ GE G G
Sbjct: 118 LHLTSL-TRENRRLKDALAGDDDYRSMVGASAALEKVYLVVRKVADSDASVLLSGESGTG 176

Query: 176 KKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANG 234
           K+ ++R +H    R   PF  VNC  I  D +E  LFG      T       GKF  A+ 
Sbjct: 177 KELVARALHARSARRNGPFVAVNCAAIPHDLLESELFGHTKGAFTGAVKDKPGKFQLADT 236

Query: 235 GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF 294
           GTI L+E   LPL +Q ++   ++   +         RLD+R++  T +++   +    F
Sbjct: 237 GTIFLDEVGELPLELQPKLLRVLQERVVTPVGGNREQRLDIRVVAATNRDIEQAISEGRF 296

Query: 295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW 354
           R+DLYYR++V  +++  LR R EDIP L    L+ FC+K+  +++   + AL++L +Y W
Sbjct: 297 REDLYYRLAVIPLHLPPLRQRREDIPLL----LRHFCSKHGAEEVRFDEAALAILQQYAW 352

Query: 355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTI 414
             NV+EL+N++ R +I    S +T +              +   +   T     K S  I
Sbjct: 353 PGNVRELENLVERLLIMRSSSSITVE--------------DLPDKIRLTVNGSAKRSAVI 398

Query: 415 LDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
             NL     P          L  +E+E++  A++      S  A+ L I R TL  ++ +
Sbjct: 399 --NLPDNGYP----------LEQLEREVVVEALERTNWNQSAAAKFLQIPRHTLLYRMEK 446

Query: 475 YNI 477
           Y I
Sbjct: 447 YAI 449


>gi|182413920|ref|YP_001818986.1| two component, sigma54 specific, Fis family transcriptional
           regulator [Opitutus terrae PB90-1]
 gi|177841134|gb|ACB75386.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Opitutus terrae PB90-1]
          Length = 467

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 99/343 (28%), Positives = 172/343 (50%), Gaps = 17/343 (4%)

Query: 134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP 193
           +E  + + +I  SP + +V+D  +        I+I+GE G GK+ +++ IH+S  R+  P
Sbjct: 134 DEKFSFEGIIGNSPKLHEVIDRVKLVAPSRATILIEGESGTGKELIAQAIHQSSSRSRGP 193

Query: 194 FFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGR 252
           F  V+C  + ++ +E  LFG +    T  + + +G+F  A+GGT+ L+E   +  + Q +
Sbjct: 194 FLAVHCAALSENLLESELFGHERGSFTGATERRIGRFESADGGTLFLDEIGEISASTQVK 253

Query: 253 IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTL 312
           +  F+ET  IE       I LDVRL+  T + L   V+   FR+DL++R++V  I +  L
Sbjct: 254 LLRFLETKSIERVGGSKPIDLDVRLVAATNRTLEQLVRDGKFREDLFFRLNVVRITMPPL 313

Query: 313 RSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGL 372
           R R+ED+P L+  ++ +F  +N +  ++I   AL+ L  YPW  N++EL+N    AV+  
Sbjct: 314 RERAEDVPLLLGHYITAFSEENGVPPLTIEPGALATLQAYPWPGNIRELRNFCENAVVLR 373

Query: 373 KDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEV 432
           +   L+E         E +              T G    T+L      S          
Sbjct: 374 RGRSLSE------YDLEPRYRDATLAGATGPAPTPGAPGSTVLGGAVPTSF--------- 418

Query: 433 RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY 475
             + + EK ++  A+   R   ++ A  +GI R TL+RKI ++
Sbjct: 419 -SVEENEKRLLREALIKSRGNRTKAAELMGISRRTLHRKIAQW 460


>gi|147676940|ref|YP_001211155.1| response regulator [Pelotomaculum thermopropionicum SI]
 gi|146273037|dbj|BAF58786.1| response regulator [Pelotomaculum thermopropionicum SI]
          Length = 515

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 130/450 (28%), Positives = 201/450 (44%), Gaps = 43/450 (9%)

Query: 70  ILKNIVDKIPIVPIIVQT----TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR 125
           +L+ + +  P   +I+ T    T+  +K +    Y+ + K F N+   ++L +  I ++ 
Sbjct: 66  LLREVKNLQPHCEVIIMTGYGTTRTAVKAIQLGAYDFLEKPFENIDELEKLIEDAI-SVS 124

Query: 126 EGVVPSQEN---EHCA--LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS 180
            G V S +    E  A  +  ++  +  M ++  +A K     I ++I GE G GK+ L+
Sbjct: 125 LGQVDSADAARWEELADQVGFVVGSTQQMRRLASIAYKIAPKNINVLIHGETGTGKELLA 184

Query: 181 RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFIEANGGTIVL 239
           RFIH +  R+   F  VNCG    + +E  LFG        +     G F  ANGGT+ L
Sbjct: 185 RFIHAASSRSGGKFVAVNCGAFPDNLLESELFGHERGAFTGAVNMRRGIFELANGGTLFL 244

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E     LAVQ ++   +ETG+         IR +VRLI  T  +L   +K   FR+DL+
Sbjct: 245 DEVGEASLAVQVKLLRVLETGEFMRIGGEKPIRTNVRLIAATNVDLEQAIKEKAFREDLF 304

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR+ V  + +  LR R EDIP LV  F+Q +        + +S + L LL  Y W  N++
Sbjct: 305 YRLDVVRLVLPPLRKRREDIPLLVSHFVQKYAKAAEYSGLRVSSECLRLLQNYDWPGNIR 364

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD------- 412
           EL N + +AV       L     V  +     K  +   E        G ++        
Sbjct: 365 ELANTIEQAVALCDGPELMPQHLVGKIRLSEAKSLQMRKEAGGQPVASGVAAGDPVSQLQ 424

Query: 413 -TILDNLSQESIPA----------------IGQDGEVRRLS--------DIEKEIIGLAM 447
             + D    E +P                 +G+  E R L+        DIE + I  A+
Sbjct: 425 ACLADEFPWEQMPTDQLLAANRLAHALIHRLGKAMERRNLASEQRFSLRDIECQSISRAL 484

Query: 448 KLYRAQMSEVARRLGIGRSTLYRKIREYNI 477
             Y    S  AR LGI RSTLYRK++EY +
Sbjct: 485 ACYGNNFSLAARALGIARSTLYRKVKEYGL 514


>gi|1177236|emb|CAA93242.1| MopR [Acinetobacter calcoaceticus]
          Length = 560

 Score =  162 bits (411), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 120/349 (34%), Positives = 175/349 (50%), Gaps = 25/349 (7%)

Query: 124 LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI 183
           L++ +    E+++   ++ +  S A  +V DL +KA    + +++QGE GVGK+  +R I
Sbjct: 228 LKKNIYTEAESDYTMFNA-VGESVAYRKVCDLLKKAAGSKVAVLLQGETGVGKEAFARGI 286

Query: 184 HESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF-LGKFIEANGGTIVLEEP 242
           H   +R   PF  VNC  I  D IE  LFG        + Q  +GKF  A+GGTI L+E 
Sbjct: 287 HNGSQRQAQPFVAVNCACIPPDLIESELFGVEKGAFTGAVQSRMGKFERAHGGTIFLDEV 346

Query: 243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI 302
             L    Q  +   ++ G+ E        ++DVRL+  T ++L   VK   FR DLYYR+
Sbjct: 347 VELSPRAQAALLRMLQEGEFERVGDSRTRQVDVRLVAATNEDLEQAVKDGKFRADLYYRL 406

Query: 303 SVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK 362
           ++F + I  LR R EDIP L++ FL  F          +SDKA + + KY W  N++EL+
Sbjct: 407 NIFPVIIPPLRERREDIPLLINHFLARFENMYNKTLKGLSDKAKNFMMKYDWPGNIRELE 466

Query: 363 NILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQES 422
           N+L RA + L D H  E +   L  +   K+ E   ETA +        D   +N S   
Sbjct: 467 NLLERATL-LTD-HQQEIKLDSLFPQH--KDLEAVGETAQSLIN---VEDLFSENFS--- 516

Query: 423 IPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL-YR 470
                       L  +E+ II  AM   +  +SE AR LGI R+TL YR
Sbjct: 517 ------------LDQLEQNIIRSAMDKSQQNVSEAARMLGISRATLDYR 553


>gi|296187936|ref|ZP_06856328.1| transcriptional regulator, Fis family [Clostridium carboxidivorans
           P7]
 gi|296047062|gb|EFG86504.1| transcriptional regulator, Fis family [Clostridium carboxidivorans
           P7]
          Length = 626

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 108/346 (31%), Positives = 175/346 (50%), Gaps = 38/346 (10%)

Query: 136 HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFF 195
           +   D +I      I+VV+ A+K  D    I+I GE G GK+  ++ IH    R   PF 
Sbjct: 315 YYTFDKVIGQDENFIKVVEYAKKISDSKSTILIMGESGTGKEVFAQSIHNYSSRVDGPFI 374

Query: 196 IVNCGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRI 253
            +NCG I +  IE  LFG  +            GKF  A+GGTI+L+E   +PL +Q ++
Sbjct: 375 ALNCGAIPKQLIESELFGYEEGAFTGAKKGGNRGKFELADGGTIMLDEIGEMPLDMQTKL 434

Query: 254 YNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLR 313
              ++ G I    S  +I +DVR+I  T ++L  +V+   FRKDLYYR++V  + +  LR
Sbjct: 435 LRVVQEGVITKIGSSKSIPVDVRIIAATNRDLKKEVELGRFRKDLYYRLNVLPLFLPPLR 494

Query: 314 SRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK 373
            R  DIP ++ + +++   +   K+ SIS++ L  +  Y W  N++EL+N++        
Sbjct: 495 ERKGDIPLIIRYLIKNISKRLEKKEPSISEEWLKEINSYDWPGNIRELENVV-------- 546

Query: 374 DSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVR 433
                     L+++ E      F       CY E      +L N+S++S+          
Sbjct: 547 ---------ELIINTESIPSGYFQN---GNCYNE------VLINISEDSL---------- 578

Query: 434 RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           +L   EKE +   +K ++  ++  A  LGI R+TLY KI++YNIE+
Sbjct: 579 KLDFAEKEHLVKVLKKFKGNITRSAEALGIRRNTLYSKIKKYNIEI 624


>gi|89094868|ref|ZP_01167800.1| two-component response regulator [Oceanospirillum sp. MED92]
 gi|89080825|gb|EAR60065.1| two-component response regulator [Oceanospirillum sp. MED92]
          Length = 454

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 132/487 (27%), Positives = 229/487 (47%), Gaps = 55/487 (11%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKEN 69
           R+LI++ D+E  + + D +E  G+D      ++  L+ +++ QV+++   +     D   
Sbjct: 4   RILIVEDDNELREALCDTLELAGFDYIEAEDAEKALALLTEHQVDMVVTDVNMPGMDGHE 63

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE--- 126
           +L  I    P +P+++ T    +          I    ++ + +    D++I ++R    
Sbjct: 64  LLSQIRQSYPGLPVMLITAFGQV----SKAVEAIKAGAVDYLMKPFDSDALISSVRRFAV 119

Query: 127 GVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES 186
           G   ++E E       IA   +  Q++ LAR+       ++I GE G GK+ L+++IH +
Sbjct: 120 GQAVTEEQEQP-----IAEEGSSKQLLQLARRVAASDSTVLISGESGTGKEVLAQYIHCN 174

Query: 187 GKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDAL 245
             RA  PF  +NC  I ++ +E  LFG +    T       GKF +ANGGTI+L+E   +
Sbjct: 175 SPRAKEPFIAINCAAIPENMLEATLFGHEKGAFTGAYNSSPGKFEQANGGTILLDEISEM 234

Query: 246 PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF 305
            L +Q ++   ++  ++E    R  I+LDVR++  T + L   V+   FR+DLYYR++VF
Sbjct: 235 DLGLQAKLLRVLQEQEVERIGGRKVIKLDVRVLATTNRKLESYVQEGKFREDLYYRLNVF 294

Query: 306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNIL 365
            +    LR R  DI  L       +C K     +S+S++  S L +Y W  NV+EL N++
Sbjct: 295 PLQWKPLRERPADIVPLAERLFLKYCQKMHRTPVSLSEQVKSDLQRYSWPGNVRELDNVV 354

Query: 366 LRAV-------IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNL 418
            RA+       IG+ D  L  D                              S+  ++++
Sbjct: 355 QRALILQTGPEIGVSDLMLNPDEL----------------------------SEAKVEDV 386

Query: 419 SQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTL-YR--KIREY 475
           + E     GQ GE  R  +   ++I  A+K       + A  LGI   TL Y+  K+RE 
Sbjct: 387 AVEDDDLAGQLGEGMRQHEF--QLIIDALKATHGSRKDAAENLGISPRTLRYKLAKMREM 444

Query: 476 NIEVDSL 482
            +++D L
Sbjct: 445 GLDLDKL 451


>gi|206890448|ref|YP_002249494.1| transcriptional regulator [Thermodesulfovibrio yellowstonii DSM
           11347]
 gi|206742386|gb|ACI21443.1| transcriptional regulator [Thermodesulfovibrio yellowstonii DSM
           11347]
          Length = 511

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 89/250 (35%), Positives = 142/250 (56%), Gaps = 1/250 (0%)

Query: 128 VVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG 187
           ++ +Q  +     +L+  SP+   V+    K       +++ GE G GK+ +++ IH   
Sbjct: 179 ILRAQLKDRYNFPNLVGQSPSFQAVLKTVMKVASTDATVLLFGESGTGKELIAKTIHFQS 238

Query: 188 KRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPL 247
           KRA  PF  +NC  I ++ +E  LFG        + + +GKF +ANGGTI L+E   LPL
Sbjct: 239 KRAKGPFVAINCAAIPENLLEAELFGSEKGAFTGAVKRIGKFEQANGGTIFLDEIAELPL 298

Query: 248 AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLI 307
           ++Q ++   ++   +E   S   IR+DVRLI  T K+L  +++   FR+DL++R++V  I
Sbjct: 299 SLQPKLLRVLQERTVEPLGSSKTIRVDVRLISATNKDLSEEIRKGNFREDLFWRLNVIPI 358

Query: 308 NISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLR 367
            I  LR R EDIP LV ++L+SFC     K +SI ++AL +L  Y W  NV+EL N + R
Sbjct: 359 YIPPLRERKEDIPLLVEYYLKSFCNIYR-KSVSIDEEALKVLVSYDWPGNVRELANTIER 417

Query: 368 AVIGLKDSHL 377
            V+  + S +
Sbjct: 418 LVVMTESSKI 427


>gi|255526784|ref|ZP_05393684.1| GAF modulated sigma54 specific transcriptional regulator, Fis
           family [Clostridium carboxidivorans P7]
 gi|255509512|gb|EET85852.1| GAF modulated sigma54 specific transcriptional regulator, Fis
           family [Clostridium carboxidivorans P7]
          Length = 643

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 108/346 (31%), Positives = 175/346 (50%), Gaps = 38/346 (10%)

Query: 136 HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFF 195
           +   D +I      I+VV+ A+K  D    I+I GE G GK+  ++ IH    R   PF 
Sbjct: 332 YYTFDKVIGQDENFIKVVEYAKKISDSKSTILIMGESGTGKEVFAQSIHNYSSRVDGPFI 391

Query: 196 IVNCGMIDQDKIEKFLFG--DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRI 253
            +NCG I +  IE  LFG  +            GKF  A+GGTI+L+E   +PL +Q ++
Sbjct: 392 ALNCGAIPKQLIESELFGYEEGAFTGAKKGGNRGKFELADGGTIMLDEIGEMPLDMQTKL 451

Query: 254 YNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLR 313
              ++ G I    S  +I +DVR+I  T ++L  +V+   FRKDLYYR++V  + +  LR
Sbjct: 452 LRVVQEGVITKIGSSKSIPVDVRIIAATNRDLKKEVELGRFRKDLYYRLNVLPLFLPPLR 511

Query: 314 SRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK 373
            R  DIP ++ + +++   +   K+ SIS++ L  +  Y W  N++EL+N++        
Sbjct: 512 ERKGDIPLIIRYLIKNISKRLEKKEPSISEEWLKEINSYDWPGNIRELENVV-------- 563

Query: 374 DSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVR 433
                     L+++ E      F       CY E      +L N+S++S+          
Sbjct: 564 ---------ELIINTESIPSGYFQN---GNCYNE------VLINISEDSL---------- 595

Query: 434 RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEV 479
           +L   EKE +   +K ++  ++  A  LGI R+TLY KI++YNIE+
Sbjct: 596 KLDFAEKEHLVKVLKKFKGNITRSAEALGIRRNTLYSKIKKYNIEI 641


>gi|241204540|ref|YP_002975636.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Rhizobium leguminosarum bv. trifolii WSM1325]
 gi|240858430|gb|ACS56097.1| nitrogen metabolism transcriptional regulator, NtrC, Fis Family
           [Rhizobium leguminosarum bv. trifolii WSM1325]
          Length = 483

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 136/493 (27%), Positives = 231/493 (46%), Gaps = 47/493 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   IS  + +++   ++  +++  ++
Sbjct: 5   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWISAGEGDLVVTDVVMPDENAFDL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 65  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALSE 120

Query: 127 GVVPSQENEHCALDS--LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
                 + E    D   L+  S AM ++  +  +     + +MI GE G GK+ ++R +H
Sbjct: 121 PKRKPAKLEDDMQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVARALH 180

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGTIVL 239
           + GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT+ L
Sbjct: 181 DYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGTLFL 236

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+DLY
Sbjct: 237 DEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRTDVRIVAATNKDLKQAINQGLFREDLY 296

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  Y W  NV+
Sbjct: 297 YRLNVVPLRLPPLRDRAEDIPDLVRHFIQQ-AEKEGLGSKRFDQEALELMKAYAWPGNVR 355

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEG---KSSDTILD 416
           EL+N L+R ++ L    +     +         + E  ++   +   +G     S TI  
Sbjct: 356 ELEN-LIRRLMALYPQDVITREII---------DAELRSDVPDSPIDKGPMRSGSMTIAQ 405

Query: 417 NLSQ----------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
            + +          +++P  G    V  L+++E  +I  A+   R    + A  LG+ R+
Sbjct: 406 AVEENMRSYFAGFGDNLPPPGLYDRV--LTEMEYPLILAALTATRGNQIKAADLLGLNRN 463

Query: 467 TLYRKIREYNIEV 479
           TL +KIRE  + V
Sbjct: 464 TLRKKIRELGVSV 476


>gi|315294338|gb|EFU53689.1| response regulator receiver domain protein [Escherichia coli MS
           153-1]
          Length = 420

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 108/383 (28%), Positives = 192/383 (50%), Gaps = 11/383 (2%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLIN---CEDDKEN 69
           +L++D D     I++  +  +GY+V + N S    + +++  V  L L +    E D   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALAN-SGRQALEQVREQVFDLVLCDVRMAEMDGIA 66

Query: 70  ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV 129
            LK I    P +P+++ T   +++     L      + +  +    L  ++  AL     
Sbjct: 67  TLKEIKTLNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH--T 124

Query: 130 PSQENEHCALDS----LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE 185
            S + E  A+ +    ++  SPAM  ++            ++I G+ G GK+ ++R IH 
Sbjct: 125 HSVDAETPAVSASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHA 184

Query: 186 SGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEEPDA 244
           S  R+  P   +NC  +++  +E  LFG +    T    +  G+F+EA+GGT+ L+E   
Sbjct: 185 SSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGD 244

Query: 245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISV 304
           +   +Q R+   I+  +++   S   I +DVRLI  T ++L  +V +  FR+DLYYR++V
Sbjct: 245 ISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNV 304

Query: 305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI 364
             I + +LR R EDIP L + FLQ F  +N       + +A+ LL  Y W  N++EL+N 
Sbjct: 305 VAIEVPSLRQRREDIPLLANHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENA 364

Query: 365 LLRAVIGLKDSHLTEDRFVLLLS 387
           + RAV+ L   +++E    L ++
Sbjct: 365 VERAVVLLTGEYISERELPLAIA 387


>gi|86357569|ref|YP_469461.1| nitrogen regulation (two-component response regulator) protein
           [Rhizobium etli CFN 42]
 gi|86281671|gb|ABC90734.1| nitrogen regulation (two-component response regulator) protein
           [Rhizobium etli CFN 42]
          Length = 483

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 135/493 (27%), Positives = 231/493 (46%), Gaps = 47/493 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GYDV I  N + L   IS  + +++   ++  +++  ++
Sbjct: 5   ILVADDDAAIRTVLNQALSRAGYDVRITSNAATLWRWISAGEGDLVVTDVVMPDENAFDL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P +P++V + Q+     IK      Y+ + K F       +L   I  AL E
Sbjct: 65  LPRIKKARPDLPVLVMSAQNTFMTAIKASEKGAYDYLPKPF----DLTELIGIIGRALAE 120

Query: 127 GVVPSQENEHCALDS--LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH 184
                 + E    D   L+  S AM ++  +  +     + +MI GE G GK+ ++R +H
Sbjct: 121 PKRKPAKLEEDMQDGMPLVGRSAAMQEIYRVLARLMQTDLTLMITGESGTGKELVARALH 180

Query: 185 ESGKRAFFPFFIVNCGMIDQDKIEKFLFGD-----VDLQTKNSAQFLGKFIEANGGTIVL 239
           + GKR   PF  +N   I +D IE  LFG         QT+++    G+F +A GGT+ L
Sbjct: 181 DYGKRRNGPFVAINMAAIPRDLIESELFGHEKGAFTGAQTRST----GRFEQAEGGTLFL 236

Query: 240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY 299
           +E   +P+  Q R+   ++ G+      R  IR DVR++  T K+L   +   +FR+DLY
Sbjct: 237 DEIGDMPMDAQTRLLRVLQQGEYTTVGGRTPIRTDVRIVAATNKDLKQAINQGLFREDLY 296

Query: 300 YRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ 359
           YR++V  + +  LR R+EDIP LV  F+Q    K  +       +AL L+  Y W  NV+
Sbjct: 297 YRLNVVPLRLPPLRDRAEDIPDLVRHFIQQ-AEKEGLGSKRFDQEALELMKAYAWPGNVR 355

Query: 360 ELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGK-------SSD 412
           EL+N L+R ++ L    +     +         + E  ++   +   +G         S 
Sbjct: 356 ELEN-LIRRLMALYPQDVITREII---------DAELRSDVPDSPIDKGPIRNGSMTISQ 405

Query: 413 TILDNLSQ------ESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRS 466
            + +N+        +++P  G    V  L+++E  +I  A+   R    + A  LG+ R+
Sbjct: 406 AVEENMRTYFASFGDNLPPPGLYDRV--LTEMEYPLILAALTATRGNQIKAADLLGLNRN 463

Query: 467 TLYRKIREYNIEV 479
           TL +KIRE  + V
Sbjct: 464 TLRKKIRELGVSV 476


>gi|283853533|ref|ZP_06370773.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio sp. FW1012B]
 gi|283571072|gb|EFC19092.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Desulfovibrio sp. FW1012B]
          Length = 456

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 124/481 (25%), Positives = 230/481 (47%), Gaps = 45/481 (9%)

Query: 9   RHK-RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCED 65
           +HK  VLI+D D     I+   +  +GY     +     ++   +   ++I + +   + 
Sbjct: 4   KHKATVLIVDDDQGHRTILLALINGWGYKAAGADDGTKAVTLAREKPFDLILMDVRMADM 63

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIK----ILNCFLYNRISKFF----LNLVSRKQLC 117
                LK I    P +PI++ T   N++     +    Y+ ++K      L L   + L 
Sbjct: 64  GGIEALKEIKAYNPSIPILIMTAYSNVESAVEAIKAGAYDYLTKPLDFDVLRLTMERALE 123

Query: 118 DSIICA----LREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFG 173
              + A    LR+ +V S + ++     ++  S AM ++++           ++I G+ G
Sbjct: 124 HVSLKAENQELRQRLVSSFDPKN-----IVGRSEAMRRLMETVAMVAPSEATVLITGQSG 178

Query: 174 VGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEA 232
            GK+ +++ IH +  R   P   VNC  + +  +E  LFG +    T    +  G+F++A
Sbjct: 179 TGKELIAKAIHFNSPRKNGPLVTVNCAALSETLLESELFGHEKGAFTGADKRREGRFMQA 238

Query: 233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH 292
           N GTI L+E   +  A+Q ++   I+  +I+   S  A+R+DVR++  T ++L  +V++ 
Sbjct: 239 NKGTIFLDEIGEISSAMQAKLLRVIQEREIQRVGSDNALRVDVRIVAATNRDLKAEVEAG 298

Query: 293 VFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY 352
            FR+DLYYR++V  + +  LR R ED+P L   FL  F   N       + +A+ +L KY
Sbjct: 299 RFRQDLYYRLNVMTLTVPPLRDRGEDVPLLAMHFLHKFAEANRKVAKGFTPQAMDMLLKY 358

Query: 353 PWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD 412
            W  NV+EL+N + RAV+ +    +TE    L +++E   E +              +++
Sbjct: 359 DWPGNVRELENAVERAVVLMPGDFVTEKELPLSVNQEKAHEEQ--------------NAN 404

Query: 413 TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI 472
            +++    E +P          L  +E+E I  A+++     +E A++LGI R TL  K+
Sbjct: 405 QLIERGPAEILP----------LEAVEREAILAALEVTGGNKTEAAKQLGITRKTLLAKL 454

Query: 473 R 473
           +
Sbjct: 455 Q 455


>gi|197123946|ref|YP_002135897.1| Fis family transcriptional regulator [Anaeromyxobacter sp. K]
 gi|220918715|ref|YP_002494019.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
 gi|196173795|gb|ACG74768.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter sp. K]
 gi|219956569|gb|ACL66953.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 489

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 131/493 (26%), Positives = 228/493 (46%), Gaps = 45/493 (9%)

Query: 9   RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLST--ISKIQVNVIFLSLINCEDD 66
           R  RVL++D +   ++ ++  +   G++V  ++ S  +T  +++   +V    +   +  
Sbjct: 8   RPARVLVVDDEPTLLRAMEALLRRKGHEVIGLDSSIAATQRLAQEDFDVALFDIKMPQLS 67

Query: 67  KENILKNIVDKIPIVPIIVQTTQDNIKI----LNCFLYNRISKFFLNLVSR--------- 113
              +L  +  + P V +I+ T    ++     +    Y+ ++K F ++            
Sbjct: 68  GLELLNAVKHRRPEVEVIMMTGHATVETALAAVRAGAYDYLTKPFEDVEVVARAVAKAAE 127

Query: 114 -KQLCD---SIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQ 169
            K L D    +  ALRE        E    + L+  S  M +V  +       A  ++I 
Sbjct: 128 RKMLFDRNRQLESALRE-------REGTPSEGLVGTSAPMREVTRMVEAVAYSATTVLIT 180

Query: 170 GEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGK 228
           GE G GK+ ++R +H    R   PF  +NCG + +  +E  LFG V    T       G 
Sbjct: 181 GESGTGKELVARALHTRSPRRSHPFVALNCGALTETLLESELFGHVKGAFTGAQRDQRGL 240

Query: 229 FIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ 288
           F  A+GGTI L+E   +PL+ Q R+   ++ G+I+   S   +R+DVR++  T ++L   
Sbjct: 241 FDAADGGTIFLDEIGDIPLSTQVRLLRVLQEGEIKRVGSADPVRVDVRVLAATHRDLPKL 300

Query: 289 VKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSL 348
           VK+  FR+DL+YR++V  I +  LR R EDIP L H F++ +  +   K  +++ +AL L
Sbjct: 301 VKAGRFREDLFYRLNVINIPLPPLRERVEDIPLLAHHFVRRYAERLGKKVRTVAPEALEL 360

Query: 349 LTKYPWIDNVQELKNILLRAVIGLK-DSHLTEDRFVLLLSREGKKEREFHTETACTCYTE 407
           +  Y W  NV+EL+N + RAV+  + DS +  D    +  R     RE            
Sbjct: 361 MCGYRWPGNVRELENAIERAVVLCRGDSVVPGDLPPAVTGRTAPLVRE----------AP 410

Query: 408 GKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRST 467
               +     LS     A  ++  +RR    EK  +   M+     +S  AR+ G+ RS 
Sbjct: 411 ASGDEAAWLALSY----AAAKEQALRRF---EKGYVEALMRACDGNISAAARKAGMDRSN 463

Query: 468 LYRKIREYNIEVD 480
             R +R+Y  +V+
Sbjct: 464 FKRVLRKYRTDVE 476


>gi|297616765|ref|YP_003701924.1| PAS modulated sigma54 specific transcriptional regulator, Fis
           family [Syntrophothermus lipocalidus DSM 12680]
 gi|297144602|gb|ADI01359.1| PAS modulated sigma54 specific transcriptional regulator, Fis
           family [Syntrophothermus lipocalidus DSM 12680]
          Length = 468

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 116/335 (34%), Positives = 170/335 (50%), Gaps = 25/335 (7%)

Query: 142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM 201
           ++A SP M QV+ +A  A      IM+ GE G GK+ ++R+IH +  RA  PF  VNC  
Sbjct: 157 IVAESPQMQQVMTVASAAAKTDSTIMLFGESGTGKEVMARYIHRNSLRAKEPFIPVNCAA 216

Query: 202 IDQDKIEKFLFGDVDLQ-TKNSAQF-LGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET 259
           I  + +E   FG V    T  S Q   G F  A+ GT+ L+E   LPL VQ ++   +ET
Sbjct: 217 IPSELMESEFFGYVAGAFTGASTQGKPGLFEIAHKGTLFLDEVAELPLPVQSKLLRVLET 276

Query: 260 GKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI 319
           G ++   S    R +VRLI  T ++L   +   +FR+DLYYR++V  I +  LR R EDI
Sbjct: 277 GDVQRLGSTSIHRTNVRLIAATNRDLKTMMAQGLFRRDLYYRLNVVPIKLPPLRERPEDI 336

Query: 320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE 379
           P L + FL     K + K+ + + + L   T Y W  NV+EL+N++ R V+     +L  
Sbjct: 337 PILANKFLDELNRKYSFKK-TFTKQTLEAFTNYNWPGNVRELRNVVERLVVTSTSDYLN- 394

Query: 380 DRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIE 439
                           F  + +    +  +SSDT   +L Q S    G    V  L  +E
Sbjct: 395 ----------------FEGDQSLPNSSR-RSSDT--SHLRQTSTVYRGTLKSV--LQMVE 433

Query: 440 KEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE 474
           KE I   +     ++SE A+ LGI R+ LYRK+R+
Sbjct: 434 KEYINQVISECEGRISEAAQLLGIHRTVLYRKLRD 468


>gi|144899196|emb|CAM76060.1| sigma-54 dependent DNA-binding response regulator [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 483

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 135/492 (27%), Positives = 234/492 (47%), Gaps = 46/492 (9%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIV-NVSDL-STISKIQVNVIFLSLINCEDDKENI 70
           +L+ D D     ++   +   GY+V    N S L   +S+ + +++   ++  ++   ++
Sbjct: 7   ILVADDDRGIRTVLAQALGRAGYEVRTTGNASTLWRWVSEGEGDLVITDVVMPDESGLDL 66

Query: 71  LKNIVDKIPIVPIIVQTTQDN----IKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE 126
           L  I    P + IIV + Q+     +K      +  + K F +L     + +  + A R 
Sbjct: 67  LPRIKKIRPDMRIIVMSAQNTLLTAVKATQRGAFEYLPKPF-DLKELVAVVNRALTAPRS 125

Query: 127 GVV---PSQENEHCALDSLIAVSPAMIQVV-DLARKAGDCAIPIMIQGEFGVGKKRLSRF 182
                 P  ++E      LI  SPAM ++   LAR  G   + +MI GE G GK+ ++R 
Sbjct: 126 APAEGQPGDDDEEKL--PLIGRSPAMQEIYRTLARLMG-TDLTVMITGESGTGKELVARA 182

Query: 183 IHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKFIEANGGTIVLEE 241
           +H+ GKR   PF  +N   I ++ IE  LFG +    T  + +  G+F +A GGT+ L+E
Sbjct: 183 LHDYGKRRNGPFVAINMAAIPRELIESELFGHEKGAFTGATQRATGRFEQAEGGTLFLDE 242

Query: 242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR 301
              +P   Q R+   ++ G+      R  IR +VR++  T ++L   ++  +FR+DL+YR
Sbjct: 243 IGDMPPEAQTRLLRVLQEGEYTTVGGRTPIRANVRIVAATHRDLTQLIRQGLFREDLFYR 302

Query: 302 ISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL 361
           ++V  I +  LR R+EDIP L+  FL    ++  + Q SI  +A+  L ++ W  NV+EL
Sbjct: 303 LNVVPIRLPPLRERTEDIPELIRHFLAQGSSE-GLPQKSIDSQAMDRLKRHRWPGNVREL 361

Query: 362 KNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLS-- 419
           +N++               R   L S+E         E A         S    + LS  
Sbjct: 362 ENLV--------------RRLAALYSQEVIGIEVIEAELAGGAPASDAMSAGDGEGLSAS 407

Query: 420 ------------QESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRST 467
                       ++S+P  G    V  L ++E+ +I LA+++ R    + A+ LG+ R+T
Sbjct: 408 VERHLREYFGSHEDSLPPPGVYDRV--LREVERPLIALALEVTRGNQIKAAQILGLNRNT 465

Query: 468 LYRKIREYNIEV 479
           L +KIRE ++ V
Sbjct: 466 LRKKIRELDVSV 477


>gi|110598910|ref|ZP_01387157.1| Response regulator receiver:Sigma-54 factor, interaction
           region:Helix-turn-helix, Fis-type [Chlorobium
           ferrooxidans DSM 13031]
 gi|110339478|gb|EAT58006.1| Response regulator receiver:Sigma-54 factor, interaction
           region:Helix-turn-helix, Fis-type [Chlorobium
           ferrooxidans DSM 13031]
          Length = 487

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 124/487 (25%), Positives = 227/487 (46%), Gaps = 29/487 (5%)

Query: 4   KKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLI 61
           K +  +   VLI D D+   +I+   V+  GY   +    +  +  +++   NVI L + 
Sbjct: 13  KTAATKKSVVLIADDDNTSRRILSHFVQKMGYVPIVAEDGEECIRCLTEQAPNVILLDIN 72

Query: 62  NCEDDKENILKNIVDKIPIVPIIVQTTQDNI-KILNC-------FLYNRISKFFLNLVSR 113
             + D   ++ ++     + P+I+ T   +I   + C       +L   +S   L +V R
Sbjct: 73  MPKKDGFEVMLHMKAHNIVTPVIMITASHDIPHAVKCIKLGAFEYLTKPLSIDRLEIVMR 132

Query: 114 KQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFG 173
             L +S + +  + ++  +         +I  SP +   ++   +  +  + ++I GE G
Sbjct: 133 NALAESSLQSQVQ-LLQKELKSQNLFRKIIGSSPVIKHTMEQVIQVMETDLNVLIIGESG 191

Query: 174 VGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEA 232
            GK+  +  IH   KR   PF  VNC  I  +  +  LFG V    T  +    G F +A
Sbjct: 192 SGKELFAEAIHYGSKRKKGPFVSVNCAAISNNLADSLLFGHVKGSFTGANTDHTGFFEQA 251

Query: 233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH 292
           + GTI L+E   +   VQ ++   ++  KI     +    ++ R+I  T ++    +K++
Sbjct: 252 DNGTIFLDEIGDMDSDVQAKVLRALQERKIRRVGEKSEKSVNFRVISATNRDFSQAIKNN 311

Query: 293 VFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY 352
           +FR+DLYYR+  F + I  LR R EDIP L+  FL  F + N ++ + ++  AL  +  Y
Sbjct: 312 LFREDLYYRLEEFPLYIPPLRERPEDIPLLIRHFLDEFSSANNLESLQLAPDALDSIEGY 371

Query: 353 PWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSD 412
            W  N++ELKN + RA +  K + +   R  L+    G    E                 
Sbjct: 372 QWPGNIRELKNAVQRAAVTRKGNLIETLRSALIPGSAGTHAAE----------------K 415

Query: 413 TILDNLSQESIPAIGQDGEVR-RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRK 471
           T+ +   ++++P      ++   L + E++ I  A K  +  +++ AR LGIGR+TLYRK
Sbjct: 416 TVPEKTVEQALPDQKAASKISYSLEEHERDAIIKAYKASQGNLTKTARMLGIGRATLYRK 475

Query: 472 IREYNIE 478
           + ++ +E
Sbjct: 476 LDKFGLE 482


>gi|330940719|gb|EGH43727.1| helix-turn-helix, Fis-type [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 471

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 131/475 (27%), Positives = 223/475 (46%), Gaps = 19/475 (4%)

Query: 13  VLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNV-IFLSLINCED-DKENI 70
           VL+++ D    + + + ++  GYD   V  ++ + ++       + +S +N    D   +
Sbjct: 5   VLLVEDDRSLREALGETLDLAGYDYQAVGSAEEALVAAEATPFSLVISDVNMPGMDGHQL 64

Query: 71  LKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP 130
           L  +  + P +P+++ T    ++     +    + + +     K L   I    R  +  
Sbjct: 65  LSLLRSRHPQLPVLLMTAHGAVERAVDAMRQGAADYLVKPFEPKAL---IALVARHALGR 121

Query: 131 SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA 190
            +  E    D  IAV PA IQ+++LA +       ++I GE G GK+ L+RFIH++  RA
Sbjct: 122 LEPAER---DGPIAVEPASIQLLNLASRVAKSDSTVLISGESGTGKEVLARFIHQNSPRA 178

Query: 191 FFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAV 249
             PF  +NC  I  + +E  LFG      T   A   GKF +A+GGTI+L+E   +PL +
Sbjct: 179 DKPFIAINCAAIPDNMLEATLFGHEKGSFTGAIAAQAGKFEQADGGTILLDEISEMPLGL 238

Query: 250 QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINI 309
           Q ++   ++  ++E   +R  I LD+R++  T ++L  +V +  FR+DL+YR+SVF +  
Sbjct: 239 QAKLLRVLQEREVERVGARKPIVLDIRVVATTNRDLAGEVAAGRFREDLFYRLSVFPLAW 298

Query: 310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV 369
             LR R+ DI  L    L     K     + +S +A   L  YPW  NV+EL N + RA+
Sbjct: 299 QALRQRTADILPLAERLLAKHVNKMKHAPVRLSAEAQQCLVSYPWPGNVRELDNAVQRAL 358

Query: 370 IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQD 429
           I  +   +    F   LS             A         ++     +S ES  A+G D
Sbjct: 359 ILQQGGVIQAQDFC--LSGPVTSLPVAAPVEAAAAVAVTTVAENAGTGVSPESAGALGDD 416

Query: 430 GEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI---REYNIEVDS 481
                L   E ++I   ++  R +  E A RLGI   TL  K+   R+  ++V++
Sbjct: 417 -----LRRHEFQMIIDTLRSERGRRKEAAERLGISPRTLRYKLAQMRDAGMDVEA 466


>gi|220917498|ref|YP_002492802.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219955352|gb|ACL65736.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 469

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 112/381 (29%), Positives = 183/381 (48%), Gaps = 34/381 (8%)

Query: 12  RVLIIDKDDEQIKIIKDHVESYGYDVFIVN--VSDLSTISKIQVNVIFLSLINCEDDKEN 69
           RVLI+D + +  + + +  + +GYDV   +     L    +   +VI   L+    D   
Sbjct: 4   RVLIVDDETDSREALAELTQRWGYDVQTASDGTEALRRAIEGHPDVILTDLVMPNMDGLW 63

Query: 70  ILKNIVDKIPIVPIIV----QTTQDNIKILNCFLYNRISKFF----LNLVSRK------- 114
           +L+ +  ++P  P+++     T Q  ++ +    ++ I K      L LV  +       
Sbjct: 64  LLRALRAELPDCPVVLLTGRGTIQTAVQAIREGAFDFIEKPLEVPRLRLVLERALEKKET 123

Query: 115 ----QLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQG 170
               QL    I AL  G              +I   PAM +V +L +K       ++I G
Sbjct: 124 MREVQLLRRRIAALAPGT------------DMIGSGPAMQRVFELVKKVSPSNASVVIAG 171

Query: 171 EFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSAQFLGKF 229
           E G GK+ ++R IH    R   PF  +NC  I    IE  LFG +    T    + LG F
Sbjct: 172 ESGTGKEVVARAIHNLSPRKDKPFVALNCSAIPATLIESELFGYERGAFTGADQRRLGNF 231

Query: 230 IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQV 289
             A+ GT+ L+E   LPL +Q +    +E  KI     R  + +DVR+I  T ++L  ++
Sbjct: 232 ELAHNGTLFLDEIGELPLELQAKFLRVLEERKIRRLGGRSEVEVDVRVICATNRDLKEEI 291

Query: 290 KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLL 349
           +   FR+DLY+R+ VF I + TL+ R ED+P LVH F++ F  +   +   +S  A+++L
Sbjct: 292 RRGRFREDLYFRLHVFSILLPTLKERREDVPLLVHHFIEKFNAETGKRVQGVSPAAMAVL 351

Query: 350 TKYPWIDNVQELKNILLRAVI 370
             Y W  N++EL+N + RA+I
Sbjct: 352 QGYAWPGNIRELRNTVERAMI 372


>gi|170724252|ref|YP_001751940.1| Fis family two component sigma-54 specific transcriptional
           regulator [Pseudomonas putida W619]
 gi|169762255|gb|ACA75571.1| two component, sigma54 specific, transcriptional regulator, Fis
           family [Pseudomonas putida W619]
          Length = 448

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 136/481 (28%), Positives = 216/481 (44%), Gaps = 49/481 (10%)

Query: 8   DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVN-VSDLSTISKIQV-NVIFLSLINCED 65
           D   R+L++D +   ++  +  +E  GY V   N  +    + + QV ++ FL L   ED
Sbjct: 6   DNQGRILLVDDESAILRTFRYCLEDEGYSVATANSAAQAEALLQRQVFDLCFLDLRLGED 65

Query: 66  DKENILKNIVDKIPIVPIIVQTTQDNIKIL--------NCFLYNRISKFFLNLVSRKQLC 117
           +  ++L  +  + P + +++ T    I             +L    S   L L + KQL 
Sbjct: 66  NGLDVLAQMRIQAPWMRVVIVTAHSAIDTAVDAIQAGAADYLVKPCSPDQLRLATAKQLE 125

Query: 118 DSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKK 177
              + A  E +          LDS    SPAM+ V++ AR+       I+I GE G GK 
Sbjct: 126 VRQLSARLEALEGEVRKPKDGLDSH---SPAMMAVLETARQVATTDANILILGESGTGKG 182

Query: 178 RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGT 236
            L+R IH   KRA      +NC  ++ + +E  LFG      T  S   LG+  +A+GGT
Sbjct: 183 ELARAIHSWSKRARKACVTINCPSLNAELMESELFGHTRGAFTGASESTLGRVNQADGGT 242

Query: 237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK 296
           + L+E    PL +Q ++  FI+  + E        R DVR++  T  NL   V+   FR+
Sbjct: 243 LFLDEIGDFPLTLQPKLLRFIQDKEYERVGDPVTRRADVRILAATNLNLEEMVRESRFRE 302

Query: 297 DLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID 356
           DL YR++V  +++  LR RSEDI  L   FL  F  + A      SD+A + L  Y W  
Sbjct: 303 DLLYRLNVITLHLPPLRERSEDILTLADRFLARFVKEYARPARGFSDEARAALLNYRWPG 362

Query: 357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILD 416
           N++EL+N++ RA I                                 C  E    + I  
Sbjct: 363 NIRELRNVVERASI--------------------------------ICPQE--RVEIIHL 388

Query: 417 NLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN 476
            + ++   +  + G    L ++E+  IG A+      + + A+ LGI  STLYRK ++YN
Sbjct: 389 GMGEQPAGSAPRVGAALSLDELERAHIG-AVLAASDTLDQAAKTLGIDASTLYRKRKQYN 447

Query: 477 I 477
           +
Sbjct: 448 L 448


>gi|168185675|ref|ZP_02620310.1| transcriptional regulatory protein [Clostridium botulinum C str.
           Eklund]
 gi|169296527|gb|EDS78660.1| transcriptional regulatory protein [Clostridium botulinum C str.
           Eklund]
          Length = 355

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 103/343 (30%), Positives = 182/343 (53%), Gaps = 25/343 (7%)

Query: 138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV 197
             D +I  +  + ++V  A+KA +    I++QG  G GK+  +  IH   KRA  PF +V
Sbjct: 36  TFDDIITKNQNVKKIVQYAKKAANTDCSILLQGSNGTGKEVFAEAIHNYSKRAEGPFIVV 95

Query: 198 NCGMIDQDKIEKFLFGDVDLQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF 256
           +C ++ ++ +++ LFG  +   T  + ++ GKF  A+GGT+ L   + LPL +Q ++   
Sbjct: 96  DCAIVPRELLKRRLFGYYEQTFTDENEEYPGKFQLADGGTLFLNNIEELPLDIQQKLLKI 155

Query: 257 IETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS 316
           ++  K     S     +DVR+I  T KNL+ +V +  FR DLYY+++V  + +  L  R 
Sbjct: 156 LDDNKTSLRKSDEK-NIDVRIIASTNKNLIDEVNTKSFRADLYYKLNVINVKLLDLEERK 214

Query: 317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH 376
           EDIP L  +FL+   + N+ K+ +I + A+  L  Y W+ N++EL+N + +      +S+
Sbjct: 215 EDIPLLAKYFLEKLNSINSNKERTIDEDAIEELRNYKWVGNIRELRNFIEKLYYLCDESN 274

Query: 377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS 436
           +T  +F+L       K  E +       +TE  +         +ESI +         L 
Sbjct: 275 ITR-KFLLDCIYNKPKCNEKN-----K