BLASTP 2.2.21 [Jun-14-2009]

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.

Query= 0031.0015.p         (482 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects 
           15,459,386 sequences; 5,307,515,862 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|YP_003777352.1| RNA polymerase sigma-N (sigma-54) factor tra...   979   0.0  
ref|YP_001355042.1| RNA polymerase factor sigma-54 [Janthinobact...   776   0.0  
ref|ZP_08274231.1| sigma N (sigma 54) factor of RNA polymerase [...   766   0.0  
ref|YP_001101339.1| RNA polymerase factor sigma-54 [Herminiimona...   761   0.0  
ref|YP_004751122.1| sigma N (sigma 54) factor of RNA polymerase ...   741   0.0  
ref|YP_003603939.1| RNA polymerase, sigma 54 subunit, RpoN [Burk...   569   e-160
ref|YP_001894245.1| RNA polymerase factor sigma-54 [Burkholderia...   568   e-160
ref|ZP_03268444.1| RNA polymerase, sigma 54 subunit, RpoN [Burkh...   565   e-159
ref|YP_004226836.1| RNA polymerase sigma-54 subunit RpoN [Burkho...   563   e-158
ref|ZP_04577267.1| RNA polymerase factor sigma-54 [Oxalobacter f...   562   e-158

>ref|YP_003777352.1| RNA polymerase sigma-N (sigma-54) factor transcription regulator
           protein [Herbaspirillum seropedicae SmR1]
 gb|ADJ65444.1| RNA polymerase sigma-N (sigma-54) factor transcription regulator
           protein [Herbaspirillum seropedicae SmR1]
          Length = 496

 Score =  979 bits (2530), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 482/482 (100%), Positives = 482/482 (100%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 60
           LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV
Sbjct: 15  LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 74

Query: 61  SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL 120
           SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL
Sbjct: 75  SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL 134

Query: 121 EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL 180
           EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL
Sbjct: 135 EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL 194

Query: 181 EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD 240
           EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD
Sbjct: 195 EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD 254

Query: 241 FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH 300
           FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH
Sbjct: 255 FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH 314

Query: 301 EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 360
           EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF
Sbjct: 315 EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 374

Query: 361 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 420
           FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE
Sbjct: 375 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 434

Query: 421 ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK 480
           ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK
Sbjct: 435 ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK 494

Query: 481 SL 482
           SL
Sbjct: 495 SL 496


>ref|YP_001355042.1| RNA polymerase factor sigma-54 [Janthinobacterium sp. Marseille]
 gb|ABR88962.1| RNA polymerase sigma-54 factor [Janthinobacterium sp. Marseille]
          Length = 489

 Score =  776 bits (2003), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 390/482 (80%), Positives = 429/482 (89%), Gaps = 7/482 (1%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 60
           LTPQLQQSIRLLQLSTLELHQELEQIL DNP+LER DD LD++VRLLADGA+      G 
Sbjct: 15  LTPQLQQSIRLLQLSTLELHQELEQILADNPMLERTDDPLDHAVRLLADGAI------GA 68

Query: 61  SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL 120
           S TT   AS EA     + E+SFE  D  PE  +GDS+WSFDDVAR+ K+P+D+DARPQL
Sbjct: 69  SGTTPEGASVEANTQTPESETSFEAPDL-PEASNGDSEWSFDDVARTSKAPEDDDARPQL 127

Query: 121 EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL 180
           EAHE TLREHLLEQ+RVT R  RDRALLEL+ DAL+D+GYLEE LE+I ARLPEEL ++L
Sbjct: 128 EAHETTLREHLLEQMRVTVREHRDRALLELIIDALNDNGYLEEELEEIHARLPEELEIEL 187

Query: 181 EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD 240
           EEL ISLK+LQS DP GVGAR A ECLALQI+R+PKV  VTRR+AL IVE++LPLFAQRD
Sbjct: 188 EELQISLKMLQSFDPPGVGARDAAECLALQIKRMPKVAMVTRRMALAIVENHLPLFAQRD 247

Query: 241 FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH 300
           FNK++KALDCDDEDLREAQA+I+QC PHPG+ FA DASDYVVPDVIVK+T+NGWQVMLNH
Sbjct: 248 FNKLRKALDCDDEDLREAQAIIKQCNPHPGSIFATDASDYVVPDVIVKRTRNGWQVMLNH 307

Query: 301 EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 360
           +VMP+LRVN+MYA+ LKQ+KGEGSL SQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF
Sbjct: 308 DVMPRLRVNSMYANILKQSKGEGSLGSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 367

Query: 361 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 420
           FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATE GGE
Sbjct: 368 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATEAGGE 427

Query: 421 ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK 480
           ASSTAIRALIKQLIGAE+P+ P SDSKIADMLAEQGMVVARRTVAKYRE LKIPPVNLRK
Sbjct: 428 ASSTAIRALIKQLIGAEDPKIPFSDSKIADMLAEQGMVVARRTVAKYREALKIPPVNLRK 487

Query: 481 SL 482
           SL
Sbjct: 488 SL 489


>ref|ZP_08274231.1| sigma N (sigma 54) factor of RNA polymerase [Oxalobacteraceae
           bacterium IMCC9480]
 gb|EGF32299.1| sigma N (sigma 54) factor of RNA polymerase [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 493

 Score =  766 bits (1978), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/483 (78%), Positives = 425/483 (87%), Gaps = 5/483 (1%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 60
           LTPQLQQSIRLLQLSTLELHQELEQ+LTDNPLLERLDD LD+SVRLLADGA+ A    G+
Sbjct: 15  LTPQLQQSIRLLQLSTLELHQELEQMLTDNPLLERLDDPLDHSVRLLADGALGA---EGI 71

Query: 61  SETTGSEASSEAAPAAADGESSFEYQDTAPEGV-SGDSDWSFDDVARSGKSPDDEDARPQ 119
            +   SE  + AAP+ ++ ++    Q+ A +   S D+DWSFDDVAR+ K+P+D+DARPQ
Sbjct: 72  RQEGASE-DANAAPSPSEPDAPAPDQNDAGDATPSTDADWSFDDVARTSKAPEDDDARPQ 130

Query: 120 LEAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVD 179
           LEAHE TLRE LLEQ+RVT R  RDRAL+EL+ DAL+D+GYL++ LE +L RLP EL V+
Sbjct: 131 LEAHESTLREFLLEQMRVTVRNPRDRALVELMIDALNDNGYLDDTLEAMLERLPAELEVE 190

Query: 180 LEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQR 239
            EEL+I+LKLLQS DP GVGAR+A ECLALQIRR P +  VTRR+AL IVEDYLPLFAQR
Sbjct: 191 PEELTIALKLLQSFDPPGVGARNAAECLALQIRRFPGIAMVTRRMALTIVEDYLPLFAQR 250

Query: 240 DFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLN 299
           DF+K+KKALDCDDEDLREAQ+VIRQC PHPGA F    SDYVVPDVIVK+TK GWQVMLN
Sbjct: 251 DFSKLKKALDCDDEDLREAQSVIRQCNPHPGAIFGGGTSDYVVPDVIVKRTKAGWQVMLN 310

Query: 300 HEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRN 359
           H+VMP+LRVNAMYA+ LKQ+KG+GSL+SQLQEAKWLIKNMRQRFDTILRVAQAIVERQRN
Sbjct: 311 HDVMPRLRVNAMYANILKQSKGDGSLTSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRN 370

Query: 360 FFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGG 419
           FFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGG
Sbjct: 371 FFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGG 430

Query: 420 EASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLR 479
           EASSTAIRALIKQLIGAE+P+ P SDSKIADML EQGMVVARRTVAKYRE LKIPPVNLR
Sbjct: 431 EASSTAIRALIKQLIGAEDPKIPFSDSKIADMLGEQGMVVARRTVAKYREALKIPPVNLR 490

Query: 480 KSL 482
           K+L
Sbjct: 491 KAL 493


>ref|YP_001101339.1| RNA polymerase factor sigma-54 [Herminiimonas arsenicoxydans]
 emb|CAL63218.1| RNA polymerase, sigma 54 (sigma N) factor [Herminiimonas
           arsenicoxydans]
          Length = 489

 Score =  761 bits (1965), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/482 (79%), Positives = 426/482 (88%), Gaps = 7/482 (1%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 60
           LTPQLQQSIRLLQLSTLELHQELEQIL DNPLLER DD LD+++RLLADGA+      G 
Sbjct: 15  LTPQLQQSIRLLQLSTLELHQELEQILADNPLLERTDDPLDHAIRLLADGAI------GS 68

Query: 61  SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL 120
           + TT   AS EA     + ++S E  + A E  +GD++WSFDDVAR+ K+PDD+DARPQL
Sbjct: 69  AGTTPEGASVEANAQTPESDTSVEAPEPA-EASNGDAEWSFDDVARTSKAPDDDDARPQL 127

Query: 121 EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL 180
           EAHE TLREHLLEQ+RVT R +RDRALLEL+ DAL+D+GYLEE LE+I ARLPEEL ++ 
Sbjct: 128 EAHETTLREHLLEQMRVTVRERRDRALLELIIDALNDNGYLEETLEEIHARLPEELEIEP 187

Query: 181 EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD 240
           EEL I+L LLQS DPAGVGAR+A ECLALQI+R+PKV  VTRR+AL IVE +L LFAQRD
Sbjct: 188 EELQIALNLLQSFDPAGVGARNASECLALQIKRMPKVAMVTRRMALAIVEHHLGLFAQRD 247

Query: 241 FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH 300
           FNK++KALDCDDEDLREAQ VI+QC PHPG+ FA D SDYVVPDVIVK+T+NGWQVMLNH
Sbjct: 248 FNKLRKALDCDDEDLREAQVVIKQCNPHPGSIFATDTSDYVVPDVIVKRTRNGWQVMLNH 307

Query: 301 EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 360
           +VMP+LRVN+MYA+ LKQ+KGEGSL SQLQEAKWLIKNMRQRFDTILRV+QAIVERQRNF
Sbjct: 308 DVMPRLRVNSMYANILKQSKGEGSLGSQLQEAKWLIKNMRQRFDTILRVSQAIVERQRNF 367

Query: 361 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 420
           FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE
Sbjct: 368 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 427

Query: 421 ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK 480
           ASSTAIRALIKQLIGAEN +TP SDSKIA+MLAEQGMVVARRTVAKYRE LKIPPVNLRK
Sbjct: 428 ASSTAIRALIKQLIGAENQKTPFSDSKIAEMLAEQGMVVARRTVAKYREALKIPPVNLRK 487

Query: 481 SL 482
           SL
Sbjct: 488 SL 489


>ref|YP_004751122.1| sigma N (sigma 54) factor of RNA polymerase [Collimonas fungivorans
           Ter331]
 gb|AEK60299.1| sigma N (sigma 54) factor of RNA polymerase [Collimonas fungivorans
           Ter331]
          Length = 493

 Score =  741 bits (1913), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/482 (78%), Positives = 420/482 (87%), Gaps = 3/482 (0%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 60
           LTPQLQQSIRLLQLSTLELHQELEQIL+DNPLLER+DD LDNSVRLLADGA+S A +S +
Sbjct: 15  LTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERVDDPLDNSVRLLADGAISGA-TSTM 73

Query: 61  SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL 120
               G    S +   +  G  +    +  PE  +GDS+WSFDDVARS K+PDDEDARPQL
Sbjct: 74  DAPVGDSEVSSSPSESEAGLDTPPAAENGPE--NGDSEWSFDDVARSSKTPDDEDARPQL 131

Query: 121 EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL 180
           EAHE TLREHLL+Q+R T    RDRAL+EL  DALDD+GYLEE LE+IL RLP EL + +
Sbjct: 132 EAHECTLREHLLQQMRETLNDIRDRALVELTIDALDDNGYLEESLEEILERLPPELEIAI 191

Query: 181 EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD 240
           EELS +LK++QS DPAGVGAR+A ECL LQI+R  KVPFVTRRLAL IV+D+L LFAQRD
Sbjct: 192 EELSTALKMVQSFDPAGVGARNAAECLGLQIKRFIKVPFVTRRLALAIVQDHLMLFAQRD 251

Query: 241 FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH 300
           FNKIKKALDCDDEDLREAQAVI+QC PHPGA FA +ASDYVVPDVIV+++K GWQVMLN+
Sbjct: 252 FNKIKKALDCDDEDLREAQAVIKQCNPHPGAPFAANASDYVVPDVIVRRSKQGWQVMLNN 311

Query: 301 EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 360
           +VMP+LRVN +YA+ LKQ+KG+G+L+SQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF
Sbjct: 312 DVMPRLRVNVLYANILKQSKGDGALTSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 371

Query: 361 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 420
           FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATE GGE
Sbjct: 372 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATEAGGE 431

Query: 421 ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK 480
           ASSTAIRALIKQLIGAE+ + P SDSKIADMLAEQGMVVARRTVAKYRE LKIP VNLRK
Sbjct: 432 ASSTAIRALIKQLIGAEDTKNPFSDSKIADMLAEQGMVVARRTVAKYREALKIPSVNLRK 491

Query: 481 SL 482
           +L
Sbjct: 492 AL 493


>ref|YP_003603939.1| RNA polymerase, sigma 54 subunit, RpoN [Burkholderia sp. CCGE1002]
 gb|ADG14428.1| RNA polymerase, sigma 54 subunit, RpoN [Burkholderia sp. CCGE1002]
          Length = 505

 Score =  569 bits (1467), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 301/503 (59%), Positives = 372/503 (73%), Gaps = 33/503 (6%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 60
           LTPQLQQSIRLLQLSTLEL QE+   ++ NPLLE  D+ + + +R+ ADG+V       +
Sbjct: 15  LTPQLQQSIRLLQLSTLELQQEVAMAISQNPLLENEDEWIASPLRVAADGSV-------I 67

Query: 61  SETTGSEASSEAAPAAADGESSFE-----YQDTAPEGV------SGD-----SDWSFDDV 104
           ++T GS  S+ A P A +G +S E      +   P+GV      SGD     S W+ DD 
Sbjct: 68  AQTPGS--SAPADPMAGNGSTSSEGNGERAESGEPQGVDEYNGLSGDGGGDTSQWNLDDY 125

Query: 105 ARSGKSPDDEDARPQLEAHE--ITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLE 162
            RSG + DD+D  P L+ HE   +LR+HL+ Q+RVT  +QRDRAL+  L ++LDD GYL 
Sbjct: 126 GRSGNASDDDDL-PPLQIHESSTSLRDHLMAQLRVTQASQRDRALITFLIESLDDDGYLA 184

Query: 163 EPLEDILARLPEELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTR 222
             LE++LA LPEEL VD++EL+ +L LL S DP GVGARSA ECL LQ+ RL   P  TR
Sbjct: 185 ATLEEVLADLPEELEVDVDELNAALALLHSFDPPGVGARSASECLKLQLLRLEPSP--TR 242

Query: 223 RLALKIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVV 282
            LAL IV  YL L A RDF +++K L   D+DLR+A A+IR   P PGA + +  +DYVV
Sbjct: 243 TLALDIVGRYLELLAARDFTRLRKHLKASDDDLRDAHALIRSLEPFPGAAYGKAEADYVV 302

Query: 283 PDVIVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGE---GSLSSQLQEAKWLIKNM 339
           PD++V++T  GWQ  LN EV+PKLR+N +YA+ L+  +G+   GSL  QLQEA+WLIKN+
Sbjct: 303 PDIMVRKTAQGWQAELNPEVVPKLRINHLYANILRNNRGDPGSGSLRQQLQEARWLIKNI 362

Query: 340 RQRFDTILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTP 399
           +QRF+TILRVAQAIVERQ++FF HG +AMRPLVLREIADTLGLHEST+SRVTT KYMLTP
Sbjct: 363 QQRFETILRVAQAIVERQKSFFVHGEIAMRPLVLREIADTLGLHESTVSRVTTGKYMLTP 422

Query: 400 HGMFELKYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVV 459
            G  E KYFFGSHV+T+TGG ASSTAIRALIKQLIGAENP++PLSDS+IA++LAEQG VV
Sbjct: 423 FGTLEFKYFFGSHVSTDTGGAASSTAIRALIKQLIGAENPKSPLSDSRIAELLAEQGFVV 482

Query: 460 ARRTVAKYREVLKIPPVNLRKSL 482
           ARRTVAKYRE LKIP VNLRKSL
Sbjct: 483 ARRTVAKYREALKIPAVNLRKSL 505


>ref|YP_001894245.1| RNA polymerase factor sigma-54 [Burkholderia phytofirmans PsJN]
 gb|ACD15021.1| RNA polymerase, sigma 54 subunit, RpoN [Burkholderia phytofirmans
           PsJN]
          Length = 503

 Score =  568 bits (1464), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 297/492 (60%), Positives = 370/492 (75%), Gaps = 13/492 (2%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGA-VSAAPSSG 59
           LTPQLQQSIRLLQLSTLEL QE+   ++ NPLLE  DD + + +R+ ADG+ ++ AP+S 
Sbjct: 15  LTPQLQQSIRLLQLSTLELQQEVAMAISQNPLLENEDDWIASPLRVAADGSLIAQAPNSS 74

Query: 60  V--SETTGSEASSEAAPAAADGESSF--EYQDTAPEGVSGDSDWSFDDVARSGKSPDDED 115
               +  G+ +SS ++  A +GE     EY   A +G    S W+ DD  RSG + DD+D
Sbjct: 75  APPDQMGGNTSSSSSSERAENGEPQGVDEYNGLAGDGNGDASQWNLDDYGRSGNASDDDD 134

Query: 116 ARPQLEAHE--ITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLP 173
             P L+ HE   +LR+HL+ Q+RVT   QRDRAL+  L ++LDD GYL   LE++LA LP
Sbjct: 135 L-PPLQIHESSTSLRDHLMAQLRVTQAGQRDRALITFLIESLDDDGYLAATLEEVLADLP 193

Query: 174 EELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYL 233
           EEL VDL+E++ +L LL S DPAGVGARSA ECL LQ+ RL   P  TR LAL IV  +L
Sbjct: 194 EELEVDLDEMNAALALLHSFDPAGVGARSASECLKLQLLRLDASP--TRTLALDIVAHHL 251

Query: 234 PLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNG 293
            L A RDF +++K L  +D+DLR+A  +IR   P PGA + +  +DYVVPD++V++T  G
Sbjct: 252 ELLAARDFTRLRKHLKANDDDLRDAHILIRSLEPFPGAAYGKAEADYVVPDIMVRKTAQG 311

Query: 294 WQVMLNHEVMPKLRVNAMYASALKQAKGE---GSLSSQLQEAKWLIKNMRQRFDTILRVA 350
           WQ  LN EV+PKLR+N +YA+ L+  +G+   GSL  QLQEA+WLIKN++QRF+TILRVA
Sbjct: 312 WQAELNPEVVPKLRINHLYANILRNNRGDPGSGSLRQQLQEARWLIKNIQQRFETILRVA 371

Query: 351 QAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFG 410
           QAIVERQ++FF HG +AMRPLVLREIADTLGLHEST+SRVTT KYMLTP G  E KYFFG
Sbjct: 372 QAIVERQKSFFVHGEIAMRPLVLREIADTLGLHESTVSRVTTGKYMLTPFGTLEFKYFFG 431

Query: 411 SHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREV 470
           SHV+T+TGG ASSTAIRALIKQLIGAENP++PLSDS+IA++LAEQG VVARRTVAKYRE 
Sbjct: 432 SHVSTDTGGAASSTAIRALIKQLIGAENPKSPLSDSRIAELLAEQGFVVARRTVAKYREA 491

Query: 471 LKIPPVNLRKSL 482
           LKIP VNLRKSL
Sbjct: 492 LKIPAVNLRKSL 503


>ref|ZP_03268444.1| RNA polymerase, sigma 54 subunit, RpoN [Burkholderia sp. H160]
 gb|EEA00006.1| RNA polymerase, sigma 54 subunit, RpoN [Burkholderia sp. H160]
          Length = 505

 Score =  565 bits (1456), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 299/500 (59%), Positives = 366/500 (73%), Gaps = 27/500 (5%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAV------SA 54
           LTPQLQQSIRLLQLSTLEL QE+   ++ NPLLE  D+ + + +R+ ADG+V      S+
Sbjct: 15  LTPQLQQSIRLLQLSTLELQQEVAMAISQNPLLENEDEWIASPLRVAADGSVIAQTPGSS 74

Query: 55  APS-------SGVSETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARS 107
           AP+       S  SE TG  A S   P   D     EY   A +G    S W+ DD  RS
Sbjct: 75  APADPMAGNGSTSSEGTGERAES-GEPQGVD-----EYNGLAGDGGGDSSQWNLDDYGRS 128

Query: 108 GKSPDDEDARPQLEAHE--ITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPL 165
           G + DD+D  P L+ HE   +LR+HL+ Q+RVT  + RDRAL+  L ++LDD GYL   L
Sbjct: 129 GNASDDDDL-PPLQIHESSTSLRDHLMAQLRVTQASPRDRALITFLIESLDDDGYLAATL 187

Query: 166 EDILARLPEELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLA 225
           E++LA LPEEL VDL+EL+ +L LL S DP+GVGARSA ECL LQ+ RL   P  TR LA
Sbjct: 188 EEVLADLPEELEVDLDELNAALALLHSFDPSGVGARSASECLKLQLLRLDPSP--TRTLA 245

Query: 226 LKIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDV 285
           L IV  YL L A RDF +++K L   D++LR+A  +IR   P PGA + +  +DYVVPD+
Sbjct: 246 LDIVGHYLELLAARDFTRLRKHLKASDDELRDAHMLIRSLEPFPGAAYGKAEADYVVPDI 305

Query: 286 IVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGE---GSLSSQLQEAKWLIKNMRQR 342
           +V++T  GWQ  LN EV+PKLR+N +YA+ L+  +G+   GSL  QLQEA+WLIKN++QR
Sbjct: 306 MVRKTAQGWQAELNPEVVPKLRINHLYANILRNNRGDPGSGSLRQQLQEARWLIKNIQQR 365

Query: 343 FDTILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGM 402
           F+TILRVAQAIVERQ++FF HG +AMRPLVLREIADTLGLHEST+SRVTT KYMLTP G 
Sbjct: 366 FETILRVAQAIVERQKSFFVHGEIAMRPLVLREIADTLGLHESTVSRVTTGKYMLTPFGT 425

Query: 403 FELKYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARR 462
            E KYFFGSHV+T+TGG ASSTAIRALIKQLIGAENP++PLSDS+IA++LAEQG VVARR
Sbjct: 426 LEFKYFFGSHVSTDTGGAASSTAIRALIKQLIGAENPKSPLSDSRIAELLAEQGFVVARR 485

Query: 463 TVAKYREVLKIPPVNLRKSL 482
           TVAKYRE LKIP VNLRKSL
Sbjct: 486 TVAKYREALKIPAVNLRKSL 505


>ref|YP_004226836.1| RNA polymerase sigma-54 subunit RpoN [Burkholderia sp. CCGE1001]
 gb|ADX53776.1| RNA polymerase, sigma 54 subunit, RpoN [Burkholderia sp. CCGE1001]
          Length = 505

 Score =  563 bits (1452), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 297/494 (60%), Positives = 367/494 (74%), Gaps = 15/494 (3%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGA-VSAAPSSG 59
           LTPQLQQSIRLLQLSTLEL QE+   ++ NPLLE  DD + + +R+ ADG+ ++ AP S 
Sbjct: 15  LTPQLQQSIRLLQLSTLELQQEVATAISQNPLLENEDDWIASPLRVAADGSLIAQAPGSA 74

Query: 60  VSE----TTGSEASSEAAPAAADGESSF--EYQDTAPEGVSGDSDWSFDDVARSGKSPDD 113
                    GS +S+ ++  + +GE     EY   + +G    S W+ DD  RSG + DD
Sbjct: 75  TPPDQMGGNGSSSSTSSSERSENGEPQGVDEYNGLSGDGNGDASQWNLDDYGRSGNASDD 134

Query: 114 EDARPQLEAHE--ITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILAR 171
           +D  P L+ HE   +LR+HL+ Q+RVT   QRDRAL+  L ++LDD GYL   LE++LA 
Sbjct: 135 DDL-PPLQIHESSTSLRDHLMAQLRVTQAGQRDRALVTFLIESLDDDGYLAATLEEVLAD 193

Query: 172 LPEELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVED 231
           LPEEL VDL+EL+ +L LL S DPAGVGARSA ECL LQ+ RL   P  TR LAL IV  
Sbjct: 194 LPEELEVDLDELNAALALLHSFDPAGVGARSASECLKLQLLRLEPSP--TRALALDIVAH 251

Query: 232 YLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTK 291
           YL L A RDF +++K L   D+DLR+A A+IR   P PGA + +  +DYVVPD++V++T 
Sbjct: 252 YLELLAARDFTRLRKHLKASDDDLRDAHALIRSLEPFPGAAYGKAEADYVVPDIMVRKTA 311

Query: 292 NGWQVMLNHEVMPKLRVNAMYASALKQAKGE---GSLSSQLQEAKWLIKNMRQRFDTILR 348
            GWQ  LN EV+PKLR+N +YA+ L+  +G+   GSL  QLQEA+WLIKN++QRF+TILR
Sbjct: 312 QGWQAELNPEVVPKLRINHLYANILRNNRGDPGSGSLRQQLQEARWLIKNIQQRFETILR 371

Query: 349 VAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYF 408
           VAQAIVERQ++FF HG +AMRPLVLREIADTLGLHEST+SRVTT KYMLTP G  E KYF
Sbjct: 372 VAQAIVERQKSFFVHGEIAMRPLVLREIADTLGLHESTVSRVTTGKYMLTPFGTLEFKYF 431

Query: 409 FGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYR 468
           FGSHV+T+TGG ASSTAIRALIKQLIGAEN +TPLSDS+IA++LAEQG VVARRTVAKYR
Sbjct: 432 FGSHVSTDTGGAASSTAIRALIKQLIGAENAKTPLSDSRIAELLAEQGFVVARRTVAKYR 491

Query: 469 EVLKIPPVNLRKSL 482
           E L+IP VNLRKSL
Sbjct: 492 EALRIPAVNLRKSL 505


>ref|ZP_04577267.1| RNA polymerase factor sigma-54 [Oxalobacter formigenes HOxBLS]
 gb|EEO28229.1| RNA polymerase factor sigma-54 [Oxalobacter formigenes HOxBLS]
          Length = 491

 Score =  562 bits (1449), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 276/482 (57%), Positives = 360/482 (74%), Gaps = 5/482 (1%)

Query: 1   LTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRLLADGAVSAAPSSGV 60
           LTPQLQQSIRLLQLS+LEL++E+ + L +NPLLERLDD L N+ R  ADG++   P S  
Sbjct: 15  LTPQLQQSIRLLQLSSLELNEEIGRALEENPLLERLDDPLANTTRFQADGSIIRQPVSS- 73

Query: 61  SETTGSEASSEAAPAAADGESSFEYQDTAPEGVSGDSDWSFDDVARSGKSPDDEDARPQL 120
            ET   E++  ++   +D  + FE       G +      +D    S + PDDE  +PQL
Sbjct: 74  GETPYDESAHGSSGEPSDLTAPFENTS----GSAEHDHLIWDSAKASDRHPDDERFQPQL 129

Query: 121 EAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPLEDILARLPEELGVDL 180
           EA   +L+EHL  Q+R+  R QR RAL EL+ DALD +GYL+E LE+++  LP ELG+  
Sbjct: 130 EAPPESLKEHLRSQMRLAVRNQRQRALAELIIDALDSNGYLQETLEEMIEWLPAELGIAH 189

Query: 181 EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLALKIVEDYLPLFAQRD 240
           +EL  +L  +Q  DP GVGAR++ ECLA+QIR +  +P++ R+ AL IVE++L LFAQRD
Sbjct: 190 KELEETLVCIQGFDPPGVGARNSAECLAIQIRLMQNIPYIVRKQALNIVENHLKLFAQRD 249

Query: 241 FNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVIVKQTKNGWQVMLNH 300
           F ++KKAL+CDDEDLREA  VIR+C PHPGA +A DA+D V+P+++V +    W   LN 
Sbjct: 250 FIRLKKALECDDEDLREATEVIRRCNPHPGAAYANDAADVVIPEIVVVKKDGAWHAELNT 309

Query: 301 EVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTILRVAQAIVERQRNF 360
           + MPK+R+N MY   LK A  + SL+++ QEAKWLI+N+ QRF+TIL+V++AI+ERQ+NF
Sbjct: 310 DAMPKIRINRMYGDVLKSASNKTSLNTRFQEAKWLIRNINQRFETILKVSEAIIERQQNF 369

Query: 361 FSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFFGSHVATETGGE 420
           FS GA +MRPLVLREIADTLGLHESTISRVTTQK+MLTP G+FELKYFFGSH+ATE GGE
Sbjct: 370 FSFGATSMRPLVLREIADTLGLHESTISRVTTQKFMLTPLGIFELKYFFGSHIATEGGGE 429

Query: 421 ASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAKYREVLKIPPVNLRK 480
           ASSTAIR  IKQLI  E+ + P SD+KIA +LA +G+V+ARRT+AKYR++LKIPP +LRK
Sbjct: 430 ASSTAIREKIKQLIATEDRKKPYSDNKIAQILAREGLVIARRTIAKYRDILKIPPASLRK 489

Query: 481 SL 482
           SL
Sbjct: 490 SL 491